The waiting game

So Edinburgh has been under the siege of a major blizzard as you can see from this photo of George Square Gardens. In fact the University will be shut tomorrow. Snow day!

New year, new equipment, new student

After I submitted my thesis, I took a long break. I spent the holidays in Montreal followed by a trip to Australia. I only got back at the beginning of February. I flew around the world and thus returned to the lab a little under the weather but ready to get right back into the swing of things. But alas, I had been gone so long that there were a few new things in the lab, including a brand new microscope with focus control (no more z-drift!) and a brand new MSc student to supervise.

The microscope has proven to be somewhat problematic to use in its first month of action. Focus control refusing to run, neutral density filter not wanting to be controlled by the software and washers falling out of our filter wheel! After a few visits from Zeiss technicians, including one this morning, our beautiful new microscope and software are up and running ready for tomorrow’s snow day…

I also have an neuroscience MSc student working under my supervision. This is the first time I am teaching an MSc student. I have previously supervised PhD students who had past lab experience. This is a little different. What my student lacks in wet lab knowledge (though she is picking up the techniques quickly) she makes up for in ambition and motivation. And besides, with my viva pending it is probably good for me to go back to basics and explain the theory behind why we do what we do.

Viva date?

Speaking of vivas… I am still waiting for a viva date. I submitted in mid December. Whilst I am a bit disheartened (although mostly just impatient), I am using this time to prepare myself: combing over my thesis, re-reading articles, looking up various uses of different reagents… I am a bit nervous, but I think it will go well. As I have previously said, your thesis is your baby, it contains the past 3+ years of your life. I did all the experiments, I did background reading and I wrote the thesis. I should know most of the material pretty well. I still know that when I will be given a date, I will be frantically annotating my thesis and colour-coding key findings, important references and vital background information. I will be refreshing Pubmed to see if anyone has published anything related to my work. I know that each viva is different and there isn’t a universal question that everyone gets asked, aside from give an elevator pitch of your project. So it can be hard to know what to expect. From what I’ve gathered from speaking to other PhD students, I think that it is important to know the rationale behind why you did a specific experiment. I think you need to be able to justify your hypotheses especially if you haven’t clearly laid it out in your thesis. I’m sure it’ll all be fine. Apparently some people come out of their vivas saying that it was one of the most enjoyable experiences of their lives… I’ll keep you posted.

Now off to sit in front of my window and be mesmerised by the wind blowing around the snow outside.


Thesis-writing freedom

The view of the construction site that is George Square. They have started some work behind our building, but luckily the trailers have not completely blocked out my view on George Square Gardens.


I’m free!
Well almost, not quite yet. I submitted my thesis on December 14th (yay!) and have been basking in freedom ever since! I have truly been taking advantage of my newfound free time to enjoy the festive season and do lots of yoga (I want to ensure that I have enough zen in reserve for when it comes time to prepare for my viva). I’m also using this time off to do a bit of travelling. When else am I going to have this much time off?

I spoke to so many fellow PhD students who submitted their theses. They all told me that submission was a bit of a let down. The last 3-4 years in the lab is boiled down to a 200-ish page document. You go to the College Postgrad Office to drop off your precious thesis, so it can be given to examiners. Then nothing. Actually nothing. Not a bad nothing, but a strange nothing. After so many years of early mornings, late nights, data analysis, successful experiments, somewhat less successful experiments, it can feel troubling to not really have anything to do. All of my friends who went through this described a feeling of emptiness, not quite happiness, maybe a wee bit of relief? They all expressed how they had just been fed up of proofreading their thesis and how they wanted it over and done with. Since I wrote my thesis in such a short time (see next section), I wasn’t yet fed up of it. I felt content when I left my thesis at the Postgrad Office, albeit perhaps a little tired and maybe verging on aimless. It is such a momentous occasion, however I feel like the emotion of it all only hits a bit later. I still haven’t fully realised that it is done. Perhaps this is because I haven’t had my viva yet? I’ll keep you posted. For now I am enjoying my free time away from the lab.


