The day has finally arrived... I am now Dr Caitlin Syme! My PhD thesis went through the various stages of PDF upload, revision, re-upload, approval, FINAL upload, and then I received the letter I'd been waiting for...
I'm looking for more 'normal' paid work while I apply for post-docs and museum-related jobs, but for now I can breathe a little easier. Thanks for joining me on this PhD journey, and I hope you continue to find these posts useful for understanding both PhD and post-PhD life. And to keep enjoying fossil and taphonomy related news, of course!
I submitted my PhD thesis in September 2016, and got word back a few weeks before Christmas that it had been accepted by the university for the award of my degree! Barring a few changes, of course. Technically, my thesis has been 'accepted with changes'.
For those who don't know how the process works:
It would have been lovely to recieve it back with 'no changes required', but hey, it would be wonderful to submit perfectly written papers for peer review and not need changes to them too, but we aren't all perfect!
I use Mendeley as my reference manager, and will sing its praises to anyone I meet asking what citation software they should use for writing research manuscripts. It's super easy to import article PDFs into your virtual library, ask it to 'watch folders' for new PDFs you've downloaded, has a pretty good stab at labelling articles in your library by looking at the metadata, and cites-while-you-write with its MS Word plug-in.
The Mendeley Desktop 'library' view. Each single PDF has a single entry in the library, which can exist in more than one folder simultaneously without creating extra copies of the PDF. I find organising papers into multiple themic folders extremely useful!
You can even highlight passages and jot down notes within each PDF in the form of floating sticky notes, called 'annotations'.
Annotations are shown as yellow sticky note symbols on the PDF page, and the contents of each annotation are displayed on the right hand side of the screen.
But I wish that those annotations were more accessible in their own right.
You might, for example, read a paper in Mendeley about the taphonomy of mammal carcasses. There's an interesting line about teeth: that while they are more resistant to weathering than bones, they can still crack and split in hot and dry environments. You highlight this sentence and add an annotation with your thoughts.
But how do you find that annotation at a later date? Until you read that paper again, you might not remember that it even exists.
Mendeley does not allow you to view all annotations you've ever created, or even indicate which PDFs either do or don't have annotations. If you remember reading something interesting and writing something about it, you better hope that you remember what you wrote, as you can find annotations by searching for key words within them. And if you're like me and just want to review your past notes, good luck trying to remember all the papers you've added annotations to over the last 6 months.
The columns in the lbrary show a star symbol for your 'favourite' papers, a circle symbol for read/unread papers, and the main paper details (author, title, year, etc.). I'd really like an annotations/no annotations column.
There are, of course, work-arounds for this: you could tag all papers you add annotations to with a key word such as 'Annotations' or mark each paper with the 'favourite' star symbol, but this relies on you never forgetting to include this step.
You could copy the contents of each annotation in to an Excel spreadsheet or mind map, and group them by theme. That way you can review your database or mindmap and find your way back to the original paper. But this feels like double handling - why not just write the annotation in the mind map in the first place? What I would LOVE is a mind-mapping tool within Mendeley, where you could click and drag annotations on to nodes/branches, but I realise this could be nightmarish to code and implement.
I can't say I've come up with a solid solution for this problem yet. Has anyone else figured out a better annotation workflow for Mendeley, or do you use other software and reference manager combinations to keep track of your research notes?
Geology is an important component of any taphonomic investigation. This helps to 'set the scene' when considering potential taphonomic pathways: what environment did these ancient creatures live in? What happened to their bodies after they died? What environment were they buried in, and how quickly were they buried?
To this end, my colleagues and I have just published a paper about the ancient environment of the Winton Formation at Isisford to better understand the taphonomic history of crocodyliforms, osteichthyan fish, and dinosaur fossils uncovered there. We propose that around 100 million years ago, Isisford lay in the middle of a river delta that flowed into the nearby Eromanga Sea.
We came to this conclusion by studying the sandstone concretions that encase each of the fossils found at Isisford. These concretions formed when sand grains were cemented together with calcium carbonate (calcite) from calcium-rich groundwater. The majority of fossils appear not to be distorted or warped in any way, and as fossilisation occurs under high temperature and high pressure, it seems the concretions surrounding the buried bones and afforded them some protection. If this calcite cement, and therefore the concretions formed before fossilisation, then information about groundwater quality where the bones were buried would be locked away in the calcite minerals themselves - specifically, isotopes of carbon and oxygen.
