the invisible hand made visible

On my way to the lab today, the usual stop at the reception to check the newspapers' headlines. The front page story being the same in all of them. The awaited rescue of some of the U.S. greatest -until very recently- banks and insurance companies by the biggest state-funded operation in history. I remembered an old post some time ago related to the "invisible hand" of the "markets", meaning their "ability" to re-adjust themselves under pressure and thought that the invisible hand was finally made visible.

It's funny isn't it? I have asked myself again and again even in past pages of this blog about economy-related stuff. Where does all the money go?, what shapes the stock market prices? and similar questions have puzzled me from time to time. It seems that despite all my questioning in older posts (and pardon the substantial self-referencing in this one), there was not much to question about. In this sense, I would urge you to NOT go back and read those previous posts because they simply talk about stuff that do not make sense anymore. It's not that things have changed, no. It's just that under the current crisis (or depression, or whatever you call it) economy cannot hide from itself any longer.

There are no invisible hands. Perhaps someone has tried to convince us about that in times of "prosperity" when everything is going as planned, because (they tell us) the markets function on their own -natural- way (that is without control). But when things really go out of control, situation gets out of hand, and banks go out of cash, then the state comes to the rescue. This -we are told- is done to save the economy, the same economy whose prime advantage was that as long as it run uncontrolled, left nothing to worry about. The new style is this. When all goes well, markets function because they are free and all the state should do is lay off private enterprise. But when the shit hits the fan the state should better put its Superman cape on and pay 700Bi to save the poor companies from going bankrupt. This translates into the following common truth: Taxpayers should get no profit from wealthy companies making money. Instead they should chip-in when the same companies are in trouble. Liberal when profitable, state-funded when problematic.

No wonder, private companies are always well-off and it's only the nationalized ones to bring all the burden.

We should not be surprised. The new dogma is like the old dogma. It has always been thus and will always be so. It's just that now it's too damn obvious not to see it.

say "welcome" to the machine!

This was yesterday's view of the corridor leading to the lab. The usual, crispy clean, futuristic hallway was blocked by what appeared to be some sort of heavy, important shipment of scientific equipment. In fact it was something much more than just that. It was our own "doomsday machine" or in brief "The Machine"!

For the more observative ones that are also aware of the latest(?) advances in the field of genomics (not that you deserve any merit for that) the inscription on the top left part of the wooden box that reads "Illumina" may say something. For the rest let me just inform you that what we are dealing with here is a third-generation genome sequencer, whose capacities involve ultra-rapid, massive DNA sequencing in short read-fragments, genome mapping and de novo sequence assembly. Oh yes! it also disposes of a bioinformatician-repeller!

Assuming this last (add-on) function, the Solexa-Illumina sequencer will soon start the process of expelling us, the entire Computational Genomics Group, from the fine altitudes of the 4th floor of the Biomedical Research Park of Barcelona, which we currently occupy, to the ground floor of the same building. I can see many of you raising an eyebrow in doubt of the potential of such a machine to kick out an entire department, but things are -as always- slightly more complicated than they seem to be. You see, this doomsday machine, is only the second to be purchased by our Institute and is very likely going to be followed by 6 or 8 more in the process of "our" Centre for Genomic Regulation becoming the "main node" in sequencing in the entire country. (Quotation marks added the way I feel like. It's my blog isn't it?")

I will skip posing the question related to whether spending tax-payers money on trying to become the "main node" is really worth it. I shall also omit questioning the quality of the data these machines are producing. No matter how hard I try over these last six months, they simply fail to make sense (or I am failing to make sense of their profound, unquestionably objective noise). What cannot pass unquestioned though, is something that has fewer things to do with the machines themselves and more with the people (us, the scientific community, or whoever they are) who manage them. Because one of the main side-effects of our dear Institute becoming the "main node" in genomic sequencing all over Spain, would be the displacement of roughly 30 or more "people who treat our data", formerly known as "bioinformaticians", formerly known as "theoretical biologists", (this last term being a remote reference to science therefore abolished some long time ago). In the course of this displacement, we are to pack books, CD, computers, notebooks and the rest to make space for the installation of "the machines", ironically the same machines which will carry on producing the data we will be asked to treat, analyze and (hopefully) interpret.

The bottom line of all of the above would probably be to ask oneself the obvious question: "Since when did people become commodities comparable to technology?".
But I am afraid the even more obvious answer would be: "When did they stop being exactly that?"

I shall leave that question to you, the (few but loyal) readers. What I shall leave to me and to my fellow colleagues is a slightly more existential (thus also more provocative) question. And that is to what extent are we ourselves responsible for such a treatment. I mean, there is a long distance from the "computational biologists" we started out to be, researchers with our own projects and ideas to the "data analyzers", the last part (human but not much less dispensable) in a high-tech pipeline that we have turned ourselves into.

