Samstag, 15. Juni 2019

Thesis diary part V

Day 34
Feeling slightly better I manage to do a fair amount of writing. Maybe I CAN do this after all? In the afternoon we play some card games which makes me happy. 

Day 35
Finally back to feeling normal. I work from home today, mostly reading papers I should have read about a year ago. Progress is slow but I do feel productive. 

Day 36
In the morning I attend a course which turns out to be fairly useless. However, it gives me quality time to bounce ideas around with our rotation student and we develop a bunch of good ideas (i think), which makes me happy. In the afternoon I deal with a bunch of stuff in the lab, no writing but it’s all towards the thesis.

Day 37
Lab meeting, various other meetings etc mean I don’t get much done but I get my LAST batch of data for the thesis and start analysing it which is very fun. I do love a bit of coding. The evening is fun because we play games with my FSIL and her husband and it’s very chilled.

Day 38
Today is Wellcome Trust presentation day which means we are tasked to “present the major findings of your PhD”. I did not prepare much because I was so preoccupied with my thesis and so my talk is mediocre. Luckily people still think it’s ok. In the evening we have a formal dinner with everyone from the programme. There’s plenty of wine and fun chat and we continue the night with more drinks at Catz bar. It’s an excellent time.

Day 39
Severely.Hung.Over.Alcohol.Is.My.Enemy. The morning does not go very well, I do a bit of work on the sofa wrapped in a blanked feeling sorry for myself. In the afternoon I move to Hot Numbers (so hipster I can’t) to work with my friend. I actually am quite productive and nearly finish the first draft of my introduction, can you believe it? In the evening I reward myself with arts and crafts and an episode of ‘Love Island’. 

Day 40
How has it already been 40 days? Anyway let’s not get too stressed. In the morning I cycle to lab to get a bunch of data from a server I failed to access from home. After analysis I send it to our collaborators to discover that they are on holiday for 2 weeks. Oh well. I spend another few hours polishing my introduction until a dear undergrad friend pops over from London. We go for a long and rather nostalgic walk through the city center, enjoy sugary cocktails at 196 followed by an abundance of Swiss fondue, Ligretto and an episode of “Chernobyl” (which I highly recommend! We’ll definitely be watching the whole series). Bliss.

Day 41
We start the day with an extravagant brunch including all the millennial trimmings such as avocado, poached eggs and small-batch roasted coffee. (all home-cooked/brewed I should say!). After an intense round of Ligretto (I LOVE this game) my friend and his partner depart. I proceed to a little thesis-stress-related cry followed by a few solid hours of work on chapter 4. In the evening we go to a pub quiz. I would say we do ok but obviously we don’t rank anywhere near the top. And I majorly screw up the “killer” round by answering “smoked breakfast fish” with “Rollmops”. When that is obviously pickled not smoked. Argh.

Day 42 
I start the day with the usual Monday morning swim with corpus and swim a few solid fast 100s free yay. I then work solidly from home including a very motivating call with my collaborator in Glasgow. In the evening the German girls and I practice hair and makeup for the upcoming May ball which is rather fun but also clipping in human hair to get more volume just freaks me out. Like. That stuff was once on someone’s head how weird?? Looks good though haha Also we rewatch some of those Tourette syndrome videos. They just don’t get old. KATZENFLEISCH.

Day 43
I’ve got a doctor’s appointment in the morning and then go get a few last essentials for the May Ball such as open-toe tights and make up fixation spray. ESSENTIALS I know. #firstworld. In the afternoon I work at a local café with my friend and we are really very productive. After dinner my fiancé and I play scrabble. I lose but I still enjoy it a lot.

Montag, 3. Juni 2019

Thesis diary part IV

Day 26
I catch a Ryanair flight to Bremen, Germany to attend a dear friend’s 30thbirthday bash. I arrive feeling sick because I’m so tired. Luckily I manage to get a good 2h of sleep in the hotel room before finishing the famous figure while watching a makeover show. Shortly after 6pm I arrive at the party. Hugging my friend, whom I hadn’t seen in 3 years actually brings tears of joy to my eyes. The joy continues with delicious food, plentiful drinks and lots and lots of dancing. It really is a blast. Just before 4 am I drop dead into my ibis budget bed.

