Closing time

Today is Good Friday in whatever is called the "western christianity".
I am starting to get a bit superstitious with the observation (or fact?) that Good Friday tends to be cloudy no matter if it's March, April or May, if it's a Catholic "Good" one or an orthodox "Big" one. Then my well-hidden scientific side rises on the surface with a profoundly sound argument which claims that since we are talking about a whole day and since it is practically impossible that a whole day remains cloudy all over the world we have to be talking about an observer-biased phenomenon. Meaning Good Friday looks to be always cloudy to me, wherever I am, and perhaps to my mother, whose superstition can only be traced back to this same observation, every year.

In any case, cloudy or not, Good Friday in a Catholic country like Spain is a holiday, which means I should be having my siesta instead of seeping coffee in the lab. Nonetheless, here I am, trying to organize my stuff before I leave for my real holiday in order not to come back in 10 days realizing I don't even remember in which folder I keep my e-mail messages, a useful -though admittedly boring- practice I learned from my previous boss Yannis. But it somehow looks that neither today's blue and moody weather nor my slightly hang-overed head can help me in carrying out this task with the minimal decency. Instead I am reading poems by Miguel Hernandez, as a tribute to today's international poetry day, I browse lyrics on the web and keep blogging with musical references. Whoever notices the subtle one in this post, as compared to the immediate previous one, shall irrevocably earn my admiration.

By the time the evening approaches and my need for a late siesta can only be battled against with a huge mug of the lab's strongest coffee, I start putting stuff into order. I sent the last updates to our collaborators, sure they want read them today and supposing they want care even when they eventually do. Then I organize my shell terminals with tags denoting the project I am working on each, thinking that I am doing it (and writing about it) just to piss off Julien and Sylvain ....(got You!). Next I post my to-do list on my google calendar and pile up properly the -mostly unread- papers on my desk. I am left with a bunch of small scripts lying around on my desktop, tiny unfinished lines of code, striving to accomplish a function which lingers undecided, desperately trying to reach the end of the loop while self-aware of their rough-hewed ends. As I try to browse through this incomprehensible stream of dos and whiles it seems to me like I am reading geeky, surrealist poetry of the strangest kind.

Then, disgusted of myself for having dared to think of such an obscene metaphor, afraid of Sylvain preparing his geek-card all the way from North California, I decide to send most of it to the recycle bin, or in any case away from my screen. I am stuck in front of the last one, which is supposed to solve a simple problem but in the fastest possible way. I slightly tilt my head to get a better view of it, thinking that I should be looking like one of this apes of the "Space Odyssey" upon facing the famous black column. Which reminds me of the news of Arthur Clarke's death, which reminds me that it's a long time since I last listened to some classical piece I really like from that great Kubrick film, which, which, which.... the series of digressions can now only compare to my friend Filipe's thoughts. I am confused....

No I am not. I just realize that today is not a day to work. Before I finally leave the lab for good for the coming ten days, I take a last look at my script and decide it would be nice if I placed it somewhere it wouldn't be lost, but without getting in my way all the time. And I guess I 'll leave it there, at the back of my mind, like a small riddle, like this pair of snickers hanging from a power cord in Barceloneta, which Julien captured one day, so insightful of the small everyday problems of a poor bioinformatician at the verge of a nervous breakdown.

It's closing time. I am off to Greece.

Grapefruit moon

Last night I left the lab at 9 pm. It was the fourth day in a row, after having been here last Saturday and Sunday as well. At some point, even the usually indifferent -about such stuff- Micha, turned to me and asked me: "Is something wrong?"

To me it looked like nothing was wrong, except perhaps from a growing headache in a shrinking head, my back that ached, my elbows that felt stiff and my shattered humour. I was coming to the end of two of the most useless weeks of my adult-so-called-productive career, which even for someone like me, whose moto is "we have to do what we have to do" could not simply look like nothing was wrong. In any case and whatever it was, I was getting over with it. Having just sent some uninteresting -according to my not so humble opinion- analysis to some experimentalist I was leaving the lab on the eve of the holiday with the soothing -yes it can be that too- voice of Tom Waits hitting me smoothly on my way out of the elevator.

