To get to the other side: finishing the doctoral thesis

I am 1 year and 3 months away from my thesis dissertation and defense deadline; the finishing of the PhD. For those in pursuit or were formerly in pursuit of their PhD, you know the feeling of that looming deadline and the intangible and yet intimidating amount of work you still need to do. Though on the other hand, I love objectives, goals, a list of things to do and thus a deadline. These parameters are what bring structure to my day and motivate me to get on that computer and crunch numbers, build my ideas and tease through the enormous pile of peer-reviewed literature. In my opinion, a little fear behind missing a deadline ends up being my strength.

Don’t get me wrong, the thesis is a process and one that I have relished over the past 3 years. Truly, my education has been and is a privilege that I don’t take lightly nor resent in any way. The past year alone has been one of the best years of my life and without the opportunities of my education; none of it would have happened. But I get this feeling that the fourth and final year of a PhD is the hardest and one where most students will waiver in their productivity and motivations.

left to right: Brandan Norman, Gill Holmes and Kevin Young. Southampton Island Nunavut 2015

So how am I planning on organizing my time and tackling my objectives over the next year and a bit? Well, for starters I opted to not be a teaching assistant. Surveying those that have come before me, I asked them what they thought was the biggest reason why PhD students didn’t finish on time and the main response was that teaching eats up too much time and prevents students from having nice chunky blocks of time to just immerse themselves in data analysis and writing. DONE. So I don’t make as much money; in the end, if you go over your 4-year time, you end up paying tuition anyways so really are you making THAT much money? Secondly, I write things as I go. Not that this has proven from start to finish that I’ll finish on time but I know I saved myself a lot of digging by just writing thoughts down, referencing works and statements from those papers that are applicable and inserted them into the section or chapter it will eventually end up in. This file is titled, “First ever thesis draft.outline”. It’s kind of an interesting file of finished pages, finished paragraphs but many bullets containing a smattering of content. This file is 55 pages long. As the content grows and those page numbers increase, it helps alleviate the overwhelming feeling as I proceed to write the longest document I will have written in my life and perhaps will ever.

So far I have found this book really helpful.

I know finishing this monster, the thing they call ‘the thesis’ on time is ambitious. I won’t be punishing myself for not finishing on time but at some point we students need to finish what we started and move on with our lives, enter the work force and start using those skills we’ve worked so hard to build. I look forward to seeing all of us on the other side.

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Attaching nanotags – a grad student perspective

If you study plants, studying how they change can be pretty easy (from a logistical stand point). Sessile plants and animals can be found where you left them. Awesome. It saves guess work or the laborious task of tracking individuals to even start and continue studying your target species in any longitudinal research. However, for many of us, studying living creatures means accommodating the fact that they move around. Sometimes across fields, across lakes or even across continents.

I study migrating birds, but not just any migrating birds; long-distance arctic-breeding shorebirds. These species fly some of the longest recorded migrations known on the planet. They never stay in one place for very long so we have to work hard and fast when they are around and prepare to monitor movement once they decide to leave.

Black-bellied Plover arriving to the breeding grounds on Southampton Nunavut. Photo by: Kevin Young
Black-bellied Plover arriving to the breeding grounds on Southampton Nunavut. Photo by: Kevin Young

Historically, the larger the animal, the easier it was track. Not only are larger animals more conspicuous but larger animals can carry larger markers like flags on their legs or brightly coloured collars around their necks. They can also carry around heavier devices which are ideal for satellite tracking requiring larger heavy batteries and larger antenna to transmit signals out into space.

Unfortunately for many of us, we could only dream of tracking our much smaller highly mobile animals across large distances. And we are still dreaming. But until some wonderful engineer makes our dreams come true and designs a satellite tracker weighing less than half a gram, we have devised (meaning lots of people, not including me) ways of tracking animals using other kinds of information-transmission other than satellite signaling.

I track and monitor migratory movements of small shorebirds weighing between 50 and 300 grams using radio telemetry. Telemetry has been around for a long time but was only really used locally where a handheld receiver could detect signals on foot for a kilometer or so depending on terrain. But collaborative efforts with academics, along with provincial and federal governments, we now have the MOTUS wildlife tracking system (http://motus-wts.org/) .

3 sizes of nanotags
3 sizes of nanotags

Small radio tags emit pulses in unique patterns on the same radio frequency that can be detected by towers set up all over Eastern Canada and the North-East coast of the US. Density of towers in the Southern Ontario region basically cover the entire area so we can monitor “microscale” movements of birds through the Great Lakes region.

An almost complete map of towers on the MOTUS Wildlife tracking system detecting transmitting nanotags
An almost complete map of towers on the MOTUS Wildlife tracking system detecting transmiting nanotags

Battery life ranges in the tags from 60-180 days and then will fall off when the bird molts . Tags are only glued to the body feathers which are “shed” twice a year (once for breeding plumage and once for winter plumage in most species). Tag size ranges based on how long you want them to transmit; larger the battery, the longer the life.

