Mind the Gap

If you are not an absolute geek, look away now.

As for the rest, have any of you ever visited the Royal Museum of Scotland in Edinburgh? I first had the pleasure one summer long ago when I ran away from home on an ultimately ill-fated romantic mission, but ended up falling in love with their superlative Science and Industry collection instead. Since then, I’ve been back several times. You wander the hushed shadowy halls peering at the objects behind the glass and feel humbled by the weight and beauty of the history of science crowding just over your shoulder: astrolabes, sextants, microscopes, difference engines, compasses, telescopes; everything chrome and brass, copper and bronze, gold and steel, knurled and sculpted and buffed like an artefact out of a Philip Pullman novel.

Swanky kit: Goes from zero to sixty in ten seconds

They don’t, I’m afraid, make them like they used to. I was thinking about this the other day when I had to do a bit of microbiology, the first since resuming my career as a bench scientist. I wanted to inoculate some bacteria into broth, so asked around the lab to see who could lend me a platinum loop. No joy. So I trekked, then, around the institute, asking people at random: I either got baffled looks, or people saying, “Well, I always just use a yellow Gilson tip”.

A yellow Gilson tip? This is what happens when you earn your PhD in an old-fashioned, God-fearin’ American Microbiology department: you become really fussy about your instruments. (You also feel reluctant to drink from anyone else’s glass for the duration of your thesis, but that’s another story.) I don’t feel I am doing justice to sterile technique with disposable plastic: once the box has been opened, the masses of amp-resistant bacteria swirling around our lab are bound to encroach. Besides, there is satisfaction and ritual in the dousing of the wire into the alcohol, the purifying flame of the gas burner, the sizzle of the molten loop in the cool agar or broth. I was never one of these cavalier plate scribblers, either: no, my streak-outs would be conducted in the strict three-area method with colonies isolated to perfection.

Dear Reader, I purchased that platinum loop and holder. A really swanky, expensive one from Fisher Scientific, with a wonderful heft and weight to it, and a wire that sizzled like a fine sports car.

It felt wonderful.

I’m afraid to say it out loud, but my lab notebook just isn’t up to the job anymore. Last time I talked about how difficult it is to display some forms of modern experimental data in a readily comprehensible fashion. But that’s not the only problem I’m having these days. Documenting my work in the trusty notebook is also growing more futile: most of my data consists of monster spreadsheets and terabytes of images and videos. I know journals have overcome this problem by exploiting online publication and supplementary data, and labs, by creating vast storage databases on their websites. But gone, for me, at the personal level, is the ability to record everything that I am doing with a pen, on paper.

This state of affairs is particularly distressing for someone of my temperament. In an older post, I explained how I am a compulsive documenter when it comes to my experiments: no piece of film, for example, is blank enough to escape my scissors and tape; no failed PCR gel is too smeary and inconclusive. I like, in short, to record every detail from triumphant eureka to notorious bellyflop, including scribbles, images, graphs and charts, snippets of email printouts from collaborators – more like a geeky scrapbook than the sort of documents a patent judge might want to subpoena.

Now, my attempts at summary grow increasingly half-hearted – most of my book is just an index, pointing to a series of files on DVD and a growing family of external hard-drives. Given the fragmented nature of the narrative, even I have problems following the logic of my activities some days. Worse, I don’t really trust DVDs and hard-drives; I’ve had enough of these spontaneously corrupt to know that I can’t rely on their permanence.

But then, it was ever thus: the ways and means of science have been briskly evolving since I entered the research game back in the late 1980s. My year in graduate school was the last group of students to paste photographs directly into their Ph.D. theses; flipping through it now, I marvel as the pages fan by, weighed down by Kodak paper and glue. I recall, too, the stab of jealousy I felt when the next year’s crop of students showed off their magna opera, all images neatly scanned and incorporated into the document. I’ve seen the conversion from slides to PowerPoint, and the PowerPoint fads come and go: yellow text on a fading gradient of dark blue; cheesy animation transitions; that entire grim year when Comic Sans was the only font you ever saw at American conferences.

