not my fault

Over the past half year or so, I have expanded my repertoire of skills and made myself important to the lab in ways I wasn't hired for. I have campaigned for the organization of our DNA constructs in electronic form and have implemented a database and web interface to take care of that. This done, I kicked a wiki into life and started harassing my colleagues about contributing their wisdom, about making their experiences and knowledge available to everyone. You can always ask, but only as long as someone remains a member of the lab. Whoever leaves – and academic labs have a dynamic turnaround – takes what he has learned and improved in the lab with him, irretrievably. Lastly, I designed and coded the lab's new website, an effort that's not complete yet because people drag their feet about adding content. But my part is done and I'm happy with it.

I know there's no reason for complacency, though. An IT project is never done when the last modification is saved and the site goes live. It requires diligent supervision, constant maintenance and painstaking error prevention. That's why I'm equipped with administrator and root passwords and have turned into some sort of mini system administrator.

Our lab's web and database servers sit on a computer that's used for regular work. In fact, it's a student's primary workstation. Today, this computer went down. Its juice was mysteriously cut and it just blanked. When the power supply was restored, it came back to life as quickly as it had faded, and everything seemed to work. Everything, that is, but the wiki. Accessing its start page only gave a cryptic php error. Something wrong with the database, apparently. And something was very wrong indeed. The database server was fine. The plasmid database worked as it should. But the wiki database hadn't shut down cleanly when the computer zonked. Data had been compromised beyond repair.

It was then that two thoughts flushed through my brain almost concurrently. First: Damn, I don't have a backup. Why did it never occur to me to be prudent? Second: I'm so damn glad I'm not professionally responsible for this database. Imagine I worked in some commercial operation that would stand lose a million pounds every minute their databases are not operational. Someone would find his way to my desk very quickly and start yelling at me as if had I gnawed through the power cable with my own teeth.

There is very little yelling in academia, thankfully. Were my boss to hear about this meltdown, he would ask with honest concern, 'Will you get it back up? Will get the data back?' And I would reply that all would be easier if I had read all the pages of the MySQL bible I bought many years ago, and not just those immediately relevant for what I was doing. We would share a laugh.

The server wasn't critical, but the database would need to come back to life eventually, and I'd like to have the data back. I went down to the department's system administrator who, professional that he is, assured me that he had done weekly dumps of the database's content and he would send me the latest version he has on backup. It will be up to me to restore it and to make sure that future backups will be more frequent. What a nice environment for learning this is.

Christmas spirit

This year, for as long as I can remember, I have experienced the least Christmas spirit. I'm walking through the streets and it doesn't strike me as if Christmas were just around the corner. I haven't heard a traditional song or the clear sound of a trombone. I haven't smelled mulled wine or the twigs of a freshly hewn spruce. I haven't seen snow. Each day, I pass my time like I would any other day.

The town is full of grandiose but ultimately pathetic decorations like blinking Santa Clauses and diode arrays to make you go blind. Inevitably, they surround advertisements and shop displays. As I don't go shopping much, I'm not much touched by how Christmas is misrepresented. And last weekend on Oxford Street, it could have been any weekend – there was absolutely nothing seasonal about it.

Living where I do doesn't help. Shepherd's Bush is full of diversity but devoid of values that are dear to me, devoid of things I associate with home, with warmth, with happiness. There are no trees, no lights and no carols. The Green has been taken over by a fun fair. Apparently, going on rides and shooting numbers for prizes is what the British like to do in winter, but it doesn't do the trick for me. Further down on Uxbridge Road, the Arabic stores do business as usual.

Maybe the lack of snow exacerbates things. In the northern hemisphere, Christmas is in winter, and I associate the sparkle of fresh white snow with the peaceful days at the end of the year. In Grenoble and Salt Lake, even if there was no snow on the street in front of your house, there were always the mountains, less than an hour away and clearly visible from town, their rich coat of snow reflecting the sunset in bright orange.