Day 27
I am hung over. Severely hung over. I spend the whole day wrapped up in a blanked on a deckchair in my friend’s garden feeling sorry for myself. We all do, in fact. Conversation (when we are awake) evolves around the fun party and also more specifically around an indecent picture that made its way onto her phone. After a bit of analysis of surrounding clothing the culprit is identified. More discussion follows. The highlight of my conversation is being asked what the most painful cancer was. God I always end up in the scientist box…The day ends with a take-away pizza and bed at 9 pm.

Day 28
I get a morning flight back, feeling in great spirits after the wonderful weekend. Another grounding experience that enabled me to see the whole thesis thing in a bit of perspective. However, that philosophical state of mind does not last long. After 90 min of gardening I rush over to my laptop to work on that thesis chapter. Working solidly I manage to produce a lot of decent text and give myself the evening off to watch telly with my fiancé. We start watching a period drama about the Tudors and I realise I should really brush up on my history….

Day 29
I go for an intense 3k swim in the morning and then work all day. By the end of it the chapter is basically ready for re-inspection yay. 

Day 30
My friend joins me for home office. We’re very productive. In a break we nip into town to buy shoes for her for the May Ball we are attending in 3 weeks. In the evening we enjoy a formal at my college with two other friends and a bottle of white (!) Rioja. Fascinating.

Day 31 
Today our collaborators from Oxford and Leeds are visiting. It’s a busy, interesting and intense day of discussions. I get fairly depressed when I’m told my data is “interesting observations” but not really a story for a paper. In the evening we have a meal at one of my favourite Cambridge restaurants. Unfortunately I don’t enjoy it very much because I am sad about my lack of paperability. I get home and go to bed pretty much straight away, feeling rubbish.

Day 32
I wake up feeling ill. I dose up on Paracetamol and drag myself to the institute for more discussion. It’s good but I feel very dizzy so I go home at noon to sleep. I can’t sleep because I’m nervous about my lack of data. I work and produce some text but it’s not great. My throat is killing me. Why. 

Day 33
I still feel crap. I try to work but my head is spinning. I go back to bed for most of the day. I find it difficult to sleep because I panic about my writing. A good hour on the phone with my friend helps to calm me down. Tomorrow's another day I suppose.

Montag, 27. Mai 2019

Thesis diary part III

Day 16
I wake up feeling very down. Luckily swimming lifts my mood. I go to the lab and do various things including some coding, a chalk talk and some immunohistochemistry. I don’t write anything but I try to feel calm. Prosecco in the evening helps. I attend an event by the guilty feminist with my lovely FSIL (future sister in law). The event is very fun but It goes on a bit longer than I had anticipated. The prospect of less than 8h of sleep and a suboptimally functioning brain makes me anxious but luckily I fall asleep very quickly.

Day 17
I wake up and I’m tired and hence upset. But I drag myself to the pool and it has the effect I was hoping for: I feel happy. I then go to the lab, finish some stainings, attend an R course and then hop on a train up North. That’s right. I’m going to spend some days at my FPILs’ (future parents in law) house – as mentioned before, I call this a “writing retreat”. My FFIL (I think I can stop explaining these abbreviations now…) picks me up from the station and we drive to Barnard Castle. After a brief walk we sit down at the restaurant with Gin&Tonics. Oh yes. My FMIL and FGMIL then join (I can tell you are enjoying this) and we have a lovely meal accompanied by lovely wine, of which I “have” to drink quite a lot as they are driving. Good times.

Day 18
It’s a Saturday but this time I want to work, after all that’s what I’m here for (and of course to spend quality time with my FPILs) (They might be reading this so I had to say that lol). So I spend most of my day being remarkably productive. By the end of it most of chapter 3 is at least drafted. Figures are in production. It’s a good writing day, finally! The day is rounded off by a walk around the reservoir and watching EUROVISION SONG CONTEST. A short summary of my opinion on the various acts:
Madonna.I don’t know. Just somehow off.

