Mind the Gap

I’ve just had an epiphany of sorts. A lab colleague of mine wanted to read the most recent draft of my second novel, still in manuscript form, but quite fancied trying out a shiny Sony PRS-505 electronic reading device that her husband had recently brought back from the States. We thought it would be fun to import my manuscript onto her reader so she could critique the draft and trial the new toy simultaneously. So I took the thing home for the weekend to see what it could do.

In short, I’m now smitten. Not necessarily with the Sony, which isn’t quite perfect, but with the entire e-reader concept. Whenever I thought about e-books in the past, I envisioned an ugly backlit screen inducing eyestrain and headaches. To say nothing of the fact that relaxation, for me, is an escape from the screens that already dominate so much of my waking life. Never mind the hype about Japanese schoolgirls reading novels on their mobile phones – could someone as traditional as I am actually curl up on the sofa with Bill Evans the cat and lose myself in one of these things?

The answer is yes: emphatically so. The technology, which I believe is called eInk and comes courtesy of Phillips, is amazing. The print is so paper-like that the page can only be read in the light – a complaint from some consumers but a distinct plus in my opinion, not being a big fan of reading in the dark. The text was also beautifully rendered, in all three handy sizes. After a few minutes perusing a sample e-Book, I found my right hand subconsciously floating towards the top right corner ready to turn the nonexistent page. To me this implies that my mind was completely fooled and thought it was a real book. Not being able to suspend disbelief would have been the death knell for this platform, but it was no problem at all.

For me, another key factor is convenience. The Sony is slimmer than a paperback and probably no heavier. I’m one of these sorts of girls who lug around too many things in a handbag, so lately my literary choices have been based more on width than on authorship and reputation. If I can’t commute easily with a book these days, it doesn’t get read. And imagine going on a trip with only one paperback-sized item instead of ten. Run out of material in a country that has no easy access to books in your language? You’re only a dodgy internet café away from topping up.

You can download your own documents onto the Sony as well, just by converting Word to rtf. It took me about five minutes to get my novel onto my friend’s reader, and the formatting was perfectly preserved. When I eventually buy a reader of my own, I will try to use it for my scientific reading. It will be easy to convert manuscripts and grants in preparation and those I’m helping to peer review, whereas I assume I can take the full-text version of a published paper, paste into Word and convert to rtf. No figures, of course, but I’m the sort of person who likes to go through the entire text first before examining the figures anyway. I’m already guilty about how much paper I waste printing out the literature (and often get a sore shoulder from the weight of my bag), so the reader could be a great solution.

If anyone out there has tried another type of reader, such as the Kindle, or has any reservations about the Sony, I’d be grateful to hear your feedback before I make the purchase.

In the meantime, I always thought I’d mourn the loss of paper books, a transition bound to be inevitable. But suddenly, I’m not so sure it will be as heartbreaking as I’d imagined. How many years away, do you suppose, are we from that world?

You might think you have some control over your life. And it’s true that you can carry on in a purposeful direction with a bit of thought and effort, but still events will tumble across your path, and nobody can stop the wind from blowing.

Parallel universe: What else is out there?

I don’t know about you, but I often become hyperaware of the invisible web around me, its threads spun from cause and effect, missed possibilities and lucky breaks. If I decide to take the bus instead of the train, I wonder what opportunity or mishap might have been avoided (or gained) in the process. Almost every job I’ve ever had has resulted from random collisions with strangers; my first position in publishing came about from a series of events kicked off by having dinner with the friend of a friend on a balcony one warm summer night in Amsterdam. It would never had occurred if I hadn’t followed the random events that forged that particular friendship, that led to my move to the Netherlands; neither would it have happened if the friend of the friend had not followed his own trail, dropping by our Dutch flat on a whim during a business trip.

And all of these possibilities go on forever, in all directions, all of the time. If you thought about it too much, it would either incapacitate your decision-making capabilities or drive you mad. But thinking about it a little, I think, is good for you. It keeps you sharp, and inspires you to put yourself in as many interesting situations as possible – the more threads in your web, the better.

