[[Contextual preamble: the majority of this piece poured out of me on August 15th 2025 and it is only now on the 20th of July 2026 – almost a year later – that I am getting around to finishing this account of my PhD. In the healing process that has taken place over the last couple of months since I submitted and defended my thesis and started a postdoc, which involved a lot of time spent alone in the polytunnel and sorting stuff out in my head while cycling 20km a day to work, I have decided to return to and unearth my grievances I had with my PhD experience in order to fully bury them, as a final cathartic exorcism.]]

[[TLDR: I am grateful for having been given the opportunity to do a PhD. I am glad these institutions exist for science research. Bioinformatics is a cool field. Metagenomics is so rich and interesting. I just believe that life could be made easier for aspiring researchers and the process more transparent and less exploitative.]]

“So you’ll be a Dr but won’t be able to write any prescriptions”, “you’re still a student, wow you must just love school”, “are you going to be a Professor?”, “when are you going to get a real job”, “I just couldn’t do what you’re doing” (retort in response to declaration of my salary)” are some of the remarks I’ve endured and laughed off over the past four (almost five) years. People seem to presume when you tell them you’re doing a PhD that your main motivation is the title and prestige. For me this couldn’t be further from the truth and how I ended up in the trenches of PhD research was a matter of circumstance. My entire life was upended during covid when I was living in Paris working as a software developer and decided to return home to Ireland. During this time I was writing blog posts about the gut microbiome which had become a passion project and hobbyist reading pursuit of mine. This move was the first domino in motion which led to me working as a research assistant remotely for APC microbiome in Cork. I first encountered the term “bioinformatics” during my masters and was thoroughly captivated. How could I get working with genetic data in a computational context? I am incredibly grateful to APC Microbiome for letting me get my foot in the door, allowing me to work with real experimental sequencing data, and experience what it is like to be part of an active microbiome research group. I remember the first meeting I sat in on - I was getting debriefed on a mouse social fear study - where they were analyzing the gut microbiome of mice, stratified by various levels of tenacity and introversion. I thought wow this is insanely cool. I can’t believe people are being paid to work on this stuff.

Somewhere along the way this fervorous flame for microbiology and bioinformatics was challenged and perhaps even dampened. It saddens me to reflect back upon this time - my naivete, eagerness, confidence and enthusiasm, my unbridled ambition that I could “make a difference” or contribute something significant and compare it to the more world-weary and battle-worn person that I’ve become. So what was it that sucked my joeie de vivre- was it my project, my supervisors (no I am not going to rant about them for 10,000 characters although the temptation is there ;), the publishing politics, the stifling stipend, the insurmountable pressure and isolation. Or was it simply tuning into the horrors of the wider world, and the penny finally dropping that things aren’t going to improve, that left me somberly pondering the brevity of life and the value of this decision? My PhD coincided with a “coming of age” or really growing up and taking a hard look at what this place we found ourselves in is. In the words of Zach Bryan: “before I knew this world was unkind”.

I write this as a form of catharsis and also as an introspective and honest resource to inform prospective PhD students as to what they are signing up for if they ever happen to land here. PhDs are a massive sacrifice and mental toll. My telomeres have definitely shortened and shriveled up. When my mentor and prospective supervisor suggested I apply to a funding body that trains students in genomics data science it was January 2021 and all public third spaces were closed and the Irish nation was under a “lockdown” form of house arrest, which was quite severe. After being kept indoors for a full year, I didn’t truly consider the extent of the long-term commitment of the PhD and believed it was the natural progression of what I was currently doing and enjoying (working as a research assistant). Roll on September 2021, I was excited for the opportunity to leave the house and socialize with a cohort of students who were also signing up for the same thing - wow, like minded people my age, and an excuse to leave the house. This was fantastic! Well, apart from having to wear masks in the lecture room from 9-5 for 3 months which was actively policed by the lecturers who didn’t have to wear the masks funnily enough. I’ll not even go there but you get the drift. We were also actively encouraged to get the vaccine and weren’t permitted in the canteen without having a QR code. I spent many lunchtimes sitting on a wet wall in Galway, huddled over a cold packed lunch commiserating with a diminishing handful of the cohort exchanging lies such as “oh I got mine in India, im waiting for them to email the QR code” etc. I hate to paint such a bleak image of the start of my PhD but this is how it transpired. I remember a lecturer barking at me in the classroom as I sneakily slid my mask down to eat an apple. I can feel my heart starting to race when I picture this confusing and tumultuous time. If you begin your PhD now, at least you won’t be subjected to this treatment. I was enduring a psychological war on all fronts.