Things change, and I’m going to have to learn to live with my stripped down, new-age lab journal. But I do confess, I won’t be able to love it quite as much as before.

The ways and means of science are changing. It’s true: I can feel the tide tugging at me. I’m that waterlogged bit of dead tree mired in beach shingle; the last few passes of the surf have caused me to start sliding in. As the tide continues to turn, I will soon be flowing out into the grey deeps, liberated from gravity and on my way – whether I want to be or not.

Too much information: Scientific datasets no longer color between the lines

What triggered this idea today was Excel spreadsheets. Like them or loathe them, it’s not really possible to analyze a genome-wide screen without a large number of them. In the past I have got round my antipathy towards the output of this hateful Microsoft product by printing the damn things out at the first opportunity, impaling them spitefully with holes and filing them in a tidy binder with colourful tabs. Soon, the printed spreadsheet would acquire scribbles, notes, a rainbow’s worth of highlighter pen marks. Thumbed through until the corners were ragged, stained with coffee, I would know exactly where my experiments were and what I had to do next. I might feel the need to update or correct the electronic version, but it was never the working copy.

All well and good, but what to do when your spreadsheet has thousands of rows and more than fifty columns? No amount of column narrowing and font reduction can force one of these babies onto a piece of A4. Print it out and your machine will spew out a monster collage that would need to be pieced together like the Dead Sea Scrolls (along with about a hundred superfluous blank pages for good measure). But try as I might, I cannot seem to think when facing a small computer screen with multiple windows of information that I need to compare. Click one open and the other is immediately forgotten; click back and you forget why you left in the first place.

But there is hope: I liken this difficulty to the mental shift I had to make, in the 1980’s, when we all had to start composing words with a keyboard instead of a pen. Remember that, those of you of a certain age? I have a distinct recollection of sitting at a shiny Canon electric typewriter in my university dorm room, trying to force my creative juices to flow without a pen between my fingers. I felt disarmed, almost crippled. The typing movements of my fingers could not seem to stimulate the same neuronal pathways. Now, of course, my handwritten journals are what is rough and artless – only with a keyboard can I produce quality material. My brain, it seems, has adopted. And I have no doubt that the next generation will be able to perform these mental acrobatics, to think in virtual space, as naturally as breathing.

In the meantime, you’ll have to excuse me: I have a tide to catch.

It may be below zero on these chill London evenings, but spring is in the air. And so is science-related fiction. On Monday, I was a talking head on the Guardian‘s ‘Science Weekly’ podcast, which was devoted to science and literature. What’s more, the formal announcement is forthcoming, but I’ve been authorized by fellow Nature Network London denizen Jonathan ‘he’s a lot less green than his avatar’ Black to leak a little trailer about an exciting new monthly manifestation: The Fiction Lab.

Exciting revelations: The new-look RI should be completed by April’s end

The Fiction Lab, coming soon to the state-of-the art bar in the newly refurbished Royal Institution on Albemarle Street, will be a reading group dedicated to lab lit and other science-related or inspired literary fiction. Brought to you by the RI and presided over by yours truly, it may in fact be the world’s first science-in-fiction salon. Once a month, starting on 9 June, we will gather together to enjoy a drink and discuss a great novel that features science at its heart. Sadly, there isn’t enough new pure lab lit fiction — novels featuring scientists plying their trade as central characters — to sustain a monthly book group, but despair not: we’ll be supplementing this rarefied genre with novels that are generally inspired by science or scientific ideas. Each month’s selection will be chosen by the group, and you’ll have a month to read the book before we convene to give it a poke and a prod.

Our first book will be The Sun and Moon Corrupted by Nature’s own Philip Ball. Ball is a prolific author of popular science non-fiction, but this is his debut novel, out in May and available now for pre-order on Amazon. It is puffed thusly: A young journalist, Lena Romanowicz, goes in search of Karl Neder, a provocative physicist whose discovery of a new energy source made him an outcast. In order to find him she must follow his trail from the castles of Transylvania to the rocket labs of NASA, from Viennese cafés to the blasted borderlands of the Soviet Union. But as Lena chases his story across the world, she is also trying to outrun the buried motives that drive her. Tantalizing stuff.