Day 19
Sunday = Funday! I wake up super late (9:00), and do some solid work in the morning before we sit down for a delicious Sunday lunch with the farmer from next door. It is followed by an equally tasty dessert. To fight food coma, I have coffee and go for a walk around the reservoir (in the other direction this time. We know how to have fun.) with my FMIL. In the afternoon work is a bit slow. I manage to make a figure but am not very happy with it. The first results chapter is now nearly ready for inspection by my boss! 

Day 20
I enter the zone. 
8:30-12:30 writing in the morning. (quick walk/seeing the hens break half way)
Walk around the quarry after lunch
15:30-dinnertime work
Fondue for dinner followed by Jass, the Swiss national card game.
Not sure Jass is popular with the FPILs.

Day 21
In the zone.
Afternoon walk with destination viaduct.
After-dinner Jass met with more enthusiasm today. 

Day 22
Afternoon walk up to Kirkkarrion and a former lead mine, very fascinating
After-dinner Jass very much entertaining. Followed by Oh Hell. Accompanied by a variety of drinks as it’s my last night up here.

Day 23
I’m leaving West Pasture today and am quite sad about it. I had a wonderful time up here and am emerging with a full results chapter written including figures, another one half done, some progress on the introduction and a generally more balanced state of mind. 
On the train I do some coding in R (really trying to improve my skills in the area of programming). In the afternoon I pop into the lab to fill a few gaps in my materials and methods and take a few pictures for better figures. In the evening I am finally reunited with my fiancé. 

Day 24
I go to lab and after a fight with my network connection manage to print my first chapter to give to my boss for inspection. My adrenaline goes through the roof. And my mood plummets as I notice he spends a loooooooooong time reading it. Not a good sign. I pop my head into his office before heading home and get a “it’s not ALL bad”. I spend my evening over-analysing that statement, unable to focus on the lovely BBQ we are having. 

Day 25 
I discuss the infamous thesis chapter with my boss. Turns out he just wants a casual COMPLETE RESTRUCTURING. I mildly freak out, spend the rest of the day helping our rotation student and going mental.  When I get home I immediately start working on a tricky figure my boss asked for. I don’t stop until late at night and then don’t really manage to sleep at all. What is this life.  

Mittwoch, 15. Mai 2019

Thesis diary part II

Don't expect me to post every single week but I'm feeling crap tonight and writing this helped me so here you go...

Day 10
Omg it’s already double digits where has time gone.  I’ve got about 7000 words written, for some of it I cheated though, as it was mostly copy and pasted from one of my two first year reports (don’t ask). I go to the lab bearing Swiss chocolate as a gift, talk to my boss, colleagues and discuss stuff with the rotation student. I also attend my weekly R session, which goes a lot better than last week (alcohol is evil). Can’t say I manage to write a lot of words. At 6:15 pm I leave the lab to attend a ceremony for student-led teaching awards. I was shortlisted for “innovative teaching” – I guess those crossword puzzles I make for the students were well received.  Unfortunately I don’t win so I go home very upset (I really like winning).

Day 11+12
I take another weekend off (such a rebel) and go to Brighton with my fiancé. (slowly getting used to this word). We have a lot of fun sightseeing, eating food, sitting at the beach, eating more food, wasting money on arcade games on the pier (£10 spending limit tho!) more beach (including drinks) etc. I have a panic attack about my thesis every 2h or so but manage to hide this from him fairly well I think. Overall it’s a super lovely weekend.

Day 13
I catch an 8 am train from Brighton to London Victoria and sit in a totally unglamorous Starbucks and write. It’s fairly productive as the Starbucks is empty and crap. I then get the tube to St Paul’s to have lunch with a friend I made at the conference I attended in March (See my relating blog post). We buy shoes for her at Topshop. I then join her at her lab near Barbican and do a very productive couple of hours at her office. I then go for a swim at the nearby Ironmonger Row Baths – highly recommended! I get in for free with my Better gym membership from Cambridge and the hairdryers are free – both these things make me very happy for some reason. I get to Clapham Junction at 8 pm where I get a Doner Kebap with a dear friend from undergraduate times. We then sit in the Jacuzzi and discuss my potential hen do and just generally have great chat and I forget about my thesis for a few hours which is great.