" Never had no destination, could not get across.
You became my inspiration, oh but what a cost."

And as I was getting out of the patio towards the beach in search for a bike, I saw exactly what Tom was singing about. A big, beautiful "Grapefruit moon" gloriously standing above the Barceloneta. As I rode the bike steering with my right hand, trying to use the left to call Demetra, I could not take my eyes off it. And neither could a great number of people who taking advantage of the holiday were strolling down the beach on this rather cool night at the doorstep of spring. When Demetra managed -by a stroke of coincidence or fate(?)- to reach me first, I had already joined all these modern city, moon-howlers, taking dangerous manoeuvres with my bike, while talking on the phone and whistling alongside Tom Waits at the same time. I guess it had only taken my stiff elbows, my aching back and my weary head, five minutes to return to normality. And it would be rather cheesy to state the obvious that sometimes the simplest things can have such an uplifting effect, so I won't say it. Perhaps because the moon -especially a full one- cannot be qualified as something simple and because it would not do any harm -even to really rigorous scientists like us- admitting the influence the stars have on us, every now and then.

Much later the same night, going down the Rambla at 3am, I found myself walking with the company of a prostitute trying to lure me into temptation on the dawn of Good Friday. As we both walked down, side by side for a couple of seconds, she noticed I was still staring at the moon, still hanging over the top of Columbus' column down the street . Then as if -I 'd like to think- the moon exercised a romantic effect on her she turned to me and instead of the typical "Let's go fuck" line, she told me: "Let me make love to you".

I stopped and looked at her for a very brief moment, until I realized that she was being professional trying to guess what I wanted to hear.

Then I thanked her very politely for that excellent choice of words and went straight home.

Scientist's block

I copy from Webster's dictionary:

Writer's block: a phenomenon involving temporary loss of ability to begin or continue writing, usually due to lack of inspiration or creativity.

carrying on from Wikipedia:

Writer's block can be closely related to depression and anxiety, two mood disorders that reflect environmentally-caused or spontaneous changes in the brain's frontal lobe. This is in contrast to hypergraphia, more closely linked to mania, in which the changes occur primarily in the temporal lobe.

I do not really know which lobe or other topological entity of my brain to look for, in order to better define my state of mind, one which I would dare to call "scientist's block". I apologise for this somehow poetic definition but it's the closest thing that my tormented frontal, back and side lobes can come up with, having gone through two frenetic working weeks with minimal if not disappointing outcome. If in the last post I was metaphorically "introspecting", looking at the interior patio of the Institute, today I can only look at it like in this photo, extending upwards, too steep to climb, too tiring just to think about going up there, and that is both metaphorically and literally.

Scientist's block has not so much to do with loss of ability to work. All the contrary, in my case at least it appears to be highly correlated with working overtime. During the last tow weeks, I found myself spending far too much time in the lab (including late shifts and Saturdays). In all, it has been a period during which I felt rather active and prone to work but -alas- it appears that the excitement one looks for in science, (this little spark that comes when looking at a long-anticipated plot) is not so easy to achieve. In the end, a load of data fell into place, some scripts were better organized, a few new R functions were perfected but that is not so much of progress and falls far from being qualified as success.

Then came fatigue and an increasing craving to take my iPod and my copy of "Voyage au bout de la nuit" to the Ciutadella park and lay on the grass until it gets dark. And perhaps I should do exactly this. I tend to tell people that working in the lab and thinking are two mutually exclusive activities and although their usual reaction is a smile of consolation, deep inside they know, that like myself, they have had their best -or like myself their less mediocre- ideas exactly when they took some time off work, a small pause to ponder and reflect about a problem of scientific nature. Therefore, having just introduced the term "scientist's block" I would tend to say that it is more connected to "mania" and "hyperlaboria" than the contrary (if not caused by them). And I would go even further to cite some of the most prominent symptoms, which apart from the obvious (fatigue, frustration, depression, denial, appearing in this order) include object-specific side-effects like : failure to blog, persistence in playing chess on the web instead of attending seminars and self-inflicted damage of the inner ear by listening to Rage Against the Machine full blast.

