Wednesday, 9 June 2010

Tania's Tales from the Lab: Part 3

I'm in the lab again today, I won't do a minute-by-minute live blog but I thought I'd write down some of my thoughts. After two months or so embedding in this lab, I feel now I have some kind of understanding of how difficult it is to ever assert that you know anything. Looking into science from the outside it seems that scientists run experiments to see if Z happens when Y is put with X, get results and hey presto, we have a new FACT. We think scientists have cutting-edge equipment on their lab benches, ultra-fast computers, powerful electron microscopes, so that they can see exactly what's what.
I mean, this is how it is on CSI, right?

Well, no.

The first thing I now have more of a grasp of is that you need to check, if not every step then every few steps and they might be many many steps in your experiment! - that you even have the right stuff in your test tubes! As one of the postdocs said to me last week, "It all looks like cloudy liquid" so how do you know what's in the cloudy liquid?

If you are interested in molecular biology, well, you run a gel... This, says Wikipedia, is:
a technique used for the separation of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein molecules using an electric field applied to a gel matrix

and this is the equipment:

Guess when this method was invented. Well, the first reports were some time in the 1930s. At least 80 years ago. And this is still, from what I understand, one of the best and most useful methods to figure out what's in your cloudy liquid. You have a wedge of gel in this bath contraption, you have a set of little wells into which you put your different samples - tiny drops of your cloudy liquid as well as control samples just to compare - and then you run an electric current which pushes the molecules of your liquid through the gel from top to bottom. Basically, the bigger molecules get stuck moving through the gel and the smaller molecules can move through a bit faster so get further. Like a race between very fat tortoises that get stuck getting down the corridor and skinnier tortoises - and all sizes in between!

After about 25 minutes or so, your gel is "done", your tortoises have moved as far as they're going to move. You take the gel out, stick it in another machine that shines UV light through the gel and you can take a photograph which looks something like this:

Clear now? Yup... I don't really know what it means either. The bands of light are molecules and some haven't moved far from the top, and some, like the guy in the bottom left corner, got pretty far...To the trained eye, this tells you everything.

Jut for fun - and a little education! - here is a 1930s concept brought into the 21st century with this cool animation about how to run a gel that I found on YouTube (with rock soundtrack):

When your gel tells you that there's stuff in your cloudy liquid that you didn't expect to be there, or something doesn't show up that's "supposed" to be there, then what do you do? Run the gel again - which involves preparing more samples etc.., can take a day or more. And if it happens again? Check all your equipment in case something snuck in. Check and re-check. And if still not...then you might need a complete rethink.

So, to sum up, to actually "see" in science isn't as simple as looking at a sample or sticking it in your fancy million-pound desktop machine. It often means using a technique developed in the 1930s and which can take days to prepare for. Anyone want to share gel stories? And talking of stories... more about the idea of "story" in science next time. Back to the lab!


Paromita said...

Very good post.I know gel electrophoresis because i read it in my college.I found it very interesting and thank you for the video.I had some confusions but after watching the video , my confusions are now clear. Can you post more updates about gel electrophoresis.

Peter29 said...

Thank you for the information.I read about gel electrophoresis but never saw the image.Thank you for that also.Keep writing.

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