AcademicalNerd @academicalnerd@qoto.org

A Scientist Is A Modern Monk

Historically, monasteries were the stronghold of knowledge.
Monks would study and copy the books and ponder the meaning behind them.
It was often, but not always purely theological.
Gregor Mendele, for example, was a monk and discovered inheritance laws far ahead of his time.

Modern scientists, I think, should strive for much of the same virtues monasteries cultivated in their inhabitants.
I am not talking about celibacy or worship of God, obviously.
These were the rudiments of the time, although there is time and place for both in the modern world.

Consider these.
Literacy, far exceeding that of an average contemporary, regardless of the field.
Strong grasp of philosophy, its fundamentals and connection to science.
Physical tenacity, while relatively rare in western civilization, was almost mandatory in the east.
The ability to thrive in quiet and solitude, working for a long time without being distracted.

It seems to be a compelling set of virtues, however, none of them seem to be quite related to religion.
Why then would I make the case about monks specifically?
Firstly because science, whether we like it or not, grew out of religion and inherited many of its structural features.
Secondly, because the pitfalls and problems in both religion and academia are similar.

Letting government’s money in slaves the organization to government’s needs, whether it be a sanctification of the king’s power or the development of nuclear weapons.
Focusing on money as the goal leads to printing meaningless publications and selling indulgencies.
Bad selection procedures for newcomers corrupt the structure, destroys its reputation and ultimately compromises the fundamental idea it rests upon.

I am mostly putting this out there for the sake of discussion and as an interesting allegory that came to my mind. Maybe it will trigger some dialogue and bring new insight.

I don’t even know if my posts make sense for readers, honestly. My English is a bit rusty and there is no feedback most of the time as I write into the void. Do you people read me? Are the texts clear? Or is it an indistinguishable mess of words?

Here is what I’ve been up to. First and foremost, new lab. Now my main work is to use neural networks to predict crystal stability. It took me a while to write and train the model for this, about a year along with studying and an internship. However, now that it’s mostly ready, I have to do an experiment.

It is not strictly necessary, but my department requires master’s dissertation to contain some experiments. I had to make one for bachelor diploma and now the history repeats itself. However, now I am in a different lab, with far better apparatus and work ethics. The experiments are mostly made with solid-state synthesis, which makes thing way easier (weigh – press – anneal – analyze – repeat).

Apart from this and an ungodly amount of papers I needed to study in the field and crippling burnout from personal problems, the last year went well. Now I have a week to finish most of the experiment and prepare something like the dissertation proposal. It is a discriminatory practice my department uses to make some students’ life more difficult. In my case it’s the theoretical nature of my work that is causing problems.

But I’ll power through this eventually.

Ugh. The Summer turned out to be quite difficult.
Anyway, here is a piece from substack where I try to write these days: https://open.substack.com/pub/academicallife/p/a-scientist-five-years-into-making?utm_campaign=post&utm_medium=web

I had a discussion with a friend today and now I’m curious: do you people cook for yourself? Does someone cook for you? Do you buy food? What do you typically cook?

I cook most of my food when I live alone and it’s usually simple and healthy “meat+vegetables/pasta/rice” dishes, salads, eggs in all varieties and a sandwich here and there.

No poll attached, I’m interested mostly in long and unnecessarily sophisticated answers. Let the 65k character limit be useful.

Today I presented my new work for the first time. It was surprisingly easy to talk about, even though my understanding of the subject matter is not perfect.

The topic is “predicting stability of solid crystals using graph neural networks”. Far more exciting than any thermodynamics I used to do.

Today a realization struck me. A simple one, but I feel like sharing it for some reason. Envy is horrible and it is not talked about for the most part. It poisons people and hurts their relationships, while the solution is relatively simple. To not be envious of someone, it is necessary to learn to be happy for their accomplishments. It mostly works for close people, but being envious towards close people is most destructive as well.

This ability to feel joy is not “free”, it has to be learned and cultivated either in the family during adolescence or consciously later in life. And I am infinitely grateful to my family and friends who seem to have taught me that over the years.

This sounds childish now that I read it, but hey, why not. Maybe it will offset some of that gloominess of mine.

Oh well, I can’t not write, can I. Here goes 2022 in review. Hectic and unpolished because I’m lazy and excited for the day ahead and the work I need to do.

It was bloody horrible. My country started a war with a neighbor, in some sense a relative, and it keeps going. There was mobilization. Some of my close friends had to flee, but I can stay with my family. For how long? That I can’t know for sure. There are other problems in my life that weren’t solved this year and that will probably persist for a few more years.

It was magnificent. I finished bachelor degree, managed to get into masters program, worked in an office through Summer. It’s not a good lifestyle for me but the experience was well worth it. New people entered my life, some of them became friends. I arranged more parties and meetups in one year than I ever had before and probably more than I ever will. That was an overkill. I am also in a better shape that ever was and probably healthier than ever will be.

All in all, it was productive and positively horrifying. The contrast between the dreadful news and the good days spices things up, for sure. This is how our minds work.

Today I heard a saying that goes among Russian journalists: we should not humiliate ourselves with hope. Oddly inspiring, albeit gloomy.

So there is a course with no textbook or any information on it other than lecture slides. Thankfully, they are quite extensive and have a text search within pdf files. I quickly dropped a “pdfunite *.pdf merged.pdf” in the terminal and saw that the output has exactly 1769 slides in it, weighing in at almost 2 Gb. Ctrl+f takes a few seconds to parse this, even with zathura. I hope this is the last time I face such monstrosity.

