Where are we? When are we? 

AHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
That is how one of the postdocs in the lab suggested I start off this blog post. Perhaps because I am a tad frazzled these days.

Time warp
I know that I have already mentioned that I do not know how time is going by so quickly, but I feel the need to reiterate this point. It feels like just yesterday I looked out the window and saw the multi-coloured Fringe posters and Underbelly tent. Then I blinked and entered some kind of time warp that has brought me to November. November! I really do not know where the time went.

Teaching
I suppose that a lot of my time this term has been spent teaching. I am a facilitator in two new courses: Our Changing World (OCW) and Clinical Biochemistry and Endocrinology 3 (CBE3). The former is composed of a series of public talks on various issues that affect our global society including happiness, traffic and multiculturalism. After each lecture there is a group discussion which I facilitate. CBE3 is in a slightly different format: problem-based learning (PBL). The students are given an actual case report from a patient and go through it meticulously to try to understand all the components (from blood panel results to vague symptoms) and how they relate to the diagnosis. After the first session, they come up with questions they need to research to fully understand the case. During the second session, they get the opportunity to give comprehensive answers to all the questions raised. I facilitate these sessions and make sure that the students stay on track and discuss the relevant information.

SfN
Last May (which really doesn’t feel so far away now), I submitted an abstract for a poster at the Society for Neuroscience’s annual meeting in San Diego. My abstract was accepted, I was awarded travel grants and I will be on my merry way to the Pacific coast next Friday. The catch, my poster is still not made and the data is not yet fully analysed because of the little hiccough that I discussed last blog post (that base insertion knocking everything out of frame). This meeting is the largest neuroscience conference in the world with over 30000 people attending from more than 80 countries! This will be quite an interesting experience. It’ll give me the opportunity to present and defend my work in front of the leading experts in the field.

On that note, I am off to finish up my analysis and make my poster!

What I have learned so far v2.0

Things have seemed to settle down a bit in Edinburgh. The grass is staring to grow again in George Square Gardens, everyone is back from holidays and freshers are recovering from freshers flu.

As I did last year, I will once again provide you with Katherine’s kernels of wisdom (speaking about myself in the third person again). I am one year wiser and I am passing along all my wisdom to you, my lovely blog readers. These “what I have learned so far v2.0” should be taken along with what I learned from my first year to provide you with a sort of manual for “How to survive your PhD 101”.

You do not have much time
Three years may seem like ages, but let me tell you, if you blink, it’ll go right past. Three years is really not a long time to complete a PhD. In North America PhDs tend to last at least 5 years and usually even longer. The duration of PhDs here is both a blessing and a curse. If you decide midway through that science and academia is not for you, you will have only dedicated a small portion of your life to research. Nevertheless, you will have come out of your PhD with lots of other important transferable skills and a great work ethic. However, if you are incredibly passionate, three years may not be enough time to go down all the winding, twisting paths where your research question may drag you. You need to make sure to carefully plan your project. Although you may want to pursue every avenue, be sure to stay on course. I think that meeting often with your supervisor is the best way to stay on track. It is good to discuss your ideas and plans for other experiments.

Stay on top of your data analysis
I must admit that I am guilty of not quite being so timely with my data analysis. I must stress that it is really important (do as I say, not as I do, right?). If you don’t look at your data, how do you know that your experiments/ protocols are actually working? Analysing as you go along will save you time and effort in the long-run. You’ll be able to troubleshoot right away and won’t have to repeat experiments unnecessarily.

Get out of the lab!
Even if your sole ambition in life is to win a Nobel Prize in Physiology or Medicine, there is no need to be in the lab 24/7. Find yourself a hobby, go to the gym, travel, paint, join a society or a committee or just go hang out at a pub or a coffee shop to wind down. Meet people from outside of your research area -if nothing else it’ll give you the chance to practice explaining your research to a lay audience and improve your science communication skills. If what you are studying truly is your one passion in life (in that case, congratulations on landing the best PhD project ever!) then go to talks and lectures on related topics. Try to do some teaching in your field as well, there are so many opportunities for demonstrating and facilitating undergraduate courses here. Just do not spend all your time in the lab, it’ll drive you crazy!

