Wednesday, 28 January 2015

And now for something completely different

I'm scared, because my next objective is to use all the sequences I have collected so far from all three genes to make a proper tree, with a root and molecular clock. This is quite exciting, because although I have been playing around making little trees, I haven't yet done it properly. But it's also scary because what if nothing makes sense? What if the program I am using (BEAST (Bayesian Evolutionary Analysis by Sampling Trees), specifically *BEAST) doesn't work on my data? I have had that problem with countless programs and data before: it works beautifully on the example data, but not on my data. A crushing disappointment similar to when you test-drive a car and it runs beautifully, but then when you take it home it blows a head gasket. There are always solutions, but they take many long and tedious hours of removing extra spaces, inserting brackets and dots, and trying capital letters instead of lower-case letters to see if any of those work.

For the last few days I have been swept up in the completely random and unpredictable science of ecology. In particular, we (myself and my field technician) have been sampling Cantuaria habitat to see if soil moisture, soil grain size, and a bunch of other factors affect the range and positioning of populations. We've also been trying to gauge the size and range of the populations using adaptive cluster sampling (ACS), which is one of the most tedious ecological sampling techniques out there, but it's also pretty good. Basically, you decide on an area large enough to contain a few burrows (I chose a 2m X 2m square). You start off in an area with burrows, mark that there are burrows and the number of them (and other stuff you're interested in), and then move onto another area the same size but to the right of the square you've just covered and repeat the process. Then you do the same to the left of the first square, and above it and below it. If, on any of these surrounding squares, you find a burrow, you then have to sample squares above, below, and beside that square. So you can find that on two sides of one square there are no burrows, and get your hopes up and think you can now go home after friggin hours of measuring out squares and looking for burrows, but then you look in the third square and there's one burrow there so you have to look in another three bloody squares. It's a good way of finding the edges of a population, but it's also a good way of making yourself wish the populations were a little bit smaller.

Also, the day that we put out some data loggers to collect temperature and humidity data about the habitat, some cattle got into the reserve and trampled everything and destroyed burrows and pulled out probes that we'd put into burrows to see if the temperature and humidity differed in burrows as opposed to in the surrounding soil. Yet another reason that cattle should not be in NZ.

Anyway, I'd better get on and begin the process of trying to begin the process of hopefully maybe beginning to make a tree. I'll let you know how it goes.

Tuesday, 13 January 2015

If I could converse with my younger self...

Arrow (My nickname as a 14 year old): Hi 26 year old self!
Vikki: Hi 14 year old self. Is there something on your mind?
Arrow: Yeah...I've been thinking about Scotland and I really miss it. Hey, do you live in Scotland?
Vikki: No, I live in New Zealand. It's like Scotland, but everyone is a bit more cheerful.
Arrow: Really? What are you doing there?
Vikki: A PhD.
Arrow: Awesome! I'm really glad that I'll manage to get that far. I guess I'll get into university after all. But what are you doing your PhD in? At the moment I'm thinking of studying virology or it one of those?
Vikki: Nope! Forget those subjects. What do you love more than anything else?
Arrow: Animals!
Vikki: Exactly. Forget humans and their pesky ailments. Go for zoology. It's just animals. Nothing else. Don't waste your time pretending to be interested in curing diseases. And don't listen to people when they say you're too weird or mad or that you should not be so obsessed with animals. You have a passion which you can run with. Enjoy it and don't be embarrassed.
Arrow: So your PhD is in zoology then?
Vikki: Kind of. That's what my degree is in. My PhD is in evolutionary biology. I'm studying spiders.
Arrow: Hmmm...kind of weird, I like birds of prey better.
Vikki: Yeah, you like handling them and training them, right? But they're surprisingly boring at a scientific level, and spiders are much weirder and more interesting.
Arrow: So I'm guessing you're not a falconer then. I was hoping by the time I got to PhD level I'd have a Bonelli's eagle, an Aplomado falcon and a black sparrowhawk.
Vikki: You wanted them for the wrong reasons. I have a New Zealand falcon. They are the best. And yes, I am a falconer, and that isn't going to change any time soon - but it is a hobby, not a career.
Arrow: Falconry is my life though! I live and breathe it. Nothing else comes close!
Vikki: Don't be so of the best pieces of advice I have been given is that you want to aim at being a scientist who does falconry, not a falconer who does science. You can live off the first, and have a much more interesting life.

*Flash forward six years*

Vikki: Hi 20 year old self. Life sucks for you. I'm here to tell you it will get a hell of a lot better.
Just get out of student halls, and life will start improving.Buzz (20 year old self): Student halls are the worst thing, but I still don't see how I will do a four year degree in this stinking city with no pets or countryside without getting severely depressed.
Vikki: The years will pass quickly, you will get pets throughout your degree, and the city isn't so bad - you get used to it. Plus, your degree becomes quite awesome.
Buzz: I guess that sounds more tolerable. Uni is kind of boring at the moment though. All we seem to learn about are people, plants and oil.
Vikki: Yeah, but work hard and get into next year and you start learning really cool things about different animals, and the people are a lot more fun to be around. Stick it out till third year, and you'll learn how birds fly and kangaroos jump. You'll take a year out and do your own research in New Zealand. Then you get fourth year, which is the most fun year of all.
Buzz: And then what?
Vikki: Then you do a PhD. Life is so much better. You live in a homely house with framed pictures on the walls and a library. You have rabbits, chickens, a falcon, spiders, three fish tanks, and a mealworm culture. You spend all day doing research and getting paid for it.
Buzz: What kind of research?
Vikki: Lab work doing molecular stuff so you can build a phylogeny of trapdoor spiders, a lot of writing, and some DNA analysis. A bit of fieldwork too.
Buzz: Molecular stuff is boring and hard.
Vikki: No it isn't, they just don't teach it particularly well at Glasgow. Stick with it - it makes you feel like a real scientist, and is so fantastically satisfying when it all goes right.