There will probably be no snow on the ground when I go to Germany this Friday. The airport will be full of blinking Santas and diode lights, and so will be the big malls. But at home, in the small town I grew up in and certainly in my parents' house, Christmas how I know it will rule. To me, Christmas means peace. Christmas means slowing down and kicking back. Christmas means Bach's Oratorio, cookies baked by mom, and a real tree with real candles. When these candles are lit for the first time, the Christmas spirit will finally hit me.

welcome, little Eee

When I came back from Paris yesterday, my latest toy had already arrived in the lab. It was an addition to my growing family of laptops but very different from the rest. Bigger is better is a thing of the past. The day it was announced, I had fallen in love with the Eee PC for its uncompromising mobility. It weighs about a kilo, fits in a lady's purse, and the battery lasts longer than you'd ever want to sit in front of a computer. Last week, I finally ordered mine. The idea is to take it with me wherever I go, letting me sit down and write wherever I am, whether it's a coffee shop in London, a plane over the Atlantic or the Syrian desert.

The Eee is brilliant. It is tiny – and also extremely cute. It weighs next to nothing (The AC adapter is the size and weight of a Mars bar.) but feels rock solid, and it's almost silent. There is no hard drive that spins; just a quiet fan if loads of applications are running. Booting is nearly instantaneous. The pre-loaded Linux, some flavor I've never tasted, works out of the box. I was using the computer less than a minute after first boot. StarOffice, Firefox, Skype, and photo and video management software are already built in. (Strangely, VLC is missing.)

Where are the limitations? Well, the size of the Eee can work against you. The keyboard is tiny and some keys are nearly impossible to hit without looking. On the upside, there's proper delete key, something even the MacBook Air doesn't have. Typing is a bit of a pain, and I would probably use a USB keyboard whenever available. However, this post was entirely written on the Eee, and my hands haven't cramped up yet.

The screen is tiny as well, but it displays the same number of pixels horizontally like my first Vaio did, and I was fine with that. The touchpad doesn't feel right, but that might just be a question of getting used to. While it comes with system restore disks, the Eee doesn't have a CD player. Apparently, one can easily create a bootable USB stick. Films make their way to the computer via the same media. Internal storage is only 20GB, but one has to travel a lot and write a lot of stories to fill this up.

My verdict: I love it. I can't wait to trow it in my backpack when I go home over Christmas. I now have a mighty ThinkPad for sale. (Of course the MacBook Pro still rules whenever sheer power is required.)

Paris, part two

I love trains. That’s how I got around when I was little. The car was a clear second. I remember weekend outings with my buddies (and an adult or two to keep things sane), and sleeper cars to Budapest. When I was thirteen, a train took me non-stop from East Berlin to Vilnius to a three-week summer camp fit for the son of Politbüro member. I have no idea how my dad got it. He wasn’t even in the communist party. The ride took 28 hours.

Ever since they opened the Chunnel, the rail tunnel underneath the English Channel, I’ve wanted to fly through it. This desire started to burn hotter and into the foreground when St. Pancras was opened after a Milliwaysian refurbishment (where little expense was spared to give the impression that no expense had been spared), making it the new launch pad to Paris, just a bit more than two hours away.

On Tuesday afternoon, I was finally aboard one of the trains, and slightly dissatisfied. For all I had been looking forward to, the ride was spectacularly anticlimactic. When we left the station, night had already descended and it was completely dark outside. When we hit the tunnel, all went black, easy to miss unless you pay attention. My perception was blunted by an earful of music. Resurfacing in France twenty minutes later, it was still dark.

Besides the nonevent of the tunnel, there was also the nonevent of speed. While the train wasn’t as smoothly cruising as an ICE3 where you can leave a bic pen on your seat table and it won't roll off, it was infinitely calmer than the bone-rattling traditional TGV that is as much about speed as it is about communicating that speed to the passenger. The Eurostar moves, noticeably, but it doesn’t shake or bounce, and it doesn’t accelerate as madly as you would expect for a train hitting 180 mph.

You know it’s going fast, though, when, while passing a station, you can’t tell where you are because you can’t even read the signs three platforms away. It’s all blurry with speed. Once the train was on its way, I collapsed into my iPod and woke up, a few hours later, in Paris. Here are some of my first impressions, put to paper that same night, but only committed to the blog just now.

The metro doesn’t give a good first impression. Discarded tickets are all over the floor, and intricate scratch designs in the windows. The tunnels are dimly lit but covered in bright graffiti. At the stations, there are no attendants. People jump over ticket gates or squeeze through in pairs. A faint smell of anarchy hangs in the air. For all the ubiquitous whining about the London tube, it looks like a clear winner to me.

