In which nature imitates science – number 327

Sometimes when you look at something from a different angle, you see something you’d never otherwise have noticed.

We’ve been trying to grow melons in the greenhouse, without much success: hundreds of female flowers have unfurled, but only a handful have set fruit. Meanwhile, we haven’t been very good about keeping the vines tidy or pruned, so they have infiltrated absolutely everywhere in an untidy green tangle, underfoot and overhead.

This morning, Richard was outside the greenhouse and happened to notice one fruit we’d missed, growing between the slats behind the lettuces and padrón peppers:




Its strange behavior reminded me of something. After a few minutes, I realized what it was:

A white blood cell l in the vessels squeezes between cells into tissue to fight infection
Remix of “Leukozytenmigration 01″ by Kuebi = Armin Kübelbeck – own work, made with InkScape. Licensed under CC BY 3.0 via Wikimedia Commons

Diapedesis: the process by which leukocytes, which patrol in the bloodstream, are attracted into tissues to fight infection. Like this melon, leukocytes manage to squeeze their very large bulk into a very tiny space to get from A to B. Once in the tissues, the immune cells home in on invaders and eat them up.

In this case, however, the meal is going to be a lot tastier.

Posted in Domestic bliss, Gardening, Scientific thinking, Silliness | Leave a comment

In which we recommend a classic lab lit novel in honor of the Pluto flyby

The big day is finally arrived: in just a few hours, we are about to get our closest look yet at Pluto. Call it what you will – planet, dwarf planet, even the last word in that classic American solar system mnemonic (“My very educated mother just served us nine pizza-pies” – sung to the tune of “Swannee River“) – it’s a big day for science, and it’s a big day for our species.

If you want to learn more about the history of Pluto’s discovery in a truly entertaining way, I can highly recommend the lab lit classic novel The Unfixed Stars (its UK title; in America it was called Percival’s Planet). Penned by the fabulous Michael Byers, it’s a fictionalised account of the painstaking identification of the heavenly body by a Kansas farm boy. Byers brings the story to life by imbedding it in a colorful and vivid story – not all of whose elements are true.

But that’s just part of the fun!

Posted in LabLit, Writing | Comments Off on In which we recommend a classic lab lit novel in honor of the Pluto flyby

In which we kill the messenger: is Twitter dystopian?

In the past week there has been a lot of talk about sexism in science. I don’t want to rehash any of the arguments (though you can hear some of my views on Radio 4 and in the Telegraph). One might summarize it like this, just to set the stage:

1. Some silly, ill-thought-out comments were made by a high-profile scientist in a very public venue, as an attempt at humor

2. The comments were shared widely via social media

3. Many people thought the comments, even if delivered in jest, were damaging to the cause of parity; others didn’t see what all the fuss was about

4. Much commentary ensued, both in mainstream and social media channels as well as in emailing lists and in the tea rooms of academia and beyond

5. Perhaps predictably, the backlash instigated a backlash, which in turn spawned a counter-backlash, and a counter-counter-backlash…so on, as the ripples radiate further afield and begin their inevitable dissipation into the vast, short-term memoried milieu of the media sea

The current reigning trope seems to be about how social media is a spiteful and devastating weapon, a kangaroo court that can decimate a reputation in minutes flat. A piece yesterday in the Guardian ascribed to Twitter “innate cruelty” and “savage power”. But while social media may at times have this effect, it can also be a strong force for good – a conduit for protest, a way to share knowledge with a swift efficiency never before possible in the history of the world. It can boost a lone cry escaping the censorship of a repressed regime, or a small-town mindset, or a lonely city of millions. With social media, even the most insignificant voice might be amplified so that all can hear. So is tarring the entire medium with one brush really fair?

First off, everyone will see their own version of social media: my timeline is not the same as your timeline. The people I follow might be more reasonable that the timeline of a troll. Can we assign one modus operandi to a medium fractured into a billion personal pathways?

