Reciprocal Space

The Guardian runs an interesting ‘”Writer’s Rooms” feature in its Review section every Saturday in which a writer (or sometimes an artist) discusses a photograph of their office or workroom, pointing out significant objects. The idea (as in Desert Island Discs) is to gain an oblique insight into the subject’s mindset.

Well, it’s hardly an original idea but wouldn’t be interesting to take the same approach with scientists? Perhaps we can get a series of our own going on Nature Network. To kick things off, here is a photograph of my office, taken just last week:

My office, late September 2008 (Flickr )

My room at Imperial is in the rather unlovely Huxley Building, named after Darwin’s famous bulldog, T.H. Huxley who used to teach at the Royal School of Mines, one of our constituent colleges. It looks out over an elegant street, Queens Gate, but I keep the blinds drawn most days because glare from the westward facing windows strains my eyes when working at the computer all day long. The computer, a sleek and silvery Apple Macbook Pro (yes, I am a fan, but let’s not get into that!). The laptop is attached to a widescreen monitor to give me a much bigger work area because this arrangement makes you more productive. I owe it all my success…

Nestling behind the monitor is an old stereo brought in from home (busted tape-deck) that I can plug into the computer when listening to music. I usually only have music on when ploughing through relatively tedious tasks such as exam marking. On these occasions I am to be found, iTunes on shuffle, reading the scripts aloud to myself. When I have sixty or more essays on ATP hydrolysis or phasing methods to get through, this mantra induces a trance-like state that dulls the pain of those dismal days.

On the shelf above the desk you can see the blue spines of old lab books – some of them mine, some from former students and postdocs. I prefer the Banner notebooks, 244 pages, all pre-numbered. Every so often I reach for one of my old notebooks to re-trace a method or show a new student the exemplary standard of record-keeping that I expect them to maintain. Alas, there are occasions when my notebooks reveal me to be a hypocrite.

The desk and table (yes, it is olive green) are scattered with papers and it is a constant battle to keep them in order. When it finally dawns on me that I am spending way too much time looking for stuff, I know that a major tidy-up is in order. The last of these was back in January and I think I am due another very soon. The only trouble is, term is about to start…tomorrow!

Peeking into the photo from the left-hand side is my whiteboard. It’s used for tutorials but when I’m trying to grapple with a new problem or project I like to wipe it clean and stand in front jotting down my thoughts, trying to impose some kind of coherence. Having a big space to work on helps me to seek out the patterns in my thinking so I can grope my way forwards. The notes then glare at me for the succeeding days, worming their way into my brain and bringing me finally to some devastating insight. That, at any rate, is the theory.

Sadly I’m showing my office and not my lab bench since I spend most of my time in front of the computer and don’t have any bench-space to call my own: I really must get myself a sabbatical and re-discover the pleasure (and pain) of wet-lab work.

So is anyone else willing to open their door? Needless to say, you don’t have to be a scientist to participate – you could be an editor, intern, a popular science writer or whatever…

It looks like SciBlog08 was very much ahead of the curve in issuing the call for more scientists to get involved in blogging.

A former student (thanks Ananyo) has just drawn my attention to an open access article on science blogging that has appeared in this month’s PLOS Biology. I’ve just read it and am still digesting but there are some very good suggestions on how universities might learn the value of blogging and enable their staff to get stuck in.

I think I will see if it stirs any interest among my colleagues.

My resemblance to Blanche DuBois has not been remarked on before but last Wednesday evening it was unmistakeable.

There I was travelling on the tube to the TalkScience event at the British Library when, like Tennessee Williams’ fateful Southern belle, I found myself entirely dependent on the kindness of strangers. Still recovering from a cold, I was suddenly overcome by a severe coughing fit. I coughed and coughed, clamped a hanky to my mouth, coughed and coughed, fought tears that streamed from my eyes and kept on coughing. In my head I was imagining my fellow passengers’ rising alarm—“Dear God, he’s got TB!”—when the gentleman next to me dug into his bag and offered me a bottle of water. I croaked gratitude and drank, the cool fluid soothing my ragged throat. If you’re out there Sir, please accept my profound thanks once again.

And thence, finally, to the British Library where I squeezed in late at a table shared by Frank and Matt and joined in a room-wide discussion on “Scientific Researchers and Web 2.0: Social NotWorking?” Afterwards I chatted to Maxine and Cameron and a couple of chaps from Mendeley. From these conversations I got tips on using aggregators and may have made a small but useful suggestion on how to enhance reference sharing. All this with people who, until recently, were strangers to me: we’d never met except via Web2.0.

