What have I been doing in Tromsø the week that has passed?

I have learned to use a lot of computer programs to analyze my data (the data I made in June that I will base my master project on), how to connect the information I get and also a bit about how to present what I find out. And today I presented my own analysis on my own data for the first time. Hopefully this is what I will do the rest of my life and today was the first! So exciting!

Two pictures from my presentation today:

This is a picture of a bar plot that you get when you do a genetic structure analysis in Structure. What you do is that you put your data set into the program and then you use Markov Chain Monte Carlo (MCMC) and some prior values to find out how many genetic groups there are in your data set. You indicate number of steps in the burn in (100 000) and then the number of steps of the MCMC (400 000) and then how many groups (values of K) the program should try and how many times it should try each K (number of iterations). Each bar is one individual and the colours indicate the frequency of each genetic group in each individual. Along the x-axis my samples are sorted by geography.

This, as you can see, is a map of the Northern hemisphere. This is where you can find my moss, Hylocomium splendens. It is found on the whole of the Northern hemisphere and also on Mt. Kilimanjaro. The circles are just another way of showing the bar plot. I have made one circle for each of my nine populations. Also here the colours indicate the three different genetic groups.

As you can see, there seems to be some genetic patters and that the colours group geographically. My groups were East and West North-America, Africa, North and South Europe and North, South, West and East Russia.

So when I get back to Trondheim I will clean my data set and get rid of all my missing data and bad groupings and then I will do all this (and more) again. The analysis to make the bar plot took 10 hours of computational time and for the data I will present in my project in the end, I will have to at least double number of steps. And I have to run the analysis many times with different priors (prior values, things I already know). This is what I will do for the next three months at least 🙂

This one is from Saturday morning breakfast cereal. You know what the bad part is? This cycle of the trematode is very common among trematodes and other parasites. I love the people making this comic just because they know all this biology stuff. And then again because of the astrophysicists 🙂

I need to buy this shirt based on this comic

Why? Because this is what I will do the next four months, waiting for my computer to finish an analysis so it can do another one. I’m not a programmer, but I still only deal with computers.

I have already mentioned that I have to translate sample labels from Cyrillic in order to understand where the samples from Russia really are from. Here are some shots that my supervisor, Kristian Hassel, took while in Russia that I have selected that will give you an insight into the life of a master in systematics…

I love this next picture mostly because it has IZBORSK in it. As Borsk it one of my nick names back home 🙂

I have heard that someone here at the Museum is actually quite good at handwritten Cyrillic. Might come in handy…

My second favorite Russian location: Ayulyuyuzyuk (I didn’t know it was possible to put that many y’s in one word)

Little blown paper bags with moss (or really Bryophytes, moss is only one group of three in the taxa Bryophytes) in them are my life, and will be for a while. But they are definitely more fun when they are from Russia or Alaska.

There are many things you learn when doing a master degree and not all of them have to do with your thesis per se. Not just that you turn into a google wizard or anything, but today I realized that I should learn the Cyrillic alphabet. And that I need to know more of current Russian geography than I do. The reason is this, my supervisor went to Russia in March to collect samples from the herbaria in Moscow and Leningrad for me and for other projects. In our herbarium here in Trondheim all specimen tags are in English and all the newly collected material is digitalized. This is because we exchange specimens with people from all over the world and then there is no use having it all in Norwegian as well as English. But this is not necessarily the case in other parts of the world. In Russia, for instance, a lot of the specimens are only in Russian (and sometimes only in Cyrillic) and then you need to translate. My supervisor has just taken pictures of all the labels, numbered the pictures and the samples and will now give it all to me, so I can translate the labels… I would never have thought that I needed to know the Cyrillic alphabet studying biology…

Today I was trying to locate my samples on a map of Russia with all the regions on it. But while trying to find all the locations I realized I know nothing of Russian geography. I could not place anything North or East of Georgia and the Ural mountains. So, since I am studying for exams, I did a tour of wikipedia on Russia and the Russian regions…

The result? I now have a favorite Russian region:

Sakha (Yakutsk) Republic

(disclaimer, everything is from wikipedia)

– it lies in the Far Eastern area (they actually call it that), sometimes included in the area Siberia.

– it has almost 1 million inhabitants, but because it is just a tiny bit smaller than India (!) the population density is 0,31.

– it is the largest sub-national governing body by area in the world.

– it is named after the Sakha people who settled there almost 700 years ago.

– As wikipedia so elegantly puts it: “Yakutia’s remoteness, even compared to the rest of Siberia, made it a place of exile of choice for both Czarist and Communist governments of Russia.”

– mineral exploitation is what feeds people there (as in the whole of the Northern Russia).

– there are two main roads, but neither has asphalt (because of permafrost), only clay cover.

– the “official” religion is Russian Orthodox, but as none of the priests want to live outside the capital, people mostly have no faith or believe in shamanism.

– the republic has 3 time zones.

– it has mountains of more than 3000 m.

– it contains the coldest place in the Northern Hemisphere.