The best laid schemes of mice and men often go awry
I think last year I was being optimistic when I said that things don’t always go well. I’m being slightly more realistic this year and I am firmly stating: things will go wrong. In fact, a few weeks ago, I found out that one of the constructs that I had been working with had a single base insertion that knocked everything out of frame. Although it was devastating to find out that what I had been working on for a long time had to be repeated, it did explain why I was struggling to see my protein of interest! I have since fixed my construct and I am merrily on my way to repeat my experiments.

Take care of yourself
I know I said this last year, but it is worth repeating again. PhDs are stressful and they do completely take over your life. Try to follow some kind of routine. Do not forget to take care of yourself and eat and sleep.

I hope that these latest kernels of wisdom prove to be useful and helpful!

12 more months…

The Fringe is officially over. The giant purple cow has been deflated, the posters have been taken down and there is no longer anyone handing out flyers. Between the tourists who have left and the students who have not yet arrived for Freshers, George Square is quiet and peaceful.

Fringe-y fun
I have a confession, I may or may not have been converted to a Fringe fan! I cannot believe I am saying this, much less writing it here for everyone to see! Although I had only bought tickets to 3 shows as of my last blog post, I ended up going to 5 shows, that’s right, 5 shows! I enjoyed all of them. I saw magic and comedy and illusions and circus and hypnosis and improv oh my! I also did enjoy having both the Assembly and Underbelly bars a stone’s throw away from the lab. All the food trucks did also make for good lunch and supper options. I immersed myself in all things Fringe this year and I did enjoy it, although I am very happy to get some peace and quiet back.

Lab work
The good new is that I had caught up on my data analysis. The bad news is that I have fallen behind again. I must just be that productive at taking images on the microscope hehehe. The problem is, if I don’t do this analysis, I don’t know whether or not my experiments are finished! I am also attempting to pioneer a new protocol in the lab, so I have been going around the building asking everyone I know for tips on various steps of this elaborate protocol. I have read and re-read papers to try to figure out the best protocols to use. Ultimately I have opted to use the manufacturer’s protocol for each step to date and let me tell you, they really work. Those manufacturers do know their stuff.

2nd-year meeting
This post has been delayed a few days because I have been getting ready for my 2nd year progress meeting which was today. This meeting is with my supervisors and the chair of my committee. There is not really a fixed format for this meeting (not like for our 1st-year meeting. In my case, I opted to do a short data presentation to show everyone (specifically my second supervisor and chair) what I had been up to since I became a real PhD student. My 15 slides turned into an hour long presentation… but overall it was extremely productive. I got some good feedback and great ideas for other experiments that would compliment what I have already done. It was also incredibly scary! I AM GOING INTO MY FINAL YEAR! The end of this meeting was spent discussing staying on-track, finishing all my experiments and writing up my thesis. It was also a chance to discuss my future plans and what I intend to do with myself after I submit. Apparently I have until Christmas to mull it over and then I should start contacting prospective supervisors (*giant apprehensive gulp*). I know I have already been in Edinburgh for 3 years, but I really feel like the end of my PhD has crept up on me. So my plan for the next 12 months is to work hard and produce the best and loveliest thesis that there ever was.

Now I will leave you, as I go ponder my future and make a detailed list (my favourite thing to do) of what needs to be done before September 2017…

Summertime analysis

Fringe time is coming, the posters have gone up, as you can see from my picture of George Square, the Underbelly venue is going up, complete with the giant purple cow! This is the first year, since I moved to Edinburgh in August 2013, that I will be in Edinburgh to experience the festival in its entirety. I cannot believe I am admitting this, but I have actually booked myself tickets to see 3 shows at the Festival this year. 3 SHOWS! What has gotten into me? Edinburgh may have finally worn me down.