Once outside the underground system, the Haussmannian gracefulness of the city is striking. The ground floor of most buildings is extra tall, with enough space for a restaurant’s mezzanine or a shop’s storage space. All windows are really French doors. Only little metal gates prevent the careless from stepping trough these doors and falling onto the sidewalk. At night, all windows are closed with metal folding shutters.

In contrast, the textbook London dwellings are dilapidated Victorian terraces. They were built at about the same time as their Parisian counterparts but should have been demolished a long time ago. Substance is crumbling. Thin walls and rickety windows let heat escape unhindered. Paint comes off the walls or has been splattered back on in the most haphazard way. Trash bags are heaped by the front door because there’s no room for them in the entrance portal. Scratch this, there is no entrance portal in the first place.

There are exquisitely elegant buildings in London as well, in the posh central districts, characterized by enormous sash windows, washed brick façades and bright white trimmings. Not unlike medieval fortresses, these buildings are inevitably surrounded by ten-foot deep trenches, revealing troglodyte dwellings for those with the delirious desire for a prestigious address but without the financial means. Herein lies an enormous difference between the English and the French. I think a Frenchman would rather camp underneath a bridge on a Seine quai than degrade himself to living in a basement. After all, where would he put his wine?

I didn’t have the time to contemplate all this upon exiting the metro because my hotel was straight across the street. I didn’t have to look for it. I didn’t even have to think about where to look for it. It was like limo service without the car. I didn’t have to walk. I just climbed a few steps and arrived. Of course I went back out again after checking in and dropping my bags.

Talking about luggage, have you ever noticed the guys selling fake designer bags in Rome or Milano, scattering their wares on a tarp so they can grab everything and run off in one go should police appear? According to a story in the Economist a while back, they all belong to a particular ethnic group from Senegal. In the cities where they operate, they have communities, rules, safe houses and soup kitchens, and ways of transferring money back home. This doesn’t exist in London, but is alive and well in Paris, except what I saw them offer were trinkets for tourists, Perspex Eiffel Towers and Mona Lisas with blue LEDs for eyes, not bogus luxury goods.

I saw these guys—this is not hard to guess—underneath the Eiffel Tower, a very special place indeed. The perplexing, entangled steel construction is a marvel of civil engineering and a piece of art to my eyes. The tower is at the end of the Champs de Mars, a large public garden and park whose name derives from the Roman god of war.

These days, it’s a much less belligerent place. There’s even a monument to peace at its other end. As I was walking by in the quiet of a cold night, I couldn’t help but be infinitely grateful for living in peaceful times, when Germany isn’t invading France every half century and England doesn’t try to rule the world by force. I prefer economic prosperity over military mastery, and fast trains over fast bullets.

Paris, part three

Last night, right before leaving Paris on the fast train, I let myself be tempted. I tasted the nuts of Old Jack. My tongue painted slow circles on the substantially sized flattened spheres, tenderly tracing surface cracks and clearly defined edges in the process. The outside had a hint of ruggedness to it and betrayed only little of the explosive tenderness I was about to receive. So much pleasure in a dimly lit room!

The day had started more conventionally. I had met with collaborators at the Pasteur Institute. We explained to each other what we had been doing between sending emails to each other, and discussed how our efforts might be turned into a publication. The meeting went well, and it was quick. By one in the afternoon I was off to do sightseeing in a city that I haven’t properly visited in eleven years.

Right away, I took the metro down to the Arc de Triomphe and ambled down the Champs Élysées. It was a very cold day, but Paris is a city that will always warm my heart. When I see the Eiffel Tower, and it’s widely visible, a true landmark, my heart skips a beat and I start bopping down the street instead of walking. Eventually, I got to the Grand and Petit Palais. These have only recently been restored to and, in all likelihood, beyond their original splendor. All I remember from last time were heavy equipment, tall wooden fences and curiosity-tickling impenetrable plastic foil all the way up to the roof. Now, major art exhibitions are staged here in the most appropriate settings.

I also spent time in the Tuileries and around the Louvre. Just about then, the sun decided to play its games with me. For only a few seconds and seemingly out of nowhere it would paint the glorious architecture in a light that makes winter so great for traveling. It was frustrating because I would hardly ever be at the right place at the right time in order to capture the splendor with my camera, but chasing the elusive rays kept me warm at least.