– the capital of more than 200 000 has no road connection every winter. The only real means of transport is by water or by air.

It sounds like a wonderful place. They have volcanoes as well. And border the Arctic Ocean. I have to go there sometime. It seems the only real means of transportation in Russia East of Ural is the railway. I should try it sometime.

8.30-11.30: work on master thesis. Mostly lab work.
11.30-12.00: lunch.
12.00-16.00: study for exams (still have three to go).
16.00-16.30: eat. Try to make dinner at home and heat it at the office.
16.30-20.30: study for exams.
20.30-23.00: free time. Scout responsibilities, SiT Service, friends, work out, work, other.

This is my plan. This is how my life will be until the 26. May. That’s two weeks. It should work. It has to work. After that I only have the master thesis and work left. I’m sure if that will be better or worse…

Today dinner is penne, one tomato, half a pepper, a small onion, an egg and basil.

When I die of boredom I read a chapter of Pride and Prejudice in Google Books. Love the concept. And I love the book as well 🙂 I’ve seen the mini series and the movie so many times that I picture it while reading. And I am really impressed by how true the films are to the story. Jane Austen is wonderful at capturing people and has this fantastic dry humor.

I miss my camera. But now the weather forecast says rain for more than a week, so it’s not the worst thing to have to be indoors and study.

I am such a statistics nerd. After meeting exiting new people in Germany this Easter, one of my fellow biologists (who is from Slovenia) send me a link from this site with statistical probability distribution plushies (kosedyr). They are wonderful! I spent some time at the site and they have everything! I am definitely going to get something from there (just need to decide what…).

This is a pattern with the two kinds of errors in statistics. Type 1 is when you reject the null hypothesis when it is actually true. Type 2 is when you don’t reject the null hypothesis even though it is wrong (yes, I have this on an exam next week…)

This is a plushie of the student t-distribution. There are many more of them, and I can’t decide which I like most…

I love this poster. Almost all of the words are part of my everyday life and is my syllabus in one or more courses this semester… Talk to me next semester and it will be everything I know…

This is just a wonderful pun. When you estimate something in statistics you give it the ^ to indicate that it is just an estimated value, not the true one. And naturally it is called hat. So this is a p hat hat 😉

I know it is uncommon for a biologist to love statistics, but it is wonderful. Today I am going to really understand approximate Bayesian computation (ABC for short). And to study for my exams, of course 😉

So I have again this semester, suddenly got ill and had to rearrange my whole schedule. 🙁 So instead of having the final exam today I had blocked sinuses (bihuler), a fever and a sore throat. No fun. Luckily my professor said that I should just tell him when I’m better and we’ll set a new date. But I’m still sick. My entire head hurts and I have no-one to look after me. Definitely the worst thing about being single and living away from home. Having to cook for yourself when you are ill.

I hope I will be better tomorrow, because I still have two exercises I need to do this week. And then it is all the lab work and the work at the herbarium. The 26th of May, I will have no more exams, only master thesis lab work and work-work. Good times!

Det er altså en liten fisk som ser slik ut. Den er ikke fra Amazonas, men heter Amazon molly etter amazonene i greske myter. Hvorfor det, spør du? Det er noen forskere med dårlig humor som har vært på ferde. Det har seg nemlig slik at disse fiskene er hunner alle sammen (hunkjønn, altså). Det er egentlig ikke så uvanlig, det er mange både planter og dyr der de kloner seg selv i stedet for å ha sex med noen andre. Det festlige med disse her er for det første at de er jenter og ikke intetkjønn eller noe annet, og for det andre at de trenger hanner for å reprodusere. Men det de egentlig trenger, er ikke det genetiske bidraget fra en hann, nei de trenger at en sperm  er i kontakt med en eggcelle. Er ikke en sperm i kontakt med en eggcelle så utvikles den ikke til en ny hunn. Det nyutviklede indivdet er en tro kopi (klon) av sin mor, men allikevel. Så hunnene i denne arten bruker hanner fra en annen art for å hjelpe seg.

Det skal sies at disse møter de samme genetiske utfordringene som alle andre arter som baserer seg kun på kloning, at man ikke får silt ut genetiske feil og at man ikke beveger seg framover genetisk heller. Dette gjør at arten fort blir stor i antall, men så blir den utkonkurrert fordi den ikke kan tilpasse seg og så blir den veldig liten.

Det er mye spennende i verden. Og seksuell seleksjon gjor det hele spesielt festlig (og fargerikt).

This one is just so me. Not only the enthusiasm, but the molds as well. That has happened so many times the last four years.

This one actually made me quite sad. Especially because I have a close friend who is struggling with cancer in his family, and then it is particularly painful to understand the statistics and the biology of it all.

Siden januar har jeg lært veldig mye om folkehelse. Hvorfor? Eksperter i Team. EiT er et obligatorisk fag på NTNU som alle som går i 4. klasse/ første året på master, skal ha. Faget er todelt der den ene delen handler om å lære å jobbe i grupper og den andre er å jobbe tverrfaglig om et tema. Man bruker det faglige arbeidet til å se på gruppeprosesser og slikt. Faget har dårlig rykte spesielt på Gløs, men jeg tror det har noe med å gjøre at supermattenerder kanskje ikke er så flinke eller interesserte i å lære å jobbe i grupper.