Lab work
As I mentioned in my last post, I was off on holiday for 3 weeks (more on that later), so I haven’t been doing many experiments these days. What I have been doing since getting back is a lot of data analysis. I have almost caught up! While looking through folders of images on my hard drive, I just kept on finding folders that had not been analysed. Once I made my way through them, I realised that I have actually done more experiments than I thought and I am probably going to have a monster thesis to write up (too much data is better than not enough, right?). In finally getting a chance to look at my data, I now know which experiments I need to focus on to have completed data sets (the aim of all PhD students). Once I completed my analysis, I also saw that all my imaging for one of my chapters in complete! Woohoo! This is the same chapter that I thought I had already finished… but at least now it really should be, aside from some Western blots to be done in the next couple of weeks. Fingers crossed.

Edinburgh Award
The University of Edinburgh offers Edinburgh Awards. These awards allow you to gain recognition from the university for an extracurricular activity that you are particularly invested in. The categories range from: charity fundraising to Gaelic outreach and sports union club management. This year, for the first time, they have launched a Digital Ambassadors Edinburgh Award. This award recognises digital skills such as Wikipedia editing, blogging, social media management… I have decided to take part in this award, so I have spent the past few weeks looking at digital footprints (the traces that we leave online), blogging, updating my LinkedIn profile, building connections through Twitter and researching the role that social media plays in science. It is all very interesting and very worthwhile, albeit time consuming especially for a PhD student such as myself who is entering her final year (FINAL YEAR!). I think that these Edinburgh Awards are a wonderful initiative by the University and are definitely worth it.

Summer sunshine
I had 3 glorious weeks of sunshine during my holidays this year. I went back home to Montreal for a week during which the weather was gorgeous and I got to take advantage of all the terrasses which Montreal is renowned for and which are severely lacking in Edinburgh (mostly due to the rainy weather- totally understandable). After my speedy visit home, I went to Greece with some labmates for 10 days. It was spectacular. I would highly recommend going to Athens and sipping a nice cold drink on a rooftop with a view of the Acropolis, or walking through the winding streets of the city centre to get an ice cream, or just eating as much tzaziki and feta cheese as your heart desired. (Personally, that last one was my favourite thing to do 🙂 .)  If you do not have any summer getaways planned, and you stay in Edinburgh for the summer, you are spoiled for choices of festivals to attend (Magic, Jazz & Blues, Fringe, International…) and if festivals are not your thing, find yourself a nice pub to watch the Olympic Games!

 

On that note, I am off to fix some cells which I will then stain, image and have to analyse. And so the cycle begins again! Happy Sunday!

 

What time is it? Summertime!

It is a gorgeous day. So sunny and warm. Blue skies with wispy clouds and luscious (albeit a bit wet) grass. And of course, just my luck, I have to image today… The silver lining to the big fluffy cloud is that I go home to Montreal tomorrow where it is hot and sunny and proper summer!

Katherine the crab
I had a little accident and poured boiling water all down the back of my hand in April- not lab related, do not worry. This has kind of delayed all my work a little bit. The coverslips that I image are very delicate and fiddly, if you look at them funny, they crack… So it was quite hard to image them while my hand was bandaged (I affectionately have been calling it the claw). I am glad to say that after 9.5 weeks of going to get the burns dressed 3 time a week, I finally no longer need to wear a bandage! The skin has finally regrown! I wish that I could say that I got all my analysis done when I realised I couldn’t do any imaging at the end of April, but if you are an avid View of George Square blog reader (and if you aren’t, I would highly recommend becoming one) you’d know that I am behind on analysis and when the claw got less swollen, I continued imaging, so I am still very behind in my analysis… On a serious note, I would like to thank everyone in the lab who helped me especially during the first few weeks when I couldn’t even fit a glove on!

Lab work
June has been very hectic! I have taken advantage of the fact that the postdoc who shares the scope with me was on holiday to image my little heart out. When I close my eyes I see cells. I think the images are burnt onto my retina. Now the next step will be do do all of the analysis, which really desperately needs to be done so I can figure out what needs to be done next. It will be done after I come back to the lab reinvigorated after my lovely 3 weeks off.