As a special treat, the first Fiction Lab will feature a special appearance by Philip Ball himself, who (after we’ve have a chance to thoroughly decimate his magnum opus – just kidding, Phil) will rather bravely drop by at the end to share his insider insights with the group.

We’ll keep you posted on any further developments!

Like many scientists, I often gnash my teeth at the way our profession is portrayed in science documentaries. Yet at the same time, I have always suspected that it is not as easy as it looks. So it was with genuine curiosity that I accepted a consultancy to help out with Science on Film, a joint project between the Wellcome Trust and the Documentary Filmmakers Group.
Science on Film brings together eight practicing scientists with eight young filmmakers, who in pairs are coached through the entire process of creating a short science documentary from initial idea to gala launch screening. The ultimate goal is to teach the participants more about what goes into making a skilled science documentary: the filmmakers will hopefully learn more about how best to portray a complex scientific topic in a fair, balanced, understandable and entertaining way, while the scientists will ideally come away with a better idea of how difficult this balancing act can be.

The course, still ongoing, spans three long weekends and teaches narrative, story research, interview skills, camera work, editing and other technical aspects. And I’ve run a few workshops with them about what science is really like: the processes, the lifestyle, the culture, the history, the myths and realities, the stereotypes – in short, the good, the bad and the ugly. In parallel, listening to the filmmakers’ point of view has been eye-opening. Aspects about science filmmaking that I despise – for example, the tired old narrative formula that BBC Horizon used to employ on every one of its films – were held up by the film tutor as shining examples to be emulated. Yet in listening to the justifications for these points of view, without being entirely converted I at least came away with something to think about.

This past Friday, they all came to my lab to practice filming scientists in their natural habitat. Have you ever tried to fit in eight cameras and affiliated paraphernalia, sixteen filmmakers, one tutor and two assistants into a lab containing only four bays? Come to think of it, have you ever had to pin down eight scientists and make them stay in the same place for more than ten minutes? The filmmaker mob descended just after lunchtime, lugging their cameras, wielding furry-tipped booms and looking around expectantly. The head tutor turned visibly pale when he saw that not a single one of my colleagues was yet in evidence. As tumbleweeds blew through the empty room, I attempted to round up my labmates by mobile phone: tutorials had run over; a train was delayed; a confocal experiment was playing up; our Italian undergradute really just wanted to finish her lunch in a leisurely fashion. I even had to commandeer a reluctant technician from the lab next door to make up the numbers.

But eventually we’d all settled down, each filmmaker pair interviewing and filming its designated scientist. I had had no idea how my colleagues would react to this strange invasion into their precious time, but soon was able to breathe a sigh of relief: real chemistry seemed to be developing and everyone was getting on splendidly. I did overhear a few altercations (“What do you mean, you don’t understand the words ‘apoptosis’ and ‘epithelia’?” the Chinese student demanded. “How else can I explain my project?”) and watched with amusement as one of the crews persuaded a post-doc who works exclusively with cell culture to hold a vial of fruit flies and squint at them down the microscope.

But now I know, at least in part, how some of those irritating scientist cliché memes get transmitted in science documentaries. When there is a camera in front of you begging for something televisual to happen, you can’t really help acting out the part. So it was that I found myself possessed by the Spirit of Channel 4, holding an Eppendorf tube up to the light and sagely inspecting it as I flicked its contents in agonizing slow motion, just as I’ve seen in thousands of canned shots before.

We all know how we’re supposed to act, and remarkably, this is exactly how it unfolds. How many other stereotypes are out of our conscious control?

It was only a matter of time before the British government cottoned on to the fact that we cavalier biological researchers were regularly engaged in perilous international ‘veterinary trafficking’ activities. Yes, you. Put down that rabbit antibody and step away from the bench, nice and slow like.

