The new zotero 3.0 comes with updated styles, but the conversion caused some errors. Furthermore, the changes we made to the PE style had not been implemented. That’s all fixed now, and you can get the new, correct style here (zip file, 9 kb). On the zotero site it will also soon be available.
This post is a 3-in-1 on Carboniferous arthropods, CT data of them, and a free program for handling such data. It covers three papers just published in PE, and was written by two of the the authors, Mark Sutton and Russell Garwood. I have added a comment on the text (in italics and inset paragraphs), regarding the Virtual Palaeontology computer program described in one of the papers.
Virtual Palaeontology is a set of techniques for working with three-dimensionally preserved fossils in the digital domain – essentially as three-dimensional interactive on-screen models (virtual fossils). Fossils can be digitised into three-dimensional models in a variety of ways, but the most important of these are tomographic (based on serial slices, either from machines such as CT scanners or from more traditional techniques such as serial grinding). Turning slices into three-dimensional models is not a straightforward process, and requires dedicated software – while appropriate packages do exist, few are free, and none are tuned to the needs of palaeontological data, which is often noisy and complex. In a new PE paper published in May 2012, Sutton et al. introduce the SPIERS package (software website) which is aimed at filling this gap with a free, multi-platform software toolkit for converting slice-images from any source into three-dimensional models. SPIERS is carefully and extensively documented, flexible in approach, and designed to run on everyday computers. It has already seen extensive use in the study of the invertebrate fauna of the Silurian Herefordshire Lagerstatte (see e.g., Briggs et al. 2008, Sutton et al. 2011), as well as for micro-CT based studies (e.g., Garwood et al. 2011, Sutton & Sigwart 2012). SPIERS has already made informal inroads within the palaeontological community through a process of osmosis and direct contact with its authors; its formal launch should help increase the uptake of these techniques within our science.
Figure 2 of Garwood and Sutton (2012), showing fossil examples of the genus Camptophyllia, the guinea pigs for the presentation of SPIERS.
This place has been quite as a grave for a long time. That downtime was caused by a number of factors, most significantly the simple fact that I was totally overworked, and that my blogging time went to my own, personal blog.
Additionally, PE was totally revamped, and a lot of papers came out of our backlog caused by last year’s special issue. Add to that a number of papers where authors’ revisions took a long time, which also made it to publication, and there simply was very much work to do for all involved, including the style editors, Daniela Schwarz-Wings and me.
Now, though, I hope to revive the blog, with a series of overdue articles.
Enjoy!
This is a guest post by Natasha S. Vitek, author of the article Giant fossil soft-shelled turtles of North America that recently was published in PE. For some reason, the scheduling feature didn’t work, and I didn’t notice, thus the late publication.
Soft-shelled turtles are strange. Over the long course of evolution, they’ve lost the outer, keratinous, layer of their shell. With the exception of one clade they’ve lost the peripheral bones on the outer ring of their shell. These and other morphological oddities make soft-shelled turtles a compelling study animal.
Florida softshell turtle (Apalone ferox),
image from wikipedia under license specified there.
A look into previous research about the fossil record of soft-shelled turtles reveals a lot of confusion. Parallel evolution and high levels of variation within species are common. Although these features might someday make soft-shelled turtles ideal for studying particular evolutionary patterns, they pose a serious challenge for scientists seeking to untangle the history of the group.
This is a guest post by Julia Molnar, lead author of the latest technical article in PE.
In this blog post, I summarize our recent paper for Palaeontologica Electronica, write a little bit about my research, and show some pretty pictures of tetrapods.
In this methodology paper, I explain a 3D modeling technique and how it can be applied to paleontology. Have you ever thought to yourself, “Wow, these scan data look terrible. I wish I knew some way to fix my data up a little bit without making it all up”? If so, you should take a look at our article on idealized models from scan data. The technique is borrowed from 3D animators, who know an awful lot about manipulating meshes. To give you an idea of what it’s about, here’s an image of the scan data, a 2D reconstruction by Coates (1996) showing what it’s supposed to look like, and a picture of the 3D model I made from the scan data. The procedure is really simple, and anyone can learn to do it.
