Ithaca

This is the best and most famous poem by Cavafy. Once, in London, I saw this poem pinned on the wall in the home of a French girl I was visiting. In a Spanish translation! Apparently, a Colombian guy had given it to her and told her it was his favourite poem. Imagine that...

The poem has become a bit of an internet meme, thanks to a video of a reading by Sean Connery, with beautiful music by Vangelis in the background:

Enjoy Sean Connery's Scottish baritone and lisp! "Laishtrygoniansh and Shyclopsh..."

Ithaca

by C. P. Cavafy

As you set out for Ithaca
hope that your journey is a long one,
full of adventure, full of discovery.
Laistrygonians and Cyclops,
angry Poseidon-do not be afraid of them:
you'll never find things like that on your way
as long as you keep your thoughts raised high,
as long as a rare sensation
touches your spirit and your body.
Laistrygonians and Cyclops,
wild Poseidon-you won't encounter them
unless you bring them along inside your soul,
unless your soul sets them up in front of you.
Hope that your journey is a long one.
May there be many summer mornings when,
with what pleasure, what joy,
you come into harbors seen for the first time;
may you stop at Phoenician trading stations
to buy fine things,
mother of pearl and coral, amber and ebony,
sensual perfume of every kind-
as many sensual perfumes as you can;
and may you visit many Egyptian cities
to learn and learn again from those who know.
Keep Ithaca always in your mind.
Arriving there is what you're destined for.
But do not hurry the journey at all.
Better if it lasts for years,
so that you're old by the time you reach the island,
wealthy with all you have gained on the way,
not expecting Ithaca to make you rich.
Ithaca gave you the marvelous journey.
Without her you would not have set out.
She has nothing left to give you now.
And if you find her poor, Ithaca won't have fooled you.
Wise as you will have become, so full of experience,
you will have understood by then what these Ithacas mean.

Here's the original, for my Greek (or Greek-speaking) friends:

Ιθάκη

Σα βγεις στον πηγαιμό για την Ιθάκη,

να εύχεσαι νάναι μακρύς ο δρόμος,

γεμάτος περιπέτειες, γεμάτος γνώσεις.

Τους Λαιστρυγόνας και τους Κύκλωπας,

τον θυμωμένο Ποσειδώνα μη φοβάσαι,

τέτοια στον δρόμο σου ποτέ σου δεν θα βρεις,

αν μεν' η σκέψις σου υψηλή, αν εκλεκτή

συγκίνησις το πνεύμα και το σώμα σου αγγίζει.

Τους Λαιστρυγόνας και τους Κύκλωπας,

τον άγριο Ποσειδώνα δεν θα συναντήσεις,

αν δεν τους κουβανείς μες στην ψυχή σου,

αν η ψυχή σου δεν τους στήνει εμπρός σου.

Να εύχεσαι νάναι μακρύς ο δρόμος.

Πολλά τα καλοκαιρινά πρωϊά να είναι

που με τι ευχαρίστησι, με τι χαρά

θα μπαίνεις σε λιμένας πρωτοειδωμένους,

να σταματήσεις σ' εμπορεία Φοινικικά,

και τες καλές πραγμάτειες ν' αποκτήσεις,

σεντέφια και κοράλλια, κεχριμπάρια κ' έβενους,

και ηδονικά μυρωδικά κάθε λογής,

όσο μπορείς πιο άφθονα ηδονικά μυρωδικά,

σε πόλεις Αιγυπτιακές πολλές να πας,

να μάθεις και να μάθεις απ' τους σπουδασμένους.

Πάντα στον νου σου νάχεις την Ιθάκη.

Το φθάσιμον εκεί ειν' ο προορισμός σου.

Αλλά μη βιάζεις το ταξείδι διόλου.

Καλλίτερα χρόνια πολλά να διαρκέσει

και γέρος πια ν' αράξεις στο νησί,

πλούσιος με όσα κέρδισες στο δρόμο,

μη προσδοκώντας πλούτη να σε δώσει η Ιθάκη.

Η Ιθάκη σ'έδωσε τ' ωραίο ταξείδι.

Χωρίς αυτήν δεν θάβγαινες στον δρόμο.

Άλλα δεν έχει να σε δώσει πια.