Men uansett, man blir puttet i Landsbyer med ulike temaer og så i grupper innen landsbyen. Jeg er i Folkehelselandsbyen der vi skal se på hvordan man kan bruke forskning i helsearbeidet i Norge. Min gruppe har endt opp med å jobbe med utvilkingen av et frisklivsenter i Innherred samkommune (Verdalen og Levanger). Et frisklivsenter skal hjelpe folk som ikke har kultur for å være aktive, til å bli det.

Det har grunnlag i at nordmenn ikke lenger trues av infeksjonssykdommer (som influensa og tuberkolose), men av ikke-smittsomme kroniske livsstilsykdommer (hjerte- og karsykdommer, muskel- og skjelettplager). Som betyr at det strengt tatt en hvordan du behandler kroppen din som bestemmer hvordan du får det senere. Jeg kan komme tilbake til Helsedirektoratets kostholdråd og mosjonsråd senere, men nå tenkte jeg å fortelle at jeg var på konferanse på Levanger i Nord-Trøndelag på torsdag.

Gruppa mi var invitert på konferansen av prosjektgruppa for frisklivsenteret de vil starte og vi hørte på spennende foredrag, fikk god lønsj og fikk prata med en del nøkkelpersoner som vi skal bruke framover mot påske. Det er mye spennende vi skal gjøre og jeg gleder meg til å lage et produkt som kan brukes til noe 🙂

Det var deilig vær, men en del vind på HINT (Høgskulen i Nord-Trøndelag) i Levanger. Her står vi og venter på toget hjem igjen. Levanger er omtrent 1,5 timer fra Trondeim. Og høyskolen ligger nesten nede i fjæra, det må være deilig der om sommeren.

…the life of the annuals.

This blog is about the things that I know and like, which means that it is all about cooking, fashion, scouting and biology, really. And as I am doing a Master of Science, I get a lot of impulses from different parts of biology. Tomorrow there is a PhD defence at the department of biology and therefore there have been two guest lectures today by the two opponents.

The one talked about local adaptation of plants of one species which they had translocated between two locations. So plants in Sweden were picked and grown in Italy, and Italian plants were picked and grown in Sweden. And then they looked at the genetics of the plant (the world famous Arabidopsis thaliana) in the context of the plants ecology. If you know nothing of biology, don’t care about this. But the remarkable ting is; after working of this for years they did a giant genetic study and they planted over 16 000 specimens! There is a youtube video of the field work they did.

The other guy talked about perennials and annuals. Being a perennial means that you are a plant that lives for many years, while an annual is a plant that only lives for one season. Which means that they are the real rock stars of the world, they live fast and die young. The different life histories, as they are called, that organisms “choose” are interesting to study in evolutionary biology. And since evolutionary biology is my life, this has been a very interesting lecture 🙂

Better known as Birgus latro, lives in the Indian and Pacific ocean. Why am I mentioning this? Well,  you come across an incredible amount of interesting, but completely unrelated information when you are searching for articles on Wikipedia, and this is one of them. Before Christmas a friend and I were writing a report on the effects of introduced species on biodiversity in New Zealand. And when reading articles from a completely different part of the world, you never know the latin names of all the plants and animals. And here, wikipedia is an excellent tool. Especially English wikipedia. Just write the latin (scientific) name in the search box and up comes all the information you need. Where it is placed taxonomically, where it lives, it’s ecology and everything else.

So when we were wikipediing (can you make a verb of wikipedia, as you do with google?) scientific names to understand the content of the articles we were reading, we stumbled upon (have you seen stumbleupon.com btw?) this article about the coconut crab. Why I still have this saved as a tab i Safari? Because it is hilarious!

Ok, it is a crab. Crabs have exoskeletons (just like lobsters and beetles) and breathe through their skin. This is not very unusual. But as they are quite rudimental creatures and don’t really have blood vessels to speak of or anything, it is believed that there is a limit to how big they can be. We believe this is the reason why there are no monster sized insects around.

However, this crab car a body size of up to 40 cm, and a leg span of almost 1 m (some speciemens up to 2 m). It usually weighs about 4 kg. And it can climb trees. It can open coconuts with its front legs. It lives in a shell as a juvenile, but discards this later. They have also developed a “nose” to smell in air (as most crabs only can smell in water). The coconut crab mostly eats fleshy fruits and nuts, but they have even been seen to eat rats.

While reading the article on wikipedia I pictured myself on holiday on a tiny island in the pacific, walking on the beach, and suddenly spotting a giant crab climbing a tree. Like a monkey. It’s like a cross between a pig and a monkey. Only it is a crab. Ah, me wants to see it! (It can also be eaten, and it is quite common as food where is occurs). I definitely have to go back to the Pacific.