Images showing a slice of sandstone concretion under a microscope. A, photograph of the concretion through a microscope, with darker coloured sand grains and light coloured calcite cement; B, the same area under cross-polarised light (helpful in finding more different types of minerals); C, cathodoluminescence showing the calcite cement fluorescing in bright orange with patches of bright yellow manganese ions; D, electron-dispersive diffraction (EDS or EDX) indicates the orange and yellow areas from C, shown in blue in this image, are all made of calcite. Image from Syme et al., 2016.
We tested the carbon and oxygen stable isotopic values of the calcite cement, and by comparing our results to what is ‘typical’ for fresh water and sea water, found that it formed in a brackish water environment. This wasn’t terribly surprising: the regional geology indicates that the Eromanga Sea was nearby Isisford at this time, but until now we hadn't known whether it affected the environment at Isisford or not. When we examined geological core logs from near Isisford, and compared it to the types of rocks we found at the site, we concluded that these animals were buried in a river delta that flowed into the sea, with fresh river water mixing with salty ocean water. Unfortunately, there aren’t large exposures of Winton Formation at the site that would allow for typical facies analysis, but we worked with the material we had and came up with some pretty solid conclusions.
Figure showing the typical carbon and oxygen stable isotope values for fluvial (freshwater rivers), deltaic, estuarine, and marine water. The stable isotope values of the calcite cements from Isisford are shown by the purple area, and overlaps values typical for fluvial, deltaic, and marine waters. Coupled with all the other information from the site, we determined that Isisford cements were most likely deltaic in origin. Image from Syme et al., 2016.
Our next question is: if these animal's carcasses were buried in a river delta, did they die there or were their bodies washed in from far away? Did they even live nearby at all? That is the subject of future papers that we will be publishing mid to late next year.
Syme, C., Welsh, K., Roberts, E., and Salisbury, S. 2016. Depositional environment of the Lower Cretaceous (upper Albian) Winton Formation at Isisford, central-western Queensland, inferred from sandstone concretions. Journal of Sedimentary Research, 86: 1067-1082. DOI: 10.2110/jsr.2016.67
I have finally handed in my PhD thesis!
I've included the title and thesis abstract below, for anyone so inclined to read it.
So what's the next step? Can I call myself Dr. Syme yet? Not quite. Over the next 3-4 months, two qualified taphonomists will examine the thesis, and note whether any changes to the text or figures need to be made. Once those changes have been incorporated, the thesis can then be formally accepted by UQ!
Now for the waiting game...
Life by the Eromanga Sea: Taphonomy of crocodyliform and osteichthyan fossils from the Lower Cretaceous (upper Albian) portion of the Winton Formation at Isisford central-west Queensland.
In 1995, the articulated and semi-articulated fossilised remains of two small crocodyliforms and a large predatory fish were discovered in the Lower Cretaceous (upper Albian) portion of the Winton Formation near the town of Isisford, central-west Queensland (hereafter referred to as ‘Isisford’). Subsequent expeditions yielded further crocodyliform and osteichthyan fossils, as well as those of non-avian dinosaurs. The crocodyliforms were described as a new genus and species, Isisfordia duncani Salisbury et al., 2006. Phylogenetic analysis found that Isisfordia was a basal eusuchian, indicating that modern crocodyliforms may have originated in the Australian part of Gondwana. A partially complete and articulated osteichthyan fossil discovered in 2005 was described as a new species of the ichthyodectiform Cladocyclus, C. geddesi Berrell et al., 2014, expanding the geographic range of this genus outside of Brazil and Morocco. As deposition of the Winton Formation is thought to have occurred in fluvial and lacustrine settings, these taxa are considered to have inhabited freshwater environments.