Κι αν πτωχική την βρεις, η Ιθάκη δε σε γέλασε.

Έτσι σοφός που έγινες, με τόση πείρα,

ήδη θα το κατάλαβες οι Ιθάκες τι σημαίνουν.

Κωνσταντίνος Π. Καβάφης 

Merry Christmas everyone!

To all 25 of my readers, and all my friends around the world, my very best holiday wishes. I wish everybody health, happiness and prosperity. 

There is not much more I can say other than that! I will keep this post brief, and simply offer you my electronic Christmas gift: A link to Raymond Briggs' The Snowman (with the David Bowie intro). I know almost everyone has seen this a million times, and you will watch it again on TV sometime this Christmas, but it is still a beautiful Christmas moment that you can now enjoy anytime you like, but with a click of the mouse! Isn't YouTube great?

(For those of you with no patience, here is a link to just the beautiful "Walking in the air" song from this animated short, which is certainly one of the best Christmas melodies ever. Enjoy that instead!)

Merry Christmas to you and all your loved ones!

Belated² 2010 Impact Factors

The Journal Citation Reports (JCR) for 2010 have been out for months, but I only just now got around to creating this post. This is miles away from my World Cup of Impact Factors post from a year ago, which was published within hours of last year's report release! Apologies for that. The above explanation covers the one "belated" of the title. Of course, the other "belated" has to do with the fact that, as always, Impact Factors for 2010 were published with a year's delay in the middle of the summer of 2011!

Controversial as Impact Factors are, they remain the main way in which journal quality is judged. The higher the Impact Factor, the more sought after the journal is, and publishing in the top journals (especially Nature and Science) can make or break a scientist's career.

So how did journals do in this yearly competition? Like last year, I have selected a few journals that I find interesting personally, and are somehow relevant to the research I am familiar with.

Journal	Impact factor 2010	Impact factor 2009	5-year impact factor
Nature	36.104	34.480	35.248
Cell	32.406	31.152	34.931
Science	31.377	29.747	31.777
Nature Biotechnology	31.090	29.495	29.065
PLoS Biology	12.472	12.916	14.376
PNAS USA	9.771	9.432	10.591
Molecular Systems Biology	9.667	12.125	13.327
Nucleic Acids Research	7.836	7.479	7.314
PLoS Comput. Biology	5.517	5.759	6.251
Metabolic Engineering	5.512	4.725	5.263
J of Proteome Research	5.460	5.132	5.617
Bioinformatics	4.877	4.926	6.326
PLoS ONE	4.411	4.351	4.610
FEBS Letters	3.601	3.451	3.399
BMC Systems Biology	3.565	4.064	3.961
FEBS Journal	3.129	3.042	3.200
BMC Bioinformatics	3.029	3.428	3.787
J Mathematical Biology	3.021	1.695	2.377

J Theoretical Biology

2.371

2.574

2.491

IET Systems Biology

1.735

2.384

2.025

J Computational Biology

1.600

1.694

2.033

As my friend Duncan over at O'Really pointed out, it certainly looks like the big journals are getting bigger, and the small journals are getting smaller. Information about all journals can be accessed online on the ISI website, but a subscription is required. Accessing the website through a university IP address will usually do the trick.

Have I left some interesting journals out of my table? Drop me a line and I will be happy to add any suggestions.

Beware of Greeks borrowing gifts

It is a question I have to answer almost on a daily basis for quite a while. Everywhere I go, as soon as people find out I am Greek, they ask: what is going on with Greece?

There is strong pro-European sentiment in Greece, despite the trouble.

In case you have lived under a rock for the last two years, Europe is in trouble, and, apparently, it's the Greeks fault. The debt crisis, which has engulfed Ireland and Portugal and today threatens to spread to Italy and Spain, is spearheaded by Greece and has put the very existence of the Euro, and even the European Union, in danger. How does a tiny and insignificant country in a corner of the Mediterranean end up jeoperdising the future of not only the European monetary union, but also the international markets?

It is often easy to forget the teachings of history, but the fact is that this is not the first time we have been in similar positions. Greece has been at the forefront of major European developments for almost 200 years. We Greeks often think that Greece is the centre of the world. Non-Greeks often believe that the last time Greece mattered was 2500 years ago. I think a much better perspective is this: we are Europe's testing ground; if you want to know what lies ahead, you will do well to look towards Athens first. In other words,  it is not a coincidence that the spreading debt crisis and the social unrest that comes with it have a Greek epicentre. 

