... being able to arrange work around major catastrophic events, such as the floods effecting Queensland and heading to Brisbane right this minute.

Torrential downpour over the Australia Day long weekend led to my office being flooded (again!). Figuring that I had only just got my equipment replaced from the last flood incident, and I might become stranded at uni if I worked there this week, I decided to pack everything up and work from home.

So that's one of the huge bonuses of being a self-managed PhD student: you don't have to get special permission to take my computer and work from home. You can decide what's going to work best for you, and what will be the most efficient use of your time, and act on that.

My only other problem is that my crocodile and fish decay experiment is situated about 20 m from the Brisbane River, but thankfully it is about 5 m above the current river height. Given that the current flood level predictions don't show that area being inundated, that the river height is only going to be half what it was in 2011, and that same area didn't go under in 2011, I figured the experiment was safe. Not that there is much I can do: I can't move anything because it's a.) too heavy, and b.) would affect my results. So now I just have to sit and wait it out.

To my fellow Brisbanites: don't drive anywhere unless you absolutely have to, consider working from home (if you can), maybe take annual leave if you can afford too, and please stay safe!

Old timey maps are awesome, as anyone who grew up reading atlases for fun, or 'The Island of Lost Maps: A True Story of Cartographic Crime', would know. And now, here is the ultimate map for a palaeontologist... an accurate illustrated map of Triassic Pangaea!

Here's hoping he creates similar maps for the Jurassic and Cretaceous too!

Nothing to do with palaeontology, PhDs, or dinosaurs, but too funny not to post!

Courtesy of Married To The Sea

I have a sick feeling in the pit of my stomach, and the muscles of my right shoulder are aching.
The cause of my malady? Trying to find a goddamn note-taking system for my PhD that works.

It should be simple. I should read the PDF papers I have, take some notes, and write relevant information into the papers I'm currently drafting. But I've spiralled into a vortex of note-taking software and hardware.

It all started when I decided to borrow a Wacom Bamboo tablet. I wanted to devise a paperless note-taking system that still allowed me to hand-write notes, and it seemed that the Bamboo tablet was the answer. Hand writing notes versus typing them out has always been my preferred modus operandi. The Bamboo would allow me to write digitally on PDFs, and ta-da! Perfection. Only problem was, I had no idea what software to use.

I searched extensively for a program that would let me handwrite over a PDF using the tablet, that works on Mac OSX and Windows 8, that is also free. Not as easy as I'd hoped! As it turns out, the best programs aren't free (PDF Annotator, Inkbook) or don't run on Mac (AutoInk plug-in for Adobe Acrobat), and the free ones don't easily allow annotation (PDFPen forces you to re-select the pen tool every time you write a new character), or don't allow for smooth writing (Skim, Adobe Acrobat).

It might sound fussy, but when the alternative is cheap paper and my legible handwriting, I want the best I can get. The Bamboo tablet did come bundled with some software that allows you to annotate a virtual note-book (Bamboo Paper - but the handwriting isn't very smooth), or write on screen and it translates it directly into text (Bamboo Scribe), to be pasted in any application. And in fact, the Mac OS allows you to do this too (Ink). But this is just a scratch-pad, and I really wish they'd let you save what you've handwritten, because Bamboo Scribe was the smoothest/neatest by far!

This leads to a second problem: integration of different methods/software. At the moment, I use Mendeley to read and annotate journal papers, and as my citation software when writing up my own results. But if I'm annotating PDFs in Mendeley, do I really need another piece of annotation software just to handwrite on them? And I'm currently using Scrivener to draft up my first papers, which has a 'research' area that allows you to pin PDFs, write notes, add pictures... again repeating what Mendeley can do to some degree. And I've heard of other people using Evernote to write up notes and sync information across multiple devices, which would come in handy when jotting down notes on my phone. But again, double-handling is the issue. Or is it...

As I though more deeply about this problem, I realised that although Mendeley allows for detailed analysis and note-taking on individual PDF papers, there is no space write about broad scale topics which span a number of papers. You can tag numerous papers with the same subject, such as 'taphonomy' or 'burial', but there is no way to combine all the information from different papers in one document. So why not just use Scrivener to do this? Well, the page layout isn't as conducive to note-taking in this way, but rather drafting and word-processing. Plus, it isn't available on different platforms (WP8 specifically) or online like Evernote is.

During this research, I found out that Evernote (on Windows) allows you to use a Wacom tablet to write directly in the program. Problem solved... or is it? To my dismay, this function is not provided in the Mac version of Evernote, but a work-around using Evernote Skitch to annotate images and import them into Evernote almost works just as well.

Evernote seems to be the solution to my woes, so I will trial writing up thoughts and ideas that come from reading papers in Mendeley, by creating a .jpg of the Cornell Method template to write onto in Evernote. This way, I can access this information wherever I am, and especially during meetings with my supervisors. I will still use the tagging system in Mendeley, so it will remain my referencing and citation software. But trains of thought and brainstorming will remain in Evernote.

Oh and the pain I spoke about before? That sick feeling that I've wasted a weeks worth of work just trying to figure out the best way to be productive. Add in a sore shoulder for not using a proper ergonomic set-up for the tablet (it was sitting too far to the right when it should have been centered in front of me). I'll keep you up to date and let you know if it was all worth it!

Smooth stones were found in the abdominal region of this specimen of this ground dwelling carnivorous coelurosaur, Nqwebasaurus thwazi, stones that are not common to the geological formation in which the fossil was preserved. So how did they get there? de Klerk et al. (2000) thought these stones were most likely gastroliths: swallowed by animals to aid in breaking down food in the stomach. 

