• Reciprocal Space by Stephen Curry

    Structured and unstructured observations from the principal investigator of a protein crystallography lab

    • From my pedestal

      Thursday, 04 Feb 2010

      I just wanted to clamber up onto my pedestal for a moment (it’s rented – I don’t actually possess one) and shout at the very top of my voice that Simon Jenkin’s has written an article in The Guardian that has made me VERY, VERY, VERY, VERY, VERY, VERY, VERY, VERY CROSS!!!

      I’ve already commented there (as scww) and have nothing more to say on the matter tonight. Is it just that Jenkins is an ignoramus when it comes to science or is this sort of awful ‘journalism’ somehow our fault?

      Thank you. I’m feeling a bit better already.

    • Puff The Biochemist

      Tuesday, 02 Feb 2010

      Thought that some of you might like to know that the latest (Feb 2010) issue of The Biochemist is running a special series of articles on Science and the Media; science communication if you will. There’s a piece by yours truly on science blogging and one by Jenny Rohn on scientists on screen (not read it yet, but you know it’s going to be good!).

      That’s not all: among other pieces, Tracey Brown of Sense About Science (a stalwart of the libel reform campaign) writes about the ‘second golden age of science communication’.

      The articles seem to be free as long as you are prepared to register your soul with the Biochemical Society.

    • Homeopathy: That's Numberwang!

      Saturday, 30 Jan 2010

      This morning I attended a my first ever publicity stunt. The 1023 overdose event, initiated by the Merseyside Skeptics, was held in cities around the UK and the rest of the world.

      Our particular group assembled in the lightly frosted but thoroughly freezing Red Lion Square in Holborn, London. I was more than happy to hand over £5 for the 1023 t-shirt—glad of the extra layer of clothing!

      1023 alludes to Avogadro’s number, 6.02 × 1023 (the number of molecules in the molecular weight in grams of any given compound). The link to homeopathy is ironic, playful, since typical homeopathic preparations involve dilutions of up to 1060. Such dilutions are extremely unlikely to contain even a single molecule of the original ‘active’ ingredient (setting aside for a moment the bizarre methods that homeopaths use to ‘prove’ that their ingredients are active) and therefore contain nothing. Recognising this, a little belatedly perhaps since Avogadro’s number was only evaluated in about 1908, homeopaths have adopted the view that water has memory and somehow can remember and impart the therapeutic benefit of molecules that have long since been diluted away. No credible molecular mechanism has ever been advanced for this memory effect. How that memory is transferred to a dry sugar pill is also mysterious.

      But not curious.

      Not even slightly interesting because the evidence accumulated in 200 years of homeopathy shows that it is no better than a placebo. There is an interesting discussion to be had on the ethics of treating people with placebos, since they are undoubtedly effective for minor, self-limiting ailments. But not this morning which was simply about drawing people’s attention to the fact that, by their own admission, Boots the Chemist sells ‘medicine’ for which they have no evidence of efficacy.

      This kind of craziness is on a par with Numberwang.*

      So this morning we stood around, chatting, stamping our feet to keep warm, watching the TV crews and journalists interviewing the organisers and celebs who had come along to participate.

      Martin Robbins tries to explain
      Martin Robbins tries to explain

      My drugs of choice, Arsen. Alb. 30C (a 1060 dilution of arsenic) came in a handy container, a bit like a sweetener dispenser that only releases one sugar pill at a time. However, with keys and teeth I managed to prise off one end so that I would be able to take the whole lot at once. If I was going the whole hog, it might as well be dramatic.

      Impotent stuff

      Just before the off, there were short speeches from Simon Singh, Evan Harris MP and comedian Dave Gorman. There was a count-down to the overdose and, along with everyone else, I filled my mouth with little balls of sugar and washed them down with water (also from Boots and, at 80p, considerably cheaper than the £5 pills).

      And then, of course, nothing happened.

