#thesis blog

[venustransiens]

Week 4: "And they were roommates”

This week has involved a lot of reading of articles and criticisms of lesbian academia and lesbian literary criticism as I prepare for my first review of literature draft. And it’s left me with even more interest in my topic, a potential line of research for a Ph.D., and a lot of frustration.

It’s amazing to encounter discussions of the emerging niche that is lesbian history and literary criticism in the 1970s and 80s. Many niches disregard criticism or analysis from older decades but to me this perspective is so important to understand where we go from here and how far we have come. I’ve read articles that describe hopes or aspirations that are directly correlated with what I am doing with my research. It feels really cool to have the unspoken connection with lesbian scholars of the past. 

Reading all of these articles can be fairly frustrating however. I come across twice as many writers that are happy to erase the true history of lesbians and queer people in general. Many researchers across decades are more than happy to wave away the validity of these relationships, rewrite definitions of terms, and just generally disregard this field of study altogether. It’s an issue I’m facing with my own journey in publishing research, queer studies get people talking in all the right and wrong ways. This both discourages and encourages me, oddly enough. On the one hand I truly do not want to fight for my place in academia, a fight that feels pointless and not mine to take on. I just want to do my research and publish my work in a generally accessible way, not according to some board’s idea of what research should be, which usually does not align with my own views. But on the other hand it makes me want to keep trying and make something happen. I’m sure some day I’ll find a middle ground there.

In other news, I think I accidentally discovered what I want to study for my Ph.D. dissertation even before I’m done with this degree. In my research I keep running into lesbian or queer women in general who spent a lot of their time researching ancient times and ancient instances of lesbianism. Anne Lister, Sophia Parnok, and Renée Vivien are just a few examples. I think the next step in my research, after this master’s, is going to be honing in my research and finding ways to look more into this topic specifically. We’ll see, of course, I also want to dabble in some folklore studies and generally older than modern literature. But this may be a good Ph.D. niche for me after all!

[venustransiens]

Week 3: Finding my place in my topic

We’re already three weeks into the semester??? I swear graduate school makes time fly 800x faster. This week I have been doing less intensive research for my thesis because I have a draft due for a big project outside of school in three weeks. But that doesn’t mean I stalled on progress altogether! In fact I think taking weeks like this and approaching everything slower will benefit me in the long run.

All of my books are here (yay!) well except one but it was on someone who I’m not entirely sure I’m including so oh well! tbh I think that book is lost in the mail so at this point my only concern is getting a refund as it was pretty pricey!

This week I also applied to present at a conference that would be a pretty big deal for me and an amazing post-grad opportunity. So let’s all cross our fingers I get in, I’ll update on what it is if I get accepted!

I have been reading about a few different topics this week but the most illuminating to me is the story of Marie Madeleine a Jewish German writer who helped pave the path for queer women writing in the early 20th century and was heavily addicted to morphine. Her poetry, story, and impact are a great reminder to me of why I’m doing the research I do. I love my research niche so much and uncovering more and more previously erased or hidden stories is a large part of why I study it.

My goals for the upcoming week are to (hopefully) finish my draft for my publication or at the least get into my last round of edits. I also want to get an outline of info for my lit review. I think those are solid and achievable goals or at least I hope so!

[puussaare-blog]

T-33/T-32: What does it all mean?

I am back with another ‘weekly’ blog to give an overview of my thesis progress. I should actually not call this a weekly blog, because of its not really published weekly. There is multiple reasons for it which I am not gonna bore you guys with.   

OK, what is the progress then? 

As I mentioned in my previous blog I was off to a writing retreat to get some words on the paper. Because of the location of the retreat was near London it took me about a day of travelling to get there and back. This made me think weather the whole thing would be worth it. I did a bit of calculation and the short answer is probably not. However being in a new environment, without your normal distractions and having a structured way of spending time on the thesis can be really beneficial. With all the travelling aside it was quite successful event, I managed to write approximately 3400 words towards my thesis. What appeals to me the most, is being away from your everyday duties, waking up and showing up to write every day. I guess I could do that at the office/home but it is too easy to find distractions. It comes done to willpower and self discipline. I have been trying different methods since being back - writing couple of hours at home once I wake up before going to the office, allocating writing time and sitting in different places in the office to get most out of it. It works some days and it does not work on others. Will let you know when I find the winning combinations for me. 