The preservation and composition of the Isisford vertebrate assemblage is in sharp contrast to that of other vertebrate-bearing localities of the Winton Formation, the best known of which occur near the town of Winton, 240 km north-west of Isisford. The Isisford fossils are found encased in fine-grained sandstone concretions, often ex-situ and laying in Cenozoic and recent alluvium. In contrast, vertebrate fossils found nearer to Winton are typically preserved as disarticulated elements in siltstone hosted ‘bone-beds’. Additionally, taxa found nearer to Winton include sauropod and theropod dinosaurs, freshwater turtles, and lungfish, none of which has been recovered from Isisford. Furthermore, a detrital zircon dating study of the fossil-bearing Winton Formation localities indicates that Isisford is 6–8 million years older than localities nearer Winton. It is not clear if these differences in fossil preservation and faunal composition are temporal, or due to dissimilar environmental or taphonomic processes. It is also not known whether the Isisford fossils are autochthonous or allochthonous, which has bearing on the interpretation of their preferred habitats in life, and in clarifying the nature of the depositional environment in which their remains were interred. With this in mind, the primary aim of this study was to record decay sequences in modern crocodyliforms (C. porosus) to better understand the taphonomy of I. duncani fossils, examine the sedimentology of the Winton Formation at Isisford to identify the depositional setting, and elucidate the taphonomic history of the I. duncani and C. geddesi specimens.
An aquatic actualistic decay experiment using juvenile Indo-Pacific crocodiles (Crocodylus porosus) revealed that on average, carcasses ‘bloat and float’ five days post-mortem then remain at the water’s surface for approximately one month. The majority of disarticulation occurs not during bloat and float, but after the carcass sinks. Excluding rapid burial, it appears that high degrees of articulation and completeness can only occur if the bloat and float phase is either inhibited or eliminated.
Sedimentological analysis indicates that the Isisford concretions consist of feldspathic litharenites cemented with calcite. Given the cement-supported nature of the concretions, along with minimal fossil deformation, this suggests that the concretions formed during early diagenesis prior to sediment compaction. Stable isotopic analysis of calcite 18O/16O and 13C/12C ratios versus Vienna Pee Dee Belemnite (delta 18O VPDB and delta 13C VPDB) indicates that this cement precipitated from brackish pore waters during sulphate reduction and methanogenesis. Given the location of Isisford during the late Albian near the regressing Eromanga Sea, along with the presence of mud rip-up clasts and fossil plant debris, it appears that the concretions formed in a lower deltaic plain or estuarine setting.
The Isisford fossils range in preservation style from fully articulated through to disarticulated skeletal elements, and show minimal signs of abrasion or weathering. The close association of discrete articulated skeletal segments suggests that prolonged bloating and floating did not occur. Additionally, the lack of tetany in these specimens suggests they did not suffer any toxic shock pre- or peri-mortem. I propose that the majority of the fossils are autochthonous or parautochthonous, and that I. duncani and C. geddesi lived and died in a delta or estuary connected to the Eromanga Sea.
The fossil taxa of Isisford should be analysed in the context of more contemporaneous taxa of the late Albian Eromanga Sea – namely those from the Toolebuc Formation, Allaru Mudstone, and Mackunda Formation – rather than taxa from the relatively younger portions of the Winton Formation. Furthermore, studies focussing on the J/K mass extinction event and radiation of crocodyliforms should list the preferred habitat of I. duncani as deltaic or estuarine brackish waters, not freshwater. And no longer do palaeobiogeographical studies involving C. geddesi need to invoke mechanisms for freshwater adaptation, as it appears it was brackish water tolerant, which has already been proposed for other Cladocyclus spp. from South America and Morocco.
What does a palaeontology student do on a typical work day? And what about a non-typical day? Head over to UQ's new blog, Small Change, and find out! Hint: it involves a little bit of reading papers, a little bit of lab work, with a sprinkle of lunch-time Twitter perusal.
Soapbox Science is coming to Australia for the first time!
As a part of National Science Week 2016, Soapbox Science will take place in Brisbane where leading female researchers will talk about their scientific projects and why they love science.
Soapbox Science is a public speaking and outreach event aimed at encouraging girls and women to take up careers in science. You can hear all about why these scientists love their jobs, ask questions about their research, and see that women belong in the sciences just as much as men do.
I will be speaking at this years Soapbox Science event at King George Square in Brisbane, on the 20th August between 1-4 pm. My talk title (coming as no surprise to long time readers of this blog) is: “Fossil forensics: how taphonomy helps us understand the death and decay of dinosaurs”. Keep an eye out for updates between now and August!