Modern day herbivorous avian dinosaurs (birds) use gastroliths to help in the digestion of plant matter, and aquatic carnivorous animals such as crocodiles, alligators, seals, and sea lions use them  for ballast or stability. However, some doubt still surrounds these theories for gastrolith use, especially as to the true function of gastroliths in non-avian dinosaurs (see the UCMP Berkeley page on gastroliths for an overall summary). Wings (2007, pp 1) provides an even more detailed review of gastrolith use, and lists the following possible reasons for swallowing rocks:

This little guy is also import for two other reasons. First, the occurence of N. thwazi in Early Cretaceous strata pre-dates the known North American taxa by approximately 50 million years (de Klerk et al., 2000). And second, N. thwazi is the oldest Gondwanan coelurosaurian (de Klerk et al., 2000). The authors cite paucity of fossil material in southern Africa as the reason for misinterpretations concerning faunal radiations: whether this clade originated in Laurasia or Gondwana. Lets hope that more discoveries like this help clear things up!

References
Charig, A. J., Milner, A. C. 1986. Baryonyx, a remarkable new theropod dinosaur. Nature 324: 359-361.

de Klerk, W. J., Forster, C. A., Sampson, S. D., Chinsamy, A., Ross, C. F. 2000. A new coelurosaurian dinosaur from the Early Cretaceous of South Africa. Journal of Vertebrate Paleontology 20 (2): 324-332

Ji, Q., Currie, P.J., Norell, M.A., Ji, S. (1998). Two feathered dinosaurs from northeastern China. Nature 393 (6687): 753–761

Wings, O. 2007. A review of gastrolith function with implications for fossil vertebrates and a revised classification. Acta Palaeontologica Polonica 52 (1): 1–16

I saw this amazing photo on Palaeoblog, courtesy of the National Geographic Photo Contest 2012. This poor sheep drowned in a meadow canal in southern Jylland, Denmark. Scavengers (most likely birds in the photographer's opinion) had eaten everything above the water, while flesh and wool stayed intact below the water.

This image perfectly illustrates just how varied the world of taphonomy is. If this sheep is fossilised as is (with soft tissue mummified), and dug up by future palaeontologists, would they be able to tell that 'dorsal tissue loss via opportunistic birds due to drowning feet-first' happened? I can't imagine trying to propose a scenario like this in a scientific paper: it would seem overly specific, and pretty preposterous.

A revelation has swept the globe (and has been doing so for at least the past 3 years): that office jobs that require sitting down for 8 hours per day, 5 days a week, for 50-ish years apparently (not surprisingly) adversely affects your health (examples here, here and here). Normally office workers counter this by exercising either before or after work, but this research suggests that even the longest, hardest work-outs can't negate the effects of having sat down for so god-damn long. One of the solutions to this problem is the standing desk: desks that are raised to elbow height when standing, coupled with taller chairs for the occasional rest. 

My PhD requires a lot of computer time at the moment, which results in my sitting at a desk for around 40 hrs per week, plus all the time I spend sitting in front of the computer and TV at home. I tend to get a sore back after hours of sitting (even with the correct ergonomic set-up), so I'm trialling a standing desk set-up at home. The suggestion that I might lose a little weight by doing so was also a huge motivator, to be honest. Now, I find that I tend to move a little almost constantly, shuffling, shifting weight etc... I'm also much more likely to walk around the house when I need to instead of feeling too comfortable in my chair to move. 

There are more studies suggesting that standing all day isn't healthy either, and the best solution is to get up and move every 20 minutes. I'm really not sure how that's going to work out, productivity-wise. When I'm in the 'zone' I hate to be interrupted, and just a small break is sometimes enough to throw me off. Does that mean I should just learn to get back in the 'zone' quicker? Maybe, but easier said than done.

So for the moment, the trial at home will continue, and at uni I will get up and move around every 20 minutes for 2 minutes. And hopefully not annoy my colleagues with the constant sit/stand/walk/sit routine.

The original description for this genus/species included "incipient nasal horn cores" (the lumps of bone over the eyes seen in the photo below) and a large rostrum (beak). However, there is some debate over whether the orbital horn cores which characterise this species were actually present in life, or were in fact a result of preservation as other bones around the eyes were 'squashed' down leaving the tougher "horn cores" poking up (Makovicky et al., 2006). Taphonomy strikes again!  Variation in rostrum size has been noted in other protoceratopsid genera, so the large rostrum has also been called into doubt as a defining characteristic of M. dodsoni. It has been suggested by Makovicky et al. (1996) that M. dodsoni might actually be a species of Bagaceratops, another Cretaceous Mongolian protoceratopsid.

I unfortunately don't know enough about ceratopsian anatomy to determine the validity of this myself, so until an official name change is published, it's still a valid taxon in my mind. Good luck, M. dodsoni!

References
Makovicky, P. J., Norell, M. A. 2006. Yamaceratops dorngobiensis, a new primitive ceratopsian (Dinosauria: Ornithischia) from the Cretaceous of Mongolia. American Museum Novitates 3530, 1-42.

You, H., Dong, Z. 2003. A new protoceratopsid (Dinosauria: Neoceratopsia) from the Late Cretaceous of Inner Mongolia, China. Acta Geologica Sinica 77(3):299-303

... it can't be as bad as this! In honour of a friend who'll be flying to the US tomorrow to start work at Disneyland!

Courtesy of T-Rex Trying...