Mind the Gap

If you view biology as spanning a scale from the very large (blue whales) to the very small (organic compounds), I have almost always lurked around the miniscule end of the spectrum. My first stint of undergraduate research involved trying to understand the sexual proclivities of a North American tree called the Osage orange (_Maclura pomifera_ [Raf.] Schneid. [Moraceae]), a less edgy relative of cannabis and the beer hop. When I was a child growing up in Ohio, we used to wage guerrilla warfare using its weird fruits: about the size of a grapefruit, thick brainlike skin, highlighter-pen green – in short, alien spores from another planet, so full of latex that even the squirrels left them alone.

Truth is stranger than GMO An aneuploid Osage orange radicle cell with only 55 of its alloted 4 x 16 chromosomes (bar = 10 microns)

So it was only fitting that I would find myself studying this very tree. I used to dissect seeds from fruit vernalized in the cold room and nurse them to seedlings in the steamy greenhouse. I loved working in the shadow of that vast and fecund lemon tree, surrounded by tropical blooms while snow fluttered against the glass panels above. Back in the lab, I would arrest root-tip cells using mitotic poisons, smash them with care and use a camera lucida to sketch their bizarrely dysfunctional autotetraploid karyotypes: my first foray into the microscopic.

Things got smaller from then on. My PhD in Seattle involved viruses, those strange not-quite-alive entities first identified not by what they were, but by what they could do: pass through filters that bacteria could not. Feline leukemia virus, a tidy HIV-related moggie menace with only three genes, was on the small end of the virus scale, though later, in the Netherlands, I worked with an even tinier one, chicken anemia virus. The human tumor cells I use now are huge in comparison, many microns in diameter.

A scientist at the small end of things has to take a lot on faith. I spend most of my days dealing with diminutive amounts of colorless liquid. Sometimes I find myself staring at the pipette tip, where the quarter of a microliter of clear fluid I’ve just drawn up is almost invisible, a mere glistening under the fluorescent lights. How could this infinitesimal amount of stuff ever do anything tangible? Yet a few days later, it’s caused a black band to disappear on a Western blot, or made a protein turn cherry-red on a slide, or forced a cell to warp its shape from ovoid to grossly triangular. Even when I split my cells, I worry that the tiny drop I transfer to a fresh plate couldn’t possibly be enough to perpetuate the strain; yet sure as rain, three day later the plate is full to bursting with life.

There is nothing mysterious about any of this. But it still surprises me, all the same.

Following on from the ingenuity of our French post-doc, the ante has recently been upped by the lab’s Italian contingent.

Continental shelf A cheap solution for all your live microscopy needs

Feast your eyes on this little beauty. Necessità was surely the mother of invenzione when one of our PhD students fashioned the device lovingly from a tissue-culture multi-well plate lid and what is know in the trade as ‘Blu-tac’. You can nest your 35mm dishes into each of the six ports, which ensures that they stay put as the microscope’s automatic movable stage zooms around taking pictures of your living cells.

Bellisimo.

This past Friday, though I didn’t realize it until well after midnight, marked my completion of a full year back in the lab. Time, as it always seems to do these days, has sped by more quickly than I would have thought possible, so much so that I have difficulty now remembering how it felt to be on the cusp of leaving the safety and security of an editorial universe for something much more tenuous.

My experience of returning to the lab has been an exercise in how not to take anything for granted. I can still acutely recall how it felt last year, in the bleak midwinter of 2007, when I had decided to go back to the bench but had only the faintest hope of achieving that goal. My scientific self then was still very much unallayed by four years in publishing, and it bled through in a thousand tiny examples. You could see it in the way I would measure water to the meniscus, and flour to the nearest tenth of a gram decimal place, when loading up the bread maker, and in how I experienced a twinge every time did so, remembering the life I had lost. Filtering my world through a scientific lens was not something that ever left me, even as my days were filled not with discovery, but tedious office politics, reams of manuscripts, freelance writing and all the other mundane trappings of a life more ordinary.