From my filtered end of it, the commentary was as varied in tone as human nature itself: measured and balanced; or humorous; or outraged; or bewildered; or hostile. Some called for heads to roll; some called for sympathy; some called for people to lighten up; some called for censoring all feminist response; some used the opportunity to widen and refresh a discussion of the underlying issues. (My step-daughter’s science class even used the affair as a basis for a lesson.) Social media was neither good nor bad; it was simply media, a channel for people to air their views in a global discussion. Do we kill the messenger, and vilify the people who had genuine concerns and wished to exert their right to air them? Or do we celebrate the fact that Twitter, Facebook and its ilk can help everyday people, not just the privileged few, make their cases public – the good, the bad and the ugly?

Actions have consequences. Ill-judged, damaging comments will provoke response, and the people who make them, for better or for worse, need to understand that there may well be unpleasant repercussions – even inappropriately harsh ones. The responses will be varied. But the people responding have a right to be heard. Free debate is not ‘dystopian’- even when it goes against your opinion, or unfairly damages a reputation. This is the nature of free speech. We reap its benefits, and we also, if we’re unlucky, feel the sting of its tail.

Posted in The profession of science, Women in science | 15 Comments

In which you can take the girl out of the lab…

I suppose most scientists have the problem of taking their work home with them. And by this I don’t mean the stacks of papers you need to read, or the manuscript you’re writing, or the grant application you’re still cobbling together one day before the deadline. No, I mean the tendency we scientists have of seeing everything through an experimental lens. For example, after a long day of thinking about finch beaks or the mating habits of barnacles or the separation of sex organs in plants, Darwin intensively experimented on his own children.

Case in point: I’ve just finished a lovely work of non-fiction by my friend, the psychologist and writer Charles Fernyhough, called The Baby in The Mirror. In it, he studies his first child from birth through to the end of her third year, charting developments in language, socializing and self-awareness. Some of these same questions were also of interest to Darwin when he put his son William Erasmus through his paces. Fernyhough’s observations are placed into context with reference to both historical and current thinking on how these processes are thought to come about. It’s a fascinating read – funny, sad, confessional – and deeply illuminating if your child, like mine, is right in the midst of acquiring language. And yes, Fernyhough and his fellow psychologist wife do describe subjecting their daughter to some of the classic childhood experiments. There are tests involving mirrors, and objects hidden in cups, and all sorts of other tasks designed to probe the innermost workings of the toddler brain.

I haven’t quite got to that point with Joshua – although I have noticed that he spends most of his time doing things that could easily be defined as experimentation. Indeed, Fernyhough in his book describes children as “little scientists”.

Bucket Scientist
Click to play the video in Flickr

But yes. My day-job lab habits die hard. And no more so than in my gardening. This year I started to keep a notebook to record what worked and what didn’t – seed varieties, sowing and planting-out dates, propagation and harvest information. I’m currently grappling with how to get my Melba melons to actually set fruit. The female flowers don’t seem to become fertilized by insects on their own, so each day (feeling like a furtive perv) I peel back yellow petals from the male flowers, exposing their stamens, and brush them delicately against the stigmata of the relatively rare female flowers. If I were Gregor Mendel, I’d have tied a piece of coloured string to each female flower and recorded subtle variations in application (apparently the lady bits are very fragile and hand-pollination often destroys them). Instead, I’m so disheveled with the necessities of getting a cranky toddler fed, bathed and bedded each night that I keep losing track of which flowers I’ve serviced each evening – so I’m none the wiser about the odd successful fruit set.

Cuke Notes

The gardening book – stained with manure and dirt and the pen running from off-course hose spray – lives in the big greenhouse where most of the most successful “experiments” are ongoing. I realized only today that – aside from being negligent about the details of my pollination efforts – I’ve been keeping the notes exactly as I would do in the lab. My lab notebook style tends to err on the side of lengthy prose, with plenty of sketches and irrelevant asides: rambling, untidy and emotional, sprinkled here with jubilation, there with despair (and the occasional four-letter embellishment). It’s been nearly a year since I’ve written in a real lab notebook: my team does the front-line experimentation now, while I supervise and, of course, write lots of grant applications in a bid to future-proof my group. The teaching duties are relentless, with year two material to prepare despite the end of term. And increasingly too, I’m being press-ganged into academic committees. I’m so grateful to finally be a real part of that club that I accept such invitations gracefully, only too aware of what a thin membrane lies between me and the abyss.