I would like to share a few tips and tricks regarding nanotag attachment on shorebirds. These little guys change body shape during migration, putting on fat and losing fat quickly over a short time frame, and when I say get bigger I mean, almost doubling their weight in some species. So we can’t place harnesses on their body in the event the body shape and size change a lot. So we go with a “semi-permanent” external attachment aka, glue that bugger on. Here is how we do it:

Fiskar scissors; good quality!

Gel super glue, not the liquidy stuff

Your tags, tag activator, receiver to check that the tag is actually on

***Activate the tag, I do this before leaving my field camp and carry the activated tags in my bag with me for the day. It saves the trouble of carrying the gear for 20 km.

  1. Cut the feathers above the oil gland on the back of the bird leaving the strongest part of the feather (the base of the shaft) intact.

    Photo by: Nick Docken
    Photo by: Nick Docken
  2. Place glue on the tag, just a decent blob, enough of a blob it covers the back of the tag at the round end, label facing up
  3. Don’t glue yourself to the bird. To avoid this, I use something thin and solid to put slight pressure on the tag to the bird but not using my fingers.
  4. TAKE A PHOTO. This can be the only evidence of who is wearing what tag if there is data entry error or you forget to write it down. I have gone back and referenced photos with time stamps in case the tags weren’t right. So important.

    Photo by: Nick Docken
    Photo by: Nick Docken

**And what about those ROUND TAGS……..

It’s not convenient to glue a marble to a flat surface, which is what the NTQB4-2 tags feel like. So I buy a non-stretch, non-fray material, to help increase the surface to glue ratio.

  1. ACTIVATE the tag. If you glue anything to the tag before activating it, it likely won’t fit in the activator hole…..bad news bears
  2. Glue the mesh square to the tag
  3. Glue the whole lot to bird. Don’t be shy with the glue, the bird only wears it for a handful of weeks and with the cost of the tag itself, you want it to stick.

There are many ways of doing this and this is simply what works for me. I have not had problems with tags falling off and the extra mesh on the larger tags may even help prevent the bird from pulling the tag off. Good luck scientists and happy tracking!

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Life is too short to spend it counting red blood cells

I wrote and successfully ran my first Macro….I have no idea what Macro means but I know it’s a piece of code used to perform a function on my computer.

I have entered the phase of data analysis in my PhD. If feels like my entire life is trapped within this little black box supposedly filled with 2 terabytes of digital what-not. As a potential future doctor of philosophy I have been stretching and yoga-ing my brain muscles and attempting to use higher order thought processing (in other words, how can I get more done in less time).

One of the numerous digital hurdles I’m entering into, is dealing with blood smears. On the tundra during summer in Nunavut our team captures breeding shorebirds and takes a variety of quick samples including a drop of blood. This drop (or even smaller than a drop) is smeared on a glass slide to generate a single layer of red blood cells so we can see them under a microscope.

Semipalmated Plover (Charadrius semipalmatus) Red Blood Cells
Semipalmated Plover (Charadrius semipalmatus) Red Blood Cells

Each slide contains hundreds of thousands (or even gazillions) of cells. Often scientists report the number of different cells or the prevalence of infection/disease within an observed 10,000 cells. It’s easy to miss the odd infected cell so the greater the number of cells the better. That’s all fine and dandy but counting 10,000 cells per blood slide for over 150 birds is just not what I want to be doing for 6 months of my life straight. My time is much better spent using my brain to do ‘science’ interspersed with watching Netflix or knitting baby hats.

So I took to the world of code and programming to solve this seemingly impossible endeavor.

Little did I know…..stuff like this can be really easy. There is definitely some trial and error but free software (Imagej) and a macro (some code thing) can run a batch containing all my images and count the cells for me.

 

 

Download Imagej if you are ever counting cells. And process your image using a macro like mine:

Convert the colours in the image to something recognizable for the program and then tell the program to count the number of those things…..

Hit the process button under a Batch function to run the macro for a whole suit of images and watch the magic happen (or don’t watch; just walk away and let your computer work). I was able to count 10,000 cells in just over 200 images in 10 minutes. I would have walked away and done something fun like eat cookies but I was sitting on a plane on my way to Seattle. Plus, I was so stoked ‘something was happening’ that I sat starring at the screen praying my computer didn’t suddenly self-destruct.

So next time you are faced with the challenge of managing large amounts of data, or with technology in general, try to experiment with some different options out there to save you time. Most of the papers out there say “we counted 10,000 cells per slide for the 1000 individuals of mice to determine….something something”, and what it should say is, “A poor unsuspecting undergrad student was roped into volunteering to count slides for 12 hours per week for 2 whole years to determine…..something something”. Likely most of us don’t have the luxury of hiring technicians or bribing undergrads with Tim Horton’s gift certificates to work endlessly on something mind numbing. So scientists, “don’t always just work harder, work smarter”, so you can free up time to have fun, (like get on a plane to somewhere exotic) life is too short to count red blood cells.

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