Molecular Lounge

It was Hesiod the first author to write about ages that preceded ours. In his “Works and days” (Ἔργα καὶ Ἡμέρα) he tells of five ages through which mankind had lived through, thus far: gold, silver, bronze, heroes and, finally, iron.

It’s just a case my last two posts refers to the term ages and, so far, I’ve only described two: glass and plastic. In my opinion science I’ve moved from the age of glass to that of plastic. Hesiod melancholically placed himself in the last and least glorious of the ages: the Iron one.

Today, I would like to talk about the age of paper, in which, I might say, I’d really like to be. You don’t miss your water till the well runs dry! Imagine a whole group (nine people, including an avidly reading boss), with a printer that, normally, refuses to print from the PC’s (take that Microsoft!) and, since yesterday evening, has sadly stopped showing its preference for Mac’s (take that Apple!). Unlike my boss, I’m everything but a massive reader of scientific papers, despite the fact I actually quite like reading per se.

This said, with perfect timing I found today just two nice papers I obviously HAD to print and read and couldn’t. Yes, I have to admit I’m not able to read science from a screen: I get distracted WAY to easily (I guess I’m not a real scientist. Or a freak. Or both: is there a difference, after all?).

Printing, though, is also vital when you want to decently present most of your data. Although, I’ve recently reached the conclusion that a basic power point presentation (even just 3 or 4 slides), is far more elegant and understandable for co-workers.

The most important reason why I want the printer to be fixed (at least in a way that allows ME to print out) is to complete the packaging of my secret Santa present for my favourite colleague, closest co-worker and somehow best friend M.S. What is all about? Well, (hopefully) come the age of paper, and you’ll see.

I’ve always liked glass. I’ve always thought it’s a fascinating material. Craftsmen can manipulate this highly viscous liquid to create the most exquisite items. Sure, in the everyday life, plastic has taken over as cheaper and far more practical alternative material. However, I’ve often thought that, in today’s eco-sensitive and eco-aware society, recyclable glass could have made a sudden comeback. In a way, that’s partly true: I’ve recently noticed, for instance, the surge of brands of mineral water using glass rather than plastic bottles (I find that thick plastic many posh manufacturers -such as San Pellegrino- use completely nonsense).

As far as science is concerned, glassware and plastic-ware (let alone other more sophisticated materials) are still, more or less, equally part of our everyday routine. Yes, glass test tubes are a thing of the past in biology, but all your buffers and most of your solutions are in glass bottles. Your beakers, conical flasks, cylinders and cell homogenizers are all made of glass.

Our (large) institute has its own glassware facility. In a quintessentially British fashion, dirty glass- (and plastic-)ware is to be left in a box on the floor just outside the door of each lab. Regularly an old man (true West Londoner) and an old lady (with true, ugly English teeth) come and collect the lot and wash it. When you need something, you simply go to the facility and get what you want. We hadn’t such a thing in my old, underfunded department and we had to clean after ourselves.

This is all very practical: since you don’t have to bother doing the washing up, you feel free to waste use as many glass cylinders or beakers has you want. But, there is a problem with glassware. To make it shine and get rid of the smallest trace of nasty stuff that might inevitably is left in, say, every bottle, these are washed with tons of detergents. However, since you’re not supposed to drink in your beaker, the detergent isn’t probably rinsed off. My boss (and, indeed, every one, including me) is well aware of this and of the danger this might represent: you don’t want to lysate your cells during an immunofluorescence, do you?

Following a bizarre result I got this week (in the sense a control gave, for the first time in months, a negative result) the age of glass(ware), as far as I’m concerned is definitely over: no longer will one of my buffers of solutions be allowed to sit in a glass container or be prepared using suspiciously shiny glassware. Hail to (the age of) plastic!