But I do wonder: am I redirecting all that pent-up, neglected and observational science directly into my gardening journal? Is it keeping me sane? I always hoped I’d be able to get back into some bench work once I’ve got secure funding and we’ve moved into our new home close to my teaching obligations. The reality around me, however, suggests that once you start to go the way of an office-bound lab head, it’s seldom a two-way street.

How do I feel about that? Surprisingly OK. If I’m perfectly honest, I don’t miss those three-hour marathon sessions in the tissue culture hood, seeding cells, pipetting tiny amount of clear liquid into 384-well plates, sweating miserably inside my nitrile gloves and white coat, longing for a blast of fresh air. I actually enjoy writing grants and papers, and chatting to my students about their work without having to do the hard graft myself. The thrill of discovery is still there – made possibly more exciting by the chance to frame it all in context, with persuasive paragraphs aimed at convincing others that the work deserves the funding to go further.

Meanwhile, I’ve got cucumbers to pick.

Posted in Gardening, Scientific thinking, The profession of science | 2 Comments

In which the small fish contemplates the bigger pond

The wandering path of my unconventional scientific life is about to shift yet again. It’s with mixed feelings that I report another lab move – same Division, another new campus. The retro digs in Bloomsbury, with its polished hardwood trimmings, were always meant to be temporary – even more so when the entire street was slated for imminent destruction to make way for High Speed Two (along with parts of Drummond Street, Camden’s famous curry street, and the incomparable Bree Louise Pub). But instead of rehousing to a newly refurbished, high-concept building on Riding House Street as originally planned, this June my team will be squeezing into a friendly existing centre in the Royal Free Hospital.

Mixed feelings? I am very happy about the move in many ways. Our current set-up is just as isolated as the previous, seeing as how we are still the sole biomedical researchers in residence. The building also lacks permanent infrastructure, the sort of kit and facilities that are traditionally shared amongst entire departments: ultracentrifuges, decent microscopy, darkrooms, cold rooms, shaking incubators. To record the results of ethidium bromide-stained gels, the rest of the known universe uses dedicated digital imagery. Not us: we slap the gel onto a second-hand UV box (circa 1978, recently taken from a skip, only one of four tubes working) and snap pictures with our phones through a protective piece of scratched perspex:. To isolate bacterial DNA, we put our stuff in a box and take the Underground to another institute in Mornington Crescent. There are no handy colleagues next door to bounce ideas off or to borrow chemicals from. It’s lonely and disruptive, and I’ll be happy to see the back of that sort of lab life.

But moving, twice in two years, also take its toll. It can eat months off the progress of a PhD student, especially one who relies on specialized long-term tissue culture models. It is psychologically disruptive. The first few weeks, you feel like a houseguest from abroad who doesn’t know where the sugar is stored or how to find the nearest corner shop.

It will all be worth it, I know. My soon-to-be colleagues are a vibrant bunch of basic scientists and clinicians working on a broad and diverse range of systems and diseases. I already see dozens of potential opportunities for collaboration. I like the idea of being a small fish in a big, nutrient-rich pond. It will be good for my career, good for my PhD students, and good for the science. So bring it on.

Posted in Careers, Staring into the abyss, The profession of science | 2 Comments

In which the forest emerges

The clocks have gone forward, the crocuses wither, the tulips unfurl. The students have dispersed for Easter, full of dread about the immunology exam that will pounce on their return.