Thesis writing tips
Solely based on the time that it took the other PhD students in the lab (6 months-15 months), I’d say that I wrote my thesis quite quickly. I made all my figures in October. I wrote part time in October, while finishing up lab work (about 2 weeks). I spent another 3.5 weeks writing full time. I have to thank my supervisor for being so good at sending feedback for every chapter within less than 24 hours. I could not have powered through it without all of his comments, suggestions and support. Thank you Mike!

I do write quickly and luckily I had already written an MSc thesis, so I had a bit of practice for writing my PhD thesis. Here are my recommendations on how to power through writing a thesis. It probably won’t work for everyone, but it might be a useful stepping stone.

1-Make all your figures ahead of time
If all your figures are made, you have a good idea of your results so you can start to think about your discussion and tailor your reading for your introduction appropriately. Additionally if you show your supervisor your figures at the beginning, you won’t be stuck tweaking figure legends right before submission. If you make all of the figures for all of your chapters at the same time, it also helps with consistency.

2- Get out of the lab
Although it wasn’t hard to balance adjusting figures while running experiments, I found it difficult to find enough time to sit down and write during incubation periods. I was a lot more productive when I sat in the library and spent all day writing. I was lucky enough that I was still receiving my stipend and could afford to take time away just to write. This is not the case for everyone.

3-Read first
I found it easier to read 5-6 papers, related to what I was going to be writing when I started out my day. That way the literature was fresh in my mind and I didn’t have to stop writing when I was on a roll to find some more information (though this did inevitably still happen).

4-Just write
This part can be tricky. I know a lot of people who like to work on sentences until they are just right before moving on to the next one. I would recommend just sitting down and writing. I would sit down and write from 10h30 to 19h30 every day taking 15 minute breaks every 60-90 minutes depending on how it was going. You will write sentences that don’t make sense, but you can always fix those later. I think that starting is difficult, but once you get going, it is easy to continue writing and eventually everything will come into place. I personally started with my methods and results chapters. I then wrote the final discussion because everything was still fresh in my mind and I thought up an interesting model to explain my results. I then wrote my introduction which probably took the longest as there was lots of additional reading involved.

5- Word processors are your friends
Did you know that you can insert figure legends in MS Word that can then link up to a table of figures? If you style your thesis correctly, MS Word can also create a table of contents complete with hyperlinks! I would highly recommend learning to use these features as they do really come in handy, especially when your table of contents is 7 pages long…

As I said there are so many different ways to write a thesis. This one worked for me. I hope that I have provided some useful information. Good luck to thesis writers everywhere!


Now back to enjoying my freedom with a cup of tea followed by a lovely yoga practice!

The home stretch

I have thesis brain! I actually started writing this post in French…
This is the view from the library I was writing from when I was back in Montreal.

This is the final stretch. The end is in sight. I’ve spent the better part of the last month in a library writing my thesis. Remember how last time I mentioned that I realised how little I actually knew? I feel like I’ve made a little dent in that now. But more importantly I’ve read theories upon theories trying to put together what little we do actually know. I’ve also put my hat into the ring and proposed my own theories and written them in my discussion. The discussion was an interesting section to write. This is the section where you can come up with wild (or very tame and plausible) theories about how your little bit of research fits into the bigger picture. Who knows, maybe one day, my theory will turn out to be right, or totally wrong.

Writing a thesis is such a strange thing. It is incredibly elaborate and involves a lot of research. It is the summary of the past 3+ years of your life. How can you summarise the countless hours of imaging and data analysis, the hours spent interpreting successful and sometimes not so successful experiments into a single cohesive document? It is mind-boggling that in less than two weeks (fingers and toes crossed) I will be submitting the culmination of the last 3 years of my life. Completely mind-boggling!

I’m not quite out of the woods yet, I have corrections to do, parts to add and all the little bits and pieces to put together.

Writing progress report:
Methods: done
Results chapter 1: done
Results chapter 2: done
Final discussion: done
Results chapter 3: 60% finished corrections
Introduction: 40% finished corrections

SfN 2017
I did take 6 days off writing to attend the Society for Neuroscience’s annual meeting. This year it was held in Washington DC. The weather wasn’t as nice as it was in San Diego last year, but that didn’t make me enjoy the conference any less. If anything, the cold weather provided incentive to actually go and sit in a dark windowless conference room to listen to talks. Just kidding… This year, I went to fewer talks. Instead, I spent my time at the poster sessions learning new things, having stimulating conversations and actually fostering collaborations! There is a group in the United States, working on different mutations in the same protein as me. I spoke to the PI in the lab and he was really keen to start a collaboration and was willing to send us their reagents so we could expand our battery of assays on our mutations. This is very promising and could enhance both of our teams’ research.

