Writing a Thesis - To Hell and Back Again (By Bilbo Baggins?)

G’day team,

Today I want to share with you an experience I had a few years ago, when I was a younger and more innocently minded science fan. In the lead up to my last year of uni I’d decided I’d studied the sciences for three years and it was time to get my hands dirty. I signed up to the honours colleges, begged a professor to let me in on a project and got ready to be a real scientist… or so I thought.

But before we get started, here’s a link to the thesis I’ll be chatting about

My thesis

What is an Honours Thesis

I’m sure you’ve all, at some point in your lives, met someone who introduced themselves as “a Docotor, but not THAT types of Doctor”… these esteemed women and men have what we call a PhD. In essence a PhD is a culmination of usually 4-6 years of tireless work in a very niche field within a very niche field… within a very niche field.

An Honours Thesis is like a mini-PhD, a taster of sorts. For young wide-eyed students who’re still in love with science and want nothing more than to start making a name of themselves. An honours thesis gives you a chance to experience the horrors of publishing research, without committing yourself to a life of it.

My lab group

Getting Started

My project was simple, my professor told me.

We’d be using recombinant DNA techniques on Saccharomyces cerevisiae to insert a gene into their genome which would allow us to determine if a loss of heterozygosity had occurred during mitosis in a specific region on a specific chromosome.

This was not simple, this was the opposite of simple.

You see my professor had her PhD, she had a post-doctorate and she was… well, a professor.

I was none of these things.

The Project

I started working diligently expecting that, like in all things in life, my work would pay off.

News flash… that’s not how science works.

Five months into my twelve month project and I hadn’t even successfully inserted the required marker gene into my stupid yeast. I had nearly a hundred attempted strains but none of them were growing nice and red on their media.

Then a breakthrough.

My lab partner created a successful strain, the project could begin in earnest now!

I stole her yeast (with permission) and got started.

For the next six months I repeated the following…

Step 1) Grow some yeast
Step 2) Are some of those year half white, half red? If yes isolate them!
Step 3) Grow up the red side and white side independently
Step 4) Explode the yeast
Step 5) Harvest their DNA
Step 6) Use a technique developed in some point in the early 1400s to determine where the yeast chromosome had broken
Step 7) Repeat…. Hundreds of times.

Here’s the thing… in each of these steps a thousand things can go wrong.

At any point where I grow yeast, I can have a contamination.

At any point where I isolate something, I can isolate the wrong cells.

At any point where I use my brain, my brain can fart and I mix the wrong enzymes with the wrong bottle and dissolve everything.

At any point where I take something out of a fridge I can accidentally leave it open and destroy all my work!

But I Get Through It

Five months later, just a month out from having to publish result, and I’m almost there. Only one colony left to clarify a break location in and I’m done!

Time to start writing!

At this point I’ve been working on this project for a year, I want to write a good thesis. So I start looking into the work that I’m building off. The research that has lead up to my project.

I don’t understand it!

So I decide I’ll start by explaining my project, and realise…

I don’t understand it!

I understand the parts of it.

I understand what I want.

But I don’t understand how they fit together and any attempt to explain it to me by my supervisor only makes me more confused.

So I read!

I read everything that’s even vaguely related to my research. I stop sleeping for a week, I subsist off energy drinks and I make great friends with the security guards at the library. Slowly the pieces fall into place. But now we have a new problem.

It makes in my head, but it’s complicated, and how could I possibly explain this on a piece of paper.
Well, I figure, that’s a problem I can deal with later.

I start writing my thesis and the words are just flowing! I’m tying in pieces of research from all over our field and linking it with the work we’re doing. I’m explaining the replication mechanisms and potential mechanics of DNA strand breaks down to a tee. At some point over the next two weeks I even regain some of my sanity and begin to tie my research back to the real world, explaining things in a way people might actually be able to understand.
I feel enlightened!

It all makes sense!

I Take a Night Off

I take a night off.

Me and a mate go and watch Godzilla with Orange Juice and Vanilla Vodka (horrible combination)
Great night!

Laughed my head off!

Can’t remember getting home.

Wake up… laptop is covered in vomit!

Thesis gone.

My last external back up? A week ago.

Now this might not sounds like a life-changing event but I’m now two weeks away from a rock-hard deadline on a project I’ve poured a year of my life into. And most of my actual writing has occurred in the last week. I’ve lost about 60% of my word count and about 80% of my word count that makes sense.

There’s Another Problem

I’m no longer enlightened.

That blissful state of balance where I understood my project and could explain it in real-world-words has gone.
If I thought the first week of subsisting off energy drinks was bad, the next two proved me wrong.

Over the next two weeks I slept once every two days, and I slept for 3 hours.