Over the past half year, I’ve blogged about resuming a research career after a four-year break. When I made the switch, it was into a relatively shaky situation: eighteen months of funding on the tail end of someone else’s abandoned fellowship. When you are as far away from your PhD as I am, the possibilities for further funding are extremely limited. Just before I started in the lab, I applied for a Wellcome Career Re-Entry Fellowship : four years of solid funding, more than enough to get me back on my feet – and pretty much my last realistic hope.

The application was reviewed, and I was selected for interview. Life may be random, but I put a hell of a lot of effort this past month into being as prepared as possible for my big day. Because I am working in a new field, I haven’t studied so hard since I was an undergraduate: I wanted to know everything from first principles. I started with the superlative Cell Migration Gateway, then graduated to basic reviews, followed by more specialized reviews and primaries. I went to an Actin meeting in Bristol, and one on RNAi. The day before the interview, I put myself through a brutal mock interview with a few lab heads at the institute that nearly finished me off: for one brief moment, I fantasized about cancelling the whole affair.

The fateful morning dawned brilliant blue. I stayed home to do some last-minute preparations. I read and re-read my proposal; penned before I started in the lab, it contained a few vulnerabilities and grey areas now obvious after half a year’s experience. I practiced looking in the mirror and saying, with unwavering confidence and excellent posture, how I would respond if they asked me why I had left science, why I wanted to come back, why my work was important, where I saw myself in five years’ time. Before I put on the suit, I took a long run in the woodlands around my house. Everything was gripped in heavy frost, delicate white lace delineating each blade of grass, leaves like crystal shards, a thin film of ice on the ponds and streams, pebbles and gravel dangerously slick. Droplets of water rained down from the canopy: sky-high ice melting in the sunlight. Squirrels, magpies, robins, even a skittish young fox, scattered before me; the air was so cold in my lungs that it hurt. I told myself that it didn’t matter how things turned out. If I got the fellowship, my journey back to a scientific research career would continue unabated. If I did not, I would probably have to leave the lab at the end of next year, but I would find something else, and this something might be every bit as fulfilling. Either way could be the right path.

Today I got the call: I was awarded the fellowship in full. Multiple paths and unknown alternative opportunities be damned: I was ecstatic.

Every so often I like to stray outside my comfort zone. You won’t find me jumping out of airplanes, but as a scientist, I do like to keep an open mind about things I know nothing about.

A hoarse of a different color: Pangdahai to the rescue?

My most recent experiment with the unknown has involved Chinese medicine. I’ve been struggling with periodic laryngitis for weeks now, and with a band gig this past weekend requiring me to be in good voice, I had tried pretty much everything Boots the Chemist had to offer. In fact, a few of my labmates swore they could sense my imminent arrival by the menthol and eucalyptus wafting down the corridors.

One morning our Chinese PhD student (and also a fully trained medic) brought in a small packet containing a handful of strange, furry-brown nut-like objects: Pangdahai – the dried seeds of the Asian tree Sterculia lychnophora. A ‘cold’ medicine, he informed me, to counteract the ‘heat’ of inflamed vocal cords.

Now, I don’t know much about the proposed explanations behind Chinese medicine, a lot of which sound to my untrained ear more metaphorical than mechanistic. But I do recognize that many of our most important Western drugs, from aspirin to taxol, come from plants, so there is no reason to think that with a few thousand years of experimentation, the Chinese might not have come up with some interesting botanicals themselves. After all, when the Neijing Suwen (_The Basic Questions of Internal Medicine_) was purportedly written around 2600 B.C., my ancestors were busy thwacking each others’ heads off with the latest must-have gadget: the bronze sword.

And then of course there’s that line from the 1987 film The Lost Boys: “Tell me, Michael, how could a billion Chinese people be wrong?”