Tonight, I’ve tasted revenge. To my surprise, it didn’t taste good at all. Of all the possible endings to this thing, this is definitely the most unexpected. In fact, I still can’t believe her group got 0 out 6 in last month’s quinquennial department review. I genuinely do not believe it. Or I simply don’t want to. I just can’t believe that, because of her group head’s mediocrity, they will all have to…flee the department and, as a whole entity, head for another place. Could be here in London. Or Newcastle. Or Scotland. Who knows? I should be happy, though: a part of me can’t still stop thinking about her. That part of me, to state the obvious, is as surprised and speechless as I’ve ever been in my whole life. But, if she HAS to go away, isn’t that a problem solved..by itself? So, why do I feel so uncomfortable now? Why am I so sad

That part of me, still, believes nothing of that is actually true. It’s all been generated in the mind of my colleague (and best friend) M.S. under the effect of the headache pill I gave her in the morning: a combination of amidopyrine, butalbital and caffeine, I normally take but she was taking for the second time ever. She told me she was told that by another member of the group, M.C., who (allegedly) said -with a bitter smile on her face- that they might have to leave within a year. I mean, we talked two weeks ago and she seemed fine. No sign of such thing at all. Is it even true?! And, if it’s, does she even know about it?!

A member of that group presented a poster for the reviewers. I, proudly, had my own one. Our group actually had two. We got a 4 out of 6. But, still, they had one and, I wouldn’t have never thought they where in such dire despair. Where? Where it all go wrong for V.Y.’s group?!

To be continued…

Since Noel (finally) left Oasis, many things have happened. All of a sudden, it looks like the single, big experiment on which my boss wanted me to focus (in his own words) “entirely” is to enter its final stage. I say this with a good dose of caution and relief: the grand finale involves an American company and lots of money. Unlike my boss, I don’t give a pig ass whether it’ll lead to a paper on some massive journal. For me, it may just mean the end of my misery: 9 months, 9, endless, appalling, months, during which I’ve been doing the same stuff, every week. Feel free to say it’s normal for a PhD student, especially on the first year, but I (still, to date) feel very miserable indeed.

I drink too much, too. This is something I’ve realized a few minutes ago: as I reached for my bottle of vodka, I poured the last bit of its liquid content. Just a single shot for tonight and then, tomorrow, I’ll have to get another one: I’m not sure, but I’d say I bought this 1L bottle a week ago. Not good, but not surprising either, giving the monotony of my daily routine.

Things have already changed, which is probably why I suddenly got the idea (and the strength) to write again here. I like to do a bit of everything and to work, at least, on two themes of (my/a) project. I never wanted to be a pharmacist to avoid monotony. In sum, I had a lot of strong, mixed feelings.

I heard on the radio, earlier on, that the EU authorities have approved a vaccine for Swine Flu for the UK. Two comments:

1. Mommy should be relieved now, although I’d rather cut of my testicles than get the vaccine
2. I didn’t know some blokes in Brussels had to validate a vaccine for a member of the EU. It sounds stupid and, somehow, wrong.

Tomorrow is Saturday: normally, I wake up around 10 am on a Saturday morning (even if I know I’ve gotta go to the lab). Sadly, the new term of my French course has been scheduled for Saturday from 10:15 to 13. Good news is I’ll have the whole “day” free. Bad (really, really bad) news is I’ll have to set the alarm clock for at least 8:30 (8 am is, however, more likely).

British summer is crap. However, this early autumn is fantastic: 20°C and sunny. Sadly, after my French class, I’ll be in the lab splitting my B-cells tomorrow. You can’t always get what you want.

Going back to the original assumption of the post, Noel has always been my favourite rock-musician: going solo can only be a good thing for him and me (as a fun). After all, he’s always been the heart, brain and soul behind Oasis, as the video (a marvelous acoustic performance of one of my favourite songs) proves.

God bless.