Day 14
I wake up at 5:30 am due to the lack of curtains in my friend’s living room. I feel dreadful. I stay at his flat for a couple of hours, doing solid writing, such that I can get an off peak train back to Cambridge. I work on the train. I go to lab and have a chat with my boss. I really need affirmation. As soon as I leave his office I feel stressed out again. I FEEL SO STRESSED. In the evening the German girls come over and we watch various Youtube videos about this guy who has Tourette syndrome. By various I mean several hours. (for German speakers: it’s called Gewitter im Kopf)

Day 15

I get up early to mark students’ work before heading to lab for 8:30 lab meeting. I discuss stuff with our rotation student. I mark more work. I stress about figures that need some analysis. I feel awful. I read some very interesting things about antigenic variation in African trypanosomes. I read equally interesting articles about epigenetic silencing of PfEMP1 via lncRNAs. I then go and teach that stuff to my undergraduate supervisees. I get home feeling crap because I have not written a single word today. I try gardening therapy (aka I do some weeding). Still crap. I empty the dishwasher, take out the bins, tidy the bedroom. Still crap. I update this blog and watch Made in Chelsea. As soon as it’s an acceptable time (aka past 21:30) I go to bed. I really need to do more writing.

Donnerstag, 9. Mai 2019

A thesis diary

Let’s start with a trivial statement. When I started my PhD project back in October 2016 I really did not expect writing-up time to arrive so quickly.  And yet it did. Here I am, about 2 years and 7 months and a few million crypts scored later, starting to write. Now I do love writing, prose more than science, but in any case writing a PhD thesis feels like a very, very daunting task. So I’ve given myself quite a bit of time and a vague timeline to follow. And a safety net of 1 month (which turns into holiday if I do succeed in sticking to my plan yay). My timeline starts on the 1st o May, 4 months before my artificial deadline, 5 months before the hard one imposed by my PhD programme. I figured it might be quite fun to look back on this time in 5, 10 years and reflect on it, so I’ll try and write a little diary about it.  Who knows, maybe reading it may also serve someone who finds himself in the same position in the future. In the worst case, I’ve provided myself with some excellent “writing warm-up” for every day (aka procrastination). Here we go.

Day 1
It is the 1st of May. My writing start date. Unfortunately I’m in the lab, having to finish a bunch of stuff and be present in case our rotation student needs help. In between those things I stare at my screen and try to make a skeleton of my thesis/ a  decent plan on paper (actual paper. I like using pen and paper much more than I like typing on a computer. I also have a fountain pen that I’ve used for every single important bit of writing I’ve ever done by hand since I was 12 years old. So yeah.) It does not go well. How on earth am I ever going to get any logical structure into this mess of experiments? I get home rather upset. I do some gardening to take my mind off it and watch Ex on the beach to push my dwindling self-esteem.

Day 2
Still working on that skeleton plus trying to start writing my first results chapter, which is all about method development. Still in the lab, same reasons as above. It’s not going well. I feel like I don’t have proper records of certain experiments I did. I panic. I go to the lab and look for microscopy slides to take better pictures. I fail to find them. I find them an hour later. They are not good enough. I panic. I speak to a senior researcher in the lab. He thinks I don’t need the pictures, just a table. I breathe for the first time in a few hours. A friend texts me and asks if I want to join for a wine tasting dinner for £30 instead of £80. I invite along the rotation student and spend until midnight drinking 8 glasses of rather tasty Bordeaux wine alongside 5 courses of delicious food. I get home feeling less stressed but positively dizzy.

Day 3
As one could have expected I don’t feel good. I cancel my morning swimming session and go to the lab to help the rotation student with some experiments, look for more of the microscopy slides, talk to my boss and just generally procrastinate.  I also attend a session about programming in R, which I find quite hard to follow due to last night’s activities. Alas, at 3:30 pm I decide there is no point and cycle to the garden centre to pick up some slug granules (They have been feasting on my sugar snap pea seedlings and hence deserve to die).  In the evening I watch Ex on the beach again and feel sorry for myself. I go to bed early, hopeful for a relaxing weekend.