My willingness to give Chinese herbal remedies a try was recently boosted by a Nature paper from Laura Parton and Bradford Lowell at Beth Israel Deaconess Medical Center and Harvard Medical School in Boston which showed that genipin, derived from gardenia fruit and used in Chinese medicine for centuries against Type II diabetes, actually exerts its molecular mechanism by blocking UPC2, a protein that inhibits glucose sensing in the pro-opiomelanocortin neurons of the hypothalamus (doi: 10.1038/nature06098). Urban myth has it that a Chinese post-doc in the lab persuaded Lowell to let him give genipin a try in their system.

So. Pangdahai. Put the seed in boiling water, and allow it to bloom into a brownish-red gelatinous mass about eight times its previous size. Drink five changes of water, the second being the most potent. Not without some degree of trepidation, I might add. The result? It made my face tingle, and it felt pretty nice on my throat.

I’m not, however, entirely convinced it felt any nicer than hot water alone. Now where did that ‘control me’ get to?

I should be above aesthetics at this stage of the game. After all, am I not a hardened professional scientist, squinting heroically into the winds of the unknown?

Heartbreaker: mammalian cell division

But bravado unravels in the face of truly beautiful data. And I don’t mean ‘beautiful’ in the euphemistic sense that Nature authors use when they are trying to explain why their latest result both kicks butt and will cure cancer. I mean ‘beautiful’ as in the sort of image that catches your breath.

At the moment, I’m playing with a new human cell line kindly provided by a collaborator. It expresses histone fused to monomeric Cherry and alpha-tubulin fused to eGFP, and I’m filming these cells as I inhibit various genes with RNA interference. I’m supposed to be looking for cell shape and cytoskeletal defect phenotypes, but I keep getting distracted by mitosis because it’s so damned beautiful. The cells round up, their cherry DNA hearts beginning to glow like molten lava. Then the chromosomes muster out of nowhere and line up in a scraggly red row, the livid green spindle jostling them into place like fingers. Then whoosh – apart go the fingers, the heart is broken into two and the greenness goes diffuse and pinches apart. The lava cools and the two daughter cells form around them, fading back into the blackness.

My brain, knowing an interesting thing when it sees it, keeps forcing my eyes to zero in on the mitotic events instead of keeping watch on their flat, unassuming interphase colleagues. It’s like being told not to think of ten bald men.

(p.s. I haven’t made stills from my movies yet, so the above image was donated by a friend who wishes to remain anonymous. Cheers, mate!)

I just can’t resist. The cat’s away for more than a week, which just happens to coincide with a big genome-wide screen I’ve been putting off for a few weeks. As there’s no one waiting at home for a nice dinner, why not go a bit mad in the lab? It will be just like the old days, staying late and sacrificing everything for my Art. I might even achieve at least one all-nighter like our new French post-doc, who stayed welded to a confocal microscope for 36 hours the other weekend (I knew immediately something was wrong the moment I saw him in the lab at 9 a.m. on a Monday morning). All in the pursuit of knowledge, mind – not to make the rest of us postdocs look bad.

All hail to the mighty WellMate, mistress of aliquotification

To be honest, I’m not sure I’ve still got the stamina of yore, especially with my current nasty head cold. The Biomek, alas, is out of action – but this little beauty is going to help me all she can. Behold the Matrix WellMate, which can fill 384 wells with a defined amount of liquid in about four seconds. Isn’t she lovely? She makes a multichannel pipette look like an Ancient Greek pottery shard. With the Matrix WellMate, I don’t need to be afraid, or alone. My life has purpose, meaning. My soul can float to the top of the lab, free of all earthly encumbrances.

Or is that just the antihistamines again?

Wish me luck!

Recently, the ex-practicing scientist Daniel Glaser of the Wellcome Trust, with mock-horror, used me as an example of the fact that no scientist leaving the lab was ‘safe’ from getting sucked back in. Even though I’ve been restored to scientific research for four months now, I am still quite regularly asked why I decided to return in the first place. It’s actually rather complicated even in my own head, and the answers often shift on a daily basis. But the truth is that my father, Dan Rohn, had a lot to do with it.

