🍏A Scholar’s Quest: Production of Knowledge

An original autobiographical fiction, 9th October 2025

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Hi Scholar,

The last time I wrote an essay for you, I warned you that it would not be correct, only interesting. I’m afraid I must warn you again - what follows is not an essay at all. Rather it is fiction, based on true events. Drawing inspiration from the previous series authored by The Critic over the summer “I’m Not Leaving Academia, But I am Standing Outside It’ (you can read Part 1, Part 2, and Part 3 in the archive), this series is an attempt at autobiographical fiction. It is very different from anything previously written by this author, so they hope you will forgive any shortcomings it may have.

A Scholar’s Quest: Production of Knowledge

-Written by The Tatler

Tuesday, May 5th, 2020

The Application

"Would you explain to us how you would identify reliable sources to inform your work?" a slightly muffled voice asked through Richard's laptop speakers.

The voice belonged to a physics professor who was chairing the PhD interview. He was sitting in the middle of a brightly lit seminar room on the university campus - about a mile away from Richard’s kitchen table in his student flat. John, who would be Richard's primary supervisor if the interview was successful, sat next to him. Both men wore face masks.

"First of all, I would always look at whether the paper answers the research question it set out to, and the evidence it provides in support of its conclusions. I would also prioritize sources published in reputable journals with high impact factors," Richard answered, desperately hoping they would not ask him to elaborate on what an impact factor was.

John nodded approvingly and scribbled something in his notebook.

"Why are you applying for this particular project?" asked John.

Well, thought Richard, I want a career that allows me to satisfy my curiosity. I've always loved asking questions about the world and finding out how things work. I enjoy the challenges of intellectual work and want to be able to define my own research agenda one day. A PhD and academic career is the surest way to get the career I want. As for this project... to be honest, any project would do. But this particular one is funded and you, John, are a full professor with an H-index of 26 who regularly wins enormous research grants.

"I find the biology of brown fat cells absolutely fascinating," he lied. "Most mammalian cells try to make the most efficient use of their energy supplies to support their function. However, the function of brown fat is to 'waste' energy by emitting heat. It’s also a tissue that has been discovered in adult humans relatively recently, which intrigues me. It is really quite remarkable."

"And if successful, when will you be looking to enroll in the program?"

"The earliest possible start date: January 2021," Richard said.

If the whole world hasn't died of COVID-19 by then, he added silently.

Thursday 21st, January 2021

Incubation Period

"Hi, Jasmin," he said, keeping his eyes fixed on the microscope as he heard the door to the lab open and close.

"Where were you yesterday?" she asked.

Richard looked up, surprised by the stern tone of the postdoc's voice. Since he’d started the program, John hadn’t set out a schedule or given him any expectations for the time he was to spend in the lab. Had he forgotten to do something for his ongoing experiment? No, he had dosed them at 8:30 a.m. that morning as he should have. 

"I was at home reading literature and preparing a short report of the data from Monday's assay for John."

"Your weekends are for reading," answered Jasmin, "and there are always experiments you can run. Every protocol has incubation periods and wait times. You should make use of those, even if they are only a few minutes, and write at your bench."

Her eyes softened, and Richard knew she was smiling, though he could not see it through the mask she wore.

"I'm only telling you this because it's important that you are proactive. It's true you only started two weeks ago, but four years for a PhD project is not a long time. You need to be sure you’ll have enough data for your thesis."

She pulled up a stool and sat down next to him.

"John has asked me to teach you how to extract RNA, DNA, and protein from the cell samples you prepared on Tuesday. It's a long protocol and usually takes me about three hours. However, because it's your first time and you'll have a few more samples than I usually do, it will probably take longer. Ready?"

Richard glanced at the digital clock on the wall, which showed 3:37 p.m.

"Ready," he said, turning to a fresh page in his lab book and regretting his absence the day before. He made a mental note to text Sam that he would be home late.