Day 4 + 5 (weekend)
For once I decide to take a full weekend off. I spend quality time with my partner, the garden and the kitchen. I also attend a 60th birthday BBQ in Woking and just generally have fun. This should energise me for the next week of writing.

Day 6
Today is a bank holiday . I travel to Switzerland to my parents’ house for what I like to call a “writing retreat”. I manage to work a little at the airport but other than that not so much, as I spend the evening with my parents. I go to bed early such that I can get a lot of writing done the next day.

Day 7
I spend the whole morning, from 7 am until 12 noon working pretty much non stop. I’m not very pleased with my writing as it proceeds very slowly, with a lot of time spent looking up references (the classic “I know this but I don’t know why I know it”). At least I do progress though. I feel stressed. After lunch I go see two friends who are secondary school teachers. It’s nice to get reminded of the “real world” and gossip about various useless people. The chat leaves me revitalized so I work for another few hours before dinner. I’m reasonably happy with my progress today so I go and watch the Swiss version of The Bachelorette with a dear childhood friend. It’s so cringe.  Love it.

Day 8
I start the day with a 6 am session with my old swim team. It’s tough but also very fun and again a healthy “reality check” as there are no scientists on the team. When I get home I have a cappuccino and do a bit of medium quality writing. Then I drive to Germany with my parents to look at wedding dresses. It’s very fun and makes me happy. After lunch I put in a few good hours of work, though I’m not really all that happy with the amount of words I’ve written. In the evening we have dinner at a restaurant with my brother and then do an escape room. My parents love it which makes me happy.

Day 9

Today is the last day of my writing retreat and so far I have not progressed too well. In the morning I work for an hour then go see a friend with a kid. We play for quite a while and have lunch and its fun but I start getting stressed about not writing. I then take a bus to the airport where  I sit and do solid writing. Very solid in fact, as a French air control strike gives me extra time for this. For the first time since I started writing I actually feel good about what I produce. I feel like some sort of cohesive narrative is coming out. I also realize there are a bunch of qPCRs I may need to run again, as the figures are ok for a first year report but not a PhD thesis. Back to the lab next week I reckon. Tomorrow in fact, to discuss some stuff with our rotation student. Anyway I land into Gatwick at 7 pm, and catch a direct train (BONUS) to Cambridge. Manage to work on a figure on the train yay.

