PhD at Southampton!

I have some great news! Just over a week ago, I went to Southampton for a PhD interview for a project on mass estimation in pterosaurs. That weekend, I was offered the project and some funding, which I officially accepted on Friday. I will start sometime at the beginning of October, and will be moving to Southampton probably in September. I'm really excited about it as I get to do some work that was directly related to some cool stuff I found in my Master's!

The project will be supervised by a combination of Bristol and Southampton supervisors, with Gareth Dyke being the main supervisor. As the project will rely heavily on CT scans, we're hoping to take advantage of the excellent CT scanner that Southampton has, and I've managed to secure access to a few specimens already for scanning. It will expand on what I did for my MSc with Colin Palmer (who will be involved in the PhD as well), which was developing a method of estimating bone mass using CT scans, which resulted in some pretty interesting finds. The masses for the bones we measured were about twice as heavy as what previous methods had found, which is very interesting. That paper is currently in review, and we are confident that it will be successful!

This PhD will expand on the MSc work by looking at more bones, and more importantly, more groups and taxa of pterosaurs. This way, we should be able to gain some insight into the bone mass of several different animals, but also how this may be related to phylogeny, and how bone and body mass may have evolved throughout the Pterosauria. Once bone mass has been determined, I am hoping to apply some modelling techniques to get an idea of soft tissue mass, using some of the muscular reconstructions in the literature.

All-in-all, I think I will be very busy for the next few years, learning all about pterosaur bones and mass. I'm really excited that I have finally sorted out a PhD, and that it's doing something that I am very interested in! Stay tuned for more details coming soon :)

Projects Galore

Apparently it has been 2 months since I last wrote a post, so I figured I should give a bit of an update on what's going on with me. In short: a lot. I have been so busy in the last month and will continue to be until I head back to Canada in June. So, what is keeping me busy you ask?

1. I'm still in the process of trying to get my first publication. I've heard that the first publication is always the hardest (although I'm not sure any of them are "easy"), but I just want this thing done! I have just spent the weekend re-formatting it to submit to a different journal than we originally aimed for, and adding some things to make it better, and we should be submitting it sometime soon. I really want to get this thing out! Stay tuned!

2. With some help and encouragement from Matt Wedel, I've decided to try to do some Air-Space Proportion work on the pterosaur bones that I have scans for. On the plus side, I already have all the information that I need, and I just need to convert the numbers. I've now done this for all the bones I've already analysed, and I need to do it on a few more partial bones that I have scans from (thanks to my supervisor Colin Palmer) but not analysed. The preliminary work is showing some pretty interesting stuff with some things coming out as completely different from what you might expect. I'm also hoping to take a look at some pigeon CT scans to compare them to. My goal is to work on this as much as possible and present it at SVPCA in Edinburgh in August. Exciting stuff!

3. I'm also still working on a paper from my undergrad thesis on Centrosaurus, which I'm hoping will be getting there soon. I spent about a month working on a matrix on mainly centrosaurines, and have been waiting to hear back from my undergrad supervisor about it. I heard a few weeks ago that he was doing some unrelated analyses using my matrix, to see if it worked, which is exciting. In the meantime, I'm planning on presenting this work in a poster at the Progressive Palaeontology conference in Leeds next month. Finally something to show from this project!

4. And finally (project wise), the project that has been taking up most of my time is the one that I can say the least about. I'm currently doing some really interesting work on some tiny fissure fossils from Wales. It's pretty neat, but I can't really talk about it much yet. If we get enough done, I just might present this at PalAss in Zurich in December!

5. I'm also preparing for a PhD interview at Southampton which will take place next month. I'm extremely nervous about it, and I'm not sure what to do for preparation. Eek!

All-in-all, lots going on for me! I'm hoping that I'll be able to get a few papers out of these various projects, which will be really interesting and exciting!

Making Data Public (and a small matrix-related rant)

In the world where there is a constant debate over the merits and disadvantages of Open Access journals and science, we are often bombarded with blogs and posts about it. I am generally a silent proponent of Open Access journals, agreeing that it is important, but not particularly versed in all of the politics so I tend to keep quiet. That being said, I have recently stumbled upon a related issue that has affected me in the last few weeks: the importance of making your data public.