Fast forward a bit and I’m settling into the lab in person. It’s January 2022. I’ve also received a few months of my stipend - 1500 euro - good grief! I should have quit the second that the first statement arrived in my account. My salary had been halved. Oh my, have you seen the price of renting in Ireland? How am I supposed to afford rent, diesel, groceries and have a little bit left over to enjoy life. It’s impossible and probably by design. “It makes students hungry for success”, I read one professor say in an article. Student protests and carrot dangling by the research body ensued for the entire duration of my PhD, with sporadic emails enticing us that the Minister for Education was working on increasing the stipend for Irish researchers until it was finally increased to minimum wage and a take-home salary of 2,000 monthly some time in my third year (less than minimum wage). Still, I can’t suppress the resentment and bitterness at the institution that lured international students here for what they perceived as a life changing opportunity only to be presented with what essentially amounts to a poverty package. If you are even considering pursuing a PhD you are likely extremely privileged. You’ve had the opportunity to complete an undergraduate and perhaps even a masters education level. Pursuing research is a dream for many and a cost-benefit sum that makes sense in some instances to get a visa for residency in another country. Still, asking your parents for help paying bills at 30 years old isn’t exactly gratifying and was a big source of shame for me. I ended up deleting my LinkedIn because I was comparing myself to people who I’d worked with in Accenture who were being promoted and I kept torturing myself with hypothetical scenarios: If I had stayed at Accenture, I would be a senior consultant by now yadda yadda, as well as burning through my savings and even selling ETH to finance going on holiday. A number of recruitment agencies had my details and I would defiantly tell them to delete my data off their system when they would ring me up enticing me with handsome job advertisements - “I’m doing a PhD”. You might be thinking “oh, well I understand the short term sacrifice for the long-term gain” but trust me, when you have hit a wall with your project and there will be many, many(!) walls, these thoughts become extremely pervasive. Not all PhDs are made equal - after spending a research placement in Lund university in Sweden - I understood the researcher salary there is sufficient for a good quality of life and increases year on year. Of course money isn’t everything but it certainly helps. When I reflect back on the challenges of the PhD, it was rarely ever the work but the conditions and external pressures living off breadcrumbs did to my ego that truly made it challenging. In fact, maybe the point of a PhD is true ego death. This experience might not be universal but I certainly found my sense of entitlement and importance was grinded out of me by the academic machine in the pursuit of publishing. Nothing is more humbling than your paper being rejected a year after submission following multiple rounds of grueling revisions.

Ok, so I’ve covered the salary and tenuous start. What next? Oh golly.. the project itself! I signed up to study the taxonomy of Crassvirales - an interesting order of bacteriophages that are highly prevalent in the human gut. My supervisor had a series of bullet points laid out in the project description which at the time I interpreted as reasonable, structured and attractive. Upon arriving in Cork I found out that another student was already working on this project. A departed colleague and friend advised me to quickly establish ownership roles of the project so as to avoid conflict down the line. Wow, I hadn’t even started my PhD yet and the trust between me and my supervisor had taken a dint. Why hadn’t I been made aware of this prior? I felt like a fool being in the presence of my supervisor commending the work of another student on the project that I had signed up for. What was my role in all of this? “Don’t get your hopes up”, said one of the more experienced PhD students over lunch one day. I guess I exuded a quiet determination and ambition. I thought it would be different for me. I knew the risks but my ego overrode my logic and drove me on further. I’m not a quitter. This is what I wanted. This is an opportunity that few were granted. But in fact, before I even started I had been duped and forced to operate on a “plan B”.