My enthusiasm may not have been blunted, but once I arrived back in the lab it became painfully obvious that the practical day-to-day skills of scientific research had grown rusty over the years, muscle memory notwithstanding. In fact, I would say it is only in the past few months that I have finally felt like my old self. I had to retrain myself to read papers like a scientist instead of an editor; to multitask experiments instead of doing them one at a time. Every time the twists and turns of my project led me to a different technique, I would hit the wall of yet another approach that I used to command without thinking but which I could now no longer remember how to approach. Having been unable to locate my old mildewing protocols and notebooks in the loft, I would be reduced to scouring the internet or pestering friends to remind me how to prepare a gradient gel or make a stable cell line. Surprisingly, it was the need to do mathematics that revealed the biggest gaps in my memory but, like anything else, if you don’t exercise your skills, they become flabby. And over the past year I have plowed through the calculations until they have again became second nature. A year on, I no longer walk into the common room and feel like an impostor.

It is a cool twilight in my garden, and my skin is still faintly tingling from the doses of solar radiation I took earlier. Blackbirds twitter, swifts cry overhead, a cloud-colored crescent moon hangs over the rooftops. I don’t know what will happen when my fellowship runs out in early 2012, but that doesn’t matter at the moment. For now, I am a scientist again, and I’m not ever going to take that for granted.

Biomedical research is a costly business. You don’t really get a visceral understanding of just how costly until you become the principal investigator on a hefty source of funding and start monitoring your own balance sheet. You can easily drop £300 on a dollop of antibody or £7,000 on a custom siRNA library, but even the day-to-day plastic consumables quickly add up.

Makeshift kit MacGyver would be proud

Perhaps because of my frugal upbringing, I have a thrifty streak in me. I despair, for example, that some of my lab mates like to purchase ready-made bovine serum albumin solution instead of making it themselves. For those of you who aren’t biologists, you essentially weigh out some fluffy powder into a beaker, add water, put a small magnetic bar into the beaker and set it tinkling on a stir-plate for five minutes or so until it dissolves: all very therapeutic. As a reference, it would actually take more time and effort to put through a purchase order request for the ready-made stuff.

In this spirit – with just a few special exceptions – I am always keen to encounter low-cost alternatives. I suspect I am not alone in this. When physicist Rolf Landua was showing me around the antimatter generator at CERN for a piece I was writing for LabLit, I was almost more amazed by the sheer amount of aluminum foil and gaffer tape in evidence than by the idea of those elusive subatomic particles being created and annihilated not two feet away from me. I love the ingenuity of scientists across the full spectrum, but somehow a solution cobbled together with everyday objects is more wholesome and genuine than the shiniest piece of technical wizardry.

So I took immediate interest the other day when I noticed something very unusual lying next to the microscope in the cell-culture room. If you look at the image above, you can see that the object in question used to be a 384-well screening plate. In its undisturbed configuration, each square plastic well can comfortably grow several thousand living cells, and the plate has a glass bottom suitable for subsequent immunofluorescence microscopy (as in the picture here). This pimped-up version, however, as crudely fashioned as a knapped flint, seemed designed to hold a 3-cm tissue culture dish. But who, how and why?

The ‘who’ was easy enough; the initials belonged to our French post-doc, a wily biophysicist who is very clever with his hands. The ‘why’ was clear from what was scrawled on the autoclave tape: it transpires that our big centrifuge has adapters for the screen plates but not for round dishes, and this baby was designed to help spin down cells for quick attachment to the substratum.

But what about the ‘how’? To discover the modus operandi, I had to ask the Frenchman himself. With his trademark cheeky grin, he explained that he had used a hot hammer – or, as he put it, a ‘ot ‘ammer. After dissecting out an 8×8 area of the well matrix, he had superheated the blunt end of the humble DIY tool with the gas burner until it glowed orange, then pressed it into the plate.

Et voilà: the lab is saved another few hundred quid.

What, you may ask, is a rainy bank holiday weekend good for? I’ve have plenty to do in my self-inflicted rota of Purgatory extracurricular tasks, such as preparing the next issue of LabLit, giving my novel one final polish before sending it off to the publishers for copy-editing, and attempting to stay afloat in the Web 2.0 universe.