By way of the two islands in the Seine, I got to the Marais and the Quartier Latin, two very relaxed neighborhoods right and left of the river that charm with their narrow cobbled streets, cafés, and quirky boutiques. I was frozen by now and looking for a place to have tea and cake. The day was nearing its end, and I knew I’d miss the sunset I had originally wanted to capture from Montmartre. But it was cold and the desire for cake stronger.

That’s when La Jacobine opened her doors for me, a small cozy salon de the inside an unassuming alley. The tea was six euros a pot and the cake eight fifty a piece, but who’s counting when you’re in Paris for the first time in a few years. I had my issues with the tea, though. If you charge an arm and a leg you’d better brew it right. Don’t just put the leaves into the hot water. Take them out when the tea is done. How do I know who many minutes have passed? How do I know how long this particular tea takes? And why do I have to ask for a little saucer to remove the leaves and prevent them from turning the concoction thick, dark and bitter? In any case, the chocolate cake was simply divine.

Warmed up and sweetened, I continued my stroll. I noticed the number of street markets and the quality of the produce. I seem to have completely forgotten about this. Carrots are orange and have lush green leaves. Apples are big, firm, and exist in a hundred regional varieties. A significant portion of the species on offer were unknown to me. This is the EU’s Common Agricultural Policy in action, the result of Germans’ paying high taxes and the French’s subsidizing their farmers. The most beautiful looking greens mankind has ever beheld, next to fresh, prime meat, poultry, and treasures of the seas.

Maybe it was from one of those markets that Old Jack’s nuts, introduced in the first paragraph, had come from. In case you haven’t figured it out yet, I wasn’t talking about some pink sort of naughtiness but noix de St. Jacques, the adductor muscles of St. James’ scallops, a huge bivalve mollusc from France’s northern shores. I treated myself to this delicacy in a restaurant near the Gare du Nord when my train to London was still an hour and a half off. It was truly delightful.

Shellfish is usually banned from my plate and palate because of its gummi-like chewiness. Only once before, at a tapas bar in Barcelonta, have I been satisfied with octopus. That was an eye-opening experience because it told me what such things can taste like if they’re fresh and prepared with care and love. Tonight was no difference. The noix had been grilled for a few instants and its slightly charred exterior hid a soft heart much like a good steak or magrait de canard does. The meal came with rice, slivers of carrot and a sauce that looked creamy and rich but was delicate and unimposing and left the meat the uncontested king of the plate. Enjoying the last little morsels, I almost missed my train.

a day to forget

Christmas is coming up in gigantic steps. It seems just a few weeks ago it was still months away. Now, it's here, in your face, everywhere, and impossible to avoid. Although our family will mark the festivities largely gift-free for the second time, I'll have to get a few little things, not the least of which is the five-pound item for the lab Santa. As every year, so I'm told, we'll each buy a small gift, wrap it neutral aluminum foil, gather the lot in the middle of the table during our Christmas lunch, and play for it. It goes like this: Each one in succession throws a die, and with a six or three, you can take from the heap what you fancy. By the time the table is cleared, some have acquired a gift while others have not. Obviously, some have amassed more than one. So far, so unfair.

Traditional Christmas values of generosity and kindness are completely thrown out of the window in the second part of the game. With no unallocated gifts left, the throwing of the die continues, except now you get to steal someone's gift with a three or a six. That's when the screaming and scheming starts in earnest, generously fueled by booze provided by our boss. Five minutes later, the game is halted, the lucky ones open their gifts and celebrate while the unlucky bewail their fate.

I've known what I wanted to buy for a while now, and today I went out to make the purchase, if that's an appropriate word for something that costs only five pounds. After a short ride on the Central line, I found myself in Oxford Street, surprised that there was not a single bus in sight. The street is normally closed to private vehicles on weekends, but on Very Important Pedestrians Day, it is complete traffic-free. To appreciate the impact of this, one has to see Oxford Street on a regular Sunday. Two parades of buses, one slowly moving west, the other equally slowly east, fill the street in its entire length. It's a spectacle in itself, and that's why stepping out of the Bond Street tube station gave me such a startling surprise this morning.