Doing stuff is easy, writing about it also, figuring out what it means is that the hard part. 

I thought the best way to get my thesis written is to kick it off with what I can write straight away - what I did and how. Writing about the studies, the context and what I designed, developed and deployed. It worked well and the words just flew out of me. 

It was a good practice to kick of the writing process and get into the zone, however I am now a not sure it was the best thing I could have done. More important for the thesis is to get the narrative right, because that dictates how the case studies are going to be written up. You can tell so many different stories of the same thing, but it is not easy to pick the one for the thesis. Also setting up the story helps to review if I have enough of data to tell this story. To be honest I was just terrified of writing this part and I thought it will put me off writing straight away. I was right about that.

Write early and often!

If I could go back I would tell my former self this suggestions. After doing something I should have reflected on it or even written down what, how and why I did something. Then I would have the material to organise into a narrative already. I see some of my colleagues having this practice and I am sure they will find it very useful when they come to write their thesis. What does it all mean? 

So I have been looking at a pice of paper (keep seeing similar ones on every thesis writing phd student's desk) that I made since Monday this week to figure out how does it all come together and what is the story. I have now produced a first draft of the narrative which is 500 words and 'it only took me a week'. Compared to the 3400 words I wrote at the writing retreat, it is nothing. However, these 500 words are more valuable to the whole process and help me set out the rest of the thesis. 

So if I can recommend something to my fellow Phd students is to kick off the writing with something easy to get yourself in the zone, but think about setting out the narrative for the thesis quite soon. Same recommendations I would give for starting runners - start off easy to get yourself comfortable with the movement and then figure out a plan to improve your running. 

[puussaare-blog]

T-35/T-34: On finding focus and positioning my work

I took a week off, hence the lack on blogging last week. Was planning to write something while I was away, but it seems that when you are not actively thinking about the thesis or as I mentioned in my first blog post - not allocating the time to working on it - it is just not gonna happen. Now back in the office with a post holiday dread and trying to get back on the schedule.

As I do not have major updates with the writing I though I will talk about how I deal with the overwhelming amount of work. Probably a lot of us have had moments when you go to work every day and have a task list that needs to be done and end the day with even bigger list. This can be soul crushing because it seems that it does not matter how much hours of work you put in, there is always more to do. The real issue is actually in lack of focus and a system of ticking things off. In addition to my hour allocation schedule for the week I described in the previous post I also use a small task list for every day. I actually learned this method from Tim Ferriss’s  book “Tools of Titans” which is a compilation of his podcasts where he interviews successful people about their habits. Here’s how it goes:

before looking at any screens (specially browsing your email) take out a notebook of sorts

write down 3-5 things that make you most anxious and uncomfortable. You can have a system of 1-5 to rate the tasks. I also integrate a variable of “if I do this task whether the other task become easier or absolute”

decide which task you are going to definitely finish today

then the most important thing - block out 2-3 hours from the day to focus on that task

You should look at that chosen task as a success rate for the day: “If I can tick that task off, my day is a success!” I have to admit that I do not do it every day, but on times that I feel overwhelmed with amount of tasks I always turn back to this method. And it has been successful for me and helped me fight my anxieties. If you find yourself in the same position, give it a go!

Is the value in numbers or valuable insights?

Another things that I have been thinking about lately is how do I position my PhD. I am doing PhD as part of EPSRC Centre for Doctoral Training in Digital Civics, which means that it will be multi-or cross disciplinary PhD. Which is what the whole Human-computer interaction (HCI) is all about. However I am getting my degree from an engineering department, which is still following the traditional scientific method. It is not to say that methods in HCI are not scientific which they are, but they also add more complexity for setting hypothesis and evaluating the work to come up with contributions to knowledge. Thinking about where my work fits in best and should I take a more engineering or human computing approach makes me a bit uneasy. I guess I will be coming back to this when I start moulding my methodology section of the thesis and talking about the evaluation of my work.

Running?

As you guessed I also took a week off running. However I did 8 days of physical activity on snow:

Now I am back on the training schedule and easing my way back to getting the marathon pace down. 

So this was a short blog for these two weeks, but next week I am actually going to a 2 day writing retreat to see if the social pressure and peer support will help me get more writing done.

