Tag: PhD

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Machine Learning

I would like to, first, apologize for the misleading title.

Wikipedia defines “machine learning” as:

Machine learning is a field of computer science that uses statistical techniques to give computer systems the ability to learn (e.g., progressively improve performance on a specific task) with data, without being explicitly programmed.

But that is not what this post is about.

You see, as a junior scientist about to embark on your career path, one thing you should do is learn to use different machines. Some machines will make something for you, whereas others will tell you that those machines are probably not working, and despite all your efforts, it will be some time before you start getting good samples or results out of any thing in your lab.

So if you work in a lab, you’ll now have a very good idea of who rules there: It’s them. Now and forward, in your time as a researcher, you’ll go into many labs, meet a lot of people, and learn a lot of new stuff… but nothing and no one will judge you like those silent machines sitting smugly atop work benches of your lab.

Many a times, I have started working with one, thinking, oh this is going to be one of the easier ones. Never has that attitude worked for me. It’s like you cannot trust any single one of them; even the ones that you think you know, won’t think twice when it is as tempting as shattering your trust in them.

They don’t care if you are enthusiastic about research and have chosen this field as your career with such joy. They will happily make you think that you have nice typical graphs* in your presentation that you are about to show in your group meeting. They want you to suffer, to taste embarrassment, like they want to see how long you are going to last in this field that you have been so passionate about …

… Until you have proven yourself worthy of research.

As a result, one of the few things I have always found myself doing in the beginning is to start gaining favor of the machines that are in my lab. To build good rapport with them. And it is not easy, not with every machine. Even after you feel you two are going along well, they will still  test you, or just throw you under the bus when they feel like it**.

If it all sounds depressing to you, let me tell you there is hope. Somehow, after you have stood beside them long hours and worked with them at odd times***, they will start to slowly accept you and let you enter the ranks of researchers. It’s blood, sweat and tears to gain that kind of trust, but you can gain the status of meh-you’ll-do in the eyes of the machines.

But don’t ever expect them to start liking you, because that’s ridiculous, they probably don’t have a heart.

 

 * Well, okay, they may have been looking a little weird to you as well, but early on, you wouldn’t know that, thinking this is probably how they are supposed to be.

** Which tends to happen most on Fridays, followed next in probability by Mondays.

*** Condition of high-levels-of-consistency needs to be met with these requirements of long-hours and odd-times.

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Culture Shock (Again)

Wait, haven’t I written about this before?

Seems like I have… But l appear to have the phrase stuck in my head.

Never mind, I’m a changed person now, so anything I write today (on the same topic) cannot be the same as what I might have written four (and something) moons ago.

So I shall write on this again.

And today, now eight (and something) moons into my PhD, I expect myself to have grown somewhat in my scientific capabilities. So we shall talk about culture shock the scientific way, the “graph” way (excuse my English, but I am a foreigner, so I can apparently do whatever I feel like without feeling as bad about it).

And well, the graph-way is the right way, or it becomes so once you start falling in love with this kind of data representation, which is inevitable if you science (again, I am a foreigner, and “science” feels more like a verb to me these days).

But anyway, back to the graph:

(Source).

Of course this is a very generalized curve, and just one “dip” in the experience is untrue for quite some people – this graph should be a lot more “noisy” if you’d plot a real one. Although this would differ from person to person, and how different of a culture you are moving into.

Also, the graph doesn’t really show your “mastery” level at your home country (or town).  But from the text available on the internet, it is apparent that you almost never reach the same level of mastery in your new culture that you had in your old culture (which makes sense if you think about it).

This always makes me wonder… Does this mean that, even after you have adjusted and adapted, you are technically still in a state of culture shock, and will probably remain there throughout your stay?

That I find scary. And a little unrealistic to mention if a discussion about culture shock comes up in, say, two years from today. What do I do then? Do I say I am still in culture shock, if this particular question comes up? (Although I would estimate that to be a highly unlikely scenario, but everything has a first time, doesn’t it?)