Sonntag, 5. Mai 2019

School camp revisited

It’s my first fully lab-free weekend in … months. (don’t ask) So obviously I can’t think of anything better to do than to write. About work.  Yeah I guess you could call me pathetic. But actually I’ve been meaning to write a blog post in quite a few weeks, basically ever since I’ve come back from what I like to describe as “basically a school camp for scientists” – my first Gordon Research Conference. Before going I had heard quite a bit about these conferences and how much fun they are but as I boarded a BA flight from Heathrow to LA on the 24th of March I don’t think I was prepared for the blast I was about to have. Honestly, writing this, with music by Sigma in my ears, I feel quite emotional, because the experience I had was really rather inspiring.
As you know I’m scared of flying so I really did not enjoy the 11 odd hours in the air. The whole thing was worsened by the person sat next to me who was Swiss, which usually makes for at least some decent conversation a la “ah yes I know someone who went to your high school. Ah yes my dad’s friend works at that company. Yeah I love fondue too”. But no. This man was a twat. He did not ask me any questions and his only topics were “I’m such a big dog I’m going to SF to promote my holograms startup.” And “my polish girlfriend is so hot look at her instagram she’s currently in Bali”. Could. Not. Care. Less. Also she wasn’t even that hot soz mate.  So yeah the flight was not great, I watched “Mary Queen of Scots” and “Zimna Wojna” (In keeping with the Polish theme lol).  Immigration at LA airport was a disaster. I don’t know if it was because it was a Sunday. But we waited a good 2.5h. And I was so tired. (Bearing in mind it was now about 2 am UK time). Obviously I missed my shuttle to Ventura (conference location) but so did a bunch of others, mainly PIs so we got chatting at the bus stop and on the shuttle. When we finally got to the hotel at 8pm local time (UK time about twenty thousand hours past bedtime) they invited me to have dinner with them so I immediately met like 4 PIs, including one of the organisers. We chatted about all sorts of stuff including their attempts at weight loss which included lots of swimming so obviously I had a lot to say about that and promised to provide a personal training session in the hotel pool later in the week (more about this later).  After dinner I swiftly proceeded to bed. Funnily my roommate never showed up so I had a twin room (American twin, so two King sized beds lol) to myself. GBA.
The first morning was very sociable. Most attendees (apart form the PIs) did not know anyone else so we all just got chatting at breakfast (a huge buffet including all sorts of hot options and waffles- oh ‘murica) so I immediately made a bunch of friends. Then the talks began. I was super pleased to see an even balance between male and female speakers. Though it was really quite interesting to see that most very junior attendees like me (aka PhD students) were female. In the next generation, when the old male bigdogs start biting the dust the gender landscape of biology will change dramatically. I hope I’ll be part of that.
So yeah, talks. It is fair to say that there was not a single bad talk, in fact, most of them were so fascinating, I did not check my phone a single time during the entire conference. But in my mind, the best part about this GRC was the friendly, collegial atmosphere. I think I had a chat with most of the attendees, junior and senior. We had plenty of social time, at mealtimes, in the afternoons (which were free) and also in the evenings at the bar. It was just so easy to strike a conversation with anyone. 
I bet some of you are now worried that I will describe the rest of my 5 day conference in such minute detail but fear not that is not the case. I will now switch gears into a more dream-like flow of consciousness as I try and capture the emotions and events of those inspiring days in Ventura.
Every day followed a similar routine, with breakfast, talks, coffee, talks, lunch, free time, drinks and posters, dinner, talks and bar. It really did remind me of the school camps I enjoyed as a kid and teenager. Except this time the teachers were our friends.
the beach near the hotel
I should mention I actually did know one other attendee - a friend from my undergrad who is now in London. Funnily we always end up attending the same international conferences (last time Berlin 2017), a great way to catch up. She also joined for part of the road trip (see below). One of the talks included skin samples. The speaker explained that his foreskin was already gone which is why he had to take a punch biopsy. Thanks for that. Another term that got coined during this GRC was “cuddling” – when cells are found in immediate proximity. Whale watching. It was breathtaking. We saw so many “jumping whales” (see picture, credits to Francois). And dolphins. Hundreds of them. It was special. That was also the day of my talk. I had practiced a LOT. I also practiced in my room every day since I had gotten to Ventura. My knees weak palms sweaty as I entered the stage but then, as I started with my “let me introduce you to the fascinating tissue that is the mammalian intestinal epithelium” all the nerves just vanished and I was able to own the stage and put it all out there. What a sensation it was to head to the bar afterwards and receive compliments from peers and senior PIs alike. To chat to these world-leading scientists about my work. It felt like every single evening and Sunday at lab had been worth it. I was on a high and stayed there for the rest of the conference. In fact I’m still partly running on this sensation. I should say that I believe I have managed to establish the term “fufi” as description of two crypts that are either fusing or fissioning. YASS. I also delivered my swimming training session as promised. Which was a bit surreal. Us girls spent significant time in the hot tub. Very chilled. One PI brought his daughter to the conference – adorable. The food was very very plentiful and different every day. All buffet of course. Amazing. At some point decided to ignore my flight to SF and roadtrip with a new friend instead. I’m never this spontaneous. But before that we had our last night at the bar, which included some decent dancing. Scientists can have a lot of fun, believe it or not. On Friday we got up a bit later than planned and drove off towards SF. Along the coast, seeing beautiful beaches along the way, staring into the sunset at Carmel beach and getting extremely frustrated at SF airport around 10pm where we just could NOT find the rental car place and I believe we accidentally entered a military area. Oops.

all. the. whales.
It’s Sunday today. Tomorrow I am flying to Switzerland to pump prime my thesis writing at my parents’ house. I feel slightly anxious, excited but mostly motivated. Inspired by the experience I had in Ventura. There is a plan in place. To get this thesis written and then swiftly move on to getting my work published, and decide on a lab and country to move to in 2020. That’s all I have to say for now, it’s 10 am and I’m gonna play the piano now, yay weekend.