Fringe benefits A good read about unorthodox science

But one obligation is decidedly not a chore. And that is reading Philip Ball’s debut ‘lab lit’ novel The Sun and Moon Corrupted, which will feature in our first Fiction Lab book group at the Royal Institution on 9 June (blogged about in more detail here). It’s a page-turner, so if you live in or near London, it’s not too late to pick up a copy and join us for the juicy post-mortem in a few weeks’ time.

I’m only halfway through, but it’s a cracker of a story. I won’t give away the plot, but it deals heavily with fringe science, which lies on a continuum between quackery and legitimate (or at least, accepted) knowledge. Often, the fourth dimension of time is the only thing that separates fringe science from its ‘real’ counterpart; anyone studying molecular biology in the 1980s will recall the scathing and incredulous reaction that Stan Prusiner and his wacky-seeming self-replicating prion proteins received in the traditional community – in stark contrast to his momentous encounter with the Swedish monarchy in 1997. Ball’s novel deals with people who doubt Einstein’s view of quantum mechanics, and offers a fascinating view into this nether, neither-here-nor-there universe of scientific culture.

But we can discuss all that on 9 June. What I am enjoying most of all are Ball’s scientific similes, metaphors and assorted descriptions. I’ll leave you with one of my favorites so far for a taster:

“Light was no longer a beautiful beam, a wave stretching from here to infinity. Light was quanta. Light was discrete. Light was particles. Call them photons. These photons won Einstein a Nobel Prize.

But Neder could no longer sit in the sun without feeling like he was being showered with fine grains. The sun was a sandblaster. The stars were tiny pea-shooters. The moon was a springboard for little shards that stung his eyes. The cosmos had come apart.”

Can being a writer actually make you a less efficient scientist? For the past few months I have been knee-deep in a high-throughput RNAi screen for pathways that affect cell shape and the actin cytoskeleton. Automated image analysis has come a long way recently, thanks to the work of people like Anne Carpenter, whose CellProfiler program revolutionized the field. But detecting the textures and shapes of subtle morphological characteristics against the backdrop of normal cell variation is still in its infancy, and nothing so far can beat the discriminating power of the human eye. Although we have a few talented computer scientist collaborators working on the question, I’ve still had to sift through nearly fifty gigabytes worth of images by eye.

Worth a thousand words: But only a dozen are permitted

Not only do I have to look at these cells, but I have to describe what I see using a controlled vocabulary. From this descriptive annotation, we can boil everything down to numbers, and thereby start to cluster and compare all the various manifestations of our gene knockdowns. Biology to numbers, and numbers back to biology.

So far, so good. You would think, as a writer, that describing what I see would be the easy part. My bioinformaticist collaborator assigned a list of about ten features, aspects such as “cell shape”, “actin”, and “cell number”, and told me to tick “yes” if what I saw differed from the negative control cells, or “no” if it didn’t. There was also a Notes field at the bottom where I could jot down any additional comments, which the bioinformaticist said was usually left blank.

But soon, as I began sifting through the images, the parade of weird and striking manifestations quite overwhelmed the simple digital system. Just in the “cell shape” category alone, the word “yes” seemed insufficient to cover the reoccurring and surprisingly regular morphological themes that unfolded: triangles; star-shapes; bipolarized elongated spindles; rhomboids. Ruffled lamellae pushing in multiple directions like a fractal pattern. Sharp-edged vertices with precise actin-rich points at their tips.

Surely, I reasoned, if these shapes were well represented enough to become familiar to me, it would be a shame not to record the information; and this was true for all the other categories too. If I did it in a way that could be retrieved later, surely we could subdivide the original descriptors in retrospect and make our clusters that much more informative. The bioinformaticist gave me the green light, so I began to use the Notes section. Copiously. Some of the images were so complicated that I ended up with paragraphs. I was incredibly careful, or so I thought, to use consistent words and phrases and to subdivide these with consistent punctuation for ease of automated text-mining extraction later.

Of course it all went horribly wrong.

“You’ve spelt ‘multinucleate’ twenty different ways,” the bioinformaticist informed me dourly. “I’d hate to be your editor.”

