Life in the Lab

I had my first dream about an experiment last night. These days I'm dreaming (or at least remembering my dreams) more frequently than a few months ago. I heard as an explanation of dreams somewhere once, that during your dreams, your brain is busy sifting through the day's events and working out which memories should be permanently stored. The dreams we experience are a sort of conscious interpretation of the television-static-like jargon that is generated during this time. Anyway, I guess the fact that I dreamt about an experiment just goes to show that I'm probably thinking about them too much.

While I'd like to blog more about life in Korea in general, being in the lab for 75+ hours per week tends to limit the variety of photographs I have in my camera when it's blogging time. I hope that Lee's Korea Blog can still manage to be of interest to a wider audience as it inevitably makes a transition to something more like a 'Ph.D in Korea-Blog'.

But I must say that I am interested in what I'm studying. I guess my biggest challenge now is trying to stimulate your interest in what I'm up to these days. In the photo above is a petri dish with different colonies of blue and white bacteria growing on it. The black text just details the names of the chemicals that we're growing the bacteria on, and the red text is talking about the type of DNA that the bacteria are holding. The white bacteria are the ones that we're interested in, whereas the blue spots are the naughty ones that didn't do what we wanted them to. Bacteria are commonly used to store DNA and copy it for us, kind of like a photocopier. We even refer to them as 'libraries' at times. Such blatant exploitation of simple organisms to meet our own needs is probably worthy of more scholarly debate. But no one seems to care about bacteria these days.

Except when we're sick.

Laboratories all over the world often use very similar equipment, and there's a whole underworld of suppliers that specifically target the laboratory market. You never hear about these companies normally, because they only focus on advertising to their specific customers. In this photo, along the bottom line of the sticker above our fumehood, are some examples of the names of the suppliers that I'm talking about.
I guess that because most of the companies are started up by retiring professors, the names rarely get more catchy than 'Lonza' or 'Mupid'.

This is where we get our water from in the lab. It's a fairly souped-up filtration system that takes out whatever it is that makes tap water dirty. Because chemical reactions are often sensitive to things like heavy metals or chlorine, we need to be careful about the kind of water we use.
Did you know that pure water actually freezes at -42 degrees celsius? Zero degrees is when impure water freezes, and the ice crystals grow by forming around bubbles or dissolved impurities in the water. Most of the ice that we're acquainted with comes from water that isn't completely pure. But if you take out all of the impurities and try to freeze it, the water has a more difficult time forming ice, because it doesn't have anything to form crystals around. So to achieve the same effect, you need a lower temperature.

This is a PCR machine. PCR means Polymerase Chain Reaction, and it created a small revolution in the science world when it was invented. It basically uses a combination of special chemicals and temperatures to amplify DNA so much that you can see it and take a photo of it. This is important because DNA is usually invisible to us, so it's very helpful when we can see what we're working with. I'll show you a photograph sometime later.

One thing I have noticed is that they seem to be a little more lax about safety here. In Australia, you're not allowed to eat in the lab. But in Korea, they have coffee machines in operation a few metres away from the fumehood. I guess what doesn't kill you only makes you stronger.

This is a rather nifty device called a Speedy-Vac. What it does is dry things out very quickly. When you work with things dissolved in liquids a lot, you sometimes need to get the liquid out so that you can work with the stuff left over. It would seem logical to just heat it and get the water out, right? But the problem is that if you heat DNA too much, it disintegrates, which (as with most recently disintegrated things) tends to make it considerably less useful to us.
So what this machine does is spin things around like a Hill's Hoist in a vacuum environment. It sucks out the air in a kind of pressure chamber, which makes things evaporate without heat. The stuff you need doesn't get sucked out, because it's getting spun around so fast that inertia will keep it in place. Cool hey?

And here is my weapon of choice for most of the week. This is a pipette, and what it does is deliver precise amounts of liquid into whatever I'm making. It's important to know exact volumes when you're dealing with biochemicals, and this little thing is accurate to one-one thousandth of a millilitre.

Remember those tobacco plants growing in the lab that I showed you a few weeks ago? Well they've just started to grow flowers, so celebrations are in order. I had never seen a tobacco flower before, and I must say they're a lot prettier than I imagined. When I think about it, I probably would have imagined them to be sticky, black, cancerous things. But these are quite pleasant.
Economically important crops such as tobacco tend to have a lot more research funding directed at them. This means that we know a lot about tobacco, rice and corn, but not so much about Sturt's Desert Pea. We're not researching tobacco at all, but we use it in our experiments because there is a lot of information freely available for it. What we can then do is use tobacco as an analogy to other systems. Tobacco has big leaves, which makes it useful for things like microscopy or to track a bacterial infection.

What we're studying is rice, which I feel better about. It's nice to think of your research as eventually being beneficial to people who need it. Our rice in the greenhouse is starting to form grains.
Did you know that one rice plant, coming from a single seed, can yield around 10,000 grains of rice? It's amazing what a single plant can do with a bit of dirt and sunshine.

