Saturday, 30 January 2016

PhD of travelling! Holy moly

I've been living in the UK now for 4.5 years. The first year and a bit was on a student visa (very restrictive, not fun), but for 3 years now I've been on an Ancestry Visa which is much better. This means that at the end of my 5 year visa, I can apply for Indefinite Leave to Remain to settle here in the UK if I choose to. I've been looking up the requirements and eligibility, and stumbled across some fun things.

One of the requirements is that I cannot have been out of the country for 180 days or more in any year. Looking back at my passport, I got a bit worried about that requirement. It seems like so much, but when I'm constantly going to museums, and conferences for work, plus the occasional vacation, it's not that much. This is how I discovered just how much travelling I've done since moving.

Growing up in Canada I didn't fly all that much. I did a few trips, but considering how far away everything was, it was typically for few long trips rather than any short ones. Since starting my PhD, I have been on no fewer than 14 international trips. The majority of those were work related in some way with conferences, field work and museum visits often being tacked onto or followed by a bit of vacation. My PhD has taken me to Germany (several museum visits and SVP conference), Italy (EAVP conference), Romania (field work), Switzerland (PalAss conference), Norway (museum), Canada (museum and field work), and the US (museum), and wanted to reflect on some of this.

Germany

I have spent by far most of my work-related travel going to and from Germany. German museums are full of pterosaur specimens from all over the world, partly because of a lot of German fossil sites like the Solnhofen, but also because of some significant German fossil collectors, and one of the first main resurrectors of pterosaur palaeontology - Peter Wellnhofer. I had a great time in Munich at the Bavarian collection where I got to work with some of the material Wellnhofer originally described, which is some of the best material for understanding pterosaur articulation and bone morphology. Also in this collection are some very famous specimens, and you can read more about it here, along with some material I saw in Stuttgart. I also spent some time in Tübingen, which is a lovely town, and Karlsruhe, where they graciously loaned me a large amount of material that I spent a year CT scanning. Returning the material was fun as we took the train down the day after the Paris attacks with an IKEA bag and a duffle bag full of fossils - 7 trains, 2 nights, and much stress later we managed to hand deliver the fossils to the museum on the 'Incredible Fossil Journey'. And of course we can't forget SVP 2014 in Berlin - my first SVP! 
The dejected bags of fossils after arriving in their final destination in Karlsruhe. Photo by Josh Silverstone.

USA

I've managed to spend some time at 2 different American museums. First, I went to LA to visit one of my supervisors, Mike Habib, and spent a week talking about pterosaurs and looking at some Pteranodon and Nyctosaurus material they have in the museum. They have a few neat specimens that were fun to look at. At the beginning of 2015, however, I got to spend 2 weeks in the collections at the American Museum of Natural History in New York, which was great. They don't have a lot of pterosaur material, but there's an amazing Anhanguera, and some pretty nice Pteranodon bits. While I was there was just at the tail end of the pterosaur exhibition as well, which was pretty cool. 

Canada

Last time I was home I managed to make it down to the Royal Tyrrell Museum of Palaeontology in Drumheller, Alberta to check out the material there. In particular, I wanted to see a partial, 3D preserved azhdarchid specimen that is famous for being partially scavenged. Some of this material has been CT scanned, and I wanted to take a look. I had some time to check out the other pterosaur material, which is plentiful, but not particularly well preserved. However, there's some great azhdarchid material which I haven't found much of elsewhere, so that's great. Plus I like to keep my ties to Canada open, so any data I can get from Canadian museums is a plus, especially when it's so close to home!

I've also got to check out a specimen at a museum in Oslo, Norway which was a lot of fun, have made it to Romania on field work twice, done some field work in Canada (even if that was a bit like a vacation!), and gone to conferences in Switzerland and Italy. 

I'm now in the "buckling down" stage of my PhD where I am heavy into analysis and paper writing, which means most of my travel is done. No more museum visits for me (except in London)! However, I still have some conferences I'd like to make it to, and maybe do some more field work. I've just submitted an abstract to go to the International Congress on Vertebrate Morphology in Washington, DC this June/July, which I'm really excited about. Then in October is SVP in Salt Lake City, which I'd really like to make it to again after missing last year. I'm hoping to submit sometime during the summer of 2017 (or earlier?), and then will definitely be heading to SVP in Calgary in August. I can't not do it when it's so close to home! 