Such is my case. Good thing though the catholics stuck with their calendar. This means Easter Sunday is this week and a long-awaited holiday is just around the corner. Let's hope I take advantage of it to do some serious work. And by this I mean, having ouzo and "mezedes", while waiting for a decent idea to pop up.

.....
Oh and in case it doesn't, I don't care.

with doubt and in denial

I 'd like to take one more look at this photo taken by Julien, just to get a positive feeling. It constitutes of a rather misleading image of our institute, with lights glooming allover. What it fails to capture, what is impossible to be captured actually, is the obscurity of the greatest part of everyday work produced in this -otherwise idyllic- environment.

Yes, I am being bitter, as you might have expected by the title of this post. Over the last week I have been thinking about a great number of very interesting projects. None of them had an even distant relation to science and the only reason for me calling them "projects" is my almost complete intoxication of "scientificism" of the "geakiest" nature. Thus, what normal people simply define as "interests" or "activities" I have ended up classifying as "projects". And it is exactly this introspection that brought about the aforementioned combination of doubt and denial. But let's take it one at a time.

My increasing doubts in the whole meaning of scientific research were largely speared by a friend's and colleague's (Sylvain's) final talk before leaving the Institute, last Thursday, the most interesting and educating part of which was the following: 5 or 6 consecutive slides quoting the reviewers' comments on a paper of his, finally published in Cell (to the unaware, one of the most highly rated scientific journals in the field of what was formerly known as Biology), after two years of submissions, appeals and re-submissions. Ordinary process one might think. Until you took a look at the reviewers' comments themselves, which were usually mean and rude, most of the times impolite and -most importantly- always contradictory. When one reviewer would talk about a "revolutionary work" the other would have no restrictions in considering the "errors so serious and grave that I [he] would suggest that someone else conducted this analysis". It ended up that it was only due to the strong drive of competitive researchers to publish their work -perseverance was a term which was used more than once throughout this part of the talk- that the paper finally made it through. And, moreover, it was only Sylvain's uncontested optimism that allowed him to carry on, until the final acceptance of the paper.

My optimism, on the other hand, has its limits. And although I 'd like to think that these limits can be stretched quite a lot, they appear to be a bit stiffer when it comes to science. After all, I have been raised and educated to think of research as an objective field, where truth, constantly under the strains of scientific rigour, is safeguarded by personal opinions. How could I then explain so contradictory views on the same piece of work? It looked to me that conducting scientific research could end up being no different than putting out a musical record, publishing a novel or painting a portrait and have half of the critics receive it with glorious reviews, while the rest deny to even compare it with rubbish. I conclude that I refuse to deal with this kind of science. After all, if this is the case, why not try art instead? It's more fun, a lot more rewarding in terms of personal pleasure and by far more useful for society no matter what people may tell you. I mean how many times have you admired a nice scientific paper compared to your favourite song or book, and by the way, DO YOU have a favourite scientific paper or theory? If yes, please stop reading.

To sum up, we are into science for two main reasons. Because it is supposed to be objective and because it pays the rent. Since last Thursday I am convinced that I am only in it for the money. And with this I am also through with denial. Now let me go listen to some Led Zeppelin while taking one more look on my miserably discouraging results.

Plans

Last Thursday I turned 30. The number may appear significant but it is merely based on our convention for counting the time passing by. Thirty is round in terms of years but it corresponds to 10.595 days (including leap years). On the other hand it corresponds to 360 months, which may also appear significant as a number equaling the degrees of a full circle. And perhaps it is for this -full(?)- circle that turning thirty appears that important for people of my generation, implying that it is time this circle closes, a new one opens, while philosophical self-doubting of a similarly low level is supposed to be taking place in the vulnerable mind of the poor thirty-year-old.

Above all, thirties means it's high time you start making plans. And this implicitly means long-term plans about the future. Settling down, getting a stable job, a -more or less- stable residence, start thinking about family -in case you are not already-, to sum up, all the things that irrevocably introduce you once and for all into the world of the grown-ups.