Micro-CT scan of Acanthostega vertebra segmented in Materialise Mimics software
2D reconstruction (Coates 1996)
Idealized model created in Autodesk Maya
This modeling technique was actually an unexpected outgrowth of my research on early tetrapod biomechanics with my co-authors, Stephanie Pierce, Jenny Clack, and John Hutchinson. Readers who are familiar with the field will know that decent (three-dimensionally preserved and complete) early tetrapod fossils are hard to come by, especially for postcranial anatomy. This helps to explain why so few people are working on early tetrapods in 3D! I pursued this topic in order to solve the problem of making good bone models to put into our other software for biomechanical analyses we’re doing.
Regardless of the difficulties, our long term aim is to build complete 3D models and simulations of the biomechanics of locomotion in early tetrapods. The goal is to examine how their musculoskeletal functions changed as they transitioned from aquatic to terrestrial modes of life. What was the first vertebrate to walk on land? How did it move? Did it resemble any modern animal(s), and if so, which one(s)?
To do this, we needed a method that would make 3D objects from partial scan data (often 2D-ish, from flattened or obscured slab specimen), and we needed to test how reproducible that method was—do subjective errors and investigator biases mean that no one can reproducibly reconstruct 3D morphology from such limited data (even, in the worst case, the same person if they repeat the whole process 5 times)?
Here’s the method we came up with: First, pick important points on the scan data that you want to make sure are reproduced faithfully in the model. Second, draw a grid on the surface of the model connecting your points. Third, use your grid to construct a smooth spline surface that follows the contours of the scan data while smoothing over any holes or rough bits. Finally, adjust your model to your heart’s content using a few control points. Simples!
We tested the method by having myself, Stephanie, and John each repeat the process 5 times, and used geometric morphometrics software to compare the resulting models made by each investigator. Thankfully, it worked out great for all investigators—we produced models that were statistically identical and repeatable. What’s more, the morphometrics were almost identical to the original data. Hurrah! That’s no small feat for paleontology; our colleagues in our lab even had scoffed about the poor likelihood of such an outcome. So I guess we showed them, and that’s a nice bonus for paleobiologists interested in 3D visualization methods. We encourage more researchers to check the biases in their 3D methods to ensure their morphology-based models are on sound footing. We all win by doing that—and the results are quite publishable!
Having spent two years studying medical illustration before entering the research field, I am passionate about the importance of good visuals. I believe that it’s important to try to make illustrations that are as accurate as possible, and to make it clear to the viewer which parts are made up. Scientific illustrations are more than just window dressing for papers and presentations – they are a very effective way of communicating our ideas, especially to people working in different disciplines.
The great thing about Palaeontologica Electronica is that it actively encourages scientists to share images, animations, and 3D models in a peer-reviewed journal. Publishing in PE allowed me to include lots and lots of colorful images and animations, including videos to make the procedures clear to people who aren’t familiar with the software.
OK, thanks for sticking with me to this point. As an extra reward, here are some gratuitous illustrations of early tetrapods. Enjoy!
Life reconstruction of Acanthostega
Life reconstruction of Pederpes
Life reconstruction of Crassigyrinus
Life reconstructions of various microsaurs
(All images ©Julia Molnar 2011)
Coates, M. 1996. The Devonian tetrapod Acanthostega gunnari Jarvik: Postcranial anatomy, basal tetrapod interrelationships and patterns of skeletal evolution. Transactions of the Royal Society Edinburgh Earth Sciences, 87:363–421.
Today, we have a guest post by the first author of the latest PE paper, Eline van Asperen.
When I started my PhD in 2006, I had no idea that not only would it take me to many dark museum cellars across Europe, but also to the beautiful mountains of Crimea, Ukraine. I had set out to study the evolution of horses during the European ice ages. Horse fossils are very common in bone collections from the ice ages, and they are one of the few species that show significant evolution over this, in geologists’ and palaeontologists’ eyes, relatively short period of 2 million years. Because many of the commonly used absolute dating methods (such as radiocarbon dating and uranium-series) are not very reliable for a large part of this time period, or can only be used on very specific materials that may not always be present on a particular site, using the evolution of animals is a good way to date sites. This is known as biostratigraphy. By looking at the stage of evolution horses are at on a particular find spot, we can date that location relative to other locations.