Although my primary research interest is in pterosaurs, I am currently writing up a manuscript from my undergraduate thesis, which was on the ceratopsian dinosaur Centrosaurus. Much to my surprise, the most recent discussion with my former supervisor (and the senior/co-author) went in a different direction than I was expecting: he wanted me to develop a character matrix and do a phylogenetic analysis. Now I've never done this before, although I've taken several courses and have a good basic understanding of the concept, I've never actually developed a matrix and done my own analysis. Upon discussion with him, we decided that I would use several published matrices and merge them together, taking several characters from each matrix.

Looking through recently published matrices, I came across the Farke et al. (2011) paper in which Spinops sternbergorum was described. I sent him an email, and he was very happy to share the matrix, and character descriptions (although those are available from the supplementary information of the paper) and he sent along the .nex file. Super helpful, because then I had it already in a matrix that I could open, copy, paste, edit, etc. Thanks so much for that Andy! Then, I had to add some taxa that were published more recently, like Xenoceratops foremostensis (Ryan et al. 2012), and Pachyrhinosaurus perotorum (Fiorillo and Tykoski 2012). The Xenoceratops matrix was published directly in the paper as a table (not as easy to follow the correct character number, but available), while P. perotorum was found in the supplementary material (in a more easily viewable format). The best, however, came when I looked up a paper on Anchiceratops (Mallon et al. 2011). On the downside, the paper is published in a non-open access journal, which means not everyone can access it. On the BIG upside, included in the supplementary material is the actual .nex matrix file which allows you to see all the characters, states, and taxa, right in the format you want. It makes it soooo much easier to access and much quicker when these are available at your finger tips, without having to send many emails to people asking for it. There are several other (mainly older to be fair) phylogenetic papers that don't post the matrix, or characters used, which makes it really difficult to figure out how they've done things.

Unrelated to my story, and covered much in other places so I won't cover it in detail here, is a wonderful story of a recent publication that used previously published data in a huge analysis. Larson and Currie (2013) were able to study over 1000 small theropod teeth from southern Alberta, using data that had previously been published and new data. A study of this scale would clearly have taken a lot longer if they had to do sit down and do all the measurements on 1183 small teeth. Fortunately for them, (and us), they were able to spend their time analysing the data already available, rather than painstakingly measuring them. They determined that the number of small theropods present from this area has been greatly underestimated, and that many species are known only from teeth. Cool! For more information, you can check out this blog by Jon Tennant.

Take home message: make your data open to everyone! For the most part, I have dealt with people who are extremely open and willing to email me stuff if it isn't posted. But wouldn't it be better if you didn't have to email every time? If you could just go online and access it? It shouldn't be some top-secret information. Post it!

And finally, a small rant on matrices. I know that there are disagreements about characters, so not every published matrix is going to use exactly the same characters, but WHY do people insist on changing character states around in a way that just makes things difficult?? For example, there are several characters in Fiorillo and Tykoski (2012) that are just different enough from all other matrices I've looked at that you can't just directly copy the states. Why is it necessary to switch it from the postorbital horncore height being compared to the basal skull length (which every paper does) to comparing it to the length of the face? Or change numbers slightly so one one paper a character is considered to be long if it's 0.8 or more, while in another it's 0.75? Pretty sure that is unnecessary! Make it easy, people!

References:
Farke, A.A. et al. 2011. A new centrosaurine from the Late Cretaceous of Alberta, Canada, and the evolution of parietal ornamentation in horned dinosaurs. Acta Palaeontologica Polonica 56: 691-702. Freely accessible here.
Fiorillo, A.R. and Tykoski, R.S. 2012. A new Maastrichtian species of the centrosaurine ceratopsid Pachyrhinosaurus from the North Slope of Alaska. Acta Palaeontologica Polonica 57: 561-573. Freely accessible here.
Larson, D.W., and Currie, P.J. 2013. Multivariate analyses of small theropod dinosaur teeth and implications of paleoecological turnover through time. PLoS ONE 8: e54329. Freely accessible here.
Mallon, J.C., et al. 2011. Variation in the skull of Anchiceratops (Dinosauria, Ceratopsidae) from the Horseshoe Canyon Formation (Upper Cretaceous) of Alberta. Journal of Vertebrate Paleontology 31: 1047-1071.
Ryan, M.J., et al. 2012. A new ceratopsid from the Foremost Formation (middle Campanian) of Alberta. Canadian Journal of Earth Sciences 49: 1251-1262.