Budding life forms

I put one grant application to bed and work on two others. I sketch diagrams for my PhD students, helping them to keep track of the bigger picture, the sweeping narrative arc of their overall research. They panic amidst the trees; I remind them about the forest.

And then I remind myself too. My quest towards academic security seems finally to be reaching a safe haven. As I prepare to move my lab to its new home, I make contact with like-minded researchers, explore possible angles of collaboration, try to see how best to fit my own pieces into the puzzle. Sometimes I feel like a neuron extending my dendrites in all directions in the dark, one moment absurdly confident, the other wondering if it’s all just bluster and bravado and a shimmering of dead-end impulses in the blackness. Maybe everyone feels this way. Or maybe it’s just me, burnt edges after too many years of seeking.

Meanwhile, back in real life, my son is a living, breathing experiment in language acquisition and development. Every day brings some new jaw-dropper: the complicated sequences of gesture and babble that manage to convey perfect meaning. The abstraction of one concept to a wholly unrelated one. The parallel development of vocabulary: one set in English, the other in some mysterious phonetic system that seems to make perfect sense to him, if not to anyone else.

The main thing is that he doesn’t seem to care what people think: he wants everything, right now.

Not a bad life strategy for a scientist trying to make it in academia. I plan to watch and learn.

Posted in Careers, Gardening, Scientific thinking, Staring into the abyss, Students, Teaching, The profession of science | Comments Off on In which the forest emerges

In which Charles Fernyhough comes to Fiction Lab

One of the great things about being the LabLit Guru™ is that I am constantly receiving interesting books to look over.

Stack o' Books
A stack of lab lit, yesterday – plus an intriguing hanger-on there at the bottom

One of the not-so-great things is that (A) I am always desperately behind on my reading, and (B) it doesn’t leave me time to read anything else except novels with scientists in them. (I think the last non-science-y novel I read was Gone Girl back on summer holiday two years ago.)

Still, there’s nothing that makes me happier than a stack of books. And I’d like to direct your attention to the third-from-top volume: A Box of Birds by Charles Fernyhough. I am delighted that Charles has agreed to be our guest at the next Fiction Lab – my monthly lab lit book group at London’s Royal Institution.

Charles is a brilliant writer and a fascinating person. I first met him a few years back when I was researching my third novel and wanted to understand a little bit about what it ‘sounds’ like when people experience auditory hallucinations. This being London, you can find an expert on absolutely anything within just a few city blocks, and so it was that we ended up in a coffee shop in Farringdon talking about all sorts. Charles is a Professor of Psychology at Durham University, a novelist, a popular science writer, a broadcaster and a whole host of other things too. To whit, I picked up my copy of the novel from him last month at the Wellcome Trust Collection, where he is (enviably) part of the first group of Residents in the Hub.

I enjoyed his first (non-lab lit) novel The Auctioneer immensely, and am still haunted by some of its images. So the prospect of reading his latest is exciting – because I can already tell it’s hard-core lab lit from the opening paragraph:

An opening line of beauty

An opening line of beauty

As intrigued as I am? Then do read the book and come along to meet Charles and discuss Box of Birds on 13 April at 7 PM. It’s free, and all are welcome.

Posted in LabLit, Writing | 1 Comment

In which life imitates science – number 264

A scientist is never off-duty, even in a fabulous Michelin-starred restaurant on Charlotte Street.

Spindle organization was never this tasty

Spindle organization was never this tasty

I think pretty much anyone with a cell biology background would have seen what I saw in this rhubarb confection:


Non-rhubarb-associated centrioles, diagram by Kelvinsong, Wikimedia Commons

But alas, my immediate dining companions consisted of a software system engineer and a cognitive neuroscientist, both of whom looked at me blankly – and with perhaps just a whiff of pity – when I excitedly pointed at my dessert and made little squeaky noises.

Posted in Scientific thinking, Silliness | 4 Comments

In which the postdoc sell-by date continues to shrivel: The MRC comes to its senses

How do you judge the worth of a researcher? In particular, can you tell how excellent she is by how quickly she gets from point A to point B in her career?