Journey into the unknown Detail from ‘Sentimental Journey’ by M. Daniel Rohn, taken on the Pelee Island Ferry, Lake Erie, 1953 (p.s. that’s my mother, Mary)

Dad, now retired in Colorado with Mom, is an emeritus art professor at Kent State University (whose academic reputation is still overshadowed by a sad incident involving four students gunned down by the Ohio National Guard in 1970). He started out as a painter and lithographer, including a stint earning his stripes as an assistant to Jasper Johns and bouncing ideas off his friend Roy Lichtenstein. Over the years, he’s worked with a variety of media and taught thousands of students, including most of the members of the New Wave band Devo (I can still remember the day he came home with the 45-inch single of ‘Whip It’). One of his paintings resides in the permanent collection of the Cleveland Museum of Art, and in later years he began to work with 8×10 platinum photography, an art form rendered obsolete by George Eastman’s discovery of the utility of silver halide for coating printing paper around the turn of the last century.

Despite the expense of its materials, platinum printing has since undergone a small revival, and I can testify to its unearthly beauty: though strictly black and white, the hand-coated platinum/palladium mixture still manages to impart a subtle warmth, and a seemingly infinite number of pixels. Dad became known in this niche field and has exhibited and won various awards for his beautiful landscapes. In fact, one of his images of Edna St. Vincent Millay’s snowy garden was featured on the cover of a prominent collection of the poet’s complete works.

But when Dad was younger, he had another active passion: singing. With a lot of hard work, he became an up-and-coming tenor in the prestigious Cleveland Orchestra Chorus. Although he has never talked too much about the tension between these two passions, it’s always been clear to me that the decision to settle on an art career was a painful one – and that, over the years of getting ground down by the many thankless and unremunerated aspects of teaching, it might have been one he had cause to regret.

Previously, I always felt fortunate never to have had this problem. With single-minded intensity of focus, I had wanted to go into biological research for as long as I could remember; in the seventh grade, I was even bestowed a cheap plastic medal inscribed with the words, ‘Most likely to become a scientist’. Nothing could deflect me from my path, I thought – until I got knocked off it in 2003 in the avalanche of a biotech bankruptcy. Four years into my new publishing career, the doubts had been steadily accumulating. But when I tried to look at the problem logically, head-on, all I could think about was twenty-something Dad, wavering on a pivotal point between art and music before taking his fateful fall into one side of an irrevocable life decision.

But that’s the thing I finally realized. Nothing is irrevocable. It doesn’t matter how old you are when you realize you’ve made a mistake – you can always start again. I guess my generation has been lucky in this regard; back in Dad’s day, you got a job and you plied it for life, for better or worse. It is only by a lucky accident of birth, being raised in an era and a society when all things are possible, that has allowed me this precious second chance to get back on the right road.

There’s a thread running on the LabLit forums inspired by a recent news article in Nature about two young scientists who have been facing an uphill battle to get their unconventional work published. Have a look at Erika Check’s piece for the details, but briefly, two youngish researchers have been compiling evidence that miRNAs can occasionally activate genes instead of knocking them down. After a lot of experiments and numerous rejections, they finally managed to get some of the findings published in PNAS. But despite a few additional supporting papers from independent labs, apparently most of the RNA interference community still doesn’t believe them. (Interestingly, one of the researchers says he’s been scanning through archives of biology message forums and found that “other scientists – often graduate students – have also seen evidence of RNA activation. But they have been encouraged to discount it”.)

Now, I haven’t had a chance to read the PNAS paper yet, but clearly, if the work is true, it’s an important piece of information for researchers to know about. Not just those who study the biology of small RNAs, either, but the even larger proportion of folks, like me, who use siRNA as crucial knock-down tools. The big journals say they can’t publish without a ‘mechanism’, but I suspect that if an RNAi luminary like Greg Hannon, Craig Mello or Thomas Tuschl had submitted this work to a top-tier journal, the referees and editors might have been a bit more receptive. In short, the inexperience of the authors was probably one of the main sticking point.