I guess this reflecting has made me realise two things:
  1. I am pretty lucky to be able to do this during my PhD. I have been very fortunate that I've manage to get enough funding to do most of what I wanted to do and the visits I needed to. For this, I am eternally grateful to my grad school, NSERC, the Geological Society, and PalAss for helping out with this. Funding is not always easy to come by (believe me, I know), and I'm so thankful I've been able to scrounge up enough to get it don. 
  2. Palaeontology is pretty awesome. There aren't a lot of sciences that allow you to do this much travel. My husband is a physicist, and sure he travels for conferences, but he doesn't get to spend a week in Germany in a museum collecting data. He sits in his lab in Bristol collecting data for most of the year, then gets to go somewhere else to present it. We are so lucky in palaeontology, and other natural/environmental type sciences (if we can get the funding of course) to be able to do field work and travel as part of our work. Of course it isn't for everyone, and it can get tiring after a while, but it's something I wouldn't trade for the world. I love doing this, and hope I can keep it going!

Friday, 15 January 2016

Look at the little baby dinosaur!

Finally, the baby Chasmosaurus paper is out! This specimen is by no means new to the media or public, being highly publicised since it was first discussed at the Society of Vertebrate Paleontology meeting in 2013, and has been on display in Edmonton, Canada for a period (at least a cast has). However, the highly anticipated description of this specimen is finally out, which is very exciting for several reasons. Not only is this a truly beautiful dinosaur fossil (nearly complete, skin impressions, may the list go on), but it's also very significant (it's a little baby!).

I remember when this specimen was found, as I was still at the University of Alberta then. If I remember correctly, the story goes something like this: In 2010, Phil Currie was wandering through Dinosaur Provincial Park (as he normally does in the summer), when he saw something sticking out of the sediment. He thought it was a turtle shell (which are fairly common in the area), but he thought he'd investigate. Once he started uncovering it, he realised he had found something truly special, but just how special wasn't clear until the animal was uncovered - a nearly complete baby Chasmosaurus, the smallest baby ceratopsid, missing just it's front limbs and part of the pectoral girdles, and a few tail vertebrae. This specimen was so special that it was hidden in the lead preparator's office (Clive Coy), and I remember them taking off the blanket that constantly covered it so I could see. The specimen was recently published by Currie and colleagues in the Journal of Vertebrate Paleontology. And here it is:
Baby Chasmosaurus from Currie et al. (2016)
Isn't it cute! While adult Chasmosaurus are typically 4-5m in length, this little one was just 1.5m long, making it the smallest ceratopsid ever found. It can be hard to determine what species juvenile fossils belong to due to the change in morphology throughout an animal's life (ontogeny), but several features of the skull tell us this was a Chasmosaurus. Juvenile dinosaurs are important because they show us how animal's grew, and can give us ideas into what features were important for adults. For example, there is virtually no evidence of the nasal horncore in this specimen, and only very small orbital horns, showing that these features grew later on in the animal's life, possibly relating to sexual maturity. Another cool feature of this specimen is that it had skin impressions preserved, which is not very common, and the reason for blocks of matrix still present on the specimen that have not been removed.
Baby's skull - look at the tiny orbital horns! From Currie et al. (2016).
Skin impressions from Currie et al. (2016)

Aside from the obvious awesomeness of the preservation and completeness of this specimen, it's also significant for what it shows about determining species in juvenile animals, and using juveniles in phylogenetic analyses. Using 2 different phylogenetic analyses made the animal move around quite a bit in the ceratopsid tree. When doing the analysis using all features, including characters that are very clearly juvenile or immature features/states, this little dinosaur comes out at the base of the ceratopsid tree, close to a juvenile Triceratops and along with centrosaurine ceratopsids. This isn't really surprising as centrosaurines are known for having shorter, wider frills, and this is obviously a feature of this juvenile, but this is also known to change throughout ontogeny. Centrosaurines also have smaller orbital horns, a feature seen in this specimen, but which is not common in chasmosaurines. When these immature features are coded as unknown (?), the specimen ends up in the right place, nestled with Chasmosaurus belli and Chasmosaurus russelli. This shows the importance of how careful you need to be when using immature specimens in a phylogenetic analysis of any kind.