I ate only wantons from the Chinese place near the library.

I lived my project, I breathed literature and I shat references.

And then it was the night before! I was just putting together my final touched before I realised something was missing.
That last set of data! The one I’d pushed aside to focus on writing, it was missing!

I’d written an entire thesis, including all my statistical analysis, out of the wrong data set.

So I ran back to the lab. Threw on my Gel Electrophoresis, and actively screamed at the tiny strands of DNA to get the hell down that lane!.

Done.

12PM

Building is closed, but I hide from the security guard in the post-grad room (sneaky undergrad tactic) and start re-writing my results and discussion with my new numbers.

2AM

I realise my p value has changed so much that my results, which were not statistically significant, are now significant.
I rapidly re-write everything with slightly different wording to try and make it make sense.

6AM

My professor is an early riser and she’ll want this first thing when she gets in at 7, but all I have to do is re-format.
Now if you’ve never written a thesis you won’t understand how anal they can be on formatting. All those buttons no-one uses on Microsoft Word become your best friend. You actually view your paper in mark-up view. It’s freaky!

7AM

I’m done

I made it

My professor arrives and I hand over the paper.

“Well done Tom, I’ll have a look when I get some time”

I make it out of her office before I almost simultaneously pass out and have a seizure.

I don’t remember how I made it home, I just remember waking up three days later.

Bliss

Now there’s a two to four week period after handing in an honours thesis that is just fucking bliss. And I don’t swear lightly (well, I do, but not on Steemit) but this really wouldn’t come across properly without the fucking. You’re free. There’s nothing else to do, except coursework. But even half a dozen projects and a few impending exams feel light as a feather after four weeks of carrying the boulder that is thesis-stress around.

I was happy with what I’d produced and part from the last minute scramble I thought I’d put together a really nice thesis, a great piece of writing and a good explanation of my project.

All there was to do was a couple of revisions and I’d be done.

In these weeks I left my university in the USA and returned home to Australia, expecting the nightmare to be over.

Revision

For those who haven’t written a thesis, after submission a panel will read it and offer revisions.

My revision e-mail came in, there were four versions of my thesis attached.

The first had over 200 comments and revisions in place, I was astounded! TWO HUNDRED things I’d done wrong. And these weren’t spelling errors or miss-placed commas. These were big paragraphs of revisions. But this professor was anal at the best of times, so maybe the others wouldn’t be so bad, right?

Wrong!

Professor 2 and 3 were a little more lenient than the first, coming in at a total of around 300 revisions. But my own professor had TORN ME TO SHREDS. Over 1200 comments and revisions, including removal of sections of my thesis that were several thousand words long AND a re-do of all my artfully crafted self-made diagrams.

It took me six weeks to complete these changes.

I didn’t do sleepless nights this time, but I swore a lot more as I removed sections of my thesis that took me days to write.

And then I re-submitted it.

At this point in the process my soul had been crushed, my view of the world had become a sombre grey and I had successfully, at least for the moment, been beaten by academia.

Revisions Round 2

I only got a single document back this time, 300 more revisions, two more weeks of writing.

This time when I submitted it was with the idea in mind that this will never end. I will, for the rest of my life, be submitting and reviewing this same thesis. Over and over and over again.

The revision round 3 email came in.

“No more changes, happy to accept this as your final thesis”

I almost cried!

Okay I lied… I cried.

It was done.

My thesis

Finally a Scientist

So I was finished.

I had my degree and my research and I was, in my mind, finally a scientist.

A fledgling, baby little minnow scientist.

But I’d made my contribution and I’d use it to back me up any day!

In Context

Years passed and I look back on this experience now. It remains the hardest thing I’ve ever done, and I’ve done some really frikkin hard shit. I was a competitive swimmer for over a decade and made it into medical school while keeping that up. But it had nothing on this project.

But what is it really? It’s just a baby step.

Thinking about what every Master or PhD candidate has to go through quite literally makes me sweat!
I’d take my degree in medicine any day, over having to do a project five to ten times harder than the one I finished in 2014.

I think back about when I was writing and I have this revelation.

Anyone with a PhD must be constantly enlightened. Their research is so engrained in their lives that they exist in the state that I obtained for a few weeks, but permanently. Constantly living in two worlds, the normal world and one where their brain is so finely tuned to the minutia of their work that it would be a waste to even try to explain to a normal person.

Going Back

Despite all I’ve said above, I want to do it again.

I want my PhD in the future, but I think I’ll give myself a decade or so to recover from that honours thesis before I brave the waters of academia and research again!

Thanks

As always thanks for reading team, I hope I haven’t scared anyone away from pursuing science :)

-tfc

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