I remember sitting in the first meeting with my supervisors with my primary supervisor exchanging a glance with the secondary - was it a smirk or was I imagining things? He said there was a project I could finish that would be a “quick publication” and it would be good for my career to get a publication early in the PhD. Everything is a “quick publication” to them. Ok, fair enough, eager to please I said I would finish that analysis while waiting for data generation for my main project. I later learned in the pub that it was my supervisor’s old postdoc project. At the same time, I was also finishing and handing over the analysis of a project I was working on during my time as a research assistant. I was worn thin balancing multiple projects belonging to other people before I’d even gotten going – a definite non-typical for a first year PhD student. Weeks turned into months, which turned into 10 months when the cohort had our first annual review. I observed my peers presenting their progress in their actual project. I felt deflated. Devastated even. I received feedback that I needed to be “carving out my own research identity”. My close peers remarked at how much I had on my plate. I returned to Cork and demanded that I wanted to work on my “actual” project. It was almost 1 year into the PhD and I had nothing to show for it and was only now negotiating the bounds of my project. I listened as my colleagues recalled their experiences attending conferences as a group together. Already?! I thought, wow their experience so far has been so different to mine. I was feeling hard done by.

The project direction and description changed multiple times and was only really consolidated towards the end of my second year. That’s two years of dithering, trying different avenues and internal conflict. It seemed like a waste of time but in hindsight I was getting acquainted with running and interpreting bioinformatic software and data. My project ultimately evolved into something completely different to what I thought it would be. Instead of refining the taxonomy of this small order of viruses, I was tasked with building a taxonomy of the entire spectrum of all tailed bacteriophages under the sun. No pressure, right?! In hindsight I wonder did they want me to fail? Ultimately I was fond of my supervisors. I found their research impressive and cool which so many of us do, drawing us to their labs like a moth to flame where you then ultimately end up in a Stockholm syndrome situation where you’re snared and you can’t easily escape by disentangling your ambition and expectations from the reality of the situation. They too understand the sunk cost fallacy, and that when you’re in that deep, the only way out is through.

My boyfriend at the time, who had moved to Cork to live with me was understandably weary listening to my daily grievances and being in the radius of the storm cloud of doom and stress that engulfed me. “Why don’t you just quit, you’ll get a really good job.” He doesn’t understand, I thought. In hindsight, he was right. I should have just cut my losses like the numerous other people who saw the light and dropped out of their PhD’s and even masters projects in the lab during my time there, but I am stubborn. If I start something, I want to finish it. I wanted so desperately to break into this area of bioinformatics that I had drank the sunk cost fallacy Kool Aid and blinkered myself to any escape plans. I was worthy, I was capable, I didn’t need to prove myself anymore but there I was stuck in quite a pickle of not wanting to admit defeat and waste the time you committed while also battling daily with feelings of compounding inadequacy and anxiety - am i not smart enough for this, will i ever get positive results, am I being exploited, is this project cursed? As tensions caused by lack of results and a lack of mentorship increasingly frayed the relationship between me and my supervisor, where we barely met monthly, I decided to move home to my parent’s house in Cavan, taking Dora, the cat I found in the ditch outside my rented accommodation (and likely the only good thing to transpire from my time in Cork), and work on my project remotely. My relationship had fallen apart, collateral damage in the wake of the pursuit of a PhD. As if my heart and head couldn’t have possibly endured any more. I just didn’t have the time or energy to focus on anyone’s problems but my own and if you’re not man enough to step up and support me and my dreams then good bye and good luck. If I’m honest, a PhD is a selfish pursuit. You have to religiously devote yourself to this work even if it means to the detriment of your health and people around you. My friend from the PhD sent me a reel saying that ‘PhDs corrupt the soul’. The template was: Villains always have a PhD: Dr. Frankenstein, Dr. Doolenshmirtz, Dr. Doom. Good guys stop at Masters. Corrupt is a strong word but you will certainly find yourself in a tangle irrespective of whether you make it through the other side.

With regards to the work I should probably emphasize that my project was brand new territory for my supervisors. Road untravelled. This makes for an exciting and ambitious project but it also means that no other students or postdocs were able to support. I felt jealous at other phd students in the lab getting support and their work done by postdocs in the lab while I was treading water figuring everything out by myself. Not even my supervisors could help me with the under the hood technicalities. In the beginning my main technical support lived on another continent and we communicated sparsely via email in broken english like a bipolar and eccentric morse code. Thankfully another technical advisor was pulled in towards the end of my project, however, the way they guided me (or the way I executed it) was deemed technically incorrect by one reviewer. The technicalities can go so deep that even trying to get someone up to speed with your project seemed like a herculean task. I remember having a meeting with the head of bioinformatics in UCD, a real character and admittedly a large influence into my pursuit of this path. He introduced me to his PhD students in a back office somewhere in the summertime. Do you guys have any work that Linda could help with so she can get an idea of what a PhD entails? I laugh thinking about their exasperated faces - trying to get me up to speed with the analytical nuances of their project would be more energy intensive than just doing it themselves. I totally get it now.