If you want to hear a bit more about this find and other dinosaurs from Alberta, check out my Palaeocast interview with Phil Currie.

This specimen has been CT scanned (yay!) and we can expect more studies on this awesome little dude in the future. Until then, imagine this little guy running around, about the size of a golden retriever (credit to Andy Farke for that comparison!) and just try not to go "awwwwww!".

Reference:
Currie P.J., Holmes R.B., Ryan M.J., and Coy C. 2016. A juvenile chasmosaurine ceratopsid (Dinosauria, Ornithischia) from the Dinosaur Park Formation, Alberta, Canada. Journal of Vertebrate Paleontology, DOI: 10.1080/02724634.2015.1048348. 

Tuesday, 12 January 2016

Scholarship applications, the bane of my existence

I've talked a lot about my situation as a PhD student that is not fully funded, and this is something I have had to deal a lot with over the years. My funding situation has meant that I have applied for a lot of scholarships or awards over my time as a graduate student. I'm not going to tell you how many have been successful, but I've written over a dozen applications/cover letters/budgets for anything from £200 to go to a conference, up to a full research scholarship worth $21000 CAD/year. Sometimes it's just a simple letter to prove your case and show why you need funding, and other times it's a full application with your background, CV, research proposal, references, etc.

Regardless what the application requires or what it's for, I always have the same thought: How do you decide if it's worth the time?

I have always gone with the belief that if you qualify for it, and there's a chance you could get it (even if that's a small chance), to go for it, if you can spare the time to apply for it. This is part of why I've applied for so many. Many of them I didn't think I'd get, but I figured why not? And one of those includes the biggest and the one that saved my PhD - a 3 year research award from the Canadian government that I never expected I'd get. Basic statistics - 10% of people need to get it, and eventually you will be in that 10%, right?

But lately I've been thinking maybe this is not the best tactic. Maybe it's because I'm getting later into my PhD and so my time is more precious, but I just can't help but think "Is it really worth it?". My husband has a strategy of working out whether or not things like this are worth it. It's related to the likelihood you'll get the scholarship (which is a bit of a guess of course), and the amount of money it's worth. Then he decides if it is worth it for that amount. Typically this means he doesn't bother applying for anything small, as the metric isn't high enough. That being said, he generally doesn't apply for anything because he doesn't think the effort is worth it, but I suppose he has less reason to apply for things like travel grants (he doesn't have to go to museums all over the world to do his research).

I have a deadline coming up for a Canadian scholarship that I have applied for before and been unsuccessful. They don't tell you why you are unsuccessful, but I suspect it's related to my number of publications. I've been debating whether or not to apply again and if it's worth it, but it's a significant chunk of money, and not a large amount of work, so I likely will. I'm sure I still won't get it, but my CV has improved, and I am on par with previous winners in most categories, so I'll give it a go.

So how do I decide whether or not to apply? I ask myself a series of questions:

  1. Do I really need the money? Will I be able to do the research/survive without it?
    • If the research won't happen without the money, then I always give it a try. If I can survive without the money, then it depends. For example, could I survive without this next one? Yes, but it would be a lot easier with it. My husband and I pay rent in 2 cities, plus transportation between them, and I don't get a stipend... so it would be nice to stop using my savings to pay for my PhD.
  2. How competitive is the scholarship? 
    • This is tough and not really quantifiable. If I can get my hands on them, I look at past winner profiles. Can I match any of them? If I'm not anywhere near the previous winners, then there is probably no point. If, however, I'm not far off, then I'll normally try it. 
  3. Finally - how much work is the application?
    • Again, hard to quantify. If the application is easy, always go for it. I normally have a fairly updated version of my CV ready to go, and sometimes all you need is a CV, cover letter, and a budget. If I'm busy, then it's probably not happening. There's a very complicated Canadian one that I applied for last year and didn't bother with this year because it involved something like 7 copies of each document, and all this crazy stuff. Not worth my time... But this is possibly the most important question. If you're too busy and stressed, then it's probably best to leave it. You likely won't write the best application if you rush it, and chances are, it's not worth stressing yourself out more. Again, if it's a really big one then maybe it is worth it.
Those are my thoughts about applying for awards and scholarships, but I'm curious about other people. How do you decide? Do PhD students generally apply for a lot of awards? Or very few? What about as post docs or early researchers? Any advice for other students thinking about scholarships?