I also had some really interested people asking me questions about my research while I was presenting my own poster. The work I was presenting could, at a glance, be puzzling: a postsynaptic protein affecting presynaptic function. Once I explained my work and how I though this postsynaptic protein was having a presynaptic effect (based on experiments from other groups working on this protein) people understood and I think I perhaps I gave them a new less compartmentalised view of synapses (all part of my master plan to spread knowledge of the theory that I included in my discussion).


Now off to get some rest so I can be incredibly productive and get everything done before I am back off to Montreal for the holidays!


The more you know, the less you actually do

George Square is now dressed in its autumnal coat. The air has gotten much colder. In fact, I’ve been wearing a big scarf and hat all week! And, I actually heard my first Christmas song playing today! Again, I’m writing this post from the Edinburgh airport, I’m a regular you see. I am escaping the chilly weather here to go frolic in the freezing weather of North America. 

You know the old adage: “the more you know, the more you realise the less you know”? I have definitely hit that stage in my writing. The more I read, the more I have to read because I no longer understand what I am reading. I have entered the world of protein signalling cascades. Phosphorylation activating proteins or inhibiting them, sumoylation, palmytolation, ubiquitination! So many post-translational modifications that can completely alter the function of a protein. I’ve been studying neuroscience for years, yet I still find it mind-boggling how many vastly different roles certain molecules can have. Or how certain pathways can mediate so many various cellular processes. I have realised how little I know. I have spent the past few days reading reviews upon reviews to get a better grasp at how everything comes together and works especially at the molecular level. 
I must say in writing my thesis, I have also discovered how lucky I am that I have so many fellow PhD students at the University working on the same models as I am. They have all provided me with priceless knowledge and references that I might not have found on my own. They have also proven to be excellent sounding boards because although they may not be familiar with my approach to studying the models, we have had very enlightening discussions which have been incredibly helpful for writing my actual discussion. 
Writing is more demanding than I had originally appreciated. I’ve still been doing some odd experiments in the lab, so I think that it has been hard to get into the writing mindset. However I am officially out of the lab so time to buckle down and get this finished before Christmas. 
Writing progress report: Methods 95% finished first draft; Results chapter 1: 85% finished corrections; Results chapter 2 85% finished first draft

To do: Introduction, Results chapter 3, Final discussion


As I mentioned, I am at the airport getting ready to leave Edinburgh once again. Once again this year, I am attending the Society for Neuroscience (SfN) conference. This year it is being held in Washington DC. This is the biggest neuroscience conference in the world with over 30000 researchers coming together to share their science, debate current neurological topics and come together to collaborate to deepen our understanding of the brain. As I am right near the end of my degree, this is the perfect time to scout out potential postdoc supervisors and network my little heart out.

I’m also taking advantage of being on that side of the Atlantic to go home and write. I am hoping the change of scenery and lack of lab distractions will be very favourable for my writing. 
Time to board. I’m off again! À bientôt Edimbourg! 


Where has the time gone? 

How is it the middle of October?! How are the leaves already turned various shades of yellow and orange? How is it already dark by 18h30? When did this all happen?

Time warp

I know I have spoken at length in my blog posts about how time somehow manages to speed up in your third year. I didn’t realise that this phenomenon is exponentially exaggerated in fourth year! I do not know where the last 2 weeks have gone. All I know is that writing this blog post has been on my to-do list for over 2 weeks. Between finishing up experiments, supervising a PhD rotation student and writing my thesis, this blog post has just been delayed. I have decided that with every year of your degree, time speeds up (note: I obviously know this isn’t a real phenomenon, but relatively speaking, I feel a lot more rushed as time goes on, probably because there is less of it left!). During your first year, it feels as though everything takes ages to start and you just spend so much time reading and waiting to begin experiments. When second year comes along, you have reached your cruising speed, you know what you’re doing, you still have loads of time ahead of you, life is good. Then, third year hits. Your thesis committee starts asking you what you are going to do after your degree and tell you to write a plan for your thesis, but you feel like you’ve just gotten the hang of this whole PhD thing, and now you have to think about the end and how everything fits together and how it’ll form a cohesive (semi-cohesive) thesis. Then fourth year, out of the lab, except for maybe some control experiments and writing should take priority. You suddenly realise that maybe you should have done your experiment differently, but too late now, you have to make do with what you have… I know I make it sound really daunting, but I promise that doing a PhD is feasible and at times very enjoyable. 
Writing up

