Bernadeta's blog

Honestly, I’m too lazy to write much… some sort of spring depression… hate this rainy and cold weather… GIVE ME SUMMER!!! At least the strawberry season is in… I can drown myself in the sweetness of red berries :0

Anyway, some things don’t require much talking… it just looks goooooood!

Oh, and here are some photos from a few weeks before. There is a very nice conservatory on the top floor of barbican center- a perfect place for a Sunday afternoon walk.

Cheers,

I’m off to eat my strawberries!

So, I’ve spent another week in Natural History Museum but this time instead of chatting with dung Beatles I’ve turned to playing with DNA  The conclusion from all of the week work is: YES, I WANT TO BE A SCIENTIST! I mean, I even find pipetting an exciting job!

Well, it’s not only pipetting that I’ve been doing, in fact, I’ve done some pretty good lab-work, it went something like this:

The research is on Brosimum alicastrum (Maya Nut) with an aim to understand the geographical patterns of the populations of this species in the Central and South America; this is an important step in order to help to make the reforestation of this species more sustainable.  During my week I was responsible for extracting DNA from the leaf samples of this tree that were collected in Panama. In addition to getting the DNA sequence that later will be used for phylogenetic tree building, we also investigated whether drying samples in a microwave (they are usually dried using silica granules that suck out the water from the sample (these are the same granules that are found in a small bag with a notice ‘not edible’ when buying shoes) has any effect on the quality of DNA. Often in a fieldtrip silica is not so readily available and microwave can usually be found in any hotel, moreover, microwaved samples look much better than the silica dried ones. All in all, if microwaved samples provide the same quality DNA that would make the life of researchers much easier!

The process of DNA extraction starts with grinding the samples into powder, mixing them with a special buffer, centrifuging them, adding chloroform and centrifuging again. These steps are not precise; the protocol also involves lots of storing in specific temperatures, collecting suspensions, adding RNAse to get rid of any RNA molecules, etc. After all of this you end up with a clear solution to which you add another million of buffers, make another million of centrifuge turns and then hope that you have some DNA trapped in a tiny filter in the eppendorf tube . As my supervisor nicely put it “by the end of the day you will be the centrifuge queen”, I would also add that by the end of the day you will not feel your thumb or have a blister on it due to the million times you have to open and close the eppendorf tubes! (I wouldn’t be surprised if in the families that have long-run science history they tend to have thumbs with a very tough skin on them). To check if you actually have DNA you then run many electrophoreses- I was lucky!!!

If you are lucky then you can do PCR, which is a very sensitive process and any contamination will make all of your efforts go to trash… The DNA we got from extraction was any DNA that can be found in a cell but then when we did the PCR we added specific forward and reverse primers for a small region on the chloroplast genome, so after the sequencing all the information you get is about this short stretch of chDNA.

Something that was an entirely new thing for me was the analysis of DNA sequences. What you get from sequencing lab is just lots of letters and curves but then you need to edit them and match forward and reverse sequences. It’s a bit of subjective process, which is why I will be a bit more critical about the sequence data in papers, but it’s, I think, another example of puzzle collecting in science, which makes it quite a fun process!

And that’s it! Or at least what I’ve managed to do during the week. The sequence data will be later used to construct phylogenetic trees.

All in all, it has been an amazing week! Interesting work, more knowledge and intelligent people – what more can you wish! I’ve basically got a private tutoring session for lab practice, nice isn’t it?  Oh, and they have a common room on the roof of nhm- I mean, come on, can it get any better?!

The chicken and egg dilemma has been solved- there was no chicken after all!

To speak plainly… Working in NHM is awesome!!!

It’s almost unbelievable that some people earn their living doing such amazing stuff! I so far have helped out with sorting specimens and also the mounting of Scarab beetles . NMH is helping for the Smithsonian museum to prepare specimens for an interesting research: someone has collected Scarab beetles over the last few years at different altitudes and they will map how populations and species’ move as a result of climate change. However, until someone can identify the exact species there are literally thousands and thousands of beetles to be mounted. I have never done anything like this before; it’s like a catwalk for beetles- strike the pose! Each leg and antenna has to be placed so that it could be seen when the beetle is mounted (it’s not as easy as it might sound, especially, when some specimens are a few years old and tend to be very fragile) and then depending on the size of the specimen you have to choose from direct pinning, card mounting or point mounting… uh…. But it’s really fun, and it reminds me of collecting puzzles :}. It’s probably not exactly what I would like to do in my science career (I tend more towards molecular stuff (that’s why I’m very excited to start working in botanical department)) but I definitely wouldn’t mind to do something like this as a hobby!