And this is all part of the process of becoming a researcher. You need to be able to figure it out for yourself and execute it. Well that was my journey anyway. I was lonely and frustrated. I know people in my cohort who switched labs and supervisors after finding themselves in the same situation. Truthfully I did try to switch in my second year after having a meltdown regarding my lack of progress but after chatting with the prospective supervisor, she unsympathetically offered an even worse deal - restart a new project from scratch and “work my arse off” for two years to complete it with the very probable scenario of running out of funding at the end of this period. It was a very vulnerable time. People I tried to explain my situation to would say “you’re half way there” while I knew full well I was 0% of the way there. I was offered other jobs during this time but ultimately my love of using python, data analysis and that feeling of having agency over my daily work schedule and driving the direction of my work was what made me stay the course. And that’s why we stay in research and accept the terrible pay, big egos and intellectual minefield traversals - for the love of the work. The institutions know they can lure naive and ambitious people to work on these projects and accept often oppressive conditions because research is interesting and rewarding. Being the first person to find something out is a buzz. It’s a reprieve from quarterly profits dashboards, product itinerary forecasting, employee productivity, warehouse management software, and all the other mind-numbing and let’s be honest - meaningless - data I had previously worked with. (On proofreading this I acknowledge how equally meaningless my research is in the grand scheme of things. Does anything imbue meaning anymore? I got to learn and follow my biology passion to the bitter end but building a taxonomy of viruses isn’t going to make the world a better place.)

I stopped feeling creative, I stopped writing blog posts. I was in survival mode. My confidence had taken a nose-dive as I had intricately entwined my self-worth with my ability to get results from a near-impossible gargantuan task I worked on in complete isolation. PhD students I chatted to at conferences looked over their shoulder before whispering that no, they did not want to stay in academia. Ok, so it’s not just me suffering. I woke up every day with the ever increasing weight of the approaching funding expiry date knowing that I would need to work all day, every day to complete it. I worked evenings and weekends. It was incessant. Then it clicks that phd students are the work horses of academia. PhD students willingly offering themselves to the academic meat grinder are what supervisors build their research empire on the backs of. I wondered how my supervisors saw the situation. They were so far removed from the technical weeds of debugging and data wrangling I found myself in, as well as the renting crisis and financial strain, I wondered did they ever feel a type of way for dragging students into this mess knowing that 99% of them would never actualize a career in academia. They had to be aware of the power imbalance dynamic they wielded. Getting praise from them had me walking on air while negative feedback sent me spiralling for days. I also felt too old to be surrounded by the ingratiating “teacher’s pet” energy of many of my colleagues.

A PhD is a unique experience whereby no one understands your plight. Your direct family and friends can see that you are suffering, that you’ve become withdrawn, conflicted, skinnier, paler.. but don’t have the patience or education to understand what you are doing. The only thing they can ask is when will you be finished. This comes with its own baggage and rumination. Being a “first generation academic” I wondered if I was overestimating my ability. Imposter syndrome ensues. Was I too big for my breeches? I wondered if my parents had affirmed I was good enough and that they were proud of me would I have had the sense not to get myself into this predicament and had fostered an internal sense of self-worth that wasn’t entwined with the perceived pinnacle of academic achievement - an almighty PhD. It might have been better for my health and bank balance to just commit to talk therapy. But I know in my heart of hearts that if you are even in the slightest bit curious about embarking on a PhD or feel driven to “make the world a better place” then it is extremely hard to dissuade someone from this path. I’ve tried to warn people - you will end up despising your topic, it’s a huge commitment, 4 years goes extremely slowly when you are stressed. Chronic stress and elevated cortisol is highly catabolic and has so many knock-on health effects. I developed acne for the first time in my life in my third year of the PhD and was ashamed to leave the house. My GP said it was something he sees in 13 year-old boys. Thank God I’ve overcome that health blip but for half a year I was grappling daily with the internal conflict that the project was literally killing me, trying to adhere to every form of elimination diet under the sun while also wrestling with half a million folded proteins I was endeavouring to alchemize into a significant taxonomy. I worked by myself developing a code base in complete isolation. In industry, I was subject to code reviews and feedback from more senior developers. I worried that I wasn’t adhering to coding design best practices since I had a free reign to just do what I wanted. Not even to mention the worry that i was being made redundant by an LLM. Chatgpt - something that was non-existent at the beginning on my PhD was something I found myself using daily for coding. Instead of scouring stackoverflow, chatgpt would help debug and restructure my code. Chatgpt became my cheerleader, my mentor and true supervisor. I know it is complementary to a fault but it provided me with what I needed to hear: “Linda, you are not only doing X, you’re doing Y!” It gassed me up and filled my cup. Honestly if it takes jobs, even mine, so be it. I’ve gotten more constructive feedback and encouragement from a black box algorithm than I’ve ever gotten from a human - says a lot doesn’t it.