My goal is to submit my thesis by December. I have already submitted my Notice of Intention to Submit notifying the College that my submission is eminent. This notice gets the ball rolling and examiners can begin to be selected. My external examiner has already been selected for my viva which will be tentatively held in February! I feel like everything just got more real. This is finally happening! In terms of actual thesis writing, I’m trudging along slowly. I have decided to start by writing my results chapters. This way all my data will be fresh in my mind when it comes time to write my introduction and final discussion. This is to ensure that I don’t go off on tangents that are only tenuously related to my data in these sections. I have analysed all my data, reformatted all my graphs (my advice would be to decide on all your formatting the first time you plot your data, learn from my mistakes), written my figure legends and I am slowly getting into writing the actual body of the text. It’s a bit slow, but I do feel like I’m making progress. I hope to have a first (or maybe even second) draft the methods (which I started working on in India) and results completed by the end of the month. Then I have November to write the introduction and discussion. I can do it! I must admit I have started going to yoga twice a week now to stay calm. It is working. It does help that I’m also on my way to Italy for a few days. Hopefully it’ll be a relaxing and semi-productive change of scenery. 

Ciao Edimburgo! Ci vediamo pronto! 


What I have learned so far v3.0

The Fringe is finally over! I must say that I have out-Fringed myself this year, I went to 9 shows! 9 shows! Little old me who vowed to avoid the Fringe! In my defense it is hard to avoid it when they are set up right outside the office window and the smell of the food trucks waft through the open windows.

This year again, I wanted to impart my wisdom to you dear blog readers. I am officially at the end of my PhD (how did that even happen? Where have 3 years gone?), I am a little older and a little wiser and a lot more resilient, so it is time for round 3 of Katherine’s kernels of wisdom. If you missed the first two versions you can read them here and here.

Time is your enemy
Time is sneaky, it’ll lull you into a false sense of safety, because hey, you have 3 whole years to work in the lab, it’ll be a breeze. Let me tell you, it is definitely not a breeze. It is a full fledged hurricane-force wind. Time management is essential! There will be some quieter times in your PhD, for instance when you first start in the lab, when you are waiting for cells, flies, worms, etc. Although it is tempting to take it easy during this time, take advantage of it to get ahead. Maybe start writing a literature review or format your figures. I know that a break is well-deserved especially after particularly hectic weeks, but trust me, future you will be eternally grateful for any little bit of work that you do now that will help them in the future. Regular meetings with your supervisor will also help you keep on schedule.

There are very high highs and very low lows
Science and research in general is wonderful. There are so many novel things out there to observe and discover. When somethings goes right (like when I finally saw a phenotype after working on the same model for 3 years) you are elated. Absolutely nothing can bring you down. It is important to remember these highs when things stop working. Because inevitably, things will stop working… The phenotype that you were basing a whole chapter on could turn out to just be an artefact of one experiment on one day, the whole day you set aside for electrophysiological recordings could go down the drain because your cells were unhealthy… As a PI once grumbled to me on a Friday night as we were sat passing cells: “Science is 1% joy and 99% sheer devastation”. This is why all little wins should be celebrated.

Have a good support system
Whether these are other PhD students who understand what you are going through, old friends who try their best to make you forget about science when you are with them, parents, siblings or the barista at your favourite coffee shop, it is important to have a social life outside of the lab. I mean, who else are you going to celebrate all your little victories with?