I always knew our days were numbered: what a luxury, to send and receive that simple Jiffy-padded envelope full of vials of living fruit flies or nematodes, antibodies or plasmids or cell lines, dispatched from far-flung labs with nothing more complicated than the standard marker-pen scribbled mantra: ‘biological samples, non-hazardous’. Such was the collegial nature of such transactions that it would have been a breach of etiquette for the sender to even hint at the possibility of postal recompense, although I once liberated a vial with a cheerful note twisted around it that said “Buy me a beer the next time you see me at Keystone”. To share materials without complication; to desire and request a strain and to have it show up a few days later, no muss or fuss – such opulence. I always knew, in short, that we were somehow operating under the wire, and that if the powers-that-be ever suspected, we’d be in big trouble.

Well, our halcyon days are now officially over, at least in Blighty. Importing scientific reagents into the UK just became a lot more complicated. The laws were passed more than a year ago, but it seems they only decided to start enforcing them very recently. Our lab noticed the winds of change last week when a purified antibody, dispatched by Fedex from the States, failed to arrive on schedule. A few days later, we received an ominous missive from DEFRA (The Department for Environment, Food and Rural Affairs), an extract of which I reproduce below for your entertainment and edification:

“The import requirements for this type of import are set out in Importer Information Note (IIN) BAL-Live 1…This states that these animals may be imported with a declaration from the exporter stating that at the time of dispatch the animals showed no obvious signs of disease and that the holding of origin was no subject to any restrictions for reasons of Animal Health. If these animals are being imported from a Third (non-EU) Country it is necessary for it to enter the UK through a Border Inspection Post (BIP). For a list of BIPs and their capabilities please follow the link below. You must give 24 hours prior notification by a Common Veterinary Entry Document (CVED) which can be obtained from your local Animal Health Divisional Office (AHDO) or BIP. Part 1 must be completed and returned to the BIP of entry into the EU. To find your local AHDO please follow the link below. Products included in this requirement include blood products, serum and antibodies. … Once received the original copy of the documentation should be attached to the consignment prior to export so that it arrives with the correct documentation at the BIP. Failures to do so may result in delays to the processing of your consignment and to the eventual re-export or destruction of the consignment.”

(Anyone out there know how to spot a diseased antibody? Tiny sneezes issuing from inside the Eppendorf tube, perchance?)

In parallel, emails started to circulate amongst collaborators and colleagues, tales of lost packages, of delayed frozen materials that had arrived several days after the last of the dry ice had evaporated, of crucial manuscript revisions delayed because an irreplaceable reagent had gone astray, of epic telephone arguments with implacable officials at Stansted Airport (our nearest ‘BIP’, since you ask). People justifiably wondered why no one from DEFRA had bothered to alert any of the major universities and research institutions that the laws had been changed. Darker mutterings were heard too, conspiracy theories that had DEFRA infiltrated by Intelligent Designists or Christian Scientists.

All of this, I must say, was sounding a bit familiar to me after a four-year stint in a lab in the Netherlands. There, I tried three times to order COS1 cells from the American Type Culture Collection. Each time, my consignment was intercepted at Schiphol Airport for seven days as the vials were duly inspected by the official in charge of preventing the illegal trafficking of endangered species. COS1 cells, you see, were originally derived from an African green monkey, which is on the official endangered species list. Never mind that the cells in question were derived many moons ago, and that in importing an immortalized cell line, I was actually helping to perpetuate, not imperil, the species’ genomic existence. But to no avail: the checking procedure took exactly seven days, regardless of the logic of my arguments, and no amount of dry ice could withstand that amount of time.

So heads up, everyone: before you request that crucial perishable reagent from a mate on the other side of the world, gird your loins, obtain and fill our your CVED from your AHDO or BIP, post it to the sender…and ask them to put it in a box the size of a house with enough dry ice to sweat out the inevitable bureaucratic delays. Because, as the DEFRA notice helpfully pointed out, “Please note that the BIP office is not staffed on a daily basis.”