But having grown comfortable with the idea of culture shock, and the (somewhat embarrassing) fact that I am still in there somewhere (although now probably in an overall better part of the curve), and being there for perhaps as long as I am in Finland, I have also realized the good this will do to my self-esteem…

So if I am not as good as I am hoping to become… heck, I am just in the wrong country!

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Other Stuff

A while back, I came across this post about how science can make you feel stupid.

I shared it, thinking I understood perfectly what it meant and felt like. I actually didn’t then, because now I know what it means and feels like. (And yet, I am not exactly sure how it feels like. Stupid can take so many forms).

When I started off my PhD, I was like any normal person, motivated about starting a new “project” that they are excited about. It’s just like new year, and we all know how that goes:

1) You start off with a long list of resolutions;

2) You start following through on almost all of them immediately;

3) You feel so good that you are following through, and how this year did not turn out like last year (and we all know how that went);

4) You start realizing how by starting everything, you broke all rules of developing new habits, and how this is not sustainable at all (did you really even want all of this?);

5) You start going back to your normal routine, and your resolutions start feeling less important to you now;

6) New year, and you have almost forgotten (almost) how last year went and are ready for a new cycle of highly-motivated-to-back-to-“normal”.

But of course, everybody knows these stages, everyone has new-year moments. And when I started my PhD, I knew I’d face some kind of a slump some of the times. People-on-the-internet told me that the PhD dip is inevitable, and it is not a question of if you will come across it but when you will actually experience it (although they also told me that this phase comes sometime around the second year and I am still in my first, so am I just going through a trailer for the actual movie that will be officially opening in months to come?).

The thing is, despite knowing this, I didn’t really plan for this time (that is another kind of stupid right there). Because, like any normal person motivated about starting a new “project” that they are excited about, I wanted to be laser-focused on my PhD and on things that would take it forward.

So if I needed a break from lab work, I could read or catch up on literature, and if I needed a break from reading, I could take some online course. I did like doing other stuff, but all of that could wait until I had my PhD a little more on routine (a thing, that I am finding out only now, was not as easy as I supposed it was, but that could be for another time).

And this is the importance of comparatively-dumber-sounding other stuff.

Because when you are doing something as crazy as a PhD, where you can go months running around in circles finding your way back to square-one’s, feeling-stupid does become inevitable. And when you see it’s been a while since you last made progress, or learnt something new, or developed a new skill, or added something to you, yourself, as a person, that can be eexxttrreemmeellyy demotivating.

But other stuff can help you here.

Because if you have a little something going on the side, like learning a new skill that may not be completely related to your PhD, it is some progress that you can, at least, show to yourself: So, yes, I still haven’t been able to decide if zinc chloride is better or if I should go for zinc acetate for my solutions, but I have completed six-hundred-and-eighty-five blog posts! That should be a milestone!

So that’s why I have started to think about starting other stuff this new semester. Like taking a language course (I have always wanted to learn another language and now might be a perfect opportunity), or starting to draw (I have some half-developed scripts for a comic on how my PhD stuff is going), or taking up other random workshops and activities where I can just change my environment and see what else is up in the world.

And there is another reason why the other stuff can be so complementary to your PhD: so now when you are moving about progress-less, you can blame it on the other stuff, and how, because of other stuff, you probably have not been able to focus on your PhD.

But the other stuff was your stupid idea, wasn’t it?

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Breakdowns

Recently, the hotplate I had been using was glitching a lot (it was fine when I was not using it this much). And then I saw this in my social media newsfeed and this seemed to hit right on point:

Currently, I think we have both started to understand each other more, so we have been getting along better. Now, I have nothing but honest praise for the hot plate.

Dear hotplate, you are the best! 🙂

(I took the image from this link but could not find whose brilliant theory this actually is).

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Doing Dishes

When I am a little frustrated, I blog about it. I have found that it clears your head and is quite an effective release mechanism.

And recently, I have found another way for times when I am more frustrated – a LOT frustrated:

Wash glassware.