Tuesday, 29 December 2015

Earliest theropod abdominal air sacs?

Skeletal pneumaticity is the presence of air within bones of animals. This is typically in the presence of sinuses (think of your face and your achey sinuses during a cold, caused by a build up of pressure in the air spaces), or in birds, when the respiratory system projects part of itself into the bones to invade and hollow them, typically seen in in many avian vertebrae and wing bones. In birds, their respiratory system is more advanced than those in mammals, with air flow being separated between oxygenated (the air breathed in), and de-oxygenated (used air being breathed out), while mammal respiration is less efficient mixing both oxygenated and de-oxygenated air.  For more background on pneumaticity and post cranial pneumaticity, check out my previous post on pterosaur pneumaticity (and the lightweight skeleton of birds.

In addition to birds, postcranial pneumaticity is commonly found in some animals in the fossil record, including pterosaurs, and non-avian dinosaurs. Sauropods often have highly pneumatised vertebrae, thought the help keep them light and facilitate movement of their massive necks, while some theropods have pneumatic vertebrae and even postcranial elements in some species. Traditional studies on pneumaticity have used just visual methods to identify pneumatic foramina and determine if elements are pneumatic, but more recently, scientists have started using CT scans to look inside the bones and determine if they are pneumatic. This allows us to see through any matrix present, and see where the foremen leads to, without destroying the specimen.

The presence of pneumaticity in theropod dinosaurs was originally thought to be something leading towards birds, as the efficient respiratory system is believed to be what allows birds to be so successful, allowing for better breathing during flight. However, the exact timing of the bird-like respiratory system has been unclear and controversial. A new study, lead by Akinobu Watanabe from the American Museum of Natural History, and published in PLOS ONE, looked at the presence of postcranial pneumaticity in Archaeornithomimus and other ornithomimosaur dinosaurs, a group of theropods not directly on the branch to modern birds. Using CT scans, they were able to show that Archaeornithomimus had pneumatic cervical (neck), dorsal (back), and caudal (tail) vertebrae, but there was no unequivocal evidence of pneumatic sacral vertebrae, although there were some possible pneumatic fossae. Watanabe et al. (2015) also looked at other ornithomimosaurs to look at the evolution of pneumaticity in this group, but unfortunately these specimens were studied without CT scans. They found that the cervical vertebrae of Nqwebasaurus (basal ornithomimosaur), Pelecanimimus, Gallimimus and Ornithomimus showed evidence of pneumaticity, while the dorsal vertebrae of Gallimimus are also pneumatic. They suggest that the sacrum of Gallimimus is also pneumatic, but without CT scans showing precisely where these foramina are going, it's hard to be sure.
Cervical vertebrae and CT images taken at specific points of Archaeornithomimus (Watanabe et al. 2015)
Now the important part of the paper - what does is mean for the evolution of pneumaticity in ornithomimosaurs? Compared to several other groups of non-avian theropods, ornithomimosaurs are less pneumatic. Basal members are less pneumatic (with just their cervical and possibly dorsal vertebrae showing evidence), while more derived members Archaeornithomimus, Gallimimus, and Deinocheirus may have independently evolved higher levels of pneumaticity, which is especially evident in Deinocheirus. Additionally, the presence of a pneumatic hiatus, or an area where the vertebrae appear not to be pneumatised between two sections that are, suggest the presence of distinct air sacs. In the case of Archaeornithomimus, the dorsal and caudal vertebrae are pneumatised, while the sacral are not, suggesting that ornithomimosaurs may have had distinct abdominal air sacs, the evolution of which has been contentious in theropods. If this is the case, this represents the earliest appearance of abdominal air sacs in coelurosaurian dinosaurs. The authors suggest that this may mean that pneumatic hiatuses have been missed before, without the use of CT revealing other pneumatic features.