Moving up in the world!

I have news! I have now officially graduated from my Masters! I now have a Masters with Distinction! Hurrah! Since graduating, I've also submitted my PhD application for a PhD at the University of Southampton. I'm super excited about this, as the project will be a continuation of my project at Bristol looking at body mass of pterosaurs. Now I just have to wait to hear from them about an interview, which I've been told should be sometime in March. Now I will start preparing for my interview. I've never done an academic interview before, so any suggestions would be greatly appreciated!

Next on my list is to get some publications done. I have (again) sent my pterosaur manuscript to my MSc supervisor to edit. I'm really confident that it's nearly ready to submit. I think I've addressed the major issues that it had, and hopefully will be sending it in shortly. Unfortunately, in addressing these issues, it has gained too many words and it's now over the word limit. Now I'm not sure what to do! I'm also still working on a Centrosaurus paper that I've been working on since my undergrad. I just have to do a phylogenetic analysis and it'll be done. Oh ya, and re-write a bunch of stuff. In a couple of months though, I could have not one, but two publications! Just need to focus for the next few weeks!

Flying things that lived a long time ago

Inspired by an awesome XKCD comic, this is what I study using only the thousand most common English words. Well, it's more of a description of the animals, but it's still entertaining. I'll work on it and get a better one later, but this is the start: 

I study flying animals that died a really long time ago. They are cold blooded animals and had some hair-like covering but lots of skin. They flew using a really long finger and skin that went from the end of the finger to their legs. They moved their arms up and down to push against the air and fly. These animals were the biggest flying animals ever, some as big as a bus, but others were small. Some had lots of teeth that they used to catch food, but others had no teeth and ate animals that live in water whole. I look at pictures of their inside hard body parts to guess how heavy they were. This can tell us if they would have been too heavy to fly, and how they could fly. Did they use their power to fly? Or just put their arms out and let the air push them? We can look at animals that live today to better understand animals that lived a long time ago.

If anyone wants to give it a go, try it out here!

Hitting the wall

Manuscript A: Alright. I have a problem. My goal was to finish my pterosaur manuscript a long time ago, and for sure finish it by the end of this month. Of course, that did not happen, and isn't going to. Part of the reason is that I discovered I did some very silly things originally that I need to correct and address in order to get it to publication quality. The problem is, this involves re-doing several of my analyses. Do you know how much time it takes to re-analyse all the CT scans I've done so far? And it's not exactly the most stimulating, it's sitting with ImageJ all day. So needless to say, I have hit the wall with this paper right now. I suspect that when I get back to the UK I'll be more productive again. But we'll see.

Then we have Manuscript B: the dreaded undergrad thesis. I have been working on this thing for a few years, and I really want to see it through, but it's getting harder and harder to stay motivated. It's on something completely unrelated to what I'm working on now (I looked at skull morphology in Centrosaurus to be exact), which makes it hard. I've started working on it again, and I need to re-learn all the ceratopsian skull terminology. Met with my former supervisor and co-author last week, and he decided that I need to do a phylogenetic analysis, which I've never done before outside of an assignment. Thanks to Andy Farke, I have a matrix to work with, and I'm slowly combining a few different matrices. I'm slowly learning how annoying it is when people use slightly different characters (like one paper uses one character as 0-75% and others use 0-80%. Why you have to be so difficult!), or switch around the character states. All in all, it's not too bad, just time consuming.

I suppose that after this year of ups and downs, I'm just burnt out. I've needed this break so badly without even realising it. What I would like to know is how people deal with the loss of motivation? What makes you push to get stuff done? I'm in serious need of being prodded into productivity... Help!