Science itself is not particularly difficult. The ideas can be complicated, but if you break things down and use less jargon, nearly everyone would understand the core concepts. The rest is just details.
To that end, I'm going to take you through the basics of a common thing we do called Bacterial Transformation. Transformation means getting some DNA (dissolved in liquid) inserted into bacteria so that they will do things with it for you. Bacteria can do all sorts of interesting things with the right kind of DNA. The first thing you do is take out your bacteria from the -80 degree celsius freezer. They live here in suspended animation when not in use.

Then you thaw them out slowly in an ice box. They're in the two circular tubes in the photo. You add your foreign DNA directly into the tubes, so the bacteria are floating around in solution.

The timer is used to keep a track of the time. Funnily enough.

Then what you do is plunge them quickly into a 42 degree celsius water bath. We call this a heat shock. For us humans, going from 0 degrees to 42 degrees all of a sudden isn't particularly interesting. But for bacteria it's another story. The 'skin' of most bacteria is actually more like an oily bubble that surrounds their inner fluids. When you change the temperature quickly, what happens is that their skins will form temporary holes as the heat stretches them rapidly. The holes eventually close up, but during this time, some of the DNA that was floating around in the liquid will enter the cell. That's how we get the DNA from the outside of the cell into the bacteria, creating a biologically modified organism. Pretty simple really.
You'd think that if it was so simple, a lot of drastic genetic modification would probably happen in natural situations.

Well, it does.

Then after their traumatic ordeal, we give the bacteria a nice shot of this stuff called Luria-Bertani broth. It's a mixture of everything that bacteria find delicious, and they basically throw a party if you give them enough. Bacterial parties are good, because they have a lot of babies and do interesting things with the DNA that we quietly slipped them before the party.

After all that science talk, you may be feeling like this. In this photo, Hoon and Eun-Hae are having a quiet nap on a Saturday in the lab. Rather than being a sign of laziness, it actually represents how much work they got done during the week.

With the weather warming up nicely, I went back to the frozen lake to have a look. It's all melted now and I tried to look for some of the fish that spend the winter under the ice.

I couldn't see any because the water was rather murky.

I'll occasionally eat out on the weekends when I'm by myself. There's not much difference between food in Seoul and Busan, but Busan has a lot more guk-bab (soup-rice). Around the corner from my place though, I recently found this dish, called kong-guk (bean soup) which I had never tried before. It's a brothy soybean stew that has cabbage and a bit of beef in it. It was fine, but nothing to go out of your way for.

Heather went to Australia this week and came back on Thursday. Because she's a good worker, the school lets her do things like that. Having not returned to Australia since arriving in 2006, I had a small shopping list for her. In the photo above are Mi-Goreng noodles and Extra chewing gum. You can't get these particular noodles in Korea, and I ate them a lot in Australia. As soon as Heather pulled them out, I cooked some up and a whole lot of memories came flooding back. Heather said they taste like Korean noodles.

I'd say they do about as much as Vegemite tastes like kim-chi.

We went out to the Gangnam area of Seoul, which is usually fairly busy. I hadn't been out this way since I moved. Seoul doesn't really have a city centre, it has hot spots of activity, of which Gangnam is one. There are a few more on the other side of the river.

This is the Kyobo building, which is the headquarters of a bookstore company. Korea has been investing heavily in education, so publishers and bookstores like this one have flourished. The country is striving for a knowledge-based economy, with electronics, robotics and biotechnology being focal points.

This guy was playing drums outside for a bar. There's always a lot of competition for exposure in Seoul, and there's only so much that a flashing neon sign will do for your business. Playing drums like this will certainly get you noticed, but whether that translates into more customers is questionable. The tune sounded something like ba-dum dum ching, ba-dum ba-dum ching!

It wasn't bad.

Here's Heather standing outside the Hard Rock Cafe in Itaewon. I had never been to a Hard Rock Cafe before, so it was interesting. All I knew about them was that they sell shirts and they're in a lot of big cities around the world.

I was right about the first two points, but I also found out that they have a lot of guitars hanging around the place.

I liked the decor and the atmosphere was classy but relaxed. When we walked in, they were playing 'You Shook Me All Night Long' by AC/DC. They're an Australian band who first got together around 30 years ago in a pub called the Pooraka Hotel in Adelaide.

The drinks here weren't especially pricey and we came back after meeting with Steve for dinner. Steve is an American adoptee who I met on the 2005 OKF tour, and is currently studying for his law degree in Tokyo. We were busy drinking and talking, so I forgot to get a photo of him. Steve reads this blog from time to time.

Hi Steve!

And to finish up with this week, here is a slippery dip on the side of a building here in Seoul. With land being so expensive, playgrounds are more of a luxury that can be easily outbidded by people with money. At least they're still trying.

That's all from me this time! I hope this blog can remain interesting and I'll continue to update for as long as I have things to talk about.