This other surprise, a few days old already, was that I've got sick in the most bizarre of ways. At night, I lie in bed, being boiling hot and freezing cold at the same time, and cough my lungs out as if I had smoked since age thirteen. In the morning I'm drenched in sweat but cold. During the day, all open symptoms vanish, no runny nose, no sore throat, no teary eyes, but my head feels as if it had been smashed into a pulp. I'm drained of all energy and can hardly keep myself on my feet.

This morning, I popped my new wide-angle zoom into my backpack to take some epic pictures. A band of Salvation armists, the bells of their eight trombones shining in the sun, would have made a good shot, if I had just dared to squat down in front of them to take it. However, I was too afraid I wouldn't get back up and, lying on the ground twitching, become an attraction myself. I continued zombiing along the street, feeling and maybe looking as if I had died last night, and blended in smoothly. Snow princesses on stilts, half the cast of Star Wars in all their shiny armor, mechanic nutcrackers, and plenty of musicians kept the crowds entertained and me invisible.

In the end, I couldn't take it any longer. I had planned to go to Southbank for some creative input in the Landscape Photographer of the Year exhibition and maybe take a shot or two along the Thames when the sun set, but I had to accept defeat. My body was so weak that even my will couldn't make it move anymore. I hopped back into the Central line and am now lying on my sofa, waiting that this episode of fatigue will pass. Oh, and I have the gift in my backpack.

bikes and cars

Riding home from lab tonight was a total nightmare. The temperature hovered near freezing and bit my fingers with insistence, but that was the least of my worries. What drove me nuts was traffic. Kensington High Street was clogged in three lanes, though the road is only two wide. Buses, garbage trucks, taxis, fat Bentleys, and ridiculous G-Wizes were all idling about and turned the road into one big parking lot, most resourcefully packed. The efficient packing led to minimal space between vehicles, making passing or squeezing through on a bike nearly impossible. One van's side-view mirror almost got me. I could only dodge at the very last moment and felt it scrape my shoulder as I yanked my upper body to the other side, nearly hitting a black Mercedes in the process.

With these obstacles, in the way but big, highly visible and immobile, my commute would be a bit slower than on a normal day but not necessarily unsafe. The danger comes from unexpected sides. Pedestrians, lurching behind these bright red buses, feel compelled to cross the road as they would a Tesco parking lot, without looking left or right, and inevitably only split seconds before a cyclist passes the bus. When your focus is on a massive wing mirror on collision course with your head, a wayward pedestrian is the last thing you need. Then there are the other bikes and scooters that all zigzag through the maze according to their own perfect trajectory, trying to make the trip home as fast as possible. These paths often intersect and only aggressive brake control will avoid disaster.

Traffic tonight was denser than ever before, a sad culmination of a few days of constant deterioration. This degeneration coincided with the news that Boris Johnson, our circus clown of a mayor, was going to scrap the congestion charge for the part of town that I ride through. What a fool he is. As the congestion charge, despite my initial fears, won’t go until 2010, it must have been the time that caused my experience tonight. London’s streets are free of charge after six. During the day, you pay, but a night, you glide (if you excuse my ill-conceived poetry).

In light of the obvious effect of free driving, a three-year old can figure out that scrapping the charge will do nothing good. The number of vehicles in the streets will go up, just as it went down when the congestion charge zone was extended almost two years ago. I’m puzzled that all drivers do not support the charge. I’d hate to ride in traffic like that every day, but I’d hate it even more to be the traffic, to be sitting in a car, in a hurry to get somewhere but unable to move, burning gas and wasting time.

In the end, it all comes down to this: Even on a day like today, when fingertips slowing going numb from the cold, riding a bike is the best way to commute here. If you don't find a better way of spending your time than being stuck in traffic, why do you live in London?

research explained

Here's a colleague of mine from Imperial College illuminating his lab's research in a six-minute video. Well produced, Stephen, well explained, and clear enough that my parents could watch it without getting confused halfway through.

Antivirals research explained by Stephen Curry on Vimeo.

Given that my research is in a closely related field, and using the same techniques, the video explains my work as well. I can thus save the effort and time of science communication and go back to the lab. Maybe once I have results, I'll give the video business a shot as well.