This morning I woke up with two things in my head. (I don’t know exactly when I’ll finish to write the whole post, so, forget me if it’s posted, say, on Sunday 2, at 0:30: what I mean is Saturday morning.) One was a strong headache, which is, at the same time, usual and unexpected: I do suffer from migraine, but it’s often gone after a good sleep (and a good dose of a mixture of caffeine and barbiturate I normally take). Rarely does headache manifest itself after a good night sleep or, as in this case, during it (it woke me up around 9:30: pretty early for Saturday morning after a hell of a week, isn’t it?).

The second thing I woke up with in my head was an idea, although I’d rather call it an epiphany (way more highbrow, eh?). This idea, which I’m basically testing right now, is a sort of plan B for a cloning I’m doing at the moment. I spent a good half of my days at work, last week, working at it. Actually, having designed a risky but quite obvious cloning strategy, I spent my time basically trying to work out a way to discern which one of the 47 (!) colonies I had picked and mini-preped  contained the right product.

Eventually, on Friday evening, while waiting for a western blot transfer to finish, I must have dedicated at least 90 minutes of my life to solving that puzzle, just to conclude that what I was doing was the only, possible restriction analysis that could let me spot the right vector. Unless, of course, I was willing to burn £162.15 of my research budget and sequence them all.

I also reached the conclusion that the cloning strategy I had used for that (last) step in the generation of my final vector was the only one I could have used. I was, of course, wrong: there is, actually, an equally complicated and “risky” strategy, which, however, now looks less risky than the other to me.

Will it be successful? I’ll let you know. However, what still thrills me and makes me feel, well, blessed, is that I woke up with idea. And with the headache.

Let’s begin, of course with the rational explanation. After a week when I’ve worked on average 12 hours, I got home on Friday and had a great (but usual) dinner: Tagliatelle with mushrooms and tomato sauce , beef steak with carrots and Dijon mustard, cheese, 3/4 of a bottle of excellent Valpolicella Superiore (I don’t like beer and I drink wine every evening for dinner), a glass of milk with a couple of my beloved malted milk biscuit and a shot of Russian vodka (again, nothing unusual for me: I’m a bit of an alcoholic). I also had spent an awful lot of time thinking about this cloning, which combined with fatigue and alcohol, might have triggered a mild day-after hangover and, finally, let my brain realise an obvious alternative to my strategy. Sound all very logical and rational but:

1. headache persisted until dinner (which hasn’t been very different from the aforementioned one), despite two capsules of my headache remedy;
2. I drink the same every night.

I prefer this second, irrational answer. As I’m sure you know, Pallas Athena, son of Zeus, was thought to be, among other things, goddess of Wisdom, Intelligence, (War) Strategy and Reason. Her birth is also suspiciously close to what I’ve experienced: briefly, Zeus was experiencing an excruciating pain in his head. Not having barbiturates or sumatriptans been invented yet, he asked Hephaestus to give him relief. So, Hephaestus took his axe and smashed it on Zeus head, splitting it in two: from Zeus’s brain, came out Athena, already a young adult, dressed up and armed for the battle.

I can’t see anything against this latter explanation: this morning, as it dawned, Palls Athena gave me her help to solve this intricate cloning conundrum (how fucking sophisticated is this blog getting?!…).

Tomorrow, I’ll begin my battle to save the planet. Yes, I know: it sounds like an obese bloke saying “Tomorrow I’ll begin my diet”, while devouring peanut butter. However, there’s a difference in my case: you see, I might deeply dislike most of mankind and certainly I’ve no interest in its fate. But, believe it or not, I somehow do care about the planet. I don’t like the fact that global warming is dramatically altering the climate, I hate wasting drinkable water, I can’t stand any waste of energy (especially electricity), etc.

Generally speaking, I have a secret hate for plastic: basically, I think every plastic item is yet another sign of the suicidal philosophy mankind has embraced. Sometimes, it’s a sign of laziness too.