Well, and to state the obvious the atmosphere of working in NHM is once in a lifetime experience. Being surrounded by this amazing architecture and animal figures popping out on every corner is just something that can only be found here!

Working space

Well, finally it’s the end of term!!! Uhhhhh it feeeeeeeels gooooooood… But I’m not planning to lie in bed and do nothing for a month, no way! I have a very busy time planned ahead.

Firstly I’ve managed to arrange some amazing practice at Natural History Museum. I have already started to work in the entomology department there and have seen the specimens that Darwin has brought from his Beagle trip! I will also work for a short time in the botany department at nhm and do some DNA extraction, analysis and construction of phylogenetic trees. If I’ll get permission I’ll definitely post some ‘behind the scenes’ pictures here :] .

Secondly, I have a full list of iTunesU courses that I want to go through, including Roman architecture, Early Modern England, Philosophy, etc…(Most of them are from Yale university, if anyone cares, they have some great lectures available online that I would definitely recommend for anyone whose in for some additional knowledge). I also saw there are some interesting lunch talks at the British Museum that I would really like to listen too, so it would be great to find time for at least a few of them.

Thirdly, I want to bake!!! I miss baking sooooooo much!!! Damn you filthy kitchen!!! My hopes are that there would be less people during holidays, so I hope that the kitchen will be in  ‘rubbish-everywhere’ free condition and I would actually get to properly bake something.

Lastly, I know its holiday but I still have 50 lectures to revise and write an essay on the origin of new genes (amazingly interesting stuff!!!). Its better to do some work now than to suffer before exams and try to cram all the stuff into your head at the last moment. Besides this time I feel quite confident about my revision, I was working genuinely during this term and know that I will not need to learn all the things anew this time because I know most of them already (not being too modest and just as a footnote I’ve got 1^st in all of my exams…YEY!!!)

And here are some Easter picks from London- love those eggs all around the city!

The beginning of spring somehow always makes me want to read poetry…

THE CHESTNUT-TREE BURSTS INTO FLOWERS

To hell with elevated art

And all long idle gloomy hours

When in the springtime in the yard

The chestnut-tree bursts into flowers.

It makes the fiery rain start pouring

And the south winds awake and blow.

It blossoms so that without warning

Our hearts like streams would overflow,

That books would fly away from tables,

That nights would stifle with their scent,

That we’d be threatened with such ailments

Which doctors still fail to prevent,

That birds would sing themselves to croaking,

That everything would burn and foam,

That mothers would at nights be weeping

Over their daughters not at home…

When chestnut-trees light silent candles

Those huge white blossoms with pink spots,

You come back home completely blinded

And with your pen make messy blots.

by Henrikas Radauskas

And if you can hear Antonio Vivaldi’s Spring in your head when looking at these pictures, then you know just how I feel.

If someone would ask me to choose one thing to take to an uninhabited island that thing would definitely be a good book! Sound dull??? No it doesn’t, and no one can prove me otherwise. I mean, the right book can take you anywhere from magical worlds and the edges of the Universe back to sometimes humorous or depressing reality, and all of this fits to a few pieces of black and white paper… AMAZING!!!

I’m writing about books because I wanted to share some of the treasures that found in the second hand bookshops, here in London. I could spend for hours on end in those places just flipping from one book to another. Mind me, I have nothing against newly printed books but they just don’t have the same feeling as the old ones do…  the smell, the thumbed pages, markings and notes it’s just irresistible! Once, I found this old book about Egypt’s archeology and it was full of newspaper cuttings there was even one which announced the finding of the tomb of Tutankhamun! Imagine that, It was discovered in 1922 and now here I am, holding a book which someone 90 years ago was studying carefully and following all the happenings down in Egypt at the same time… it’s as if the time machine does exist!!!

Anyway, not surprisingly, my favorite books are those that relate to science in one-way or another (though, I’m definitely not restricted only to these). The secondhand bookshops don’t have very large shelves dedicated to science but they still have some and among them there are quite a few that are worth buying (I don’t like saying ‘to buy a book’, I prefer to think of it as an investment).  From those that I’ve bought I would probably recommend most of them but here I will write only about two must-reads:

First, are books written by Oliver Sacks. These include: “The Man Who Mistook His Wife for a Hat”, “An Anthropologist on Mars” and many others (including the film “Awakenings” starring Robert De Niro and Robin Williams, which is one of the best movies I have ever seen (probably one of the saddest too)). All of Sacks’ books are related to neurological diseases and lesions but It wouldn’t be right to say that they are only for people who study or work with neurosciences, and that’s, actually, the best thing about his books: they are understandable for anyone who has any interest about how the brain of human works. Moreover, Sacks writes in a very objective way, i.e. not only as a doctor (he is a professor of neurology and psychiatry at Columbia University Medical Center) but he also tries to see the condition from a patients point of view, which makes all of his writing very intimate and humane. Here’s a link to a short talk of his on TED: http://www.ted.com/talks/oliver_sacks_what_hallucination_reveals_about_our_minds.html