Spelling was the least of our problems. When he tried to extract phrases separated by commas, it soon became clear that I’d mistyped or missed out commas in many places, or used them in list series as you would in prose. When he decided to bin the phrases and just take individual words (1274 words with more than two letters, to be exact), the decoupling of adjectives from nouns – and the mingling of different aspects in the same paragraph – was deadly. Of course it’s so clear now I should have stopped annotating early on as soon as I realized the scope of the problem, subdivided all the digital descriptors and started over, but at the time, it had all seemed workable. So I’m cleaning up the list now, and will need to go back and manually reannotate. The bioinformaticist is trying to restrict me to twenty terms; I am secretly fomenting rebellion.

When scanning down the spreadsheet of all the nouns, adjectives and adverbs extracted from the Notes section, removed from context, I feel heartily embarrassed. Did I really see fit, over those long weeks, to use terms such as “beads-on-string”, “curviness”, “cross-hatched”, “raggedy”, “stellate”, “splotchy”, or (oh God) “fried-egg”? My inner novelist, impossible to avoid. But it did make me start to think how Henry Gee the great writers of the ages might have annotated my screen. Perhaps Homer would have seen a “wine-dark” quality in particular nucleoli, or considered a wonky spindle to be “well-greavéd”. Robert Browning, when contemplating a wispy actin phenotype, could have evoked the long grass amongst Roman ruins where lovers lie, “such a carpet as, this summer-time, o’erspreads/And embeds”.

And I like to think that P.G. Wodehouse might have deemed a particularly spectacular set of stress fibers “dashed decent”.

Sometimes works of the past can reach out across the centuries and speak directly with a timelessness and universality that their creators never dreamt they’d inspire.

Still life Old natural history drawings continue to resonate

Yesterday I attended an RSA Fellows evening at the Queen’s Gallery in Buckingham Palace. There, we were treated to a private viewing of the superb exhibition Amazing Rare Things: The Art of Natural History in the Age of Discovery, which was assembled by David Attenborough and the Royal Collection curators. (The exhibition is on until 21 September, so if you live in or near London I would highly recommend taking a look. And if you don’t, the accompanying book is lavishly illustrated and well worth the modest price.)

The exhibition was pitched to capture the excitement of enquiry at a time when so much of this planet’s flora and fauna was still unknown to civilization, and spans the 15th through 18th centuries. Many of the drawings and paintings seemed to me as lucid and vital as if they had been created only last week, glowing behind their protective glass like a portal through time and space. In some cases, the species depicted have lapsed into extinction, so the strange connection felt even more imperative.

Leonardo da Vinci’s sketches were an obvious attraction for my inner geek. The Queen owns an astonishing six hundred of his drawings, thanks to the acquisitive instincts of Royal Society founder Charles II, and a few dozen of his best were on display. That anyone could have wrought such fine details using a piece of sharpened red chalk is almost as remarkable as the state of their current preservation. I was in another universe, arrested before oak leaves and filigreed acorns bursting off the page, blackberries swelling on bramble begging to be picked, casual feline poses immediately recognizable to any cat owner. Snapshots from half a millennia ago. Nothing, it seemed, was beyond Leonardo’s shrewd inspection, a drilling down into the essence of life; he could make even the hindquarters of a horse or the dissection of a bear’s paw into a work of art.

Although Leonardo was obviously intended as the headlining act, I think for me, German naturalist Maria Sibylla Merian (1647-1717) stole the show. Fascinated with insects and spiders all her life, she went to Surinam in 1699 to document the weird and wonderful species to be found there – a remarkable feat for anyone, let alone a woman at that time. In addition to the published product of this venture, _ Metamorphosis Insectorum Surinamensium_, she produced deluxe poster-sized watercolors on vellum of many of her compositions (one of which is pictured on the book cover in the image above). For compositions these are: not sketched as seen in the wild, but rendered as idealized tableau of plant and animals in complex and wondrous interactions. For Merian, beauty seemed to encompass death, and death, beauty. I stood entranced before caiman devouring false coral snakes, giant water bugs overpowering tree frogs, a hairy tarantula bringing down a hummingbird, all in deceptively serene Garden of Eden-style backdrops of passion flowers, water hyacinths, pomegranate trees and cassava roots.