When I got home I read Pamela Ronald’s beautiful post on her experience of a moment of scientific creativity, left a comment to express my admiration and got a reply from her containing the line “Encouraging words from fellow scientists helps to keep one going…” Which is certainly the case – even if they are strangers. Richard Grant’s “recent post”:http://network.nature.com/people/rpg/blog/2008/09/14/on-depression—a-personal-perspective on depression (and the ensuing comment thread) was a further stunning example of that.

But then again, it struck me that one of the finest features of the scientific culture is that we are not strangers to each other. We know that engaging is simply part of the process. One of the Mendeley chaps—a programmer, not a scientist—asked me how I linked up with collaborators. Conferences are a good route, I told him, but it is also possible to read a paper, think up an experiment that the author and I might usefully do together and then just send them an email and take it from there. Most times, an interesting discussion and possibly some valuable science will ensue. The intercourse is not benighted by discussions of fees or contracts (though advisedly some thought may need to be given to authorship of future papers!).

I know, I know – there is plenty of ruthless competition going on as well and the world is not just. But that baseline connectedness between scientists is a thing of wonder and is for me one of the most delightful aspects of being a scientist. You can depend on it. I know I do.

I have been thinking about this for a quite while, but finally got a kick up the backside. And now it’s done.

With two members of my group I’ve put together a short movie on our research and, thanks to the good folks at Nature Network who enabled video embedding just last week, it is presented here for your… delectation?

What can I tell you? It’s a moving but ultimately uplifting tale of triumph over adversity set in lab in a once fashionable part of London. The production values are sky-high and you get to enjoy my mellifluous Northern Irish lilt.

The well-placed kick was aimed by the organisers of a conference on Control of Foot-and-Mouth Disease that will be held in Sicily next month. Noting the dearth of FMD videos on the internet (how did that happen?), they asked participants to come up with short movies on their research. This is a trend that Heather flagged up recently.

Our FMD work is focused on the poetically named 3C protease from the virus that causes the disease. We’ve used X-ray crystallography (did I mention that already?) to determine the structure of the protease and are keen to pursue antiviral drug development, though this is likely to be a long and arduous road.

The conference audience will mostly be veterinary scientists whose primary focus is well above the molecular level so I have tried to keep the story relatively simple. I hope that the material might also be suitable for a wider audience – and might be able to engage the public. Now I realise that most people around here are already terribly scientifically literate (and in so many other ways too) but I would still be interested to hear any responses. It was an interesting project to undertake – one of the most tricky aspects was how to streamline the story without distorting the underlying science.

(For those without 6 minutes to spare, there’s a cool bit starting at 1 min 50 sec…!)

Thank you for watching – you’ve been a wonderful audience!

Update: 10-10-2008: the video is now also available on Vimeo. Thanks to Eva and Marco for pointing out this higher-quality service.

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In my last post I tried to elucidate the classy and artful double-entendre title of this blog. My Reciprocal Space, I explained, is a place for exchange, but the name also belies a play on words that invokes the peculiar mathematical construct used to interpret the X-ray diffraction patterns from crystalline samples. Reciprocal space inverts reality and reflects it back at us in ways that are not immediately obvious or revealing, as those who have grappled with the concept will know; but it can reward persistent analysis.

Now I promise that am not going to keep harping on about this, but I have just spent a few days in Chicago and two artistic encounters evoked alternative types of reciprocal space. So let me beg your indulgence on this topic one more time and then I’ll drop it – at least for a while!

The first encounter happened last Sunday on a dismal grey afternoon as incessant rain glossed the sidewalks and seeped into my shoes. I took refuge in the Art Institute of Chicago and came upon Ivan Albright’s The Picture of Dorian Gray. The painting was commissioned for the 1945 film of Oscar Wilde’s famous novel of the same name. In the book Dorian Gray maintains his youthful looks and pursues a life of debauched hedonism at the expense of his portrait, which—locked in the attic—decays slowly to reveal the terrible degradation of his soul. Albright’s painting is laden with corrupting detail (his signature style) and reveals the late stage of decay of the portrait. It is a truly shocking reciprocal to Dorian’s supremely indulgent lifestyle; the inversion is ugly, repellent – even the cat is disgusted with its master.