Part of my 'investment'

Second is the one and only Richard Feynman. Man he’s good! I have never been very good in physics but I do enjoy a good bit of physics and at this point Feynman is definitely the best place to look for it. Now I’m reading his “QED”, which is a collection of his lectures on quantum electrodynamics. Who would’ve thought that it’s exciting to read such things in your spare time – but when it’s presented by Feynman IT IS!!! I also have read his “Surely you’re joking Mr. Feynman!” where he writes about his small adventures in life. It’s a very inspirational book, when I’ve read it I thought- now this is how the real scientist should be like! I love his attitude of physics being a sort of a play and science as a whole a one big puzzle; the thing that matters is not the result you get but the process by which you found it, the way you figure out and discover which bits and pieces come together in this puzzle.

So, this is my short book review, if I may call it so. Hope you will now be tempted to read some of these books. BOOKS ROCK!!!

No news for quite a long time in this place…….. well there wasn’t much to be written about since it has been a long month of revision.

Sunday afternoon in my room...

Anyway, exams are finished and the results won’t come until the next month so its better to forget them for now and live a ‘normal’ stress free month.

And what can be a better way to celebrate the end of exams than to spend three amazing days with ‘The Big Brother’!!! So, here are the three highlights of our brother-sister London tour:

1. Markets

The thing I like about London markets is that they are not only some shopping places but a sort of fun experience too. Old school items in the stands, street music, and street food create an amazing atmosphere in these buzzing places.

Belgian waffles in Portobello market....mmmmm

2. A walk along the Thames

The most romantic thing ever! If you would ever get a chance to walk along the Thames between London and Tower bridges it’s really worth doing it, especially if you need a place for some philosophical thoughts- To be or not to be?

3. Magical London

Yes, It’s Harry Potter time! Platform 9 ¾, Diagon Alley… you name it, and there’s full collection of Harry Potter characters’ wands in Hamleys shop… It kind of makes you want to cry that you don’t live in such a magical world… But that’s one of the reasons I love science – full of little bits and pieces of the magical world…

Just a bit further and I'm in!!!

I haven’t written in a while… well it was holidays … so, I just want to say that I’m still alive and I’ll be writing as usual!

I had the most amazing holidays ever!!! I went back home and then my family and I flew to Austria for a skiing trip. Ahhh… I love mountains… I just feel so goooooooooood going down the mountain, as if nothing else exists in that minute or few… it’s just surreal…

I'm a dot somewhere in the middle... feeling small...

me and the best snowboarding companion- The Brother

The present pile under our family’s Christmas tree is growing larger and larger every year but the biggest present for me this year was just being back home with my family again (Santa got my letter !!! ).

But, holidays came and went- it’s time to go back to the real world and embrace the upcoming three weeks of revision and take the exams for the dessert. If I’m gone away for a while again, please hope that the pile of books and notes haven’t crushed me down yet.

Uhhhhh… It won’t be easy…

Simple ideas are ingenious and just 2 min from Wilson House one such idea can be found- the Rolling Bridge. I’m not sure if many people know of it but it’s really cool!!!  Here are some photos of it:

It’s made by Heatherwick Studio, which has done some really amazing projects and I hope to try to go around London and find some more of those masterpieces. If anyone would like to see the bridge it’s in Grand Union Canal at Paddington Basin and is activated only on Fridays at noon.

On a more Christmassy note- London is a great city for Christmas. Back in Lithuania Christmas decorations in towns come really late… and I mean late… like a week before… if at all. Moreover, you get the same decorations for ten years… on and on again… In London Christmas spirit starts in mid November and decorations are, indeed, amazing!!! I love how even the smallest streets are full of lights, Christmas trees and Christmas baubles. So, on Sunday evening I cycled to St. Pancras station for one special purpose (some might think I’s a waste of time, but I’m sure that those who, like me, are obsessed by puzzles and spent their childhood playing Lego games will understand)- to see the largest LEGO CHRISMAS TREE.

Chi chi... temptation

Someone had a lot of work putting all the bricks together…

P.S. St. Pancras station is one of the most impressive stations that I’ve seen so far. The inside of the building is like any other station but the outside… it’s more like a castle than anything else!!!