The exhibition made me wonder what damage modern technology has done to our appreciation of nature. Of course the camera can render beauty, and remarkably well, but what the naturalists in this exhibition were trying to achieve seems far more than a precise scientific record of their subjects. Yes, they are painstakingly and anatomically correct, but the manner of their presentation – the artistic lens applied, in colors, composition and arrangement – seems to impart an emotion that even the most skilled camera operator would be unable to muster if restricted to real life. And if, like me, you respond to nature as much emotionally as scientifically, this distinction can make a big difference.

Back in the days when my hair was longer, my blood hotter and my T-shirts, more tie-dyed, I used to be a rampant feminist. I earned my undergraduate degree at Oberlin College, which my fellow Americans will recognize as one of the most liberal of the liberal arts colleges. Founded in 1833, Oberlin was the first American university to allow in black students (1835), female students (1837) and, more scandalously, the cohabitation of male and female students in the same hall of residence (1969). My four years there earning a BA in Biology seem like a haze of protests, marches and carefree gigs as one of the three barefoot tenor pan players in the Oberlin College steel drum band. Despite this, the academic regimen was fierce: alongside the rigorous science classes, I was also exposed to elective coursework as diverse as Ancient Greek, anthropology, Hispanic poetry, ethnomusicology and Ultimate Frisbee.

Hippie days Spot the blogger in this impromptu gig underneath Mudd Library, circa 1989

I should clarify that I am still a feminist, if you define feminism as the desire to see women enjoy the same opportunities and rewards as men for expending the same amount of effort. I adore men too much to be in the man-hating, bra-burning category, and neither am I a person who deludes herself that women and men are not different. Instead, my feminism these days is lumped into a larger ethos, that of loathing injustice in whatever guise it might take; for example, the thought of earning less pay for doing the same job quite understandably irritates.

Today I had the pleasure of enjoying my first female power lunch since joining the ranks of staff at University College London. Organized by the indefatigable Uta Frith, a well-known developmental psychologist and Fellow of the Royal Society, these lunches take place six times a year at the RS and offer an opportunity for so-called ‘high-flying’ female academics in the sciences to network – so I was thrilled to finally get the nod.

What transpired? We discussed a recent Current Biology article that Professor Frith had sent around for us to read beforehand, a thoughtful and balanced meditation on a female life in science by the Nobel-winning developmental biologist Christiane Nüsslein-Volhard. There was a lot of musing about why many at the table were earning less than their male colleagues, how UCL could get away with allowing a particular science committee to be held at an all-male private club, and what could be done to set up less formal and more frequent female get-togethers. All in all, thoroughly enjoyable.

Still, I must confess that I have always wanted to be a fly on the wall at an old fashioned, God-fearin’ old-boys-club networking session. In my mind’s eye, men are so sorted that they don’t have to talk about their situation. They are, I imagine, free to socialize and chat about sport or politics or whatever else takes their fancy. Women, on the other hand, get the opportunity so infrequently that they can’t afford to be anything other than meta about what they are trying to achieve by coming together. So I suppose that we’ll know we’ve arrived when the lunchtime topics are free to roam far beyond the constraints of gender.

Everyone seems to be writing papers at the moment. The other day in the office, two of my labmates were sitting at a computer, thrashing through the proto-Results section of their jointly first-authored magnum opus. In such close quarters, the rest of us were unable to avoid being included in the audible brainstorming process.

I started thinking, then, how many stock phrases occur in manuscripts. Why is it, for example, that adverbs like ‘interestingly’ seem always to be deployed for the most boring results? When I voiced this rhetorical question aloud, we decided to stage an impromptu competition for more original adverbs.

“Earth-shatteringly, there was no significant difference,” someone proposed, getting into the spirit. Other top picks included ‘astonishingly’, ‘tantalizingly’, ‘mind-bogglingly’, and – a personal favorite – ‘Lo and behold’.