Just grab a brush, pour a dollop of soap and take it ALL out on the stupid organic stuff sticking in there that just won’t go away. Bonus points for you if you can get it sparkly clean (suitable for a dish-washing soap advertisement) and a gold medal (albeit imaginary) if you can make that water “sheet” over your glassware during your distilled water rinse (nothing more spiritually satisfying than that).

Washing glassware is my research-bane: it’s the rate limiting step to my progress – where I’m most likely to procrastinate when starting a new experiment. To a normal human mind, washing some glass bottles and beakers could look like a mundane and quick step, but it can be quite tiring and time-consuming depending on how finicky you are about your glassware (and of course, we scientists-of-the-wet-labs, have specific procedures for washing our dishes.)

(Also, if you would like to read in depth about the many things that can get your beakers sparkly clean (except for cracks and scratches, where the only remedy might be to get new sparkly-clean glassware), I highly recommend this link).

So if I can have really clean bottles in my cabinet and methodically washed glass slides in my drawer, I have one less excuse to laze around and can start working on my next steps. It’s like killing two birds with one stone and so this is where I can channel the frustration of my failed-lab-experiments.

Now, from my recent frustrations, I have accumulated a fair number of glass bottles and washed slides and I am good for a couple of upcoming series that I should be running.

After I run out, I can think about learning the art of strategic frustration so that I can always have some clean glassware at hand in future, or when needed (not sure how that would work, but if I do, that can be for another blog post).

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Problem: Solutions

Lately in science, I have been trying to dissolve a  couple of salts in some “solvent” – I have now tried some options, but nothing has really worked so far.

So today, after around 3 weeks of trying to dissolve that salt, I sat down to compile the results of all my mixtures of salts-and-solvents – they could definitely not be called “solutions”.

And that was exactly what was wrong with these, not only scientifically and technically, but also on a literary level: What do I call them when I am writing my report to send to my supervisor?

We, scientists, are supposed to be very specific in terms of technical terms. So I could call them “solutions”, because I was ultimately aiming to make a solution but just was not getting there. But then, they weren’t really solutions, so how could I call them that? If I did, what kind of a scientist would that make me? Would I even be able to sleep at night?

It was a relief I could use the word “suspension” appropriately enough for some of them. That was really so considerate of that particular salt-solvent combination to give me the freedom to use another word.

For all other… Mixtures? Salt-solvent systems?… What do I call them? Or do I just craftily go on writing about them, carefully avoiding sentence structures where I would need to use the you-know-what word?

It’s crazy what people expect of a PhD student: they have to be a scientist in the lab, a writer when writing reports and papers and dissertations, and  an excellent communicator when they are supposed to present their work (and the best sales person if they choose to go into entrepreneurship).

And being a writer at that particular moment of time, how many times could I allow myself to use the word “mixture” over and over again? Or using the same sentence structure for every next line?

I do not know how I managed all that today. I just hope I can sleep at night.

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Bad Day for Science?

It hadn’t been past 12 yesterday when I had officially declared it a bad day for science.

The hot plate I was supposed to be using extensively broke down (again!) and I discovered that one of the good things going on seemed so rosy because I had been miscalculating some things (and misleading myself and others about how it was going so good at that end).

Having been through all that by 11, well, what could happen now that would make it a better day?

But in retrospect, I think I may have labelled yesterday a little too soon – because the day itself didn’t turn out that bad after all.

We, scientists, we label. And that’s a good thing. You should label all your solutions and chemicals as soon as possible, even before you put your stuff in a blank bottle, but essentially ahead of forgetting what you put in there (and until you have labelled these, your life hangs in some kind of a science-purgatory where you keep chanting the words in your head until you have penned it down where it belongs).

But today – today when I was again tempted to categorize the day in the bad-days* section, I reminded myself that a scientist should not label her days as hastily as she should label her sample bottles.

 

* A “bad” day for science constitutes all days that are worse than your usual days, when it’s normal that things don’t always work the way you want them to. A “bad” day happens when you discover having an outlier compared to your average kind of day (which can normally be rated quite close to each other on a scale of 1 to 10).

