Winning a discussion

I've started writing the methods section of my thesis, and it's not going very well. This afternoon I was really into it, obsessed, excited, tired and sick of it at the same time. I couldn't get the words right and nothing I did helped.

My supervisor then told me to stop working, go home and sleep.
- Then you'll see everything clearly tomorrow and you'll be able to fix this.
Being (not very) grown up I said something like: but.... I don't wan't to!
Yes, both my supervisor and the other student on the project laughed at me, and a new rule was created: we're not allowed to hand in the same text twice in one day. Go home and sleep on it first.

Although my gut told me my supervisor was right, it still didn't wan't to stop working. That was when I discovered the new PhD Comics:

That's it!
I won the argument!
Once you have a comic (especially something as brilliant and all-knowing as PhD Comics) on your side, you automatically win. So go home and read don't sleep - read comics!

- Also check out some Norwegian comics, like Nemi, or Pondus:

You need a life... or a hobby

A common problem with students, whether they're bachelor, master or phds, is that they think working hard is the same as working a lot - in hours. They spend 10-12 hours at their desk, several days a week, and then continue staring at the computer/article/text book when they finally go home. As I think you know, we drown in a feeling of guilt once we try to not work, even though the "work" ends up being an empty gaze into the air.

I do this a lot myself, although I know that eventually I might as well be working in my sleep - I just go stupid. Luckily I'm also crazily happy when I'm exhausted, which means that I spend a lot of time laughing, to the annoyance of my supervisor (who I unfortunately find extremely funny at times).

The long hours is typical of science and it's been a big issue on twitter and blogs these last months. I've therefore made the very profound, huge, life-changing decision to actually have... a life, in addition to all the science. In order to have a life, I needed something that I could do, something relaxing that wouldn't require too much of my not-so-functioning head in the evenings. The solution?

A good friend of mine decided to teach me knitting. And my Mum agreed to teach me quilting. I've now had one evening of knitting and one with quilting and can definitely recommend a hobby if you're looking for a way to get the elusive besides-the-science-life. Reading a book in the evening doesn't count. You need to do something that don't require too much thinking, no staring at tiny letters and it should be fun and possible to do in company with friends.
Sports, gaming, baking, blogging, sewing, knitting, dancing... there are lots of choices, so just pick one and get started.

....and NO, pipetting is NOT a hobby!

What's worth skipping for?

As I think I've mentioned a couple of times now, I currently do 3 experiments a week.
When most of the samples are prepared, there's about an hour when something needs to be stained or placed in the fridge every 10-15 minutes. This is when I usually eat my lunch, which means I'm running back and forth between the lab and the cafeteria.

All this moving around got me thinking about Michael McIntyres talk about how we walk - and why our walking is so slow. He suggested that we stop walking and start skipping while moving our arms synchronously, which is SO much faster.

Standing at the end of the long, long corridor, with my lab in one end and my delicious, warm coffee and a newly baked cinnamon role in the other, I came dangerously close to testing the skipping theory. I took about to "skipps" (not anywhere near enough to reach top speed) before I realized that all the offices ahead had glass walls, and all had an average of two scientists inside.
I must confess I didn't take the skipping theory any further. I just ran.

Later though, skipping or any other kind of happy-walk seemed even more tempting. I managed to do a quick data analysis while the last samples were being analyzed by the flow cytometer today, and everything looked great. Results are clear, significant and simply very good - at last!
How do you walk from the lab to your office knowing you're getting great results, that your on to something, about to discover something?
(Yeah, that's how it felt anyway, we'll see later if it's true....)

At this point, I think McIntryes skipping might be the correct approach.
If the corridor is ever empty, I might give it a try!

More plates and more bad luck

I just had a very annoying experience that I thought I'd share if you - like me - need to produce loads of agar plates each week. I've already made it quite clear that I think making agar plates is THE most boring routine job in a lab, however I also have amazingly bad luck when making them.

This time I used the type of sterile bench that comes with a glass front you can slide up and down, and that also has an extremely powerful fan. The medium was made, autoclaved and poured without any problems. After the plates had solidified I put the lids on them and left them in the bench until the next morning. I usually do this to get rid of some of the moisture so they won't be too wet when I plant the seeds.

When I got there the next morning to collect the them, the extreme fan in the bench had completely dried out half of the agar plates - even though the lids were on. The agar was so dry that it had shrunk and didn't even cover the bottom of pertidishes!

Oh, I got so mad, and sad, and annoyed and... felt completely tired. I guess that's what I get for complaining about a little routine task that everyone does. As my supervisor told me: forget about it and just make some new plates.

Right... so I'm going to stop complaining about agar plates - AND I'm going to stop using the crazy-super-extreme sterile bench!