This paper highlights the need for CT scans in fossil data, and the numerous questions that still exist in understanding the evolution of post cranial pneumaticity in birds, dinosaurs, and of course in my favourites - pterosaurs. As postcranial pneumaticity evolved in all of these groups, several questions about their evolution exist. Derived pterodactyloid pterosaurs appear to have had abdominal air sacs as well, so did they evolve first in a common ornithodiran ancestor, and were subsequently lost by ornithischian dinosaurs and other pterosaurs? Or did they evolve in a basal saurischian ancestor and pterosaurs separately? Or possibly they evolved several different times? We still don't know the answer.

Reference:
Watanabe A, et al. (2015) Vertebral Pneumaticity in the Ornithomimosaur Archaeornithomimus (Dinosauria: Theropoda) Revealed by Computed Tomography Imaging and Reappraisal of Axial Pneumaticity in Ornithomimosauria. PLoS ONE 10(12): e0145168. doi:10.1371/journal.pone.0145168

Wednesday, 9 December 2015

Where to publish?

As a student, choosing where to publish your next paper is extremely important in order to showcase your research and build your reputation. Perspective employers look at the journals you publish in to rate your research and decide how employable you are, which makes it very stressful making the decision.

So how do you decide? This is something I really struggle with. On one hand, I believe in the Open Access movement, and think that papers should be open and not behind a paywall. I also agree with the thought that impact factor is fundamentally flawed, and doesn't necessarily say anything about the quality of research. Often papers published in the highest impact journals are not the best scientifically, but are "sexy", so they make it in, while extremely important and excellent science gets published in lower impact journals because they may not be as sexy. While I don't feel the need to chase for higher impact factors, the more I talk to senior academics and post doctoral researchers, the more I am told that it is still important. Everything I've heard about getting a job later is that employers look at the journals you have published in, even if they maybe shouldn't.

I'm looking for a bit of advice, combined with giving a bit of my own, from what I've been told after talking to other people. Of course in palaeontology there are a few journals specifically for the topic, such as the Journal of Vertebrate Paleontology, Palaeontology, Acta Palaeontologica Polonica, and more. These are typically good for descriptions of new taxa, new localities, and more specifically palaeontology-related topics. Other journals such as Biology Letters, Proceedings of the Royal Society B, Journal of Anatomy, Journal of Evolutionary Biology are good for papers that have a wider interest than just palaeontology. Then there are open access journals such as PeerJ and Plos One that allow you to publish any aspect of palaeontology that you want, including a lot of data and supplementary material, which is extremely useful. For me, I think about what I'm trying to publish (do I have a lot of data? Is it strictly palaeontological, or is there a wider use for my work? Is it ground-breaking, or just a bit more data to add to an already painted picture?), the reputation of the the journals (more so than impact factor), and personal experiences with specific journals of myself or people I know.

I have a paper that I'm getting ready to submit, that is not sexy, but has some important data. I was planning on submitting it to a Canadian journal that is not high impact, but is well respected and they like publishing palaeo papers. Then I was going to submit it to a new journal, which is completely open (free to submit, and free to access), but after talking to some senior academics (including the editor of the new journal), I was encouraged that as a student I should not submit to any journals that are new and do not have impact factors yet. So my question is, what about submitting to new journals that are published by well known publishers like the Royal Society or Canadian Science Publishing?

What other advice to people have when deciding what journal to submit to? Especially keeping in mind that I'm a student and have a lot of things to think about... And advice for lots of other people reading as well!

And don't forget to do the survey!I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers. If you complete the survey, you will be entered to win a prize, and be given a high resolution science photograph.

It only takes 5 minutes to complete the survey. Begin here: http://bit.ly/ScienceBorealisSurvey

Sunday, 29 November 2015

Dimetrodon is Bathygnathus? Or Bathygnathus is Dimetrodon?

While the west of Canada is known for Late Cretaceous dinosaur fossils, the east has a number of Paleozoic outcrops with some early terrestrial tetrapods. In 1845, before Canada was even a country, a fossil of an upper jaw and some teeth was found on Prince Edward Island, and was first described in 1854. As the second ever vertebrate fossil to be found in Canada, this specimen has had an interesting history.