Monday 8th, March 2021

Controlled Variables

"What's the difference between Minimum Nutrient Broth and Modified Nutrient Broth?" asked Richard, unscrewing the lid of the bottle. He was working inside a tissue culture hood, preparing more cells for experiments later that week.

"Modified Nutrient Broth contains more vitamins to help the cells stay healthy," answered John, looking over his shoulder.

"Do you know which vitamins are added and why the cells need them?"

"Not really," said John. "It's a standard preparation that nearly every lab in the world uses when they grow their cells. I used it when I was a PhD student."

"I wonder how the added vitamins change the gene expression in these cells... Wouldn't it be interesting to compare cells grown in Minimum Nutrient Broth with those grown in Modified Nutrient Broth? I would imagine there would be at least some differences, maybe even in the genes we are stud–"

"Richard, pay attention," John interrupted him. His tone was firm but still kind. "One drop of broth containing cells from Treatment A almost fell into the tube reserved for Treatment B.”

Friday 28th May, 2021

Good Data

"These curves are beautiful," said John, tracing the line plotted on the screen of the computer that sat on a bench at the back of the lab. "I can see from the nanodrop readings that you have cleanly isolated the RNA as well. It must have been a little boring focusing on just one technique for the last five months, but all the practice is paying off. This kind of data is vital for your thesis, and by the end of the year we should be able to move on to the next phase of the investigation. Well done."

Richard’s heart jumped at the praise. He had begun the protocol on Tuesday, and while he was tired, he was satisfied with his work. It was becoming increasingly common for him to spend twelve hours a day at the bench; his ability to concentrate for long periods had markedly improved - sometimes going four or five hours without a break. As John said, the practice was paying off; he was producing good data. Moving through the steps of the protocol, he had noticed - and savoured - the calm assurance he felt that comes from knowing exactly what you need to do and how to do it.

"Make sure to include this data in your six-month progress review next month," John called after him as he hung up his lab coat and walked out of the lab into the hot-desk area that formed the centre of the building.

"Mate, that is rough. I can’t believe you got scooped." Max, another PhD student in his third year, was saying to Susan, a PhD student only a few months away from her submission deadline.

"It’s bad enough that a paper has published basically the same thing my project is working on, but you know what’s worse? It was published like a year and a half ago. I’ve only found it now while updating my literature review."

"Damn, how could you have missed that?"

Their voices faded as Richard walked out of the hot-desk area toward the staircase that would lead him into the late evening sunshine. The elation brought on by John’s praise just a few minutes earlier was rapidly draining away. He didn’t need to hang around to find out how Susan had missed the paper. Her write-up period had begun in October, a few months before he started, but he’d seen her running experiments in the lab opposite his, late into the night until April. As he unlocked his bike from the rack outside the building, he thought about how it had been months since he had properly engaged with the literature on his topic and tried to calm the rising panic in his chest.

Tuesday 13th July, 2021

Artifact

"It has a tail!" announced Jasmin.

There was a buzz of excitement in the lab that day. A flask containing the extra fat cells Richard had prepared yesterday was being examined using a new machine - capable of imaging cells in 3D - that had arrived last week.

"Fascinating!" cried John. "I am not aware of any other literature reporting this kind of fat droplet shape naturally occurring in fat cells before. We need to move quickly to get this published. I always imagined fat droplets to be a perfect sphere; that's certainly the way they look down the microscope…"

John and Jasmin hurried out of the lab, no doubt to begin sketching the outline of the paper.

Richard sat down at the machine, flipped to a new page in his notebook, and began to sketch the shape of the cell and its fat droplet displayed on the screen.

He thought about what John had said - could the shape of the fat drop really be "naturally" occurring? Sure it had been reported that fat droplets are extremely tensile, and he had seen how the droplets in his cells changed their shapes over the life cycle of a cell. He began to sketch another cell next to the one he had just drawn, mimicking the way the cells grew all squashed up against the bottom of the flask and each other…

Richard suddenly sat up. This tail shape… was it because of the pressures exerted on the cells in the flask? Would this tail shape still be there in a free-floating cell, not attached to anything?