I am not fully aware of whether I am going through a turning-thirty crisis or whether I have been going through it since the moment I was born and thus I am now facing it with courage and "as having been ready since long time ago". But the truth is that I never felt the least envious for the grown-up world. I never really liked long-term planning. I know I like dreaming more than average, a tendency which people sometimes attribute to my star sign, I delve into day-dreaming far more often, a tendency which people attribute to my inherent laziness. I like to plan holidays, trips and the such but when it comes to answering questions of the type " how do you see yourself in 5 years" I come upon insurmountable problems.
Linking this tendency to an attribute of my character is easy for most people. It cannot but be due to an obstinate immaturity, that has been resisting for three decades.

Well, I beg to differ. I sincerely think it has to do with my experience about life itself hating plans more than I do. I have been around enough time to see people's plans being smashed and shattered in a single moment. It is not necessarily tragic. It is the pure essence of life, uncertain and volatile. Plans are to be made in any case, but just for the fun of it. Most of the times they won't work, and quite a few of them will be transformed into glorious failures overnight.

I was just thirty years and two days old, thinking about all that, when I read about this on the paper. During Friday night, a metro train, stationed at Pireas' terminal, slipped off the tracks (probably because of a malfunction of its break system) and went through the wall surrounding the terminal only to be stopped by friction and debris in the middle of a main avenue. As it was very late at night, the train was empty of passengers and the avenue void of cars, there were almost no people harmed. Almost. You see, the train had pierced through the wall right at the point where a homeless guy used to spend the nights -the neighbours said-. He was killed on the spot.

I can bet that unfortunate German -the neighbours said- fellow, had no big plans about his life. He probably arrived in Greece some years ago with no clear plans whatsoever and just got stuck there. He must have been a grown up -as the neighbours would not mind testifying- but all he could plan about would be making it for one more cold night, right by the wall of Pireas' terminal station and then perhaps get some breakfast in a nearby cafeteria, side by side with rudely awaken workers and grumpy immigrant waiters.

It's just that sometimes, even plans as simple as that, do not seem to work out.

today

It's too early yet in this world, hear you

the beasts have not been tamed yet
my blood lost and my sharp, hear you,
my sharp dagger
like a calf that flies the skies
smashing the branches of the hanging stars
hear you,
It is me, hear you
I love you, hear you
I hold you, I behold you, I dress you
with Ophelia's white wedding gown, hear you
Where are you leaving me? where are you parting to?
and who
holds your hand over the deluges?

Odysseus Elytis

The Monogram, Canto IV

The winter of the patriarch

Yesterday, out of the blue, Fidel Castro announced that he won't be candidate for the presidency of the Cuban Parliament. A piece of news with such an impact, that he had to repeat twice even though it was in written form. It looks like the "Commandante" is eventually going out in style and dignity. I remembered an old post, written last January when Castro was close to dying and I was becoming to emotional. Then Castro got through it and the post remained unpublished. Today I finally post it partly because I re-read it and liked it, but mostly because the meaning is still there. Castro's stepping down somehow liberates Cuba from the constant threat of its adversaries, above all it can serve in removing the argument of lack of democracy, fed on his remaining in power for almost half a century. It also opens the way for reforms, but -I hope- without any compromise for the Cuban Revolution.

---

Winter is here, my general.

The winter of our discontent is here. The vultures are already out there, sharpening claws, you may not hear them but it is only because you lie there unconscious. You listen no more to the news, that your one-eyed courtiers read you everyday, because you don't want to, because you are fed up with the lies you read about you as much as with the lies they invent to protect you. To protect your venerated image of saint, patriarch, supreme leader, father of the country, because a saint, my general, cannot be dying.

The people, your people, are looking at the vultures spiraling down from the skies and are afraid. Afraid that all the prophecies will come true. That this will be the end of the passing of the comets, that they will take our sea away and sell it to the landowners of deserts piece by piece, that the days will get shorter and shorter until finally the sun rises from the west, that the sand will turn to powder and the rivers will be mixed with alcohol. That the "Granma", will shipwreck once again, one last time , and will be silently covered with seaweeds and corrals. They are afraid that our children, your children will forget the letters and the words and trade them for shiny marbles and mirrors. That our sick, old people will be thrown out on the streets, because the vultures prefer the beggars, the crippled and the fools to the poor, the barefoot and the curious.