You want an example? Well, for ages, biologists have used for plating out and picking bacterial colonies, respectively, a glass pipette (turned into a hook by heating the tiny capillary at its end with a Bunsen burner) and toothpicks. Now, however, it seems you’re a moron if you keep using these “ridiculously outdated” tools. All you need is some sort of white, plastic stick, with a small loop at its end: these inoculating loops can be used to spread the bugs on the agar plate and to pick a colony.

What’s more, you don’t need to autoclave anything: the loop is sterile, safely placed in a sealed, plastic (argh!) envelop. Who needs to place those toothpicks in a small beaker, close the top with a double layer of tinfoil and autoclave? Or  why wasting time making funny hooks out of a pipette, when you can simply open a user-friendly envelop and extract the loop in it?

I hope to be wrong, but I think these inoculating loops are far more damaging for the planet then a toothpick or a (reusable) glass pipette. I hope I’m wrong when I complain about the fact that some moron decided each loop had to come in its own, unique, plastic container. Because, my soul cries every time I pick 12 colonies and, on my left, at the end of this operation, a pile of plastic bags is left and the GM waste bin keeps filling up with plastic rods. So, I hope I’m wrong in saying this new way of doing cloning is worsening the condition of the planet and global warming as well, in the name of easing the work of the average researcher.

Anyway, even if I’m wrong, tomorrow, I’m gonna put some toothpicks I’ve just bought at the supermarket in a glass beaker and close it at the top with tinfoil. And, next time I’ll plate out something, I’ll use a flamed Pasteur pipette.

As a kid, I was 100% into the whole manga/anime universe. I used to watch Dragon Ball, Lupin, Daitran 3, Mazinger: you name it, I watched it. However, my favourite will always remain the unforgettable Saint Seiya. I still shiver when I see an episode (I’m obviously a keen collector of this sort of stuff). Perhaps, that is still influencing my opinion about Japan: you see, the whole anime was, basically, a series of tense fights between super-heros. However, with hindsight, there was always something odd about those fierce fights: the opponents talked way too much, especially in the very middle of the battle. They also announced their next move, had choreographic attacks and, above all, the length of the struggle was way too long, mainly because of all the talking and acting.

That is weird in the West, but there, it was just a modern adaptation of the traditional Kabuki genre. And such examples can be found in nearly every anime: even when preposterously huge robots are involved, Kabuki epitomes creep into the main battle between the hero and the evil antagonist. To us, non-Japanese viewers, this looks very funny and bizarre.

However, in the years, I’ve kept wondering whether they do the same in the labs. Do they shout or glow when they pipette into a multi-well plate the c-DNA? According to hours of anime watched over the years, I think so. I think you go slightly mad keeping such insane working hours.

Yes, I think we have all heard of horror stories about people (not only students) working in their labs from 8 am to midnight, as if that were the most normal of the routines. In fact, a Japanese post doc told me that and, like yesterday, you can only safely bet your money on a Japanese being the last person to live our department at night every day. If this ain’t frightening, then, what is? I guess I’ll never understand Japanese people. I mean, people say anything about Germans and their attitude, but let’s not forget, Japan is a country that had to be hit twice by nuclear bombs, before it realized the war was lost. Twice!

So there you go: my opinion about Japanese people is entirely based on watching anime in my childhood and stuff told to me by almost strangers (even if we share the same office…). Oh, and simple historical facts. Like Sofia Coppola (director of Lost in Translation), I might be accused of cultural chauvinism and inability to understand the differences in the context in which Japanese (and, more broadly speaking) Eastern cultures have developed. Believe what you want. However, if you do, then, I am getting ready for Japan as my next destination after my PhD. Right now, I’m struggling to type and think: honestly, I feel like the most tired person in the world. In the last two weeks, I’ve been working, on average 12 hours a day. Still,  I’d quite fancy to have a fireball-firing pipette…

Sadly, I haven’t been able to perform special moves, so far: my micropipette doesn’t self ignite, the table-centrifuge doesn’t evoke any blueish tornado when utilized, etc. Which makes things quite boring and predictable after 12 hours.