TRIGGER WARNING: Depression
Some caveats to begin with:
Everyone experiences depression differently, and to different degrees. I’m describing my (abbreviated) personal journey through my depression. This will not be the same for everyone, and is not The Answer™, just one answer. But I hope it will be useful to someone going through depression, or a friend or loved one who wants to know how depression may feel.
PhD programs can be stressful. If you didn’t know that, now you do. It is fantastic that people discuss how they’re feeling about their PhD workloads and how stressed they may or may not be, using Twitter hashtags such as #phdlife.
The issue comes with normalisation - thinking that it’s ok to always feel stressed during your PhD - and then just living with the stress.
Don’t get me wrong - in small doses, stress is a great motivator. A problem arises when those feelings of stress persist even when there isn’t, for example, a looming deadline. And then it can lead to depression, limiting your ability to deal with any upcoming deadline at all.
When stress isn't motivating, but crippling. Image by Loading Artist.
And therein lies the problem. I had great supervisors, and an interesting project, so I counted myself as one of the lucky ones. I also had a fantastic, supportive partner (and still do!). Stress was a ‘normal’ part of the PhD, so what did I have to worry about?
There were days where I just couldn’t get out of bed. I wished that the day would remain on ‘pause’ until I decided I was ready to get up and face the world. Even though my PhD was progressing nicely, I still felt stressed and sad.
I couldn't concentrate on reading a paper for more than 2 minutes before my vision blurred for no apparent reason. I couldn't write a sentence without having three other trains of thought (relevant or not) interrupting it. I’d also find myself walking to or from my office and feel the sudden urge to sprint down the corridor. But I had no energy to do anything of the like.
But I figured that I mustn’t really have depression, because what do I have to be depressed about? Perhaps I had just spontaneously become scatterbrained.
Over a period of a few months, things got worse. My morning sleep-ins became longer, I sniped at my partner, I still felt sad and always felt like crying. Even my favourite computer and console games felt boring.
I figured that yes, maybe now I do have depression. But only a little bit. Just a light case.
Turns out, this doesn't work. Also, you should definitely read this article+comic by Allie Brosh about how depression affected her. Image by Hyperbole and a Half.
I didn’t see a doctor about how depressed I felt for a long time because, again, I thought it was a natural part of the PhD process. It wasn’t coming out of nowhere, as it does for some, but from a definable stressor. I likened it to someone repeatedly hitting their head against a wall: their head hurts, they know why it hurts, so wouldn’t it be silly of them to take some painkillers and merrily continue on their head-smacking ways?
My doctor nodded when I described this scenario, and said, “Are you going to stop doing your PhD?” I said no, the PhD program was fine, I was just stressed and depressed for no apparent reason.
“So”, she replied, “Why don't you medicate yourself while you continue the PhD, and when you’re finished, if you want to, you can slowly come off the medication?”
And there was the seemingly obvious answer. If the cause of my depression was the PhD, I needed to take some antidepressants to continue the program. If it wasn’t the PhD, but the beginning of clinical depression, then I would have refused medication for the entire PhD program for no reason.
Here was a new option: finish the PhD program WHILST AT THE SAME TIME feeling better about myself and the world in general.
I have to remind myself that, sometimes, maybe, doctors just might know what they're talking about.
Image from KnowYourMeme.com.
(A side note: when you have an upswing in mood, and everything is feeling a bit better with the world, go see your doctor. This may seem counterintuitive - after all, you’re feeling better - but now is the time you’ll be motivated enough and able enough to step outside and talk to someone about how you’re feeling. If you wait until you are at your worst, you may not feel able to talk to the doctor about what your going through and just put off the potential diagnosis and help.)
This is the way I personally feel about antidepressants (besides complicated issues of overprescription): if the medical community has spent millions of dollars and decades of research into helping people with depression, why not take advantage of their hard work? Why suffer in a time where you have options to feel better?
I know that not all cases of depression can be easily fixed with medication. In my case, it did work. Some people need to try different types of medication, or find that the medication only takes some of the depression away.