My own lab’s papers are not the only ones I’m helping out with, however. Over the past few months, word has spread throughout the institute that I used to be a journal editor. Now, I find that I have become an agony aunt of sorts. Hardly a day passes without someone making that pilgrimage up to the third floor, sheaf of papers in hand, to seek out my Delphic advice on various points of manuscript etiquette:

Does this cover letter sound too aggressive/wimpy/cocky/demure/over-confident/smarmy/fatalistic?

I realize they’ve rejected my paper outright. But if you read between the lines, do you think they might secretly want it back?

How can I imply that referee 2 is an imbecile without sounding defensive/insecure/unbalanced/violent/vindictive/petty?

Which of these experiments does the editor really want me to do, and which are just window-dressing?

Do you think I can buy four more weeks for this revision effort if I tell the editor that the first author is on maternity leave?

It’s only since I’ve been back in the lab that I’ve realized how much the publication process is like an elaborate mating game. With its rituals and codes, artifices and conventions, it is ultimately a relationship in which the authorial side was never meant to truly commune with the editorial. For me, understanding and empathizing with both sides is both a blessing and a curse. When it comes time to write up my own paper in a few months’ time, I can’t decide whether I’ll feel more like a schizophrenic or a double agent.

The history of our fair profession is riddled with stories. First and foremost are the journal articles themselves, which seek – in their own characteristically arid way – to describe an incremental advance and thereby place it into the context of wider knowledge. But these are not, in many ways, the truest or most interesting stories that science has to tell. Behind every journal article is a drama enacted by a cast of characters on a high-pressure international stage. And for every sentence that makes it into a paper, there must be thousands for which there is no room. Inevitably shunted to the background are the narrative details that would bring these discoveries to life, breath color and meaning and passion into the collective human acts that resulted in each official snapshot of hard-won knowledge. That such papers do not – or cannot – flesh out the narrative has been a cause for chagrin as much as humor with some of my LabLit authors.

Rapt: Even the PRS likes a good story

When you strip away the formal scientific record, all that is left are the stories of the people who were part of creating it. Of course some scientists write autobiographies, but our collective library of scientific tales is primarily a verbal one: pub stories, rumors, speculations, fading memories, back-stabbing mutterings, second-hand accounts and urban myth. We know that even first-hand retrospective accounting is bound to be flawed and incomplete, warped by the perspective. Like snowflakes or Henry Gee’s anecdotes, no two are likely to be alike. And as scientists age, especially those who have made pivotal discoveries, we risk losing their crucial stories. This is why projects such as The People’s Archive, and others like it, are so important.

Last night I enjoyed the privilege of dining at the Royal Society with a small group of scientists who’d been invited to celebrate a public lecture given just before by Eric Kandel, professor at Columbia University and recipient of the Nobel Prize for Medicine in 2000. I was already primed to think about scientific memory thanks to the contents of Kandel’s excellent talk: an account of the neural systems and molecular mechanisms that contribute to learning and long-term storage. After the desserts were cleared away, Kandel tapped on his glass, uncharacteristically serious, and began to reminisce about the story behind the key discovery typically attributed to him. Was it this way, he asked; or was it that? Did this post-doc or graduate student make a key finding that pushed the momentum in the right direction? Did that colleague give up too soon, paving the way for someone else to take up the slack? One by one, the other men around the table who had been involved in the narrative began to offer their own accounts: Tim Bliss, John O’Keefe, Richard Morris, tossing the ball back and forth and seeing where it led.

I’m not sure if anything conclusive was decided in this spontaneous reexamination of reality, but it was a magical moment for me, and for the rest of the table too, to judge by our hushed attention – unexpected witnesses to a reassessment of history.

At one point I leaned over to Martin Rees, on my right, and whispered that it was a shame nobody had brought along a tape recorder. He nodded solemnly, then whispered back that it was a good thing I was taking notes.

I look at these now, and they are nothing: just a few random scrawls, dead on the page. The real story has been imported into my short-term memory, firing up second messengers and action potentials somewhere deep in my hypothalamus. But it will never be the same as the living, breathing moment that has already passed.