Can the Euro survive Greece?

Still, it is absolutely true that Greece has been living way beyond its means for at least the last 20 or 30 years. Greece has been borrowing heavily for quite some time (not that this is a practice that is any different than the one the majority of world countries have been following of course), while the government's income has always been heavily curtailed by wide-spread tax evasion, bad management, and lack of proper investments that would take advantage of the country's natural resources. For a time, the situation was sustainable due to the fiscal help provided by EU structural funds, investments related to the 2004 Olympic Games in Athens and, allegedly, "clever" book-keeping (the fact that this was later denied by both the Greek government, and our partners-in-crime, Goldman Sachs, leads me to believe that it's probably true). The perilous route of our economy was finally derailed when the international financial crisis of 2008 struck. As Warren Buffett famously said, "it's only when the tide goes out that you learn who's been swimming naked". And Greece has been skinny dipping for some time.

And then there is the gigantic problem of corruption. It is difficult to describe accurately the rampant spread of malfeasance and nepotism in Greece, especially to someone who is not familiar with the system from the inside. I am actually really conflicted about writing on this issue, because it's impossible to be fair; it is very easy to both exaggerate it and understate it. There is a wide-spread notion in Europe that finds it preposterous that Greeks are demonstrating and striking on a weekly basis, wasting public funds, after years of taking advantage of a corrupt public sector to enjoy large salaries and 3-day working weeks. But this view fails to consider the silent masses, the rest of the population that did NOT profiteer, or try to take advantage of the system, never avoided taxes, and who are now paying the steepest price for the debt crisis.

Financial mismanagement and favouritism have created an unsustainable economic model. The Greek economy and society completely depended (and still do to a very large degree, because the reforms and austerity measures are heavily resisted by the corrupt system) on the public sector. For decades, the state functioned as a mediator between foreign funds and the Greek people. Borrowing and  funds allocated for investment and development would go either to guaranteeing the support for the ruling party through the constant enlargement of the public sector, or to a select group of privileged entrepreneurs. The result: a gigantic, counter-productive, politically polarised and profligate public sector, and a private sector almost completely dependent on the state, surviving as supplier of the public sector and/or through getting involved in construction. Big business in Greece depends on a special relation with the state, or special privileges that they have been awarded by governments. Small businesses mostly survive through profiteering and tax evasion.

The problem goes deeper than finance. One of the biggest problems with the breadth of corruption is that it leads to apathy and social decay. An intimate knowledge of Greek reality reveals to anyone who will stand and take notice that what is going on in Greece, and what has been going on for decades before the consequences finally became evident, is not a debt crisis; this is just the symptom. It is a moral and ethical crisis. It is a moral collapse, which has come about because of our geopolitical situation, our specific historic circumstances, our characteristic Mediterranean temperament, and our culture which, uniquely, stands half-way between Europe and the Middle East.

Strikes and riots are a staple of everyday Greek life.

It is a situation I do not condone, but I can understand how people get drugged into. It is not easy to be the knight in shining armour when everyone around you, from the local councilors to ministers, from the corner-shop owners to bishops, from clerks to lawyers to judges, is involved in some way in the corruption. Greek society reached a point a decade or two ago, when the one who did not "use his connections", "go with the flow", "grease the hinges" (the one who did not steal, profiteer, embezzle or otherwise take advantage of the system for financial or personal gain, to do away with the metaphors), suddenly found himself on the opposite side of the fence: he was the one who was considered the outlier, the stearer, the fool. The current debt crisis is only the natural extension of that. It is also why the majority of Greeks, the silent masses, the ones who are not on TV demonstrating and creating havoc on the streets on a regular basis, are in fact pretty much stoic in dealing with the situation. We know very well that, at some level, either by our direct participation, or even simply by our indifference, we have all been part of the problem.

My only hope is that we can also be part of the solution.

Polis

The city

by C. P. Cavafy

translated By Edmund Keeley and Philip Sherrard

You said: “I’ll go to another country, go to another shore,

find another city better than this one.