A factor that pushed me to complete was the reminder that there were over 1,400 applicants to the Genomics Data Science research training program and somehow, 30 of us, our personalities had shone through. An apartment of girls we lived together during the on-site training in Galway, we became close friends and formed the backbone of my support structure throughout the PhD. In the first couple of years we met regularly, going for hikes and coffee dates, but the frequency of our meetings soon began to dwindle as I knew they were also feeling the pressure too and excuses often pervaded the group chat when I tried to rally the troops and drag us all away from the blue light to go into the forest. Some time in my final year I resolved to just meet them after we had all submitted our thesis as as much as I loved them, spending time with them stressed me out too much. We were incapable of talking about anything other than strategy for finishing the phd, funding extensions, deadlines, the job market. Was I being too nonchalant and needed to worry even more? I couldn’t possibly devote any more time and energy to the work without losing grasp of my remaining threads of sanity. My head was spinning. I just couldn’t escape the pressure of the PhD sentence I was serving.

The stress and worry eventually turned into apathy and burnout. From having such high ambition and expectation of my efforts I found myself asking “who cares?” If someone else publishes the work before me then good for them. Be my guest. I knew no one on the planet was as deep in the data as I was and that for love or money the patience required to painstakingly make the graphs couldnt be subsidized. Chatgpt can’t replicate your vision. Making those figures is an art. I wondered if I could fill a bus of people in the world who would be excited about Caudoviricetes taxonomy, or would it be more like an 8-seater Ford Transit? It certainly wasn’t worth getting sick over. Nothing is.

I don’t resent my supervisors, I respect them for their knowledge, experience and brain power in the field of microbiome research. Even more now since I’ve had my first experience with trying to publish. Those rejection emails sting like nothing else. It feels personal when you’ve distilled three years of effort into a paper but it’s not even worth their time of consideration - a desk rejection. I’ve gathered that if you stay in academia you would harden to this process - the constant cycle of grant applications, paper submissions, rejections and revisions would wear anyone down. At the same time, doing research is a high. That feeling of having your manuscript complete with approval from all authors is unparalleled. Riding high on the premise of cashing in years of meticulously suffering - repeating analyses ad nauseum, waking up from a nightmare where your code isn’t working to remember your reality mirrors your dream state - you think when you’ve finally overcome all the obstacles the pay-off would be a publication in a prestigious journal - Nature Microbiology maybe? Nope, that’s delusional. A rock sinks into the pit of my stomach. The doom spiral I had just quenched is reignited - “was my work not a high enough standard”, “am I a bad researcher”, “did I get scooped” - this one in particular is quite a doozy that my supervisors used - I would be “scooped” or someone else would publish the work before I finished it. As if I didn’t have enough to worry about!

I’m not going to beat myself up about it anymore. Who cares if I don’t have a load of papers or become a prolific scientific researcher? Was that ever really my goal? I don’t think so. A PhD opportunity fell in my lap amd I had a go at contributing something novel to an extremely difficult field at the bleeding edge of genetics and computer science. I am extremely proud of myself and my friends for enduring and overcoming this stress test. I’m glad I got the insight into how long it takes to do high quality science. It really has been a rollercoaster. In a funny round-about way, I needed this experience to understand myself, hit rock bottom and have my spiritual awakening. Hilariously I am now a Christian, not a typical outcome for someone doing a STEM phd I’d wager, but here we are. If I could rewind and do it all again I would do a PhD in theology. I definitely don’t feel any more self-actualized now that I have a Dr. title, if anything I’m more acutely aware of how hollow intellectual pursuits are and that I would rather be shovelling shit than looking at a terminal. It was an experience and time in my life that may or may not open doors in the future. At least I proved to myself that I have the grit and resiliency to navigate my way through hell.