Stay away - student has not been fed today!

I've been doing my flow cytometry experiments 3 times a week for 3 weeks now, and have learned one major thing: I've got to stop eating.

From what I hear, lunch is not compatible with most protocols. I'm lucky though, as mine usually leaves me about 20 minutes to sit down and eat something around 2.30.
It's a looong time since breakfast but the day is so busy that I'm just not bothered by the aching stomach.

My hunger usually sets in when I get home around 6. By then I'm a hungry, evil, monster that should not be approached by anyone - and definitely not talked to. There's only one way to avoid the danger: head straight for the fridge.

Unfortunately my boyfriend don't always see the warning signs, but lately he's got a very effective tactic. He gets home late. So late in fact, that we don't bother making dinner.
The idea seems to be: eat breakfast (if you have time), try get lunch, don't bother about dinner.
Therefore I've concluded I should just do the thing properly and stop eating.
Think about how much time I'll save?
It's simply brilliant!

Sending email to you super-brilliant-awesome-smart science hero

My research project consists of three parts that are not as closely linked as they perhaps should be, and each could easily be a project on it's own.

One part of the project is studying the cell cycle of Arabidopsis thaliana using flow cytometry, although flow cytometry in plants are not as straight forward as with animal cells. No one in my group has done plant flow cytometry ever, so when I started on this project in September I began researching a protocol. After a LOT of literature search and long discussions with the phd-student that helps me out, I decided to go for Galbraith's protocol.

The short version is:
The plant tissue is chopped using a razor blade in Galbraith buffer. The chopping release the nuclei from the plant cells into the buffer. The homogenate is then filtered to remove the rest of the tissue, treated with RNase A and stained with PI.

This protocol was first published in Science and has been described as genius in later articles. Therefore, understandingly,  Galbraith turned into "the flow cytometer super-hero"!

From Semptember to January I just couldn't get the flow cytometer analysis to work and was SO close to emailing the hero. Today I actually did.
I've been struggling with understanding how to analyze my data and decided "this time I want help - fast!" I gathered all my courage, took forever to write a very simple email and pressed send. So proud! So very proud that I dared contact the super-hero!

It took less than an hour to get a reply... a very nice and helpful reply asking me a question about the method that I (very shamefully) couldn't answer right away. I'm therefore sitting here, anxious to get back to work  and check up all details - and I just can't believe my awesome, super-brilliant-science-hero that help me out right away!
I seem to be meeting the nicest scientists everywhere

It takes time

I spent the last six months getting my protocol to work. It's not that it's incredibly difficult or complicated, it's just that no one, in all those articles I read, included how to do the flow cytometry analysis in detail. Turns out there are some tweaks to doing flow cytometry on plant nuclei that's just not intuitive when you've never done it  before (I'll get back to that later).

We didn't get it right until I stumbled upon a so-called white paper by Galbraith that describes everything to the last detail. Very well, at least the flow cytometer analysis works and I'm able to visualize the nuclei. But so far, none of my treatments have shown anything (except for the one where I seems to have killed the plants, but that wasn't really useful!). I KNOW it's not supposed to work yet, as I've only done it a couple of times and tested very few treatment regimes. But after spending half a year getting the analysis to work at all, it would have been kind of...nice, to just get an indication that I'm on the track of something.

Well, that's what everyone tells you about science - you need to try for ages and ages.
So, it's time to role up the sleeves and get to work. Next run is tomorrow, my plants have been treated for 48 hours. Maybe that'll do something...

Being tired/stressed/forgettfull...or just a little stupid?

This was one of those annoying days where the simplest thing goes wrong!

Making agar plates is THE simplest routine chore you do in the lab. Or it should be, but usually I manage to make a big deal of it. Mostly that is because it's so boring, but also because I'm really strict about keeping all my plates as sterile as possible, as we don't use any antibiotics.

That takes us to today's problem. I made a big batch of MS agar and used two sterile benches to pour the plates. It was enough to pour two stacks of plates, which I guess is around 40, in each of the two benches. One of these benches is weird though. There's no logic whatsoever concerning what button turns it on, off or half-on - the only easy thing is turning the light on. And as the light was on, and the bench was humming, I forgot to check the rest of the buttons before I began pouring the plates.

Not until I was going to turn off the bench, after cleaning everything up, did I notice that it had been only half-on all the time!!! Oh, I got so mad with myself for not noticing right away. I didn't throw the plates out though (I mean, the bench was half-on...?) but I marked them with B - for BAAAAAD!

Then I went home to stay on the couch for the rest of the night. I usually don't mess up that bad when I'm on my couch.