"Please tell me you haven’t shut the machine down yet, Jasmin didn’t save the image!" John burst back into the lab. "Isn’t it so exciting? Who knew that fat droplets had tails!"

"Do you really think the tail shape is natural?” Richard pushed his notebook across the bench. “Could it be an artifact of growing cells in the flask? They get all squashed up against each other. Maybe that creates the tail?"

"Um… maybe?" John said slowly. "It’s an interesting theory, but we’d have to run additional experiments to confirm if the tail was there under different conditions. Our lab - or, for that matter, any lab in the world - doesn’t have the equipment to image these cells unless they’re grown in a flask like this. To be honest, we don’t have the time either. There are research grant deadlines coming up in the next few months, and it would be really helpful for our applications to have a paper on this novel, exciting observation in review by then."

He paused, perhaps noticing the smile fading slightly from Richard’s face.

"Look," he said gently, "in case you haven’t noticed, very little attention is paid to the fact that basic research is done in cells grown under highly controlled and artificial conditions. The kinds of questions you’re asking are very interesting, but they’re difficult to answer. My job is to make sure that you can generate enough data for your thesis and help build your publication record before you graduate. Spending time on questions or projects like what you’re proposing will make it harder to advance your career. You need to be able to show outcomes, by that I mean papers, that come from the research you do. My advice is to focus on building upon previous work that has been done. If you begin to pose questions about the possible effects of your experimental conditions on what you’re observing… well, it would be more trouble than it's worth."

Saturday 2nd October, 2021

Month Ten

"Oh, this is ridiculous. I don’t want to be here today," Richard muttered under his breath.

The lab, bathed in the soft orange light of the setting autumn sun, was deserted. His hands moved robotically, metronomically, as he refreshed the nutrient broth on the last of several large flasks of cells inside the tissue culture hood. Tightening the cap on the flask, he let his forehead rest against the cool glass pane in front of him, relaxing slightly now that his task was done.

His legs, numb after hours on the hard plastic stool, felt far away, like they belonged to someone else’s body, as he stood up and carefully placed the flasks inside their incubator. He sighed heavily as he shut the incubator door, knowing the cells would be there, first thing on Monday morning, waiting impatiently for his attention. It had been a long week. Hell, it had been a long ten months. Standing alone in the lab, watching out the window as the last rosy tint on the clouds faded to grey, his throat began to tighten.

"What am I doing here?" he snapped to himself. If I have to be working on my PhD on a Saturday, can’t I at least read something? Write something? God, I can’t remember the last time I thought about what I was doing instead of spending all my time doing things! It’s just producing and producing and producing. It sounds strange, but somehow I feel dumber now than I did in January. I haven’t really expanded my knowledge of my topic - though I’ve definitely become a better technician in the lab. But to be honest, anyone could have if they’d spent as much time practicing these techniques as I have. Is this a PhD in molecular biology or an apprenticeship in laboratory techniques? Can I really do three more years as a PhD student and then ten years as a postdoc? I don’t think so. I’m out. This is not for me. There’s got to be something else I can do.

He started up his laptop, opened the LinkedIn job search, and typed “molecular biology” into the keywords box.

"Medical writer, science communication officer, pharma sales rep, journal development assistant," he read from the list of job openings that appeared on the screen. 

He’d seen enough. Opening his email inbox, he clicked “Compose new email”.

Dear John,

I hope you’re well. I’m sorry to be telling you this…

Apples can only say so much! If this essay stirred something, be it a question, a reflection, a story of your own, I want to hear it. Even if it’s something negative, it’s okay. The Scholarly Letter exists because we believe that knowledge and scholarship begins in conversation and communing. Respond to this email, Scholar, we want to hear what you have to say and share.