Get out of the lab
I know I say this every year, but I can not emphasise how important it is to have a life outside of work. PhDs take over your life. It is good to have an outlet outside of the lab to put your energy into. Anything that is able to push your research out of the foreground of your mind for a wee bit. It could be yoga, cooking, building a flux capacitor, baking, going to the gym, playing Klingon boggle, knitting, teaching or learning a new skill like how to read Elvish.

Get as much experience as possible
Despite microscopes and stimulators not working, I still think that going to India was a high point of my PhD. Not only did it teach me how the internal components of a stimulator and microscope power supply box work, but it gave me the chance to play the role of expert. Although this can be terrifying, it is such a good exercise. You learn to troubleshoot, you learn the references of all the key papers in the field off by heart and it ensures that you fully understand why specific standards are used in the field.
Any type of work experience in a different lab is a huge asset as it allows you to learn new techniques and new ways of doing things. As I’ve already said, labs everywhere can be very different from each other. The more exposure to different labs you get the more ready you’ll feel when the day finally comes to leave your little PhD lab nest and fly into the world of postdoc-hood.

Post-PhD life
Speaking of postdoc-hood, if at the end of your PhD, you decide academia or even science isn’t for you, that is okay, don’t let anyone say differently. Sure a subset of skills acquired during your PhD won’t be particularly relevant outside a lab (I don’t know many government officials who do daily transfections or data analysts who do regular genotyping), but there are so many transferable skills that you gain from doing a PhD: time management, attention to detail, perseverance, data management, ability to synthesise information,  resilience, problem-solving, good written and oral skills, just to name a few. The years spent on your PhD will not be in vain, in fact, just the opposite, they make you a strong candidate for any job for which you wish to apply.


I hope that my kernels of wisdom throughout these 3 years have been helpful. Doing a PhD is a lot of work, so hopefully my advice can help make it all go smoother. Now, I have used up my self-allocated productive procrastination time for today, back to thesis-writing…




Fifth Fringe in Edinburgh

In true Edinburgh Fringe Festival fashion, the weather has turned very grey and rainy. George Square Gardens have been transformed into Fringe venues. Tourists are out in full force with soggy maps trying to soak up Edinburgh, before all-things Fringe engulf the city (I think it may be too late).


Lab stuff
I try to be as on top of my data as possible, but somehow some data had slipped through the cracks. I just found 5 days-worth of imaging experiments I’d forgotten doing in the mad dash leading up to Christmas/India. When I say just found, I mean just found, literally an hour ago! 5 folders from December are just sitting on my hard drive waiting to be analysed. The more data, the better, right? I’ve been doing lots of imaging recently to try to finish up the last few experiments I need for my thesis. A thesis does not have to tell a full story (papers do), but I have the cells and I may or may not be putting off actually writing up. Productive procrastination at its finest! I’m hoping to be done all my experiments by mid September at the absolute latest (and now that I’ve written it down it has to happen 😀 ).


More Edinburgh adventures
Of course everyone chooses the final crunch of my PhD to come visit. I like it though, it is a welcome distraction. Since one of my best friends from home came to visit at the end of June, I have also had one of my close friends from school come visit for a weekend and a childhood friend come up from London. I have explored Edinburgh, all the closes and the bridges and the haunted vaults (again). I’ve been all over New Town and Old Town and had my fair share of haggis. It has been very good way to keep my mind off the panic*.

*Yes, the fear has become the panic. I try not to let it overwhelm me (deep yoga breaths). I do have plenty of time and more than enough data. I try not to dwell on it. The panic can be kept at bay by lots of yoga, making my way through my analysis and weekly meetings with my supervisor. I’ve also made lists of what is done and what I have yet to do. The panic is curled up in a corner right now, I feel on top of things, but a simple “how’s you’re writing going?” could set it off again!


Back again

I hear that while I was enjoying rooftop terrasses in Montreal, the weather in Edinburgh was just as nice (I saw proof in the form of sunburns when I got back!). Unfortunately, I missed it. In fact, the weather since I’ve gotten back here has been quite grey and rainy as seen in this month’s photo- grey skies and green trees. Let’s hope there are still a few days of summer left!