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What Doesn’t Make It To THE Thesis

I recently attended a PhD seminar of a student at the Physics department. One interesting question that came up was: What didn’t make it to your thesis?

After deep thought and much analysis, I have realized this is such a good question. It let the candidate show other things he did and learnt in his PhD that didn’t make it to his thesis, because they may have been slightly irrelevant or might have been disregarded as not-important-enough.

But with this question, he could highlight this stuff because he still did those during his PhD (or more likely, he could highlight this stuff well if he’d been prepared for such a question to come up – this may not be your average kind of opponent-speak).

But hang on, is it just this stuff that doesn’t make it to your thesis?

When I was doing my Masters, we’d always joke about how everybody should write 2 theses: One the more formal, “required” document; the other, a document of “failures”: the questions that we asked, and what we tried in the lab, that then didn’t work out, and that we then dropped… which then obviously wouldn’t make it to the thesis. The kind of information that you jot down in the side margins of your lab notebook, along with angry and frustrated emoticons and hashtags and exclamation marks.

Jargon that only the person who owns the lab notebook may understand – And now I realize how I don’t make much useful or interesting notes in my lab notebook :'(

The kind of information that doesn’t make it anywhere.

Because that information is also useful, although it mostly just tells you what NOT to do (which is quite the time-saving information). But this kind of information doesn’t have much space in the scientific world. Like people in all other fields, we just want to make noise about the best work that we do, disregarding the important stepping stones that our failures were that got us there.

So yeah, a lot of stuff doesn’t make it to the thesis at any level (or any important document, for that matter – except may be some internal lab communication).

There’s also a lot of other stuff that doesn’t make it to the thesis: the hardwork and energy that you put in, how you picked yourself up after repeated failures, how your informal collaborations helped you (and the people around you)…

… Although if you end up doing really good work, the thesis can become a reflection of it.

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Fast Lessons

So for the last month, I have not been blogging much.

I’m a Muslim, and we recently ended our month of fasting, in which we don’t eat or drink from pre-dawn to a little after sunset. In Finland, particularly in Åbo, that makes about 20 hours. So while we are fasting, we often switch to this energy saving mode to get through the day with grace, while not completely going into some kind of hibernation mode (which we (most of us) do go into if we are on vacation).

So, for reasons mentioned above, I was not much into anything apart from food thoughts and how-to-get-through-the-day-while-keeping-some-lab-work-going techniques (and managing my sleep deprivation issues).

But all this down-time also helps you reflect on what you are doing, and why you are doing it, anywhere from life in general to specific PhD related stuff. And this year, Ramadan (that’s what the fasting month is called) taught me something that I think I’ll be needing much reminding of in the four years of my PhD:

That you think you cannot do it, but you can.

Whenever this thing came up about me (or us Muslims) not eating or drinking anything for 20 hours straight, people would mention how they cannot go through without food and water for this long. Even we, Muslims, who get this training repeatedly every year for 30 days, cannot think of going without food and water for this long when we are not fasting.

But when we are fasting, we do.

And this is quite strange for me, because now that Ramadan is coming in summers*, we always have this big worry on our minds about how we will get through it this time, specially without water (I, in particular, whine a lot about this one). It sometimes seems so hard, and at times, so impossible.

And yet, when we start fasting, we do. Every time. The whole month.

And this year, I realized, how we are always making assumptions and excuses about how we cannot do something, without really trying it out. We don’t take into account the fact that the human mind and body are very flexible and adaptable, and we become what we make out of ourselves.

 

In my PhD, I know that I’ll come across multiple instances when I’ll think I cannot do this anymore, or how I am not able to try any further with a particular experiment, or when taking the next step forward will seem like the most difficult thing to do.

But all that will just be stuff in my head unless I try and find out that I was able to do that all along (or not).

And that, when the start is difficult, it only becomes easier as you move forward.

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* Ramadan shifts by 10 days every year because we follow a Lunar calendar for this, which is 355 days long compared to the more-common 365-day solar calendar.