Is it my idea, or are we in the process of losing something more significant than our 4th floor sea view?

Have a nice (Lady) Day

I must be (in)famous for my difficulty to wake up in the morning. That is a lie. Or at least only a half one. Alike Marilyn Monroe (or was it some other star?), who once said that she wouldn't get out of bed for less than a thousand dollars (or was it more), I find it very difficult to get out of mine when I know that it is a thousand DNA sequences that await for me. On the other hand, I have never had trouble waking up to catch a boat to the islands, a bus that will take me to some nice place up on the Pyrenees or in general to any sort of activity that a normal person cannot but anticipate.

Today being a Thursday, like many others and many more to come, I found it a bit hard to force my body out from beneath the sheets. And as I found myself strolling down Carrer de la Merce on the way to the lab, I sensed I needed the sort of soothing music that would bring my mind in a tranquil and at the same time functional status. I chose Billie Holiday.

As the first notes of "In my solitude" started streaming through my headphones and my mood was slowly going back from frustrated to normal, I realized that I was passing by a number of bars that I have only seen full during the evening. Still, it was 9.30 and most of them had at least a couple of groups of customers who chatted while having their morning coffee, or having a light breakfast while reading the morning paper. I felt an indescribable envy. Right there and then I had just realized what would get me out of bed almost every morning and that was the promise that I could have the chance of starting my day, every day, in such a relaxing way. Walking in a bar, ask for a cup of coffee, a tostada or a scone, sit at a quiet table at the back and unfold my newspaper, or my book, or whatever it were that I might be reading. Now lets imagine that at the back of this coffee-shop there is a wide window facing the beach of Barceloneta, the sun is only starting to shine and Billie Holiday is discretely singing through the bar's speakers "God bless the child".

I could not help of thinking about other places and other times, where other people -more inspired than I am- were lucky enough to consider this dream of mine their daily routine. I thought about Joyce strolling down the south bank of the Seine, Freud walking into some Viennese cafe asking for a fresh croissant, Pessoa meeting with his friends in "A brasileira". And then I went on my walk to the lab, with the useless consolation thought that probably none of them was so happy about their mornings.

And that they all lived before having the chance to listen to Lady Day comforting them in the playful way she was doing it for me.

"Good morning heartache"...

How should one read a science paper?

Yesterday night, while sitting at my living-room's table, having dinner, a strange thing happened. I read two scientific papers.

This was rather unusual because I cannot quite recall the last time it happened and this is something for which I tend to blame science more than I blame myself.

Still, I read two papers, one by a group of people, whom one of my bosses like to refer to as "competitors" and the other suggested by another of my bosses (I only have two but sometimes I feel they are more). As I was going through the first one, I realized I was facing inherent difficulties in comprehending it. What was really puzzling about it, was that although the title and the brief summary preceding it were describing a clear concept in a quite straightforward manner, the main body of the work was going around the subject in a way that to me appeared rather obscure. I forced myself to go on, putting aside my glass of wine and blaming my recent paper-reading idleness for not being able to grasp simple scientific truths. But the harder I tried, the worse I was getting entangled in its twisted structure. Right when I thought the answer would pop up in the next page I would find myself staring at exotic scientific terms, which I was coming upon for the very first time, funny-sounding acronyms which said nothing to me and all this combined with plots, where I could not make out the real data from the simulated ones.

I reached the end of the paper seriously questioning myself and thinking whether I had become inept for activities of this sort. I gathered all the strength I had left and went on to the second one.

I found myself in front of a similarly clear and straight-forward title, so I thought "not again!" To my relief it was not the case. This one was as clear as its title, the concepts were all well-explained from the start, the necessary "catchy" acronyms had been clarified in the very beginning, the plots were self-explanatory. As I was regaining my self-esteem, my questioning gradually started to direct itself towards the writers instead of the readers. Some papers I thought are good and some bad. And that's that. I took some notes at the margins of both articles, washed the dishes and went to finish my wine on the couch with my book.

To this point I should make clear, that the whole process did not take more than what a normal person needs to finish off a salad, perhaps only a bit more, so I guess we are talking about 20 minutes or so. And I hope you find I am right when I say that one should dedicate no more than 10 minutes to go through a scientific paper. It's not that I am a fast reader but I guess if on average it takes one about 10 days to read "Mrs Dalloway" or "Crime and Punishment", it is imperative that he doesn't devote more than 10 minutes to the average science paper he comes upon. (And in case I realize someone has devoted more than 2 minutes in one of my few papers I will be more than happy). This comparison is not entirely unrelated to the fact that right after fulfilling my nocturnal, scientific duties I found myself on the sofa with an essay by Virginia Woolf entitled "How should one read a book?"