I’d like to personally invite everyone living in or near London to our much-awaited free RI/Nature Network blogging event tomorrow night, already bigged up by our esteemed Editor but worth another mention. I’m already feeling seriously outclassed at the prospect of being on the same panel as Ed “He Writes Like A Veritable Angel” Yong and Ben “His Pseudoscience-Bashing Fury is Terrible To Behold” Goldacre, but very much looking forward to swapping ideas with a friendly audience, hopefully with a minimum of rotten veg propulsion and sceptical, House of Commons-style jeers and guffaws.

Anyway, we’d love to see you down at the Apple “It’s Really Quite Scarily White” Store on Regent’s Street from 7 PM tomorrow, and for a drink afterwards.

Thanks to some gentle, skilled persuasion by Bora Zivkovic (a man I would advise you to avoid as a poker opponent), I have just assumed the mantle of Editor of The Open Laboratory 2008. As many of you know, Open Lab, now in its third year, is an anthology highlighting the best science blog entries of the year. Famously, the entire shebang is assembled and published by hardworking volunteers in only a few weeks over Christmas and New Year, and proceeds go to support the annual Science Blogging Conference that occurs every January. The last two years the book was published print-on-demand via Lulu.com (urbanely edited by Bora along with guest editor Reed Cartwright). You can buy the most recent book over at Lulu, which contains a number of specimens from Nature Network denizens, and which was recently reviewed by that well-known rag, Nature.)

It’s never too soon to start thinking about seeing your name in lights, or those of your blogging friends, so feel free to begin nominating! You can nominate as many entries as you’d like, written by you or others and starting from 21 December 2007, by making use of this form.

As someone interested in the culture of lab life as much as the knowledge that emerges from it, I’d like to make a special editorial call for posts that transmit what it’s like to be a scientist in today’s world. I know that in some quarters the term ‘science blog’ has become almost synonymous with ‘science news’, albeit much more in depth than what you normally read in the newspapers. Although many bloggers do what is essentially great, unpaid, independent science journalism – and long may this continue – I’m also interested in fostering the more personal side of the scientific experience. Such rare glimpses into a hidden world of science life can be just as illuminating for non-scientists as are the explanations of the fruits of its labors. The previous Open Labs have included a number of excellent examples of both sorts, and I hope that we again get good balanced representation for the 2008 edition.

There’s an old British expression, ‘A change is as good as a rest’. I never gave it much credence before; after all, hard work is hard work, so how could it ever be relaxing?

Enter my mini-sabbatical at the European Molecular Biology Laboratory (EMBL), an idyllic outpost nestled on a steep wooded mountain overlooking Heidelberg. Founded in 1978 and supported by twenty European member states, the institute houses over 800 biologists of many different nationalities and performs cutting-edge research in the fields of cell biology, biophysics, developmental biology, gene expression, and structural and computational biology.

Clean living: yet another shiny robot welcome me to Germany

It also houses international conferences; I attended one ten years previously, although the only thing I can recall – naughty me – is ducking off from a few sessions to eat Brezel, drink Bockbier and play a fiendishly clever card game called Skat in a smoky bar with a few other post-docs (you know who you are). And of course, I remember the food. The canteen is resoundingly famous amongst biologists: for a few paltry euros, you can gorge yourself on gourmet fare every day.

I’ve been sent here from London for about three weeks, thanks to the financial largesse of the European Molecular Biology Organization (EMBO), and the kind accommodation of my host lab, to learn more about high through-put RNA interference and automated timelapse microscopy. I got a bit of a shock when I was introduced to my lab space: they’d issued me an entire empty half bay, a tissue culture hood that hardly anyone else uses, ditto the microscopes and the freezer spaces, with an incredibly competent research technician who was eager to help me. Everything is spotlessly clean and tidy, which has had a wonderful effect on my brain: faced with so much order, I feel my actions and thought processes somehow aligning to fit in with my environment. In the evenings, the setting sun bronzes the woods outside the window by my desk, filling the lab with a coral-colored glow, and all the world seems infused with a little bit of euphoria.