Whatever I try to do is fated to turn out wrong

and my heart lies buried like something dead.

How long can I let my mind moulder in this place?

Wherever I turn, wherever I look,

I see the black ruins of my life, here,

where I’ve spent so many years, wasted them, destroyed them totally.”

You won’t find a new country, won’t find another shore.

This city will always pursue you.

You’ll walk the same streets, grow old

in the same neighborhoods, turn gray in these same houses.

You’ll always end up in this city. Don’t hope for things elsewhere:

there’s no ship for you, there’s no road.

Now that you’ve wasted your life here, in this small corner,

you’ve destroyed it everywhere in the world.

And now for the Greek original:

Η πόλις

Είπες· "Θα πάγω σ' άλλη γη, θα πάγω σ' άλλη θάλασσα.

Μια πόλις άλλη θα βρεθεί καλλίτερη απ' αυτή.

Κάθε προσπάθεια μου μια καταδίκη είναι γραφτή·

κ' είν' η καρδιά μου -σαν νεκρός- θαμένη.

Ο νους μου ως πότε μες στον μαρασμόν αυτόν θα μένει.

Οπου το μάτι μου γυρίσω, όπου κι αν δω

ερείπια μαύρα της ζωής μου βλέπω εδώ,

που τόσα χρόνια πέρασα και ρήμαξα και χάλασα."

Καινούργιους τόπους δεν θα βρεις, δεν θάβρεις άλλες θάλασσες.

Η πόλις θα σε ακολουθεί. Στους δρόμους θα γυρνάς

τους ίδιους. Και στες γειτονιές τες ίδιες θα γερνάς·

και μες στα ίδια σπίτια αυτά θ' ασπρίζεις.

Πάντα στην πόλι αυτή θα φθάνεις. Για τα αλλού -μη ελπίζεις-

δεν έχει πλοίο για σε, δεν έχει οδό.

Ετσι που τη ζωή σου ρήμαξες εδώ

στην κώχη τούτη την μικρή, σ' όλην την γη την χάλασες.

Κωνσταντίνος Π. Καβάφης 

Update: As evident from the above, I was inspired to start posting poems of my favourite Greek poet, and one of the most important poets from Greece, but also from Europe, in the 20th century. Constantine P. Cavafy spent most of his life in Alexandria, but he was both passionately Greek, and inexorably cosmopolitan. I will not try to summarize his biography here; Google can easily take care of that for you if you are interested. But I will say that his poetry has been translated into numerous languages and published all over the world, so I encourage everyone to go out and discover it in any form or language you choose.

Mr Miyagi's pearls of wisdom

So here I find myself once again, in a hotel in Luxembourg with not much to do. Last time I was here, I watched Karate Kid in my hotel room, and ended up keeping a running diary on Facebook of Mr Miyagi's best lines. In memory of that evening and in honour of the great, late Pat Morita - one of the nicest actors Hollywood has known, I am collecting all those posts here to make it an official entry. The words were just too good not to. I will say it again, Karate Kid (the original, please don't talk to me about the "Kung Fu Kid" remake) is a great movie, and one of the greatest sports films of all time. So here you go, words to live your life by:

RIP Pat Morita

"Close eye. Trust. Concentrate. Think only tree. Make perfect picture... If picture come from inside you, always right one." 

"To make honey, young bee need young flower, not old prune." 

"Daniel-san, you look (for) revenge, start by digging two grave." 

"No such thing bad student, only bad teacher. Teacher say, student do." 

"In Okinawa, belt mean no need rope hold up pants." ‎

"Win, lose no matter. You make good fight, earn respect. Then nobody bother." ‎

"Walk on road: walk right side, safe. Walk left side, safe. Walk middle, sooner or later get squeeze, just like grape." 

Wait for it.... ‎

"Wax on, wax off." 

"Man who catch fly with chopstick, accomplish anything." 

"First learn stand, then learn fly. Nature rule Daniel-san, not mine." 

"Balance good, karate good, everything good. Balance bad, better pack up go home." 

 And to top it off, Miyagi's nod during the crane kick scene!!! That makes the whole movie. That's what Daniel-san is fighting for, not to get rid of the bullies, not for Ali, or for the tournament. What he's after is Miyagi's approval for a kid from New Jersey who grew up without a father. Survivor's "The moment of truth" over the end credits is just icing on the cake! Just a great, great film moment, and a great movie.