In reply to @FailForward ‘s Christmas post.

New Year mood: notes, essays due on a weekend, exams in two weeks and everyone’s ass is on fire these days. Happy New Year, wish everyone to survive ‘till the next one…

(okay, okay, it’s not that bad, I’ll survive, but no cookies for me this time around)

A few typos there, but I got emotional and didn’t do a proper proof read. Maybe it’s better this way.

I’m a city dweller. I pray on coffee and sandwiches on the go, sounds of cafes and subway soothe me and car fumes etched my lungs while I was infant, crippled my immune system for good. The city breathes, it has its own heartbeat, trembling under the streets. There are demons lurking in passages and walleys in the night, there are shadows of doubts and passions and sins imprinted in crosswalks and pave tiles.

I think it was in 2014 when I saw this the first time. The shift in people’s feelings, the surge of excitement and a feeble protest that was smothered in a matter of days. There were subtle hints that I couldn’t quite pick up at that age, unfortunately. Or maybe for the better.

Now I see with my own eyes, no goggles needed, the consequences of the past year. First, the police came. Two guys armed with pistols in every station, just standing there, talking to each other and squeezing money out of illegal immigrants on the occasion. Two more, with AK each, standing at the entrance during rush hour. I wonder if these weapons are off safety?

Every day I ride the subway and every day there is a drunk man lying on the floor. I haven’t seen this in a while in the city center. They don’t look homeless or too poor, you can usually tell by looking at the shoes and the coat. They look like they are lost, fell out of place, somehow ended up in the center instead of the suburb slum. Maybe boarded the wrong train or skipped a bus. Sometimes police takes them somwhere, sometimes they just watch, smirking.

I go to malls in the city for clothes and presents. Shop windows are shining with new goods, closed stores (h&m, cropp, uniqlo, and others) are replaced with new ones, either local or chinese-owned. Mostly the latter, but no one seems to care. It all looks very modern and quite civilized, there is even a robotic coffee kiosk at the entrance for some obscure reason. Someone couldn’t tolerate an old-fashioned coffee machine, can’t say I blame the man.

And now it’s not just the glamour and the overspending. It’s empty syringes in restrooms and fear in the eyes of the school students who go there for an ice cream when the weather is bad. I saw a few couples there over the years – boy with a boy, girl with a girl. Dyed hair, good clothes, albeit expressive, holding hands and laughing louder than considered polite. The capital was always a touch more tolerant than other cities, at least in places like this. Not anymore, not since December the first. Look over the shoulder before telling a joke, just in case. Not a paranoia, but a well-justified caution.

I will keep doing what I must, and try to tell the tale while I still can. Not because I am good at it, but because I cannot do it any other way, it seems.

I am a materials science major. It means that I have to often listen to the wonderful and promising properties of perovskites and the capabilities of various materials based on them. Every single one of these talks ends with a remark about low stability of these materials preventing the real-world usage. I can’t help but wonder, maybe these compounds are doomed to be decomposing to respective oxides after a few minutes? Will there be a point when people get off the dead, oxidized horse and move on?

This semester almost had me. The end is nigh, two more weeks to survive and a couple of exams in January, but I’m burned to the crisp. Not the first time, not the last, unpleasant nonetheless.

But I learned last week that our masters program is awkwardly structured: approx. 60% of all subjects and academic load is focused in the first semester. The rest should be a breeze to get through. Which is good, I’m now sure whether I have enough juice for another semester like this.

Working with supercomputers is a pain in the ass. It’s a miracle these things even boot up with so many devices to keep track of, but using software gets far more weird. Half the operations work on one version and another half works on the other, but only if the number of used processors is even… Maybe it’s ompi shenanigans, who knows. Weird.

Solving dependencies for conda packages used in computational chemistry is spectacularly annoying. But while I’m at it – why not write something here.

It’s been three months of work with machine learning, and over four full years of theoretical modelling overall. I learned an important lesson: the values your model predicts are not important. It is relatively easy to make a prediction using numpy, scipy and a bunch of polynomials.

It is far more important to know the applicability domain of the model, its error and trust intervals of obtained parameters. Clean the dataset, reduce the number of parameters, write out the necessary equations and try to reduce the error using first-principle approach. Modern science studies deviations and reproducibility, and rarely values themselves. Which is a good thing.

Conferences now became quite close-minded and elitist: the same people, year after year, polished presentations, barely any input at all. There are a few large ones every year, but they are expensive and quite limited number of people are allowed in. Which raises the question: does anyone know a platform or a website where one could post unpolished results and discuss them with other in hopes of feedback, corrections or even collaboration?

I’ve been working with a bunch of ML and quantum chemistry lately. At this point the hardest part is to actually come up with the problem (i.e. translate chemistry into reasonable mathematical expressions) and then make all the servers and packages work. The code and NN architecture themselves are like 10-20% of the work.

Now, a more personal note. For now I stay: to finish the education, to help the family. In some sense to see what happens next from the inside and maybe to tell the world. I will not be drafted in the near future and I think I will come up with a bailout in the next few months just to be on the safe side.

What has been happening over the last 6 months is awful and wrong and I hope it won’t last for long. The consequences will be dire for everyone. God help us, even though I do not think there is one.