Dorian Gray corrupted

The second occurred on Tuesday at the nearby Millennium Park where Anish Kapoor’s sublime and very shiny sculpture, Cloud Gate sits gleaming in the sun. Known more commonly as ‘The Bean’, since that is exactly what it looks like, this is a fun piece of public art. The smooth, polished contours of the huge steel sculpture reflect the surroundings, playfully bending the linear, cornered cityscape into friendly curves.

The Bean

But more enchanting still is to walk in underneath and gaze up at the convex metal surface which bounces and duplicates your reflection, casting it all over the place. Your image shimmers, stretches, separates and squeezes as you wander around. The pattern of reflections is so complex that you cannot easily make out the surface of the mirror—real and reciprocal spaces are conjoined—and you have to be careful not to bump into the metal walls. I stood and stared upwards, smiling with amusement, and trying—ever the scientist—to figure out the symmetry of my reflections.

Me, multiplied

There’s nothing terribly deep in either of these observations but, as I say, they did put me in mind of reciprocal space. I wonder have others chanced upon works of art that had echoes of their scientific interests? I would be glad to hear any reciprocal views…

It’s the name of this blog. But why?

Well, in Web2.0-land, a blog (can you hear my teeth grinding?) is quintessentially a space for the reciprocation of views, the exchange of ideas.

So far, so good, but the title is also a rather cheesy crystallographic pun because reciprocal space is a real thing. Well, actually it’s a weird, imaginary thing, a mathematical construct used by X-ray crystallographers to interpret the diffraction patterns of spots that we record from our crystals. In the crystal, the molecules are arranged in orderly rows and columns, stacked like bricks in unit cells. The orderliness is the key to strong scattering of the X-rays in the directions allowed by a mathematical rule known as Bragg’s Law.

But if you follow the maths—that damnable white rabbit—it takes you down a hole and before you know it you are in reciprocal space, where it is the spots of the diffraction pattern that are arrayed in rows and columns. But all the dimensions and angles are inverted – reciprocated. Crystals with small molecules packed into small unit cells create a huge reciprocal lattice where the spots are widely separated.

A slice of reciprocal space

And, oddly enough, that’s where the book discussed in this week’s Fiction Lab comes in. As has been mentioned elsewhere, on Wednesday evening I railed against the scientific inanities of the plot of “As she crawled across the table”, a novel based on the creation, in a basement physics lab, of a portal into a parallel universe that wholly absorbed — metaphorically and sometimes literally — those who gazed into it. It was a very strange story. I hated it and yet, though I almost dare not admit it, there is a kind of resonance with my own fascination with reciprocal space.

As a protein crystallographer I make occasional visits to reciprocal space, usually to take a look at a strange entity that lurks there known as the Ewald Sphere. It’s an absorbing place. But if you make the effort to get acquainted, to get to know the angles and the curves, it will ultimately reward you with a beautiful new molecular structure. It can be hard work, but the exchange is a worthwhile one.

And such are my aspirations for this blog.

Attending the SciBlog 2008 conference last week gave me a chance to weigh up my opinion of blogs, bloggers and blogging. And I’ve decided that I hate them all.

Not the concept or the people or the activity, you understand, but the words. They stick in my throat. As I would have said when I was growing up in Northern Ireland, they make me want to boke.

I know the etymology: web-log, b-log, blog. It makes perfect sense but it’s such a silly-sounding word that it seems to demean the process. I would be embarrassed to admit that I do it, just because it has such a stupid name.

And yet the call went out from the conference for more senior people to get blogging and that struck a chord that has been twanging — a little mutedly perhaps — at the back of my mind for a few months now. Not that I regard myself as so very senior. Yes, I am a professor and I’m serious about my science; but I’m still just shy of my mid-forties and like to think of myself as a young man. However, the truth of the matter is beginning to weigh on me; I now have to lift my eye-glasses to read the date on my watch, so I guess I have to face facts.

So here goes. I won’t promise to post regularly; that way I will avoid the repetition of future apologies for failing to write. I won’t promise to be unembarrassed to admit that I am a blogger. I won’t promise to have anything terribly insightful to say.

But I will share my experiences of science — such as they are and as frankly as I can — and look forward to engaging with the community on Nature Network. Indeed, I have already enjoyed that burgeoning sense of community these past few months while lurking in the background, only stepping forward now and then to comment. One of the real joys of the conference, as Dr Rohn and Dr Kushnir (among others) have remarked, was finally meeting in the flesh some of those people (OK, OK… bloggers) whom I’d only come to know from their online persona.

And you never know, perhaps one day I’ll get comfortable with the idea of… blogging. But even then, I’ll still loathe the phrase ‘Web 2.0’.