Is Systems Biology doomed to fail? (NO!)

In early 2010, Sydney Brenner, wrote an article for the journal Philosophical Transactions of the Royal Society entitled 'Sequences and consequences'. In this article, Brenner claims:

The new science of Systems Biology [...] will fail because deducing models of function from the behaviour of a complex system is an inverse problem that is impossible to solve.

Brenner goes on to label Systems Biology "anti-reductionism", and even calls it 'low input, high throughput, no output' biology. 

Now: far be it from me to criticise Sydney Brenner, arguably one of the great biologists of the 20th century. He was one of the fathers of Molecular Biology in the 60s and 70s; his work led directly or indirectly to the discovery of tRNA and mRNA, the elucidation of the genetic code and the development of the central dogma of molecular biology (i.e. that information flows from nucleic acid to protein). He practically single-handedly established C. elegans as a model organism and the research on this organism and its genetics played a big role in the development of the Human Genome Project. For his research on genetic regulation of organ development and programmed cell death, he was awarded the Nobel Prize in Physiology (along with Robert Horvitz and John Sulston).

Nevertheless, it seems to me that Brenner's article is basing its critique of Systems Biology on a narrow and even incorrect definition of what Systems Biology is and does. Brenner is basically claiming that all of Systems Biology is nothing more than top-down simulation and high-throughput measurements.  This simply is not true. For the part that I can speak of (the simulation part), there are many many systems biologists who are working on the problem of systemic behaviour with a bottom-up approach, and are very consciously basing their efforts on the work and achievements of molecular biologists of decades past (which Brenner is exalting in the aforementioned article). So not all Systems Biology is "black box modelling", but this is not to say that inverse modelling is pointless. When there is no other information about a system other that its observed behaviour, then inverse modelling is very appropriate, and can be used to improve our understanding, until more information about the parts can be collected and forward modelling can be applied. George Box famously and repeatedly wrote that 'all models are wrong, but some are useful'. Physicists and engineers do not need to be convinced of the usefulness of holistic approaches to systems with complex, non-linear, and emerging behaviours, because they have been applying them successfully on a daily basis, for decades. Brenner's unfair criticism is an indication of the work that we still need to do to convince many biologists.

I would also contend that many of the approaches that Brenner does put forward as the correct solution to the problem of complexity in biology are in fact Systems Biology approaches. In my view, the research programmes of several Systems Biology research centres, including both my former (MCISB) and current (LCSB) homes, are not at all far away from what Brenner has in mind. For further proof of this, one can contrast Brenner's CELLMAP idea with the Virtual Cell initiative. Systems Biology is already doing middle-out. 

For a (kind of) rebuttal to Brenner's paper, but mainly for an overview of how far Systems Biology has come, you can read this article by Athel Cornish-Bowden, in which he replies to Sydney Brenner:

It takes a certain amount of chutzpah for a molecular biologist (whose field was memorably defined by Erwin Chargaff as "the practice of biochemistry without a license") to make that particular criticism [...]

For a more accurate definition of what systems biologists mean when they speak against reductionism and promote the holistic approach, I always appreciate Yuri Lazebnik's 'Can a biologist fix a radio? Or, what I learned while studying apoptosis', which is not only didactic but also very amusing.

Finally, for a rather different view on the importance of genes (which not only contradicts Brenner's claims, but also radically opposes the classical view of 'living organisms as vehicles for the replication of genes' as proposed by Richard Dawkins), and a brilliant explanation of emergent behaviour in living organisms, I thoroughly recommend Denis Noble's book, The Music of Life. Noble, as the creator of the Virtual Heart, has been living proof that Systems Biology works, even before the term 'Systems Biology' existed (his original cardiac model was published back in 1960).

In the end, it comes down to definitions. I cannot help but feel that we, as systems biologists, are somewhat at fault here. Systems Biology is notoriously ill-defined as a principle, partly because of its multidisciplinary nature, partly because it often serves as a 'hook' to attract funding for all kinds of research. In my mind, a trench war over whether we should focus on studying just the parts or just the whole is missing the point. Systems Biology should be about understanding the parts in terms of the whole, and bringing everything together.