The essay is a good and pleasant read, (I assume especially for those who unlike myself are more than simply familiar with British literature) but it was mostly the main point of it that made me think twice about reading in general, and yes -even- science papers in particular. Woolf's main argument is that when it comes to a book the reader has above all a responsibility. For reading it carefully, for realizing the difficulty of writing in general, for judging it with a sincere kindness and a kind sincerity. Furthermore though, -she concluded- the criticism for which we readers are responsible (and in the case of science, readers coincide with critics although not to an extent that I would dare consider desirable) is mostly to be based on brief impressions, images and thoughts that flow as one reads without having to go into detail. Because this is what really matters.

I am not sure science papers are meant to be read as books. But considering the pleasure I get from reading books while my bosses' "paper recommendations" are piling up on my desk, I think I 'll follow Virginia's advice about it. I mean after all, we are supposed to take an expert opinion before serious undertakings, aren't we?

time

Time is relative. This we all know.

What we sometimes do not realize are the conditions that impose this relativity in our daily lives. Time is after and above all, OUR time, and while we are supposed to make of it what best suits us we are also responsible for defining it on the basis of our limited perception of duration within the confines of eternity. The fact that I had to wake up at 6.30 a.m. last Saturday to welcome my friend Kostas had nothing relative about it. It was the simple consequence of Vueling having setting up a flight schedule that is meant to torture its Greek customers.

The relativity of the whole thing makes its sudden appearance only under comparison. And such a comparison was painfully made this morning, just two days after Kostas' arrival. According to the earth's axial tilt and the geographical longitude of Barcelona, the difference in sunrise between two days is marginally less than 2 minutes. I can assure you though that the temporal distance between some days, which calendar-wise seem only slightly distant, can be huge. Especially if we are dealing with the distance between Saturday and Monday.

This was my case, last weekend. Kostas woke me up at 6.50 a.m. on Saturday, but it was a smooth waking up, simply knowing that I would go back to bed. There followed a nice nap, interrupted every now and then by the joyful sounds of a beautiful weekend morning, the smell of fresh coffee coming from the kitchen and the promise of the newspaper lying on the couch. Then all these promises were fulfilled and the day started, carried on and ended in the midst of the Fiesta Mayor of the city of Barcelona, in the company of a rather reassuring sun.

This morning, though, less than 48 hours later, when the alarm went of at 6.30 a.m. so that Kostas would catch his flight back to Boston, it seemed more like life on a different planet. A planet, where every day is Monday morning, grey and dull, with the threat of too many boring stuff piling up on your desk, where the coffee tastes like boiled leather and where there are no more fireworks or disguised people dancing in the streets. Most important of all, you cannot go back to bed. I know because I tried. But it just felt so that the atmosphere on Monday planet is too dense and too humid for me to fall asleep.

At 6.50, as the street lights started to go off, I was already waiting for the bus. It looked like it was about to rain. Through my headphones Radiohead sang "I might be wrong".

and then there were three

There are a number of ways for one to realize he is getting old. The most painful being without doubt, loss. By the time "The dark side of the moon" came out, I was not even but a distant intention in my parents minds, I wasn't even speaking during the "Wall" tour and I did not listen to Pink Floyd until long after they had split. Somehow though, I not only felt that they "belonged" to me, but also that -in a strange, metaphysical manner- I have always been a post-modern witness of their glorious past. It was probably due to the lack of good music after the legendary 60s and 70s and their unquestionable genious, that I felt that more than re-discovering them, I somehow "deserved" them.

The only time they played a gig in a place close to me, on May 31st, 1989, I was probably celebrating my little sister's 10th birthday in our small flat in Athens, most likely completely unaware of such an event even taking place. This meant I never had the chance to see them live and given that a prohibitive number of years had passed since the days of "Wish you were here" and "Animals", I was not expecting to ever have the privilege to do so. Last Tuesday, when Rick Wright left for his own last gig in the sky, he took a lot of things with him. Among those I was not so much saddened with the irrevocable vanishing of hope for a reunion, as with the feeling that actors -no matter how insignificant- of my life's play are passing behind the curtain.

It came to me then that you may know you are getting old when your heroes are long gone, but it is at an earlier stage that you become aware of aging and this is when you no longer create new heroes to replace the ones that have departed. On Tuesday I realized I have no replacements for Pink Floyd. It has little to do with their immortal music but with their physical presence.
And you have to trust me, it is less superficial than it sounds.

today

Souvent, pour s'amuser, les hommes d'équipage
Prennent des albatros, vastes oiseaux des mers,
Qui suivent, indolents compagnons de voyage,
Le navire glissant sur les gouffres amers.