It was first identified as an extinct 'saurian', then as a dinosaur, followed by a theriodont, and finally correctly identified as a sphenacodontid, a group of early synapsids (a group of tetrapods with no temporal fenestra, or holes, in their skulls, consisting of mammals today) which includes the famous extinct sail-backed reptile Dimetrodon grandis. It hails from the Lower Permian, 283-290 million years ago, and was called Bathygnathus borealis. The fragmentary nature of the fossil made it difficult to determine the exact affinities of this specimen. Over the years it has been studied by a number of people, and similarities have been identified with Dimetrodon, Sphenacodon, and Ctenospondylus, but the similarities have never been major enough to warrant an official change. That is, until now.
ANSP 9524 - type specimen of 'Bathygnathus' borealis (Brink et al. 2015)
Dr. Kristin Brink worked on Dimetrodon and similar animals during her PhD research at the University of Toronto (Mississauga) and studied the specimen which is now housed at the Academy of Natural Sciences in Philadelphia. Primarily working on tooth of these similar animals, she was able to study the specimen using CT scans and compare it to other sphenacodontids[1]. She re-described the specimen and underwent phylogenetic analysis and found some interesting results, including that dental characters appear to be extremely important in sphenacodontid taxonomy. Based on phylogenetic analysis of morphological characters, Dr. Brink found that 'Bathygnathus' borealis appeared as a sister taxa to Dimetrodon grandis, and nestled within 3 species of Dimetrodon.
Cladogram showing position of 'Bathygnathus' borealis (Brink et al. 2015)
'Bathygnathus' borealis has the same tooth count, denticles, and tooth roots as Dimetrodon grandis, characters only found  in D. grandis. Brink et al. (2015) concluded that 'Bathygnathus' borealis was actually Dimetrodon borealis, making this specimen the first and only Dimetrodon in Canada.

The interesting and very important thing about this paper is related to the the rules of taxonomic nomenclature and priority. Bathygnathus borealis was named 20 years before Dimetrodon, meaning that by the law of priority, Bathygnathus should have priority and replace Dimetrodon. However, Dimetrodon is a well known and very famous fossil and no one wants to lose that name. Exceptions are occasionally made when there is a strong reason to retain initial names, and they have started a case with the International Commission of Zoological Nomenclature (ICZN), the group responsible for taxonomic names and problems like this. If they succeed, we won't lose Dimetrodon, but gain a new species of 'Dimetrodon' borealis!

And don't forget to do the survey! I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers. If you complete the survey, you will be entered to win a prize, and be given a high resolution science photograph.

It only take 5 minutes to complete the survey. Begin here: http://bit.ly/ScienceBorealisSurvey

References
Brink KS, Maddin HC, Evans DC, and Reisz RR. 2015. Re-evaluation of the historic Canadian fossil Bathygnathus borealis from the Early Permian of Prince Edward Island. Canadian Journal of Earth Sciences 52: 1109-1120.

Wednesday, 25 November 2015

Survey time! Please take part :)

To my readers...

I've teamed up with Science Borealis, Dr. Paige Jarreau from Louisiana State University and 20 other Canadian science bloggers, to conduct a broad survey of Canadian science blog readers. Together we are trying to find out who reads science blogs in Canada, where they come from, whether Canadian-specific content is important to them and where they go for trustworthy, accurate science news and information. Your feedback will also help me learn more about my own blog readers.

It only take 5 minutes to complete the survey. Begin here: http://bit.ly/ScienceBorealisSurvey

If you complete the survey you will be entered to win one of eleven prizes! A $50 Chapters Gift Card, a $20 surprise gift card, 3 Science Borealis T-shirts and 6 Surprise Gifts! PLUS everyone who completes the survey will receive a free hi-resolution science photograph from Paige's Photography!  


It's a great chance for me to get feedback on who is reading my blog, and for Dr. Jarreau to get more detailed feedback about Canadian science blogs in general, but of course, you don't need to be Canadian to take part. Please take the time to fill out the survey, and you may even win a prize!

FYI I'm registered with Science Borealis as Liz Martin-Silverstone, so that is probably the name to use when they ask.

Thanks to all in advance!
Liz