But if you are on the road to some kind of recovery, please don’t feel guilty about the time you’ve lost. You were unable to work during that time, just like with many other illnesses. But when you feel better, capitalise on it. Use this time to talk to your supervisors, get a clear idea of your tasks, and create plans to get work done.
This doesn’t mean you should work yourself into the ground to make up for 'lost time'. It means you should work efficiently and at your normal pace, to keep that good feeling going for as long as possible. Also explore whether you can extend your PhD program deadlines, or go part-time for a little bit (if you are able) for more time to get back on your feet.
And read ALL the papers! Images by Hyperbole and a Half.
I still suffer from periods of depression. But those depressive periods are much shorter and much less emotionally exhaustive than before. And I can bounce back to the pure enjoyment of research much, much quicker.
Now, I’m off to read about fossil preservation in deltas and estuaries, and tonight will play video games I’ve actually been looking forward to!
A huge thank you to my Twitter friends for reaching out and showing support. You guys rock!
With guest author Kaylene Butler
Is it ironic that we’re going to give you advice about writing by talking about ignoring the advice we’ve been given?
But the point is to keep an open mind and try changing up your techniques and habits, even if you think you’ve already found the best way to go about it.
So here are some habits we’re currently unlearning. Many of these habits were originally learnt from undergraduate lecturers, high school teachers or our peers:
1.) Writing the abstract last.
EEEHRK, WRONG. It’s actually been a lot more useful to write the abstract first as a guide or primer for the rest of the article. You then have a succinct outline you can show to your supervisor or co-authors, and a pre-written submission for conferences talks and posters. It’s easy to edit later when you have some more conclusive results.
2.) Dot pointing sentences if you can't write a whole coherent sentence.
MLEEERP. This just makes your draft more annoying to read and edit later. We found that we had to start brand new blank documents and write the ‘nice’ whole sentences in to create a readable draft. And our supervisors really detest trying to read over sentences interspersed with dot pointed ‘insert clearer sentence about XYZ’ and ‘###need better word here###’.
3.) When reading edits or making changes, doing whichever ones you want in whatever order so you don't get stuck.
BRAWWP, WRONG AGAIN. We found that when you do all the easy, achievable edits you wind up with only hard and time-consuming edits. Which slows down the whole. Re-writing. Process.
4.) It’s okay, it’s just a draft.
Your draft may be a work in progress from a results perspective but try to remember that your co-authors, or supervisors, still have to be able to read it. This ties in with point number 2. ‘It’s a draft,’ is no excuse to not have whole paragraphs. Most importantly edit your draft properly before you send it (‘but this is just a draft’ is not an excuse most supervisors like to hear). A happy supervisor means less red when you get your draft back and more focus on the actual content of your writing instead.
5.) Write first. Format the document after you finish writing.
For journal articles, have an idea of which journal you want to submit your paper to before you start writing. For things like assignments (looking at you, undergraduate self) or grant applications, you’re given the formatting requirements (e.g. line spacing, formatting of headings, reference style) in advance. We find it easier to write the document using the required format form the start, instead of writing first and having to go back and change everything later (this is especially true for referencing styles).
Some people find it easier to write first and format later and that is fine. Find a system that works best for you. But at the very least try to have the document formatted correctly before you send a draft to your co-authors/supervisors. This allows you to save your co-authors time spent writing comments like, “This isn’t formatted correctly for the journal you just said you were going to submit to”, or, “Is this consistent with journal X?”
It is important to remember that sometimes people find a different method for writing which is more efficient for them. Not every suggestion is relevant to every person and writing advice often varies in the literature. But make sure that your writing method really is the most efficient, not just the most familiar.
Belcher, W. L. (2009). ‘Writing Your Journal Article in 12 Weeks: A Guide to Academic Publishing Success’. SAGE Publications, Inc., Los Angeles, USA. 351pp.
Gardiner, M. & Kearns, H. (2010) ‘Turbocharge Your Writing: How to become a prolific academic writer’. ThinkWell and Flinders Press, Adelaide, Australia.
‘How to write a scientific paper.’ http://conservationbytes.com/2012/10/22/how-to-write-a-scientific-paper/. Accessed 21 May 2015.