- Thinking of the whole thing now: I can't even remember if I did turn the bench on and then off again, without thinking about it - and only noticing after I'd already turned it off, thinking it had never been on...
I confuse myself, where is that couch?

Neglected tropical diseases

I attended the debate "Science for a better world - vision or illusion?" tonight, hosted by Café Nord-Sør and Universities Allied for Essential Medicines.The debate was centered around neglected tropical diseases that according to WHO affects up to 1 billion humans, without much research being done to discover vaccines or cures.

One of the speakers was Karita Bekkemellem, a former politician who is now the director of the Association of the Pharmaceutical Industry in Norway. She talked about how cooperation between industry, government and scientists is going to be essential if we are to produce cheap and effective medicines in the future. Another speaker was Lars Slørdal, professor in pharmacology at NTNU, who talked about how the problem is "not neglected diseases, but neglected humans" meaning that poverty and poor health are strongly correlated. He also took the opportunity to point put that the pharmaceutical industry is heavily influenced by the urge to make (great) profit and how this is not for the benefit of the society or the patients.

This lead to a so-called "heated discussion" between Slørdal and Bekkemellem, which was really entertaining for us in the audience. Bekkemellem was very defensive in her opening talk, so it seemed to me like she expected exactly the kind of criticism she got. I don't think the discussion was to the point though, as it's obvious, as Slørdal pointed out, that the global pharmaceutical industry do not necessarily invest research and money where it's most urgently needed (in antibiotic resistance, for instance). However Bekkemellem responded by talking about the Norwegian industry with it's 4000 employees, and how they're all "nice people". That's not really a good discussion in my view. Slørdal is right that the pharmaceutical industry has some moral issues - but Bekkemellem is right that pointing fingers isn't going to take us anywhere.

The two other speakers were Kårstein Måseide, senior adviser in the Research Council of Norway and Stig Slørdahl, from the Faculty of Medicine at NTNU. They talked about ongoing projects on research on neglected diseases and specific examples of aid - like a small, hand-held ultrasound device for medical sonography.

When the debate was over we managed to talk to some of the speakers about a cooperation with BUG - we might even get some of them to talk on the BUG seminar about antibiotic resistance, or other future events!

Sciency days and cake for lunch

Today was a picture of how life will be if I continue with research after my masters degree, I think. I was constantly late, with so much to do, remember and think of all the time, that sitting down or eating was completely forgotten. To begin with, I didn't have time for breakfast.

After not eating breakfast I met one of my PBL groups for the first time. 5 very shy girls sat there and expected me to...teach them stuff I guess. Well, I think I got them to understand the concept of PBL, and after a while a very careful/nervous discussion about HeLa cells took place.

Then I ran down to my desk and ate some cornflakes before running to the lab to prepare my samples. That went surprisingly smooth, I even remembered to tape up my ice box to keep it from leaking (some one took my box, so I only have this stupid leaky one).
Then I suddenly had time to prepare the ITC solutions for the 24 h exposure I'm going to run. But when I went the get the plants I was going to use, I discovered that I had 12 plates in stead of 10. Very weird, I've no memory of the two extra plates at all...
I took 10 plates and prepared 8 of them for the ITC exposure, as planned. What to do with the extra two?
I exposed them to high concentrations of ITC.

The whole exposure-business took forever, so I was really late for my appointment with the engineer that's teaching me to use the flow cytometer. I ran with my plants to the growth room, made a mess on the way, tried to clean it up and then ran upstairs  to the flow cytometer. As the engineer was even later, I decided I could try starting the flow cytometer myself - for the first time. Of course I got error messages that I've never seen before: carousel  error, blue laser power error...
Being very wise, I sat down and waited for the engineer (who told me nothing was wrong after all).

The analysis went okay. Now, dying from hunger I ran down to our lunch room and as the master students were having a cake lunch I managed to get... eh, some cake for lunch. It was now 3 hours since I'd left those poor seedlings with high doses of ITC. - They're dead by now, just throw them out, my supervisor told me, and went on: you're evil Signe, killing plants for fun. -Hehe...

The next sequence of events was me trying to get to a work out class on time, having to talk to a speaker I invited to the BUG seminar in stead, then trying to get dinner, running down to a later work out class, playing Zelda for about an hour and then finally, at 11 pm, beginning to prepare for tomorrows experiment. I guess this is what science-days are like (all days from now on then?). You start trying to teach someone something, then you run around in the lab for a few hours, maybe get some cake for lunch (or no lunch at all) and then end up in all kinds of meetings you had no idea were going to take place.

Luckily, a day can still end with a boyfriend making dinner, a bit of Nintendo Wii, work out and sleep.
Oh, how I love the sleep!