3-minute thesis
The 3-minute thesis format is taking Academia by storm. And of course my fellow second-year PhD students from the Centre for Neuroregeneration (CNR) and Centre for Integrative Physiology (CIP) could not escape the trend. Basically you have 3 minutes and a single slide to describe your work. Yes, you read that correctly:we had 180 seconds to describe our work which has taken up the vast majority of the the last 2-years of our lives! Friday, we had to present in the lecture theatre in front of students, postdocs, PIs and heads of centres… gulp. This is what second-year students now have to do (when we were in first year we had to go through the whole 8-month report if you can remember that (again, if not please become an avid reader so you don’t miss out on these important milestones in my PhD 🙂 )). I suppose it is an efficient way to go through 16 student presentations in 2 hours. What no one mentioned to us while we prepared for this symposium, was that there was actually going to be a contest with a prize for the presenter with the best 3-minute thesis. I am quite glad that they didn’t tell us about it, but it did add to my nervousness right before my presentation. And guess what, I was a runner-up for best presentation! Yay me! In all seriousness, I am just glad that it is over, I think this presentation actually stressed me out more than my 8-month report and first year meeting.

On that happy note, I am off to do some imaging. The sooner I start, the sooner I finish, right? Then I get to go and pack and get ready for my early flight tomorrow.

Running a little behind…

I know that this post is quite late. It has been on my to-do list for 2 weeks, but somehow lab experiments and trying to get my yearly dose of vitamin D in 14 days just took up all my time…

Lab Stuff

You know when you’re just sitting there twiddling your thumbs because you have nothing to do? And then you blink and all of a sudden you have 4 days back-to-back on the microscope? And then you blink again and you have tonnes of molecular biology experiments to do? And you slowly realise that this analysis is never going to get done? Anybody? No? Just me? 

Well that perfectly sums up my month of May. With each breath I took, the work just seemed to pile up. Maybe if I take slower, deep yoga breaths it’ll stop… I said that I didn’t know where the month of April went, well I certainly don’t know what happened to May! But although May has left me in the rearview mirror, it was thoughtful enough to leave me 50 GB of data to analyse…

Non-lab stuff

Although last month was filled with experiments and multiple days on the microscope- I set a new personal record: 96 cells imaged in a week (!)- it was also a month filled with fun little activities that filled my time when I did finally part with my scope at the end of the day. We had our first BBQ on the Meadows. It was so nice. Because there are so few days of gorgeous weather, when it gets above 15 C and it is not raining, everyone flocks to the Meadows with disposable barbecues (just an aluminum pan with some charcoal) ready to have an epic grilled feast. We definitely went all out for our barbecue, with veggie skewers, lamb kebabs, spicy chipotle burgers and cheesy buns. Another fun event last month was the Eurovision Song Contest finale. My friend had the best party to celebrate. It was fancy dress with each guest dressing up as one of the finalist countries. She made cupcakes and brownies topped with edible flag cake-toppers of all the participating countries! Although I had never actively followed Eurovision in the past, this party may have made me a convert! 

Now I am off to enjoy the gorgeous Edinburgh weather and to start topping up on next year’s dose of vitamin D! 

Work/ life/ friends/ family/ grants/ science/ blog balance

Edinburgh weather never ceases to amaze me. Last week, everyone was sitting around in the Meadows having barbecues and this week it either snowed or hailed everyday!

 

Updates
This month has just flown by! I feel like I cannot account for my time since February! There must be some sort of conspiracy to speed up time that I was not made aware of… This month has been full of wonderful visits. At the beginning of the month, my friend from home came to visit and we got the chance to explore the cobbled streets of Old Town in the rain. And just last week my dad came to restock my freezer with home-cooked food for a lovely visit haha. It was nice to have people from home around. It was also strange to hear how my accent has changed over the past few years. Don’t get me wrong, everyone can tell I am from North America, I have not picked up the Scottish accent (much to the dismay of my best friend’s family), but I have picked up the vocabulary. I say trousers instead of pants, football instead of soccer and I try to make a conscious effort to pronounce the H in herb.

In my September post I spoke a bit about applying for additional funding for my 4th year. The results of that studentship applications came out and -drum roll please- I was not successful in my application. Oh well… On the bright side, this gives me extra motivation to get my PhD finished as soon as possible to go on to bigger and brighter things.