[puussaare-blog]

T-36: Setup aka things I can do to not actually write

Second week in and I was really hyped to start putting some time in to produce content for the thesis. However happened something that always does, I needed everything to be working perfectly and already in the right format. In other words all "the stars have to be aligned". So here’s what I did:

First I went through all the folders on my computer/cloud storage related to my three years of doing the degree and collected all the pieces of text I have written - papers, notes, proposals, abstracts, presentations, comments of papers and books etc. Then I dumped them all in one folder.

Next I had to find a home for the thesis document. In the back of my mind I had already decided that I will use LaTeX to write the thesis, because the idea of chasing those little points that Word creates when the formatting does not work makes my head ache. Also talking with some people from my research lab they said that they wished that they had used LaTeX because word has issues when the document gets too big (no problem of mine at the moment). I already started to dabble with LaTeX for some of the peer-reviewed papers so I know my way around it. In addition I could use an online LaTeX called Overleaf which will add some stuff like commenting and rich text editing. Only issue with overleaf is that it is not completely free service, it is £6/mo for students. Newcastle University should get the institution licence eventually to get it for all the students. In the meanwhile I am happy with the free version for my thesis, because I am the only collaborator. Things that I would like to have which are not in the free version though it are 'real-time tracking’ and ‘full document history’. Also another thing is how to back everything up, but I will come back to it later.

Overleaf also has templates for 'everything’. But of course it is missing one for Newcastle University Thesis to conform with the Guidelines for the Submission and Format of Theses. A bit of digging around and I found the 2 templates that people had made previously for their submission. Had to chase people down a bit because, but I eventually got a good template that fits the guidelines - https://github.com/AndreGuerra123/NUTT. Big thanks to André who dusted the old thesis files and put them up in GitHub upon my request.

And voila:

Got it started and even got some of it filled from the things I had written before:

But it is only accessible online and where are the backups?

All off us have heard horror stories of people loosing their whole thesis just couple of days before submission because their hard drive got corrupted or they spilled some coke on their laptop. So what I am gonna do to avoid this situation. Having a software development background I am used to code repositories and git. This will also help me with keeping track of the changes, not real time but enough to go back on what I changed with every commit. Luckily Overleaf has a Git integration and it seems to work well. I can sync it with my computer and work on it offline using other LaTeX programs. Overleaf also integrates with GitHub. Ideally I would like to sync to both Overleaf’s Git and GitHub. It seems to work fine with pushing from Overleaf to GitHub, but I already had issues when I tried to push from GitHub to Overleaf. Found this blog post which might be worth investigating - https://ineed.coffee/3454/how-to-synchronize-an-overleaf-latex-paper-with-a-github-repository/.

What is the plan now?

Now I don’t have any more excuses. The document has been set up nicely and seems to work well just filled with a lot of titles and bullet points. When I feel that there is an overwhelming amount of stuff to do I always go back to My Draft Schedule that I made in one of the time managing courses provided by the university. We often fill our calendars with meetings, book in lunches and events, however we rarely block out time for real work - the thing that really matters and gets us where we want to go. It has been working for me previously, however I need to modify this a bit to allocate more time for writing. Going back to my first blogpost about putting the time in I need the time to only focus on writing, but I also need to figure out what times I am most productive at it. I’ve noticed that mornings are the best for me so perhaps increase the morning time. Also I am quite productive at the end of the work day.

It has to be trial and error, but most importantly I need to put the time in.

But what about running?

I have not forgotten my commitment to running. A friend of mine once pointed me to the Runners Connect site when I was training for my first marathon and I found it really helpful. It talks about how to train specifically to marathon and what are the common misconceptions and mistakes that beginner runners make. So I also made a plan for running which I have been able to stick to.

[puussaare-blog]

T-37: Reality check

In my second year of PhD I came across a blog series by Tony Chu which described his process of getting his PhD thesis done. I promised myself that I would try to do something similar at some point in my PhD. I also did some maths. My studentship ends in September 2019. That makes 8 months and 22 days or 264 days. That divided by 7 is roughly 38 weeks. That means I am committing to write 37 blogposts until the submission. Although this is a hard deadline I am setting myself, I actually want to get it written done in half of the time.

So where I am with the writing? Is it feasible?