One of the places I visited to study horse fossils was the University of Wrocław in Poland. The researchers I worked with there were involved in the excavation of a cave in Ukraine, Emine-Bair-Khosar cave on the Crimean peninsula. Amongst other animals, they found a large number of horse remains. And so I found myself on the Chatyrdag plateau in Crimea to study the horse remains from the cave, the results of which my Polish and Ukrainian colleagues and I just published.
Apart from experiencing beautiful sunsets and seeing the Black Sea, I had a chance to study some extraordinarily well preserved fossils. At the present day, the cave has several entrances, but the animals whose remains we excavated ended up in the cave by falling through a hole in the plateau. This pothole is located at a spot where wind-blown snow tends to accumulate at the edge of the plateau in winter. The animals may not have spotted the hole in these circumstances, and will have fallen to their deaths as the snow gave way under their weight. This explains why some animals seem to have fallen into the cave in pairs. It has also led to an accumulation of relatively complete skeletons at the bottom of the hole. Palaeontologists look out for caves with potholes as they tend to contain rich, well-preserved faunal remains.
View from within the Emine-Bair-Khosar cave to the
top of the pothole through which the animals fell into the cave.
Photo by E. van Asperen
What is really interesting about the Emine-Bair-Khosar horses is that there are two species present: a heavy-built horse and an ass-like animal, now extinct but similar to the Asiatic wild ass. Emine-Bair-Khosar is the only place where we have found complete skulls of this ass-like animal. Extant Przewalski horses and Asiatic wild asses live together in the Bukhara Breeding Centre in Uzbekistan (Bahloul et al., 2001). They manage to survive in the same area by eating different foodstuffs and using the landscape differently. Likewise, the fact that the ass-like animal is more common in the Emine-Bair-Khosar fossils shows that the two related species used the area differently. Horses are more reliant on water sources than asses, and although there are no water sources on the Chatyrdag plateau itself, there are many springs and a river in the foothills of the plateau. The horses were probably more abundant in the foothills, while the plateau was frequented more by the ass-like animals.
The Chatyrdag plateau in spring. Photo by E. van Asperen
Horses and asses alive today form two different social groups: the harem, consisting of a stallion and several mares and their foals, and groups of young males that form unstable bachelor groups. The bachelor groups tend to live in less productive habitats than the harem groups. In contrast to the remains of other species in the cave, which are dominated by remains of young animals, foals are underrepresented. This leads us to infer that the plateau was mainly the domain of bachelor groups. In accordance with this idea, one of the ass skulls belonged to a young male, old enough to have left his natal harem band but too young to have acquired his own harem.
The Crimean peninsula is a very important region for ice age palaeontologists. Because of its relatively stable and warm microclimate, it functioned as a so-called ‘refugium’ during the colder parts of the ice ages, a place to where animals adapted to warmer climates retreated as Europe froze over (Hewitt, 1999; Stewart et al., 2010; Markova, 2011). When the climate got warmer again, these species spread across Europe from these often isolated refugia. The Crimean peninsula is located near the junction between the European temperate plains and the Central Asian steppes. During the ice ages, the range of steppe-adapted species will have expanded into eastern Europe. The Crimean fossils can tell us much about the movements of animals, both animals adapted to warm climates and those adapted to the dry, cool steppes of Central Asia, under the influence of a rapidly changing climate. It’s a fascinating and beautiful place to visit, and the many caves still harbour much new fossil evidence.
It was great to work with Ukrainian (Bogdan Ridush, Chernivtsi National “Fedkovych” University and Iurii Proskurnyak, National Museum of Natural History) and Polish researchers (Krzysztof Stefaniak, Wrocław University), who have much experience with working in caves, dealing with sediments that were deposited by very complicated processes. This interaction between experienced cave researchers and my specialist knowledge of Pleistocene horses enabled us to reconstruct how these animals lived in the Crimean environment.