They say my general, that it cannot be true that the father of the country is getting old, that he is not recovering, that he is drowning in his own feces. Because they are afraid and they forget what we humans, really are. That we are this small vein in our head that pops open, this tiny bead of grass stuck in our artery, this gut that suddenly bursts and refuses to heal. They cannot believe, or they refuse to believe, my general, that your wound is refusing to heal, that it is left open, one more open wound on the face of this land, your land.

But it is true, that the wound is not healing.

And the vultures are out there pecking the barbed-wire fence you put around the country, trying to break in, drawn by the stink of a wound that won't heal and the sacred smell of the shit in your belly. This is what we are, my general, this is what you are. You are the open wound drawing the vultures and we have become the fence that is keeping them out. It's time you go now, but we' ll stay put.

Godspeed, my general.

---

PS. Similarities -or direct references- to G.G. Marquez's "Autumn of the Patriarch" are hereby declared to be obviously non-accidental.

Back to the stone age

Going through one of the least productive phases of my life over the last years (work not being done, books remaining unread, blog not updated) I am dedicating my time in more passive activities. No wonder then that finding myself in Razzmatazz last Saturday for a concert by the Queens of the Stone Age, I was already surrounded by an aura of anticipation for self-fulfillment.

I arrived at this famous Barcelona Club, dizzy and tired from the previous night's hungover, looked for a quiet spot at the back and waited for the set to start. Then, as the first notes of "Regular John" started floating in the air I had it. The perfect flashback.

I suddenly realized that the last time I had listened to this song live was a long time ago, in some distant stage in Agios Kosmas in Athens, during a summer festival. As I started calculating the exact time distance, based on memories of people standing next to me, albums just released and football championship titles I realized that it was back in July 1999, with the Queens having only one album and with me just about ready to become the modest chemist I remain to date. As the band carried on with "Avon", (being the second track of the first album, having just followed the first track of of the first album) I took some time off my headbanging -doomed to look ridiculous at my age as most of my friends would be so kind to verify- and drifted off in a trance of recollections covering these nine years.

First came the people. I remembered people there with me on that concert, whom I now occasionally only talk to on facebook, some that I knew back then but have lost completely now and some that I didn't know then but met in the coming years only to share distant, separate concert memories. It was a different place back then. Climate change simply meant a cool April following a warm March, my hometown Athens had not seen snow for decades -since then the airport has been shut down three times due to heavy snowfall-. Ronaldo was still a phenomenon and Zidane a rising star, Greek football was in a limbo unaware of the greatness of a European Cup to follow. Kosovo was still part of Serbia -perhaps slightly more aware of foreign-office-supported greatness to follow-, New Orleans was still in its place and so was Baghdad. The Taliban were the good guys. Saddam was just being a bit stubborn before assuming the role of the personification of evil. Some people had mobile phones, none had one with a camera. Pavarotti was still alive and so was Pinochet. People were worried about Y2K. Ground Zero was still World Trade Center. September 11th was still simply the birthday of my friend Giorgos.

Personally I was just into my early 20s, much less anxious than today, only a bit more ambitious, equally lazy and frustrated with women. My hair looked more or less the same -thank God-, I was still walking around in shorts and hiking boots, wearing T-shirts with band names on them (it was Blur and Radiohead back then, Tool and Radiohead today, some things have not changed a bit). I had just returned back home in Athens after four years of college, I still wanted to become a journalist, I had no idea what Bioinformatics was -and somehow I think neither did Bioinformatics itself-, I had never been to Barcelona, nor ever ridden a plane.

As the third song -I think it was "Do it again"- steered the crowd to rhythmical "heys" I was rudely awaken. This was 2008, two world cups and five Queens' albums later, with so many things in the middle between myself and the "stone age" I had been tripping back to.

But aside of all that, I was still headbanging at the same pace, like the old times, like that distant hot July afternoon in Athens, so pleased and so reassured, that at least some things don't change. And the song remains the same.

Slowness

I spent the first half of yesterday's workday reading the blog of a friend and old colleague, which proved a worthy activity from various points of view. It was there, where I came upon this article by Anna Damianidi, for which I have to be grateful to both her for conceiving and writing it as well as to my friend for posting it. For the non-greek speaking, -probably the majority of this blog's rather limited readership- I can try to summarize the concept of that article, simply by translating the first phrase:
"I wonder what will our lives be like when we stopped being in a hurry".