 

Collaborations
My supervisors and I have a longstanding collaboration with a group in India. In fact within my first month in Edinburgh, I was already included in Skype meetings with our Indian collaborators and their findings have dictated a large part of my work- which proteins to probe for, which assays to do, etc. Just this week, 2 PhD students from India have come here to learn new assays. I will be introducing one of them to the fabulous world of live-cell imaging and all things microscope-related. This will be a sort of microscope bootcamp, she has to learn the ins and outs of everything so that she can go back to her own lab in 3 months and set up the microscope, stimulator and perfusion. It will be quite a task to teach her everything I know about imaging and to teach her how to troubleshoot any problems she may encounter while setting up and imaging in the lab in India. This is going to be a great experience for me to go over all the imaging basics and remind myself of all the details that I may have forgotten.

 

NatureJobs
Last month, NatureJobs has a contest running to get the chance to blog at The NatureJobs Career Expo. I decided to throw my hat into the ring and write a blog post for consideration for the contest. Out of the possible subjects, I chose to write about whether or not scientists can have work/life balance. Although I did not win the contest, I want to share my insight. Here is my submission:

 When I told a postdoc in my lab that I intended to write an article suggesting that scientists could indeed have work/life balance, she looked at me and asked: “Are you really the most qualified person to write that?” It is true that as a PhD student, I do work ridiculously long hours and weekends in the hope of a breakthrough result that will pave the way to my Nobel Prize in Physiology or Medicine. That being said, I still manage to travel, go to the gym regularly and have a few hobbies, making me the ideal candidate to write this.

I think that work/life balance is possible for scientists, however not in the traditional sense. A scientist’s work hours are rarely nine-to-five. This means that we cannot compare our work/life balance to those who do only work eight-hour days and who can leave their work at the office at the end of the day. If we do this, we will be miserable.

Let it go… or not
Firstly, I do not think that the work and lifestyle that we attempt to balance needs to be the dichotomy that it is made out to be. As scientists, it is often hard to completely tear ourselves away from our research. I think that it is completely fine to always leave science (work) on the back burner, gently simmering, even outside of a lab or science setting. In fact, it is quite unpleasant to actively try to push something out of your mind while attempting to enjoy life.

Homeostasis
The “balance” in work/life balance does not mean 50% work 50% lifestyle, family, hobbies, extracurricular activities, etc. As scientists, we need find a homeostatic set point between our lab work and our life outside of the lab and try to maintain it. This does not mean that we are able to make that spinning class at the gym at 5PM or stay out late on the eve of a new experiment, however we can still have a life. It is quite an effort to follow a rigid, fixed schedule particularly when experiments can be so unpredictable. Hobbies that can be done on one’s own time-unstructured hobbies- are ideal for scientists.

No working hard and playing harder
There is no need to compensate for working too hard. During quieter weeks, there will be plenty of time to make up for it. It is important not to worry about work/life balance. The more we worry, the more we overcompensate. The more we overcompensate, particularly by trying to spread ourselves thinly and equally between “work” and “life”, the greater the chances that we realise we cannot do it and go on to do one or the other and lose everything that we have been working toward.

In conclusion, unfortunately, unlike in our lab work, there is no recipe or protocol that will provide us with our own personalized, ideal work/life balance. This requires optimization, which is something that we, as scientists, happen to be very good at.

 

And with that kernel of Katherine’s infinite wisdom (and yes, I apparently think so highly of myself that I am referring to myself in the 3rd person), I wish you all a happy Saturday!

The ghost of the past, present and what is yet to come

Can I just express how happy I am that the sun is already up when I get up and sets when I am leaving the lab? I am delighted! I know that that first part will change when we set our clocks forward this weekend, but the sunlight along with the daffodils in the Meadows are a sign of Spring (and potentially some warmer weather)!

Facilitating MB1
Again this year, I facilitated group discussions in Medical Biology 1. One of the topics up for debate was the same as last year: “Should triparental embryos be used as a treatment for families with mitochondrial disorder?”. It was interesting to see how a new group of students approached this question, particularly since the UK has since voted to allow more experiments to be done in this field. This topic was debated in the first report. After submission of the first report, each student was given individualised feedback, followed by a general feedback session for the whole group. This feedback was given before the submission of the second report, the grade of which does count toward the student’s final mark. It is so fulfilling to mark reports that have taken all the feedback into account. I feel so proud that these students have listened to what I said and, in doing so, have improved their mark.