Bahloul, K., Pereladova, O.B., Soldatova, N., Fisenko, G., Sidorenko, E., and Sempéré, A.J. 2001. Social organization and dispersion of introduced kulans (Equus hemionus kulan) and Przewalski horses (Equus przewalski) in the Bukhara Reserve, Uzbekistan. Journal of Arid Environments, 47:309-323.
Hewitt, G.M. 1999. Post-glacial re-colonization of European biota. Biological journal of the Linnean Society, 68:87-112
Markova, A.K. 2011. Small mammals from Palaeolithic sites of the Crimea. Quaternary international, 231:22-27.
Stewart, J.R., Lister, A.M., Barnes, I., and Dalén, L. 2010. Refugia revisited: individualistic responses of species in space and time. Proceedings of the Royal Society B, 277:661-671.
by Timothy Patterson, professor of geology at Carleton University. Tim is a former PE editor, and staunch supporter of open access publishing.
Fifteen years ago Palaeontologia Electronica made history when it became the world’s first fully electronic, open access paleontological journal. Free of the restrictions of the printed page PE remains a pioneer in electronic publishing. Although most journals are now available online, PE’s earth science peers continue to lag PE as most only publish an electronic copy of the print journal. PE permits authors to embed movies, animations, computer programs and other media not possible in a print journal. When we were establishing PE we wanted to set ourselves apart from our peers on another front, by making the journal a freely accessible open source publication with no subscription or access fees. This was important to us as the subscription fees for publications put out by the major commercial publishing houses were straining library acquisition budgets.
Fifteen years later, the journal fees charged by these organizations are straining library budgets more than ever. To encourage young researchers to adopt the new open source, open access publishing paradigm begun by PE, Carleton University has begun offering scholarships to graduate students who publish in open source journals. Sponsored by the Graduate Students Association (GSA), the Library, and the Office of the Vice President (Research & International) the Carleton University Scholarly Communications Selection Committee annually selects the five best research papers published by graduate students in peer-reviewed open access journals to be recipients of a $1000 CAD Graduate Student Open Access Award.
Lisa Neville won a Graduate Student Open Access Award
with her publication in Palaeontologia Electronica
Lisa Neville is one of this year’s recipients, in recognition of her 2010 PE paper “Seasonal environmental and chemical impact on the amoebian community composition in an oil sands reclamation wetland in northern Alberta” (PE Article Number: 13.2.13A). In addition to being available free of any charge at the PE website, the paper will be made freely available through archiving in Carleton’s new institutional repository (CURVE), which is mandated to collect, preserve and make accessible Carleton’s digital research materials. To encourage more graduate students to publish in open source journals the awards will be made at a publicized award ceremony later this spring. Awardee bios and other publicity material will also be placed on the university web site.
The logo of Carleton University’s open access repository CURVE
Congratulations to Lisa Neville for writing an excellent research paper and publishing it in Palaeontologia Electronica as well as to Carleton University for launching such a proactive initiative. Hopefully other universities will soon follow suit making open source journals a more attractive venue for young researchers to publish their research results.
The Gliridae, the dormice, are small rodents most people don’t even realize exist. Most genera and species live in Europe, some come from Africa and Asia. In Germany, the Edible dormouse Glis glis is proverbial, the German name “Siebenschläfer” refers to the long hibernation of six months or more of these animals. Aside from that, because glirids are nocturnal and did not adapt to human settlements as aggressively as rats and mice, they mostly fly under people’s radar.
Hazel Dormouse (Muscardinus avellanarius). Picture from wikipedia under license mentioned there.
EDIT: I forgot to put this here: the post below is a author’s guest post by Peter Falkingham of the School of Earth, Atmospheric and Environmental Science,
University of Manchester. Enjoy!
This blog post coincides with my latest paper on open source photogrammetry software that appears in Palaeontologia Electronica yesterday. I want to briefly summarize the paper, but also to tell you about where the technology seems to be heading, and try and communicate some of my excitement.
Using just a normal camera, free software, and a desktop computer,
you can generate 3D digital models of everything from hand specimens,
through mounted skeletons, and beyond buildings and outcrops.
