Reflecting on my PhD journey so far

As I approach the final stretch of my PhD, and we throw ourselves into 2025, I thought it was appropriate to reflect on my PhD journey so far. It's crazy to think how fast these last three years have gone.

I've recently found myself struggling with low confidence and fluctuating moods at work. A few days into 2025, I'm trying to turn a new leaf. But, the looming seven months ahead feel like an impossible mountain filled with hidden pitfalls ready to catch me out.

Many of my peers have recently celebrated their vivas, leaving me feeling (of course) proud of them, but slightly left in the dust. These feelings are apparently normal in the final year of such a monumentous academic challange (which is slightly comforting).

It’s easy to forget the progress I've made when I’m caught up in the daily grind. To help improve my outlook, I decided to reflect on my PhD journey so far—a journey that, I'm trying to recognise, has been filled with challenges, growth, and accomplishments.

Here’s a year-by-year breakdown of my progress as I navigate this closing chapter (pun intended). Reflecting on my accomplishments has helped me feel proud and reminded me of the massive amount of work invested in this project.

I hope this reflection piece also provides helpful insights into what a PhD journey can look like.

First year: Groundwork, admin, and research freedom

At the beginning, I was completely overjoyed that I had even secured a PhD in the first place. I immersed myself in a broad range of activities and experiences that laid the groundwork for my research.

A significant portion of my time was dedicated to PhD training and admin tasks, including getting to know my supervisors and developing a deep understanding of relevant methods. Coming into the program, I had never even heard of environmental DNA, but I dived deep into the topic with hours of reading and took on training in all things omics. It was made more difficult being the only researcher in my supervisor's group.

I've generally had very little structure in the project from day one due to my hands-off supervisory team, so the whole project was entirely my own from the start. I'm not suggesting a hands-off team is necessarily a bad thing—it's taught me to be a truly independent researcher. But I've not always found it easy working alone for the majority of the PhD.

I've always found it difficult to decide on specific research questions because I'm a big-picture thinker. It took a while to define my research proposal (or at least the first draft, as it's changed so much over the course of the PhD).

Slowly, my research began to take shape as I conducted a small pilot study to test my methods, explored existing data, and developed a rocky shore eDNA protocol from scratch. I also structured my literature review, which served as the basis for my introduction chapter.

I completed my first field season, which included ten-day-long trips to South Wales and the Scottish Highlands. The trips involved lots of preparation, failed data collection, long days, and being in close living proximity to my primary supervisor!

I also trained in bioinformatics tools, got set up on the high-performance computer server, and learned shell commands. I finalised lab methods for my target species and wrote a grant proposal to cover lab work. I gained teaching experience, delivering a workshop on social media in science that I've now developed over the years. Conference participation was another highlight of the year - I attended my annual DTP conference, British Ecological Society conference, EuroSeas workshop and MBA postgraduate conference.

Outside of the PhD, I graduated from my undergraduate degree (delayed due to the dreaded covid), gained a higher eduction teaching qualification, and built new professional connections within the eDNA community. On a personal level, I faced the unexpected loss of family members and grappled with the experience of death for the first time.

Second year: Completing fieldwork and finding confidence in the lab

The second year built on the foundation established in the first by delving deeper into data analysis, fieldwork, and lab work. I analysed the pilot data collected in the first year, which put my new bioinformatics knowledge to the test.

My first significant lab stint lasted three months in Sheffield, where I sequenced my first round of samples and navigated the logistical challenges of arranging short-term accommodation. Side note, I moved in and out of accomodation seven times over the last three years—and I wouldn't recommend it! In the lab, I carried out DNA extractions, PCRs, library preparation, and sequencing for the first time! There was a lot of information to take in.

I completed all fieldwork, which involved three trips to North Wales, Northeast England, and Southwest England throughout the summer. By the end of the project, I hand filtered nearly 300 liters of seawater!

In between fieldwork trips, I jumped into analysis, where I began testing various bioinformatics pipelines and exploring different parameters to find the best approach. I also fleshed out my literature review and created a thesis structure in LaTeX on Overleaf (this is where it started to actually look like a real thesis!).

Teaching continued to play a part in my PhD experience (when I was actually in Liverpool!), as I gained another higher education teaching qualification. I presented posters and gave talks at numerous conferences. I also organised my first conference, which was a mixed experience but still valuable.

Toward the end of the year, I finished all fieldwork and started my main data analyses. I attended a time series modeling course, which was insightful but proved less directly useful to my current research. To be honest, I struggled to concentrate in that course due to being ridiculously burnt out from traveling so much!

Third year: Completing lab work and lots of coding

I don't know whether you can tell from the pictures, but the PhD started to take its toll from the third year onwards!

Third year began with another three-month lab stint in Sheffield to process the other half of my samples, during which I managed 1.5 times the workload compared to the previous year. I ran bioinformatics analyses at lunchtimes and between lab days, and wrote a manuscript in the evenings.

Once lab work was completed, I temporarily moved back to my parents' house to save some money and prevent moving (again) to another unfamiliar accommodation. I then undertook a deep dive into data analysis, developing code for data tidying, community analyses, and modeling. My code currently spans thousands and thousands of lines!

Halfway through my third year, I started to struggle with health issues, probably as a result of burnout. I had quite bad post-viral fatigue and had to request official sick leave, so I was given a one-month extension. Other health issues snowballed over the year. Currently, I'm the best I've been physically in a while, but only after reevaluating my overworking habits and reaching out for help.

On the plus side, I won the university 3MT competition and the best talk award at our school conference. I ended up teaching the same bioinformatics course I attended two years ago, which really shows how I went from being a newbie to becoming an expert in the field (full circle moment!). I helped to organise my DTP conference, as well as research group seminars as a student representative. I also contributed to a book (which should be out next year!).

I made significant strides in writing. I published my master's work (first-author, hell yeah!) and started collaborating on a second paper with my master's supervisor. I also continued to write my thesis, preparing my data chapter 1 for publication, with progress on the introduction, methods, results, and discussion.

For data chapters 2 and 3, I worked on reformatting data and completing ecological analyses, even though some paths led to dead ends.

As the year drew to a close, I relocated with my partner of nine years—a significant personal milestone! I also supported him through his thesis revisions and celebrated his passing of the viva. I secured a placement which extended my PhD funding by three months.

Fourth year: Placement, final slog, and digging deep for positivity

We are now two months into the fourth and final year, during which I've made limited progress on the PhD due to being on placement. Here are some final insights as I go into probably one of the hardest work years I'll ever experience.

I think the biggest challenge of completing a PhD is not the science, the writing, or the experiments, but the ability to stay positive and motivated when everything seems hopeless. When you're trapped in a hole of analysis with no solution in sight, when words fail you and praise is non-existent. When you crave encouragement but find no one to provide it. When months speed by without any rewards or successes.

I believe the true lesson of a PhD is the ability to persevere, alone, through the hardest times.

I currently feel like everything is unfinished, and the work ahead is too much to cram into seven months (minus 1.5 months dedicated to the rest of my placement!). But I'll continue to believe I can get this PhD done.

Let's finish this thing.