In some ways, I suspect it’s healthy to have your skepticism dial turned up to eleven when faced with inexperienced researchers. Not only are they more error-prone but, let’s face it, they are also packed full of youthful excitability. I can still recall in vivid detail during my first year of graduate school, on several occasions, racing from the darkroom to my boss’s office, so flushed with a good result that I didn’t even bother to check the precise order in which I’d loaded my samples onto the gel. And Julie would give me that look, frogmarch me back to my notebook – and I’d belatedly realize the whopping dark band I was celebrating was actually just the positive control.

How times have changed. These days, I’m treating cells with siRNAs targeted to novel genes and looking for phenotypes. I’ve had a beautiful phenotype staring me in the face for weeks; I’ve repeated it five times using different conditions, made cautious scribbles and sketches in my notebook about how there “appears” to be an effect – the images are annotated with circles and arrows and everything. I’m camped out by the microscope. But somehow, I just haven’t been able to truly believe it. And here’s the crux: I think it’s also about age, but this time the other side. We might be hyper-gullible about our results when we first start, but as we get wiser and more cynical, it gets harder to convince ourselves that our own data is real, let alone that of some green newbie fresh out of grad school. (Disclaimer: I am speaking generally. Some of my best friends are green newbies fresh out of grad school.)

Of course, thanks to hearing about this weird new activation role of small RNAs, my scepticism feels entirely justified. Just as I was feeling comfortable with my phenotype, I suppose I am now obliged to suspect that it was an artefact all along.

But no, it’s too late – I’ve already given it a name!

(See, I knew reading Nature was dangerous. Cheers, Erika.)

Maybe some of you will recognize the following scenario. I was ill a few days ago with a bad cold and forced to take a few days off from the lab. As I lay in bed, too drained to do anything but doze, I found myself strangely elated. How, I wondered, could such a miserable condition be in any way cheering? And no, since you ask, it wasn’t the antihistamines. It was the realization that I was in fact too ill to do anything. Even if I did feel physically up to sitting at my computer, I did not have the mental wherewithal to exert myself intellectually. In short, I was being forced to relax and do nothing.

Non-negotiable oblivion

Had I really reached the state where being ill was only thing that could excuse me from my (entirely self-imposed) obligations and ambitions?

Now I know I’ve made quite a fuss about how it’s personally important for me not to spend too much time in the lab. But the truth is that I work very hard outside of the lab on personal projects. In addition to a variety of freelance activities, including writing, editing and consulting, I am trying to get several novels published. And of course, I edit LabLit, where we try to publish at least two new pieces a week – a goal that requires a lot of attending events, commissioning and chasing as well as editing and production.

This looming docket of duties, which are more of less omnipresent, makes it very difficult to relax. Whenever I am not working on something, I am fretting because I feel I ought to be. This past Sunday was case in point. It was a glorious autumn day: bright sunlight, spectacular clouds, a fresh wind, the last of the summer roses shedding petals onto the grass, golden leaves raining down in the woods around my house. When I rose at half eight and put on the coffee, I had the entire Sunday ahead of me. Unusually for me, my extracurricular workload was more or less under control and ticking over – I could easily have kicked back.

But it’s not so easy. A beautiful weekend day is not quite as good an excuse as a rhinovirus, is it? So out came the laptop, the only thing that can smooth away the guilt.

I rather think some reprogramming might be in order. Can anyone think of a non-infectious way to get me into that chaise longue next weekend?

When I look back on my research career, one thing that stands out over the years is a particular sensation deep within – a nagging, pressing imperative that preys on your innards. It’s so subtle that you can sense it only during the rare idle moments that punctuate otherwise endless stretches of adrenalin-fuelled activity: leaning against the centrifuge, say, waiting those final few seconds for the rotor to swish to a stop and the lid-lock to release with a satisfying clank; resting your forehead against the plexiglass shield of the tissue culture hood, watching the hypnotic dribble of your pink medium through the membrane of the vacuum filter device; zoning out as you rub a frozen tube between your hands, trying to speed up the thawing of its contents.