In the paper, I present some freely available, open source software for producing high resolution 3D models of specimens ranging from centimetre scale to outcrop scale, using photographs taken with an ordinary camera and processed on a desktop computer. The software was developed by researchers at the Graphics and Imaging Laboratory of the University of Washington, principally to generate 3D models from the growing databases of photographs online (see, “Building Rome in a day”). My paper describes where to get the software and how to use it, and presents a number of examples to illustrate the quality of the models. Great models comparable to those acquired through laser scanning can be generated using any consumer camera, without manual point matching or calibration. The idea is that I wanted to make it explicit to people that the realm of 3D data acquisition is no longer restricted to expensive photogrammetric reconstruction software or laser scanning equipment.
Production of 3D digital models of palaeontological specimens is far more than just making pretty pictures for publications. Previously, digital models have been used to look at body mass reconstructions (Bates et al., 2009a, 2009b; Hutchinson et al., 2011), ranges of motion (Mallison, 2010), conservation (Bates et al., 2008, Adams et al., 2010), or visualisation e.g. cross section/profiling (Falkingham et al., 2009), among many other uses.
Digital models provide an objective data source that can be distributed and shared among researchers as easily as sending an email. The key word there is ‘objective.’ It means that you or I can perform a study, or analysis, and then give the model to someone else to either repeat the analysis or build upon it using the same base data. Journals which are embracing the internet as a medium for publication, like Palaeontologia Electronica, provide a fantastic outlet for presenting this kind of data with publications.
Of course, the problem with trying to publish on rapidly advancing technology is that it does just that – it rapidly advances! When I first submitted the manuscript last year, the commercially available photogrammetry software I was aware of was all very expensive, and required camera calibration and/or specific markers in the images. Since then, the price of commercial software has really plummeted, and they’ve only got easier to use. $200 can get you software with a nice graphical user interface (GUI) to generate the 3D models with the click of a button. There have also been a number of online web services appearing that allow you to upload your photos, and then download the finished model, either for free or relatively small fees [though if using these you should read the terms and conditions carefully, as they might take copyright of the photos and digital models]. This all makes generation of 3D digital data even easier (while the programs described in my paper are easy to use, they are not always entirely easy to set up).
Nevertheless, I maintain that the open source community is where the bleeding edge of the technology lies. The programs used in my paper seem to handle larger data sets more capably than the affordable commercial software (undoubtedly because this is what they were originally intended for with sourcing thousands of images online). They are also being actively developed – take a look at VisualSFM, which provides a GUI for the previously mentioned programs, and importantly takes advantage of the graphics processing unit (GPU) which, in certain cases, can act as the equivalent of hundreds of processors. This enables the software to match the photos into a 3D model in real time (check out the video on the VisualSFM website), using a desktop computer [dense reconstruction still relies on PMVS and runs on the CPU, but this is actively being developed to run on the GPU instead].
It’s very easy to get lost in the possibilities of photogrammetry in the immediate future. In my paper I allude to using photogrammetric software on smartphones. This year, we’ll be seeing smartphones with quad core processors and 1gb of RAM or more, making smaller models easily within their processing power. Already there are apps available for android and iphone that can generate [admittedly basic] 3D models from 3 or 4 photos taken with the phones built in camera.
But it’s not just making the current process easier or faster, it’s the novel possibilities that are really exciting. For instance, how about capturing the 4th dimension, time? Or how about creating accurate 3D models of specimens which were photographed, but are now lost or damaged? One could imagine a fossil tracksite visited by hundreds of tourists each year but exposed to weathering; by using google image search and filtering by date, one could generate 3D models year by year, retrospectively documenting the rate of erosion.
The production of digital models through both laser scanning and photogrammetry has been around for some years. But now that the affordability and usability have reached a level where anyone can produce digital models as needed, I look forward to seeing the ways in which palaeontology can grow, both through novel applications, and through dissemination of data.
Adams, T., C. Strganac, M. J. Polcyn & L. L. Jacobs (2010) High Resolution Three-Dimensional LaserScanning of the Type Specimen of Eubrontes (?) glenrosensis Shuler, 1935, from the Comanchean (Lower Cretaceous) of Texas: Implications for Digital Archiving and Preservation. Palaeontologia Electronica, 13, 1T:11p, http://palaeo-electronica.org/2010_3/226/index.html.