And here’s where we get to the restful bit: it is wonderfully liberating to have only one problem to work on, and to chip away at it without any distraction. Back home, I have a lot of lab chores, and my attendance is required at an endless parade of research talks and group meetings. The research, as it is, seems perennially interrupted, such that you fit in your experiments around the obligations, and not the other way around. Here, free of any distractions, the only thing that matters is the sole scientific question: can I spot a microarray of siRNAs onto a glass slide and achieve transfection and imaging conditions such that I can follow my cell morphology phenotypes in focus over time and space for a forty-eight hours period? After a week here, I’ve made good progress, and though I work hard and return to my guest room exhausted, I still manage to feel exhilarated.

Everyone should get away once in a while. Perhaps periodic lab sabbaticals should be an integral part of every scientist’s research life, built into the budgets of their fellowships and grants. It doesn’t cost very much to send someone somewhere for a couple of weeks, but the mental and research benefits can be enormous.

A room with a view: looking west out of my room in Gastehaus Eichwald

You’ve probably all seen it by now: Scientists for Better PCR, an advertisement for BioRad’s 1000-series thermal cycler. Fabricated as a music video and available on YouTube, the song is a deft send-up of the 1985 classic “We Are The World” in which, for those of you too young to remember with excruciating clarity, luminaries such as Michael Jackson, Cyndi Lauper, Billy Joel and dozens of other stars got together to croon for Africa with such lines as “There’s a choice we’re making/we’re saving our own lives” and “We are the ones to make a brighter day, so let’s start giving”.

Gospel truth: Lab kit advert targets GenX

In contrast, the ‘scientists’ in the BioRad advert, sporting headphones and the occasional cowboy hat and sunglasses, take turns singing lines such as “There was a time when to amplify DNA/You had to grow tons and tons of tiny cells” and “It’s amazing what heating and cooling and heating can do”. Many of the actors in the video resemble the original ‘US for Africa’ performers, such as Bob Dylan, Kennie Rodgers and Diana Ross, but in an intriguing twist, a few of them have also been given a subtle scientist look as well, so subtle that I cannot quite put my finger on what they have done to their hair and clothing to suggest this.

Undoubtedly the funniest part of this song occurs in the chorus. We’re told that one of the virtues of PCR, besides detecting mutation, solving crimes and facilitating recombination, is “when you need to find out who the daddy is”, at which point the gospel backup vocals respond with “Who’s your daddy?”. Near the end, as the chorus is reaching epic stadium proportions of poptastic euphoria, a thermal cycler is thrust into the choir and passed hand to hand overhead until one of the singers passionately embraces and kisses the humble apparatus. At the end, the earnest American voiceover declares: “For all the scientists out there doing PCR, BioRed salutes you.” A scientist friend of mine confessed she actually got a tear in her eye at that point – although she then owned up to having consumed an entire bottle of Pinot Grigio just beforehand.

The link has been e-mailed to me over ten times from a broad geographical area, which means that it has gone about as viral as anything scientific is likely to get. (I mean, we can’t really compete with sneezing baby pandas or shockingly inarticulate American beauty queens.) And the tune is perniciously infectious: in the past few days I’ve caught myself humming it several times.

I have a deep admiration for this clever bit of marketing. Not only is it refreshing to see a biotech supply company leaving the safe territory of cheesy slogans and puns that we all know and cringe over. But they are intimately communing with the perfect demographic on this occasion. I mean, think about it: who is actually in the market for a brand-new thermal cycler? Certainly not an old-timer, whose lab would already be well kitted out. And not a post-doc or graduate student: these folks don’t hold the purse strings. No, it’s precisely my age group they’re targeting – scientists who are old enough to have just started their own lab, give or take a few years, and are in need of core equipment.

And just at the right age, too, to have been in super-formative mode when “We Are The World” first came out. Scientists tell us that memories laid down in late adolescence remain the freshest and most precious. For recognizing this weakness and exploiting it, I can only say, on behalf of scientists everywhere:

“BioRad, we salute you.”