A peine les ont-ils déposés sur les planches,
Que ces rois de l'azur, maladroits et honteux,
Laissent piteusement leurs grandes ailes blanches
Comme des avirons traîner à côté d'eux.

Ce voyageur ailé, comme il est gauche et veule!
Lui, naguère si beau, qu'il est comique et laid!
L'un agace son bec avec un brûle-gueule,
L'autre mime, en boitant, l'infirme qui volait!

Le Poète est semblable au prince des nuées
Qui hante la tempête et se rit de l'archer
Exilé sur le sol au milieu des huées,
Ses ailes de géant l'empêchent de marcher.


Charles Baudelaire
L' albatros

Emma Bovary's eyes

Emma Bovary's eyes are irrevocably black.

I spent a wonderful five days in France last week, during which I bought a copy of Flaubert's great novel and remembered how Emma Bovary's eyes have steered a great deal of controversy and how Julian Barnes has so wittingly criticized literary critics, using the colour of Emma's eyes as a starting point, in his great book about Flaubert. (chapter 6 for the lazy ones)

Emma Bovary's eyes are naturally black.
Nonetheless there is a flowing ambiguity when it comes to their appearance. Sometimes they appear blue, others brown, most of the times it's hard to tell. Given my somewhat frustrating situation at work it is hard not to think about Emma's eyes when I look at the results on the screen of my computer. Quite often the numbers appear reasonable, but sometimes they acquire rather unfamiliar values, strange shapes and weird distributions. But science -we have been told- is objective, therefore my plots and numbers should be naturally making sense, or not. There should be no inbetweens, no greyzones, no conflicting conclusions. Alas, this is not the case.

Emma Bovary's eyes are most ardently black.
But the real wonder in them is their ever-changing impression, their transcendental hues, their unequivocal ambiguity. Sadly though, Emma Bovary is a fictional character of a great French novel while my results are the mere outcome of a poorly supported, sloppily applied algorithm. And since poor science cannot even remotely compare to the literature of masterpieces, my plots' changing shapes have nothing transcendental or charming, romantic or mysterious. These are simply bad results. There is nevertheless something comforting about them and this is exactly the fact that when one (me in this case) tries to present them in their lack of clarity, when one tries to explain why a plot of the same kind looks sharp in Figure 1 and suddenly bends over in Figure 4b, the resulting feeling is more to the frustration than to the amusement of the reader. Science, it is, cannot be converted to literature, the romantic ambiguities remain safe under the pen of geniouses of a different caliber and we are ascertained that the joy we get from a good book will never be spoiled by bad science.

Emma Bovary's eyes are wonderfully black.

today

Φίλοι κι αδέρφια, μανάδες, γέροι και παιδιά,

στα παραθύρια βγείτε και θωρείτε
ποιοι περπατούν στα σκοτεινά
και σερgιανούν μες τα στενά
φίλοι κι αδέρφια, μανάδες, γέροι και παιδιά.
γράφουν σημάδια, μηνύματα στο βασιλιά,
σαν δε φωνάξεις, έβγα να το γράψεις
να μη σ’ ακούσουν τα σκυλιά,
βγάλε φωνή χωρίς μιλιά,
σημάδια και μηνύματα στο βασιλιά

Ήταν στρατιώτες, καπεταναίοι λαϊκοί,
όρκο σταυρώσαν βάλαν στο σπαθί τους,
η λευτεριά να μη χαθεί,
όρκο σταυρώσαν στο σπαθί,
καπεταναίοι στρατιώτες λαϊκοί.
Κι όπου φοβάται, φωνή ν’ ακούει απ’ το λαό,
σ’ έρημο τόπο ζει και βασιλεύει
κάστρο φυλάει ερημικό
έχει το φόβο φυλαχτό
όπου φωνή φοβάται ν΄ ακούει απ’ το λαό.

Γη παιδεμένη, με σίδερο και με φωτιά,
για κοίτα ποιόν σου φέρανε καημένη,
να σ’ αφεντεύει από ψηλά, τα κρίματά σου είναι πολλά,
χτυπούν το σίδερο θεριέψαν τη φωτιά.
Καίει το φιτίλι ξεθηκαρώνουν τα σπαθιά
κάνουν Βουλή Συνταχτική και γράφουν
το θέλημά τους στα χαρτιά
κι η κοσμοθάλασσα πλατιά
κάνουν Βουλή ξεθηκαρώνουν τα σπαθιά.

Τρεις του Σεπτέμβρη, μανάδες, γέροι και παιδιά,
στα παραθύρια βγείτε και θωρείτε
τι φέρνουνε στο βασιλιά
βαθιά γραμμένο στα χαρτιά
τρεις του Σεπτέμβρη μάνες, γέροι και παιδιά.

Ιάκωβος Καμπανέλλης
Το μεγάλο μας τσίρκο