And honestly, I don't think there's much to say beyond that. The article goes on describing some beautiful images of everyday slowness, where everything is seen, felt and perceived in slow motion, therefore regaining its initial meaning and becoming once again important. Then an image of a very beloved person came to my mind, one of these people that never get stressed or anxious, lying on my couch, silently enjoying her cigarette, while reading Milan Kundera's "Slowness", postponing doing the dishes with a charming smile and with her delightful state serving at the same time as a self-referential proof of the book's point.

"What will our lives be like when we stopped being in a hurry?"
If you ask me, they would be very much like Tammy reading Kundera on my couch, smoking.

I spent the second half of yesterday's working time, messed up in between program optimizations and high-throughput sequencing, neither of which has anything to do with slowness, nor could possibly help in its appreciation. Then I re-read the post, sticking to the first sentence once more, realizing that there was an optimistic "when" where I would have expected a dull, utopic "if".
"I wonder what will our lives be like *when* we stopped being in a hurry".

And I said, let's see.

I went back home, cooked for my ex flatmate Pauline, then we watched "High Fidelity" and then I read a bit of Lobo Antunes's "Natural order of things" before going to bed. I slept for a good ten hours straight only to wake up at 10 a.m., to make me a nice breakfast, which I felt no guilt for enjoying on my couch, re-reading parts of "Fever Pitch" by Nick Hornby. During all this, I was listening to Chopin's Nocturnes, which apart from amusing served as another demonstration of this new concept of slowness. A concept whose practice I carried on, arriving late at work, slowly browsing through yesterday's results, unhurriedly walking to the cafeteria for lunch, leisurely discussing with my student Sonja about her progress, while having coffee.

And here I am, at 7 p.m., blogging my slowed-down experience, having done fewer things than I could have done in one day, but certainly having entertained myself far more. In the end, work will be done, programs will be as optimized as possible and the sequence reads will eventually take their place on the genome (or the endless series of failed experiments). And it will all be done the right way, the slow way with me in the middle of all this, at the center of all this, realizing their true meaning, or at last being given the opportunity to judge if there is such a bigger meaning in mapping sequence reads than listening to Chopin.

I mean, after all, how meaningful would it have been if Tammy had done the dishes instead?

---

Thanks once more to Julien for providing the photo for this post, a collaboration I 'll try to keep ongoing.

February 8th, 1981

The rain is dampening the freezing air. But nobody's cold.
Embraced in a song that seems never-ending, only to be interrupted by cheers.

One, two-nil.
And the song goes on until half-time. It doesn't stop even then. This festival goes on in the midst of this cold, as the scarves leave the necks naked and start dancing in the air. Their voices keep them warm.

Three, four-nil.
All they are waiting for is the final whistle. The score does not matter anymore. No need to worry or argue. They are already fantasizing the goals on tonight's news, their father stunned while listening to their stories, their friends afraid of their rag, looking for a place to hide. They think about tomorrow's happy Monday at school, at college, at work. This next happy week, full of laughter, until next Sunday comes and then the next, until the league is over and then the last Sunday of May with the title, then the transfer season, the summer break and then the first Sunday of September.

Five, six-nil...
Thoughts dancing around the Sundays to come and the songs that don't stop. They all go down the corridors, out of the stadium, back home, to the bars and cafes where the neighbours are waiting for an account of the triumph.

But the doors are shut.In front of them, the Sundays of the ones ahead are tumbling down the stairs. Behind them, the Sundays of the ones to follow are pushing them forward. Their own Sundays, stuck in the middle, crumble, trip and fall. The eyes fill with fear, that six-nil disappears, tonight's news, the rags and laughters, the league and their father waiting, they 're all pressed against the walls. All their Sundays condensed into this single afternoon, all their memories become one...

That of their mother, a few hours ago, as they were getting ready for the game, when she straightened their scarf around the neck, before telling them...

"Take care my son"...

---

PS. This message goes out for the 20 Olympiacos and one AEK fans who died a day like today, back in 1981. (Thanks to anonymous referee V. for reading, commenting and correcting)