30.04.2008

The old professors

Recently I am reading a lot of scientific papers, which given the fact that I am writing my thesis is not remarkable in itself. The scary thing is that I started to enjoy some of them. Yes, really! The reason of this weird phenomenon is of course starvation, resulting from the lack of time to read anything more entertaining.
Additionally, it seems that I started to be a connoisseur of sorts. For any sane person scientific paper is something that you have to read in order to assimilate knowledge and get ideas for your own work, as well as see what competition is up to. That is a case with me of course, but I have also found that if you are reading some papers that have been written by the old professors they can be really entertaining (in relative terms, there are thousands of more entertaining stuff around).
I read two such papers in recent weeks and I would like to write few words about them.
First one was written by prof. N. Tolbert - one of the scientists responsible for the elucidation of so called photorespiration. This process takes place in most of the plants, where if carbon dioxide is limiting, oxygen is fixed instead. This process is frequently considered wasteful, since it leads to decrease in crop yields during hot and sunny days.
Prof. Tolbert's paper (Annu. Rev. Plant Physiol. Plant Mol. Biol. 1997) is a review devoted to photorespiration, but what makes it so interesting is that it was written from his point of view and contains a lot of personal details about him and people he was working with. It makes really huge difference from normally strict and bland scientific style. I did not learn many new things from this paper but for sure I had a lot of fun reading it and I was laughing frequently. And on top of that I found out that Prof. Tolbert is making something that philosophers of science call a bold prediction. He claims in his paper that process of photorespiration is one of the main agents responsible for the ratio of oxygen to carbon dioxde in atmosphere. In other words, the fact that we have 21% of oxygen in air results from the fact that any more than that in atmosphere containing ~300 ppm of CO2 would lead to increase of photorespiration that acts in this system as a reverse feedback, leading to increased production of CO2 and decreased oxygen evolution by plants. Now, the catch is that global rise in CO2 shifts this balance. Prof. Tollbert predicts that a new balance will be 27% oxygen! I am really interested if anyone checked if we really observe any measurable increase in oxygen concentration over last 100 years.
Another paper I was enjoying greatly was written by professor John Allen "The function of genomes in bioenergetic organelles" (2003). This one is not really that entertaining as far as writing goes, but has a paramount importance in putting my work in a wider context. Such a shame I did not read it before. I am not exaggerating when I say that I was totally hooked up on the ideas presented in the paper. To make long story short - we all have in our bodies descendants of bacteria that underwent, so called, endosymbiosis. Mitochondria, which I have in mind are the powerplants supplying energy to our cells. Plants have mitochondria as well but they also posses chloroplasts - these are endosymbiotic entities (a proper biological term is organelle) that are responsible for conversion of light energy into biologicaly available energy. The significance of these two organnelle is hard to overestimate, explaining why there is so much research (of which I am lowly participant)devoted to elucidate inner workings and regulatory mechanisms involved in this structures.
For those not knowing, I explain - mitochondria are not only producing energy, but they are also playing an important role in many diseases, of which cancer is probably the most important. The chloroplasts, on the other hand, may not be a focus of so much attention, but given the impending fuel crisis and increasing scarcity of food, it is not hard to realize how much we are dependent on plants and algae.
So know, when I explained what are these two organelle, I can explain why I consider prof. Allen paper to be such an important piece. The organelle are hiding one very puzzling secret. Why is it so that they contain their own genome? Both mitochondria and chloroplasts have DNA encoding a relatively small subset of genes. Why is it such a big deal? Well, as I have already mentioned mitochondria and chloroplasts are involved in production of energy, and this process is not without its dangers. Conversion of energy is very efficient but not perfect, leading to production of small amount of very reactive chemical entities called reactive oxygen species. They are damaging everything they come in contact with. Of course there are defense mechanisms in place but, as everything, they are not perfect. So having a DNA exposed to a source of highly damaging chemicals does not seem as a particularly good idea.
This fact is widely regarded as a curiosity that is hard to explain. Why natural selection did not take care of this?
There are several competing hypotheses:
1) Transfer of genes is still not finished.
2) Certain proteins cannot be imported (transferred from cell cytoplasm into the mitochondria/chloroplasts).
3) Some evolutionary event blocked gene transfer.
4) Few others that are modifications of the above.
5) Co-location for redox regulation (CORR) - the hypothesis that I like the most is the one presented in the Allen paper.
This hypothesis takes in the fact that there is statistical irregularity in the distribution of the organelle genes in different species. Namely, subset of genes involved in production of energy, as well as genes encoding proteins involved in the regulation of first subset are overrepresented in the organellar genome. This may mean that it is advantageous for an organism to retain certain genes due to the fact that they have to rapidly respond to changes in the environment and such localization allows them to do so in the most efficient manner.
I do not feel confident to summarize the whole paper as well as multitude of experimental research that went into forming of CORR hypothesis but I would like to explain why I think paper describing CORR is such compelling and important paper.
Allen took a great care in highlighting facts that form his hypothesis, described alternative hypotheses and presented several possible points that can lead to refutation of CORR. To me this paper is something that places my own work within a research program as understood by philosophy of science. It made me realize few important ideas that help me to deal with background and implications of my work.
I hope I showed that scientific papers can be entertaining and gripping from time to time. Thank God for old professors!