Old postdocs may not be as stale as they look

Old postdocs may not be as stale as they look

The funding bodies used to think speed was of the essence. Hence the ‘sell-by’ or ‘expiration’ date of post-docs applying for fellowships: “Thou shalt not be be X years beyond the awarding of your PhD” – where X would tend to be about 4-7 years.

I’ve written about this before, and just to give you an example of how sell-by date is a lousy measure of excellence, here’s the example I gave in that older post:

Postdoc A does his first postdoc in a high-powered lab, stepping neatly into a project, initiated by a departing PhD student, that is just starting to bear fruit. He doesn’t have a family, so is able to work 12-hour days and throughout the weekend. He ends up with two top-tier papers in four years, and is able to secure another high-profile postdoc in an allied field, consolidating his reputation as an up-and-coming star with two more decent papers. Adding those to his 2 publications from his PhD, he has 6 first-author papers after 7 postdoctoral years. Moreover, his boss is happy for his protégé to take the line of research with him, so he’s in a great place to apply and succeed at a fellowship like the URF.

Not so Postdoc B. She does her first postdoc in a small but respected lab, but gives birth to her second child in year 2. The project is disrupted by her one-year break, so by the end of four years, she has only one co-first author paper (shared with the postdoc who took over her project while she was on maternity leave) and one small first-author paper. She has had to leave the lab every day at 5 PM to pick up her kids from daycare, and can’t work weekends. Most funding bodies would disqualify her break, so she’s effectively done a 3-year stint. From this, she secures a second postdoc in another decent lab, but the boss wants her to develop an entirely new system, which takes her three years to perfect: it’s a highly intricate technological advance, clearly innovative and incredibly powerful. In her third year she manages to publish one first-author paper about the system, but her boss doesn’t want her to take the bulk of this desirable prize as seed-corn for an independent fellowship; she attempts arbitration, but the head of department sides with the lab head. So instead she leaves it all behind and does a third postdoc in a high-powered lab on a project that’s quick off the mark: four years later, she has two top-tier papers, one decent one, and a portable line of research. Her track record is now the same as A’s – except that she’s been in the postdoctoral system for 10 years (not counting the break), so is not eligible for the URF.

So three cheers for the UK Medical Research Council, which yesterday announced the results of its 2014 Careers Review consultation. Here’s the key bit:

We are taking a fresh approach to supporting careers by removing eligibility criteria based on years of post-doctoral experience. This will allow for variations in career paths, recognising that the speed of career progression can be affected by factors unrelated to a person’s scientific potential.

The Engineering and Physical Sciences Research Council abolished the sell-by date years ago – and there may be other major funders that have followed suit. (Can you let me know if you know of any?) This current news is definitely a step in the right direction: it’s a victory for older scientists, for scientists with complicated family or personal lives, for scientists who dabbled outside of academia, for scientists who maybe just had a string of bad luck or a series of unsupportive supervisors.

For scientists who are human, in other words, and not charmed charmless turbo-gunners with ten Nature papers and no social life.

Posted in Careers, science funding, Staring into the abyss, The profession of science, Women in science | 1 Comment

In which I invite them in

Although engaging with the public about science is famously not about – heaven forbid – ‘teaching’ it, the two endeavors do share some common strategies. I’ve been organizing and executing a lot of undergraduate educational sessions these past few terms, and I can report that the humble analogy is equally effective in both spheres.

It’s true I sometimes weary of science similes and metaphors, especially when they stray into overtrodden cliché territory. The DNA-as-letters/chromosomes-as-books/genome-as-library trope, once so apposite and fresh, has been trotted out so many times by the unimaginative over the years that is has become almost greeting-card sickening. Other metaphors are so engrained in our science vocabulary that people have even forgotten they were metaphors in the first place – concepts such as ‘immune surveillance’ or ‘protein translation’, for example.