Bates, K. T., F. Rarity, P. L. Manning, D. Hodgetts, B. Vila, O. Oms, À. Galobart & R. Gawthorpe (2008) High-resolution LiDAR and photogrammetric survey of the Fumanya dinosaur tracksites (Catalonia): Implications for the conservation and interpretation of geological heritage sites. Journal of the Geological Society, London, 165, 115-127.
Bates, K. T., P. L. Falkingham, B. H. Breithaupt, D. Hodgetts, W. I. Sellers & P. L. Manning (2009a) How big was ‘Big Al’? Quantifying the effect of soft tissue and osteological unknowns on mass predictions for allosaurus (Dinosauria: Theropoda). Palaeontologia Electronica, 12, 33.
Bates, K. T., P. L. Falkingham, D. Hodgetts, J. O. Farlow, H. Breithaupt Brent, M. O’Brien, A. Matthews Neffra, W. I. Sellers & P. L. Manning (2009b) Digital imaging and public engangement in palaeontology. Geology Today, 25, 134-139.
Falkingham, P., L. Margetts, I. Smith & P. Manning (2009) Reinterpretation of palmate and semi-palmate (webbed) fossil tracks; insights from finite element modelling. Palaeogeography Palaeoclimatology Palaeoecology, 271, 69-76.
Hutchinson JR, Bates KT, Molnar J, Allen V, Makovicky PJ, 2011 A Computational Analysis of Limb and Body Dimensions in Tyrannosaurus rex with Implications for Locomotion, Ontogeny, and Growth. PLoS ONE 6(10): e26037. doi:10.1371/journal.pone.0026037
Mallison, Heinrich. 2010. The digital Plateosaurus II: An assessment of the range of motion of the limbs and vertebral column and of previous reconstructions using a digital skeletal mount. Acta Palaeontologica Polonica, 55:433-458
At the age of 15 years, compared to other fully-electronic palaeo-journals PE is quite old by now. But that doesn’t mean that PE is outdated and old-fashioned. The editorial board always strives to adapt the journal to changes (I am a bit hesitant to use the term “progress”) in technology and science.
Today, I have the pleasure to announce some big changes for the very near future.
First of all, PE will no longer publish all articles in two regular and one special issues. Instead, nearly all papers will be published immediately. That is, once a paper is submitted in its final version, the production of galleys will be done as soon as our staff can manage (remember, most of us are volunteers, the rest are part-timers). Then, the authors are sent the proofs, and once they OK them the paper can go online right away.
Does this really make a difference? That depends a bit on timing. In the old system, if your paper happened to come in one day too late for the second regular issue of a year it would have to sit around for nearly half a year! Obviously, nobody would rush the galley production, but it would still be quite a wait. On the other hand, I have seen papers go from final submission to publication in a matter of days. In the future, you can expect a wait of a few days to a week or two at the most, unless something unexpected happens. The steps in the publication process that take longest will very likely still be peer-review and author’s revisions.
The new publishing schedule is only a small part of all the changes at PE. Starting now, PE will be published using a new Joomla content management system and will have a completely new look. We are still fiddling with the details – to be honest, manging editor Jennifer Rumford and technical editor Mark Sutton are. They are tech wizards and surprising us every day by fixing things to look the way we want them. I’m happy if I manage to have a list show on my blog the way I want to. Jennifer can do these things in her sleep, I believe. She’s a master at making the site perform, and we all look forward to the new look and feel. Mark is also behind the technical aspects of this blog, so if it doesn’t work (a very unlikely event), blame him.
We will also have a RSS feed for new articles, so that you can get notifications every time a new contribution is published.
Now, we all realize that no new design will please all. And PE will not stand still. Yell in comments here or email us about things that you want us to improve. If what you wask for makes sense, and if we can do it, we will!
We’re also planning to get DOIs for our content. This will take a little while, though.
Enough change for now. We look forward to the first articles of 2012, which will go live in a matter of days now.