05.04.2008

To Holmgard and beyond!

Yesterday I was, for a first time since long ago, on a metal concert. And it was awesome!
When few days back I spotted posters proclaiming that "Turisas" is coming to town I knew that this is the time to finally fulfill a dream of mine and join the fellow headbangers for an epic evening.
Turisas have been one of my favorite bands for a long time now. I have found them on last.fm, while reading about another great band "Ensiferum". As I found out, both come from Finland - I am wondering what is with this country that it breeds so many excellent bands - most of my favorite bands comes from there.
Of course I was a bit shy at first with my decision. I do not have any metal friends in Stockholm and I wouldn't like to drag my wife to the concert, knowing that she would not enjoy this at all. Well, world belong to the courageous, or so they say, so I bought a ticket and headed to Klubben hoping that I want be consumed by flesh eating satanic norwegian Loki worshiping pagans.
I was quickly calmed and even a little bit disappointed by the fact that all people seemed to be quite normal. On top of that, I was actually feeling more at home than anywhere in Stockholm. All foreigners are quick in observing that Stockholmers are clothing themselves a tad bit eccentric.
Well people outside the Klubben with a few exceptions were all clothed in black, sporting metal themed t-shirts. I felt like I was in Krakow in "Rotunda", more than in Stockholm. Nice.
So after waiting for 30 minutes concert started with a support band called "Månegarm". I will just say that it was a serious down to earth guitar shredding and cookie monster singing. In other words serious business. Of course I was stunned in a short time, and be saying stunned I mean in literal sense deafened by a wall of sound and hellish growls. I guess orcs of Mordor would be proud of this guys. That being said, after the third song I have started to really enjoy their performance. Maybe that is way death metal bands can survive? I can hardly imagine how I could listen to that music at home, but at the concert they were fantastic!
So finally there was a time for a serious ear-drum kicking by "Turisas". They jumped on the stage, clothed in furs and hides with faces painted in red and black. If that is how Vikings looked when they were descending from their boats to put towns and villages to fire and sword, I can imagine the fear their victims must have felt.
I know that most peoples would consider this funny and stupid. I say to hell with you. I enjoyed this theatrical costumes and a play they were making on the stage. This really added a nice touch to the story of Varangians.
Fuck the guitar Solos!

So know I will tell you why I like "Turisas" and metal so much. It is because of whole experience around this music. It is, in my opinion, unlike any other kind of music I know. Metal, at least the one I am listening to, is inspired by fantasy, sci-fi and often, as in case of Turisas history. It is not concerned too much with contemporary problems and I am fine with that. It tells the stories of heroes and villains, of battles and horrors. The music is usually very energetic and convey, at last for me, strong emotions. And that is what I love about it.
The Turisas concert was promoting their new album "The Varngian Way". The album tells the story of vikings going to Novogrod (Helmgard) and further down south until the gates of Byzantium. It has everything I expect from such a work. There are battle songs, crazy "party" song "In the court of Jarrisleif" and last but not list epic "Miklagard overture". I enjoyed it immensely while listening on my media player and I enjoyed it even more on concert. That is true that my eardrums would be pierced to pieces if I were not protecting them, but I think it was an amaaizing experience to scream and wave my hands and applaud the band. And I couldn't not to do this. I may be overextatic about the whole thing but it seems to me that guys and a gal from "Turisas" were having as much fun as the public. It was a great evening and I am happy I was there.