The 70 kg Quetzalcoatlus debate

Last week, a press release went out from Texas Tech University on some findings that were presented recently at Geological Society of America annual meeting. This is not abnormal. What is unfortunate, is that the press release covers a talk based primarily on a study by Chatterjee and Templin from 2004, and other results that have not been peer reviewed. Mark Witton, Mike Habib, and Brian Switek have all done a great job discussing why this is bad, troublesome, and poor science (you can check those out here, here, and here), so I won't get into that. For me, having spent the last year looking at pterosaur mass and how we estimate it, my big problem is the mass of Quetzalcoatlus associated with this study.

For a super brief explanation on how some mass estimates are determined for pterosaurs, check out my previous post on pterosaur mass estimation. Chatterjee and Templin (2004) determined that 70 kg was the absolute maximum that Quetzalcoatlus could be, based on estimates by Atanassov and Strauss (2002). This was determined using a principal component regression method based on different skeletal measurements. For more information, check out their poster here. The rest of the conclusions in Chatterjee and Templin (2004) are based on the 70 kg mass, and fail to take into account recent studies like the quadrupedal launch hypothesis by Habib (2008). They determine that if Quetzalcoatlus was more than 70 kg, it would not have been able to take off, and that at 70 kg, it would have needed a hill or cliff to successfully take to the air. This is based largely on the theory that pterosaurs took off the same way as birds, from two feet, rather than the quadrupedal launch. When accounting for the quadrupedal launch, and other adaptations, a higher mass is possible. Other estimates for Quetzalcoatlus range from 259 kg (Witton 2008) to 544 kg (Henderson 2010).

Aside from that, there is a huge problem with a 70 kg Quetzalcoatlus, which has been discussed by Witton (2008): in order for Quetzalocoatlus to be 70 kg, it would have required it's body to be about 60-90% full of air. Recently, the 70 kg estimate was put into prospective for me. First of all, an important piece of information is required. Quetzalcoatlus is about as tall as a giraffe, with a wingspan of 10-12 m, as seen in a great image by Mark Witton:

That is a HUGE flying animal! Now picture a 70 kg giraffe. For the record, giraffes are about 1600 kg on average. Putting it down to 70 kg is a bit impossible. This was even more obvious to me when I realised that my brother is about 70 kg, and probably pretty similar in size to the guy in the picture. So now imagine taking that mass, and spreading it over the size of a giraffe. It doesn't work! Yes, pterosaur bones are lightweight, but they are not THAT lightweight. According to Witton (2008), the skeleton itself was 18 kg, and other evidence suggests that might be a low estimate (Martin and Palmer 2012). How then is it supposed to have only 52 kg (maximum!) of muscle, still be able to successfully cover its body in skin and muscle, AND be able to fly?! It's not possible! I do not understand at all how someone can justify a 70 kg pterosaur with a wingspan of 10-12 m, and to my knowledge, they have not tried to explain it, or to scientifically address the heavy mass estimates. Not cool!

So basically, my question is this: how does anyone expect a 70 kg Quetzalcoatlus to have the muscle necessary to fly, walk, or even live?! The answer: it doesn't. Which is why the 70 kg estimate and anything based off of this estimate is incorrect.

References
Atanassov, M. and Strauss, R. 2002. How much did Archaeopteryx and Quetzalcoatlus weight? Mass estimation by multivariate analysis of bone dimension. Poster at Society of Vertebrate Paleontology annual meeting. Download here
Chatterjee, S. and Templin, R. 2004. Posture, locomotion, and paleoecology of pterosaurs. Geological Society of America Special Publication 376: 1-64.
Habib, M. B. 2008. Comparative evidence for quadrupedal launch in pterosaurs. Zitteliana Reihe B 28: 159-166.
Henderson, D. M. 2010. Pterosaur body mass estimates from three-dimensional mathematical slicing. Journal of Vertebrate Paleontology 30: 768-785.
Martin, E. G. and Palmer, C. 2012. A novel approach to estimating pterosaur bone mass using CT scans. Symposium of Vertebrate Palaeontology and Comparative Anatomy oral presentation. Abstract on page 18 and can be downloaded here.
Witton, M. P. 2008. A new approach to determining pterosaur body mass and its implications for pterosaur flight. Zitteliana Reihe B 28: 143-158.