I've just published my first academic paper in the journal 'Palaeogeography, Palaeoclimatology, Palaeoecology', with my co-author Steve Salisbury. Our paper is called "Patterns of aquatic decay and disarticulation in juvenile Indo-Pacific crocodiles (Crocodylus porosus), and implications for the taphonomic interpretation of fossil crocodyliform material."
What is the paper about?
Essentially, the paper looks at what happens to crocodile carcasses when they rot, undisturbed in fresh water – whether the carcasses float (they do), how long they float for (about a month), whether parts of the body fall off while they float (a few ribs and hip bones do, but not much), and what happens after the carcasses sink (they crumple into a pile of bones, but parts of the skeleton still stay attached to one another).
We also examined the difference between (1) crocodile carcasses buried in sand, versus (2) carcasses left in water to rot and buried once they sank, versus (3) carcasses left in water to rot and left unburied.
We were interested in how this applies to the fossil record: when we examine fossil crocodiles, can we tell where they died, and how long they were left to rot, and whether they were buried quickly or not?
More details: 'Bloat and float'
Here are some diagrams that show what happened. The carcasses bloated due to bacteria inside the carcass eating soft tissue and creating gases (I'm sure you've all seen swollen or bloated roadkill before, it's the same process). These bloated carcasses float in water, a phenomena (not surprisingly) called 'bloat and float'.
Side view illustration of carcasses in the experiment bloating, floating, and sinking. Image from Syme et al. (2014).
The carcasses stayed intact while floating (except for a few ribs and hip bones that drifted away thanks to fly maggots eating flesh), and sunk after about 32 days. Large portions of the skeleton stayed intact after sinking, but some portions separated from one another - for example, the whole left leg may have stayed intact, but disconnected from the rest of the body.
Top-down photographs of one carcass as it decayed. You can see that while the carcass floated, the limbs, tail, and head stayed connected while slowing sinking below the water's surface. Once they sunk and we very gently drained water from the tank, the carcass looked a lot more disconnected! Image from Syme et al. (2014).
Burial: what difference does it make?
Part of the experiment was to determine the effect of burial on the carcasses. Two crocodile carcasses were buried in sand at the beginning of the experiment, and by the end of the experiment their skeletons looked like this:
Three crocodile carcasses rotted in fresh water, as I described earlier, but as soon as they sank they were buried in sand. At the end of the experiment, they looked like this:
And finally, three carcasses were left to rot in fresh water, and after they sunk, they were NOT buried. Here's what their carcasses looked like:
You can see that the carcasses buried at the beginning of the experiment look pretty much perfect – all the bones are connected and where they're supposed to be. That's not surprising, because the sand surrounding the body stopped anything from moving (there was an added complication as one of those carcasses actually floated up through the sand! But read the paper for more details).
The carcasses buried part-way through the experiment, as well as those not buried at all, look more similar to one another. Chunks of the skeleton stayed together, but other bits separated (disarticulated).
What are the most important conclusions?
The buried carcasses 'survived' the best, and much better than the other carcasses decaying in water. This is a little surprising, because the water was left undisturbed during the entire experiment: there was no water current, no large animals were allowed to scavenge the carcasses, etc. It was purely the action of floating and sinking that caused the bones to separate and move around.
What does this mean for fossil crocodiles? We might think that a really well preserved fossil might have resulted from a carcass being quickly buried, which is a fair assumption. But we might also think that a carcass left to decay undisturbed in fresh water could also be really well preserved and look the same as a buried carcass. The results from this experiment show that this is not the case for modern crocs, and therefore may not be the case for ancient crocs!
Syme, C. E., and Salisbury, S. W. 2014. Patterns of aquatic decay and disarticulation in juvenile Indo-Pacific crocodiles (Crocodylus porosus), and implications for the taphonomic interpretation of fossil crocodyliform material. Palaeogeography, Palaeoclimatology, Palaeoecology, 412:108-123. doi: 10.1016/j.palaeo.2014.07.031
About the author
Dr Caitlin Syme is a palaeontologist studying the taphonomy (preservation state) of fossil non-avian dinosaurs, crocodiles and fish from the Winton Formation, Queensland, Australia. Think forensic science or CSI for fossils, and you're on the right track!
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