Experiments
Alas once again our lab has been plagued by unhappy cells… I’m sure that I jinxed it by writing about how well things were going last month. So does that mean that in writing about my sickly, unhappy, unimage-able cells this month, they’ll go back to being perfectly happy and responsive next month? Well that is the strategy that I am going for! At least my break in imaging has allowed me to get back on track with my data analysis. I have been analysing my little heart out. I have t-tests and ANOVAs coming out of my ears! I have become one with post-hoc tests. My relationship with GraphPad has now evolved to a whole other level. GraphPad has definitely seen me in the best of times (p< 0.01) and the worst of times (What do you mean that’s not significant?! How can that not be significant? The error bars are miles away!). As a minor caveat, it is important to note that in science, particularly in biological/ biomedical science we should not have the sole goal of getting those asterisks above our graphs. Sometimes data are not significant and that is okay. It is important to keep the hypothesis in mind and look at our results in the context of our original research question and not concentrate wholly on the quest for significance. In a biostatistics course I took in college, the teacher pointed out something super important: statistical significance does not always equate to clinical significance and vice versa.

What lays ahead
Although I am mid-way through my PhD (MID-WAYYYYY!!!!!! Deep yoga breath. Okay mini freak out over), the other 3 students in the lab are all in their final year and all in the process of writing up. It is nice to view them writing up from a safe distance, nonchalantly commenting on their figures and offering data analysis advice (I am one with GraphPad) when needed. It is foreshadowing the events to come. What I find slightly unsettling about the whole ordeal is that I will be the only PhD student left in the lab in August! Our numbers are dwindling, send in reinforcement! I jest, but the high turnover rate in our building is incredible. I guess that is what it is like with 3-year PhDs.

I will leave you on that note of contemplation (I think that my GraphPad will be jealous that I spent so much time away from it! Happy Easter weekend!

Just keep swimming 

I cannot believe that February is almost over! That will mean that I am half-way through my PhD! That is quite a scary concept, and one that my brain refuses to come to terms with at the minute…

Lab work
Things have finally picked up this month. I have finished all my cloning- all the sequencing came back okay. I have been transfecting my super tricky toxic construct -the cells haven’t died on me. I have been imaging my cells -more than half the data is usable (ie responding cells, no drifting and no human error). I am not used to everything working, so I am behind on my data analysis! All in all things are looking up. I have to take advantage of this momentum and try to do get everything done- okay perhaps not everything, but at least check a few things off of my never-ending to-do list.

Finished?
I think I am, dare I say, finished with one part of one of my project. I am saying this in a whisper so that the lab fairy doesn’t come and ruin things for me. All of the analysis is completed and the graphs are made, though I still haven’t decided on my final colour scheme. I have even spent the last few days reading up on my protein of interest to try and fit my results into the story. I currently have so many tabs open on Google Chrome, I am amazed that my computer hasn’t crashed yet! I guess that this means that I am in the pre-pre-pre-stages of writing up. My inner-self is holding her hands up to block her ears and singing loudly in denial.

Podcasts
Speaking of data analysis, in some cases it can be mindless work such as counting cells or analysing immunohistochemistry staining. I’m lucky that my analysis, although very time-consuming , is not too labour-intensive. That means that I can do other things while I click. I am pretty obsessed with listening to podcasts, from true crime, to marketing to law and storytelling podcasts and everything in between. I listen to everything and pretty much anything. I was even listening to a podcast on how to make a podcast! It gives me the chance to learn new things in a pressure-free state of mind and it keeps me alert during my lengthy analysis. I also have time to listen to podcasts while on the microscope because we have set up automation on my beautiful new microscope (well not so new anymore). That means that it stimulates the cells and changes the perfusion automatically on the frame number we enter into the computer! I love technology!

 

Now I am off to start my day and keep busy so that the inner me doesn’t have time to think about my impending (not that impending) thesis submission.