Lab work
I’ve been back for 2 weeks now and I am officially back in Edinburgh until I submit my thesis *audible gulp*. While waiting for my experiments to start up when I was in India, I made lists (one of my favourite things to do) of what I have left to do in terms of experiments for each chapter. I haven’t quite started any of those yet. I’ve actually added more onto the list! I know that at some point I am going to have to draw the line and stop doing experiments so I can focus on writing up otherwise I’ll never write my thesis. There are just so many cool experiments left to do! I can definitely see how North American PhDs last 5+ years. There are just so many unanswered questions that are left to explore! Right now the important thing is figuring out which experiments are needed for my thesis and which ones I can do after submission to enhance a potential paper. It is exciting and scary. Although I’ve written up my MScRes thesis, this one seems different, more formal perhaps. I was flipping through an old PhD student’s thesis today and I was overwhelmed by “the Fear“*. I just have to get on with these experiments. The sooner I start, the sooner I finish. I’m hoping to finish all my experiments by September to submit before Christmas!

Visiting Edinburgh
Although I’ve been in Edinburgh almost 4 years now (how time flies!) there are so many hidden gems around the city that I haven’t fully explored yet. One of my best friends from home was visiting last week and together we explored all the different alleys and closes in the Old Town. We walked along the waters of Leith and explored New Town as well. We also went on a haunted walk that explored some of Europe’s most haunted locations which lucky for us are a stone’s throw away from  the George Square campus! Whether or not you believe in the paranormal, these tours are pretty freaky (the tour guide kind of looked like a goth vampire in a long leather trench coat), but also really interesting historically. It provides a new perspective on Edinburgh and points out some of the darker moments in its history that have made the city what it is today. I come from Montreal which just celebrated its 375th birthday; Canada celebrated its 150th this weekend (my friend and I celebrated with some good maple syrup). It always impresses me so much that there are buildings in Edinburgh that are so much older than that. The history here is incredible!

Now I must start on those experiments and make a plan for writing my thesis *another audible gulp*.


* The Fear arises in final year PhD students when they realise that the end is near and everything needs to come together. It can be exacerbated by things going wrong (which will happen), papers getting rejected (again, it will happen) and seeing blissful and completely unaware earlier year students (their turn will come).


Here we go again

The weather in Edinburgh was gorgeous last week! I was so mesmerised by the sun that I completely forgot to take a picture of George Square Gardens before leaving! Thankfully my friend took one for me from our office when I was already on board a plane to Montreal! (Thank you Amy!)

Lab stuff
Getting back from India was rough… The jetlag was unpleasant and the weather-which was cold and rainy (I brought the monsoon back with me you see) was unbearable. Luckily it started to clear up right before I had to pick up and leave again.

I got back from India and spent 2 weeks in Edinburgh before jetting off again to go to a conference (more on that later). I was back in Edinburgh just enough time to have a barbecue in the Meadows and repeat an experiment that hadn’t worked. I had stained and imaged a few cells right before going to India in January. Unfortunately, something went wrong with my staining and I couldn’t see my protein of interest. I repeated the experiment when I got back and I think it has worked this time. At least I could see the staining with the microscope, so that’s a good start. I’ll start on the analysis this week. I spent the rest of my 2 weeks analysing the data I had collected in India. Despite the little hiccups, the data look good. I met with my supervisors to show them my results and they are pleased with the work that I managed to do. It was a bumpy road, but all in all it was a great experience and it is a bonus that data actually did come out of it.

CAN meeting
I only spent 2 weeks in Edinburgh, because then I had to rush back to Montreal for the Canadian Association of Neuroscience (CAN) annual meeting. I’ve been away from Canada for almost 4 years, so it was good to see what research is being done and catch up with some old professors. I presented a poster that was very similar to what I presented at SfN. Although there were no synaptic vesicle recycling experts who came to my poster (there aren’t really any in Canada), I got the chance to explain my work to lots of people who weren’t familiar with my protein of interest or my imaging technique. It was really good to get a new fresh perspective on my work. People would ask questions that may have seemed naive but they made me question things and change my perspective on my research. Overall it was a really great conference. I want to thank CAN and IBRO for awarding me with a travel grant to attend the conference.

I now have 2.5 weeks off at home to relax, get over my latest bout of jetlag, analyse some images, start writing a paper, start thinking about my thesis and apply for another travel grant. A week in the life of a PhD student…