Still, I can’t resist a really nice analogy, as long as it’s evocative and – above all – original. So I tend to collect them as I find them through life’s little happenstances.

Yesterday when I was leaving the local high street home improvement superstore with my family, I was accosted by a wild-eyed, cheap-suited man who’d set up temporary shop in the foyer next to a folding table covered with leaflets. His suit wasn’t nice enough to be a Jehovah’s, although there was something of that vibe about him. In a fraction of a second I’d analyzed the leaflet being fanned enthusiastically in my face and had him pegged as a double-glazing salesman.

In a moment of terrible weakness, I decided to accept a leaflet. After all, there are a few single-paned windows in the back of our new house and Richard and I have discussed replacing them at some point in the future. What harm could one leaflet possible do?

As I tried to walk past with the brochure, the man actually grabbed me by the arm and informed my that I couldn’t get the forty per cent discount without registering. Heart sinking, I realized I was falling into a trap – a proper fruit-fly-lodged-into-congealing-jam trap – but I somehow couldn’t stop myself from scribbling my name onto his form. And, when prodded, almost robotically, my mobile phone number. I was that mesmerized maiden, inviting the vampire past my threshold. Except vampires are a lot more charming.

Desperate to escape now, I attempted again to pull away.

“Stop!” the man barked imperiously. “We need a second phone number!”

“What? Why?” Fortunately I couldn’t remember my new land line number yet, and told him as much. The fly, managing to pull half of its legs out of the jam, soon starts to wake up and sense freedom.

“What about the gentleman’s?” he barrelled on, looking over to where Richard, with a don’t-you-fucking-dare expression, was holding our squirming son, who had started to howl with hunger and fatigue. Or maybe he just doesn’t like double-glazing salesmen.

“I’m not going to give you another phone number!” I had to shout to be heard over toddler indignation. “Why do you need more than one?”

As he was muttering something about ‘security’, drowned out by unearthly shrieking, we finally managed to make our escape. There was no way I was going to give my custom to any company that would rather bully a potential customer than allow her to get her screaming baby home to lunch.

As the morning dawned foggy and morose, I knew I was in for a protracted siege. Sure enough, four missed calls from the number on the leaflet between 9 and 11 AM – but no voicemail. Don’t they comprehend that some people cannot take private calls at their places of work? (If you’re interested in science analogies, you can start paying attention again now.) I used my iPhone to block the caller. About 20 minutes later, another call – the same number except the last three digits. The second time this one called, I blocked that one too. Starting at 2 PM, I started to get calls from unknown numbers. Including one just now, as I type these words.

Screen shot from phone

The stupid, make it stop

But it wasn’t all bad. Actually, I started to realize, it was a lot like host/pathogen interactions. When you co-evolve over many millennia with an ancient enemy, as humans have done with bacteria, viruses and other parasites, you are constantly shifting to stay one step ahead. We have developed an elaborate immune system to keep out invaders – so elaborate that we are struggling to summarize it all even at a basic level for our students this term. But the pathogens seemingly shrug such barriers off and, often in no time at all, have mutated to get around our defenses.

Imagine a flu virus, which is covered in coat proteins that can latch on to our vulnerable cells. Our immune system amplifies antibodies that can stick to these virus attachment proteins and neutralize them – as my iPhone blocked the first number. But the virus, with its sloppy genome copying system, can mutate to make subtle variations in its coat proteins – subtle variations that the first antibodies no longer can recognize. That’s their related number, a few digits different, that my iPhone failed to block. I block the second number – as the immune system rebounds to generate new antibodies that can bind to the revised version of flu coat proteins. And the flu counterattacks: just as the company switches to phones that will not trigger caller ID, flu periodically makes more major coat protein changes – the so-called ‘antigenic shift’ that can sometimes be the harbinger of an epidemic. And so on, ad infinitum.

In summary: parasites…vampires…double-glazing salesmen. You get the idea.

This will be on the exam.

Posted in Science talking, Scientific thinking, Silliness, Students, Teaching | 14 Comments