Honestly it is not looking particularly good. I have written couple of papers which will contribute to chapters, I have a rough plan what the thesis will consist of and I have some notes scattered here and there, but I don’t have any systematic way set up to get the writing done. That is the reality of the situation. One good thing in all of this is that I’m not alone in the boat. I am working in a research lab where we have over 50 PhD students in different stages of their studies - just started, half way through, in the writing up stage, almost done writing, just defended the thesis and got their doctorate. This means that somebody is always either going through the same thing or just gone through the thing you are facing.   Every individual is different, however there are things I can learn from others what to do and what not to do. Talking with others and sharing my plans of writing up in approximately 5 months, people do not seem overly enthusiastic. People tell me that writing the thesis they have developed a new level of procrastination. General consensus is that it can be done, however it needs 100% focus and dedication. And  this is hard in a lab where there is always something interesting going on. New projects, new opportunities for collaboration.

What I need is a systematic approach to writing. How would that look like? First thing I need to figure out is what I have and consolidate that in some form in one place - the thesis document. Second thing I need is the actual system for producing words. One approach that comes to mind is the one that Haruki Murakami explained in his memoir. He took a very primitive approach to writing, where he said that writing is skill which needs to be practiced - like running. You do not just wake up one day and run a marathon without any previous training. He set a dedicated time in a day where he would just sit in the office and try to solely focus on writing. Even if nothing is appearing on the paper, he would still sit and try. I believe adapting his approach for myself could work. Also I can not forget running in all of this as I have secured a place in London Maraton on the 28th of April 2019. That is in 15 weeks, which is a good time to review both - running and writing progress. In short I need to come up with my training schedule and writing schedule for the next 15 weeks and execute it. Wish me luck! 

[arabidopsister]

Some Good Science Shit™ Begins!

So I feel like most thesis blogs are awesome things like vision boards and ~cool stuff~ but honestly this is going to be a place for me to blow off steam about my thesis project. For those who don’t know me, I’m Kaitlyn, and I’m a Biochemistry/Biophysics (and Asian Languages & Civilizations!) major! (but I’m doing a Biochem thesis). I’ll probably talk about the stuff I’m doing in lab, annoying things about Dat Lab Life™, and (mostly) all the COOL SHIT I get to do as a science thesis writer. I’m excited to start this lab work, but I’m also kind of terrified of taking on something so big.

So what the hell is my thesis about? Good question. SO.

DNA doesn’t just float around in your cells’ nuclei willy nilly. It actually gets stored wrapped around these special proteins called histones, and these structures are highly dynamic and able to have the DNA unwind and rewind around the histone. Why do we care about what the DNA and the histone do in their private lives? Well, if the DNA is tightly wound around the histone, then any genes in that stretch of DNA can’t be accessed by transcription proteins, i.e. the gene doesn’t get expressed. But if the DNA isn’t wound around the histone, then transcription proteins can easily assemble on the genes.

It turns out there are certain modifications you can make to the histone’s subunits in order to cause the DNA to either wind up and suppress genes or unwind and express genes. These modifications can even be passed down to other cells and even future generations, the study of which is called epigenetics. My research revolves around one such modification called histone H3 lysine 27 trimethylation (H3K27me3), which has been shown in recent years to be a genome-wide gene suppressor modification in the plant Arabidopsis thaliana, and among the many genes it suppresses are a set of iron homeostasis genes, which my lab particularly cares about. Iron is essential for plant growth, but too much iron is actually toxic to plants. Therefore, plants must tightly regulate iron intake. Understanding more about how the H3K27me3 modification regulates iron transport will help us understand more about how Arabidopsis maintains iron homeostasis. In a broader, Big Science scope, knowing how iron homeostasis in plants works means that we may gain insight on how we can genetically modify plants, specifically crops, to have increased iron content, which could have massive benefits for regions of the world with nutrient-poor soil that are suffering from iron deficiency.

THAT’S THE LONG STORY SHORT! I’m really excited to be embarking on this project in my professor’s lab (she’s Awesome!). Who knows what the next year has in store?

Come for the hot lab gossip, stay for the spicy memes and existential thesis crisis. Either way, thanks for stopping by!

[nessro]

I thought that it’d be cool to have each team actually be color-coded, to really make the separation really obvious. I figured that the POV team would be in red, because USC (lol).