Snacks: should be budgeted into the lab grant

What is this urge? It’s not the desire to succeed, to win the Nobel, to cure cancer, to get your paper in Nature. It’s not even the desire to make the world a better place. No, it’s hunger. And I don’t mean hunger in an aesthetic, I’d-quite-fancy-a-honey-roasted-chicken-sandwich-with-aioli-and-pesto kind of way. I’m talking nutrition. Enough nutrition, specifically, to make it through the day (and night, if applicable) without passing out and being discovered by the cleaners lying on the floor in a wild tangle of lab coat and electrophoresis leads at 6 a.m.

I don’t know if it’s just me, but I often find myself not eating for long periods at the lab. This wasn’t such an issue in the editorial office; I’d work intently at my desk, snacking as needed. But in a lab, you have to make a definitive break: remove your gloves, wash your hands, locate your wallet and seek out that carbon source – overall, an activation energy barrier that sometimes proves too high to overcome.

I have to say that my current building is woefully underequipped. I’m a salty snack kind of girl, and the only sustenance provided in the Common Room besides coffee, tea and an array of sweet or chocolatey items is a small basket of Mini-Cheddar packets, usually decimated like a gazelle carcass on the savannah by 3 PM. There’s no vending machine and no canteen. Of course UCL is situated around hundreds of cafés and delis, but that would require actually leaving the building altogether (see above). I miss trekking to the basement for an icy-cold can of Coke, or dithering between ten different forms of fluorescent orange, processed cheese-inspired items, or – best of all – trying to decide which plastic-wrapped sandwich on the multilayered refrigerated carousel is least likely to be infected with Salmonella.

I’m not the only one obsessed by this topic. As a community service, one researcher rated all the many vending machines in his building, which includes the Vendtastic Burger Machine, the Junk Food Machine and the Fridge of Destiny.

I can only dream of such riches.

I’d like you all to meet my new friend, the Biomek FK – a very expensive piece of kit. She’s a robot. She’s meant to make my life a lot easier, and my experiments more reproducible. She can take the contents of a stack of 96-well plates and distribute them into a dozen replicates of 384-well screening plate in about the same time it would take me to manually pipette two rows.

And she looks a lot sexier doing it, believe me.

Better living through robotics

I just had the opportunity to use her services, and I am smitten. You guys ever ten-pin bowl? As the gleaming bank of arrayed yellow tips levitates over the mother plate, preparing to swoop down and pipette up a discrete amount of siRNA, that’s what she reminds me of: the apparatus that picks up all the pins and sweeps the fallen ones away when you’ve just choked on the strike. The machine that erases your embarrassment in a clatter of lost moments to clear the way for future triumphs.

High through-put is not all it’s cracked up to be, though. Working with this so-called ‘labor-saving device’ has been the most exhausting thing I’ve yet done in the new lab. Sure, the actual automatic aliquoting only took a few hours. But the mother plates still have to be created by hand: it took two of us most of a day, after which my thumb and wrists were trembling with fatigue. And the thing about generating dozens and dozens of plates is that they still need to be labelled, sealed, spun, frozen and thawed, manipulated in bulk, treated with kid gloves. Like preparing a meal for thirty people instead of two, you worry that some quality has been sacrificed.

And ultimately, of course, once the experiment is done (by further robots), the images will need to be analyzed by eye. We’ve got people working on the algorithms, but for most cell biological readouts, no computer can yet beat the human eye. And then there’s the mound of data that has to be annotated and stored: spreadsheets with fifty columns, that sort of thing. To say nothing of working out What It All Means.

Genome-side screens are amazing, and if they work, they can generate tons of interesting data. But I will admit to a bit of wistfulness for my previous stint, when I worked, painstakingly and lovingly, one just one protein. I knew its quirks and habits intimately, and the hypotheses were linear, not trapped in an infinite matrix of possibility.

Still, I love a challenge. Together, the FK and I are going to change the world. One well at a time.