      Mass overdose
      Nothing happening to a large crowd being filmed

      There were a few more interviews, a few more hellos and goodbyes and people dispersed. I made my way to South Kensington and to Imperial for a couple of hours work. A quiet Saturday morning is a good time to get down to some of the donkey work needed for an upcoming paper. Appropriately perhaps, the paper will be about how drugs bind to a protein, human serum albumin, which is abundant in the blood stream and can cause problems for drug delivery since many compounds stick to it too tightly. If that happens, you have to give a higher dose to make sure that a sufficient drug concentration reaches the target organ. Because you need to have a high enough number of drug molecules at the site of action to have an effect.

      This problem of drugs sticking tightly to albumin is commonly encountered in drug development and needs to be overcome if a successful therapy is to be brought to market. Our crystallographic work shows exactly where and how drugs stick to HSA, and could be used—we hope—to influence drug design and so enhance delivery and efficacy.

      Molecules binding to protein
      Superposition of diazepam (lilac) and a dansylated amino acid (light-blue) bound to drug site 2 in HSA

      The particular study we are hoping to publish will report several new structures of dansylated amino acids bound to albumin; these are fluorescent compounds that can adhere to the drug binding sites on HSA and are commonly used during drug development in assays to determine where any new lead compound might be binding to the protein. The figure shows that one of the dansylated amino acids in our study (the stick molecule with light blue carbon atoms) binds in exactly the same place as a molecule of diazepam (lilac carbon atoms). This result neatly explains why molecules of diazepam would reduce the fluorescence of a mixture of HSA and the dansylated amino acid: the drug displaces the dansylated amino acid out of the binding pocket and into solvent where its fluorescence is quenched.

      After a slightly surreal morning, it was nice to return to a reality where numbers add up and things make sense.

       




      *Apologies to our international friends who may not know Numberwang, a pointless game show comically imagined by Mitchell and Webb, who were also responsible for one of the best homeopathic sketches ever seen.

      Many thanks to @carmenego, my drug-dealer du choix, for supplying my hit!
    • Still Running

      Tuesday, 26 Jan 2010

      After a slight delay, I had an idea for a blog post and I’m going to run with it. Hope you can keep up.

      I have started to run. I have known for a long time that I needed to do this but it took a build-up of pressure to get me moving. It is for my own good. I am feeling the pain but also—still somewhat to my surprise—the benefit. 

      So far I am managing to go running about three times a week. I am the slowest jogger in the park but that’s OK—it’s not a competition. I am not racing. Most definitely not racing. In fact, part of the reason for running is to get away from from my racing mind, from the constant streams of thought that the life of a scientist drives through your head. In a sense I am running to find a way to stand still.

      I say running but strictly I’m jogging. Well, I say jogging but in truth it’s more of a slow plod. And as I plod I am usually plugged into my iPod. I tend not to listen to music – too fast. The slower pace of the human voice is more in tune with my motion. On Monday of last week as I pounded around Kensington Gardens I was listening to Front Row, a Radio 4 review of the arts. I heard Mark Lawson’s polished back-of-the-throat voice (that I find strangely appealing) as he spoke to Jonathan Miller about an exhibition of photos that Miller has curated for the Estorick Museum.

      Rather appositely for my run, the exhibition is called ‘On the move’ and seeks to show how photography came to give new insights into the motion of people and animals and to influence the work of artists, who had sometimes struggled to capture the true dynamics of movement in static media such as painting and sculpture.

      Miller waffled on a little too portentously for my liking but I my interest was piqued and so on Saturday I made my way to the Estorick in Highbury and Islington in north-east London. I took the train—it’s a little far to run.

      The exhibition starts with the work of the improbably named 19th Century photographer Eadward Muybridge who was commissioned by Leland Stanford, a horse-racing governor of California, to settle a bet about how horses ran. Because of the speed of movement as they galloped over the turf, no-one was quite sure how their legs moved and, crucially, whether at any point, all four legs left the ground. Eventually—the work was interrupted by Muybridge’s trial for the murder of his wife’s lover—by using a clever arrangement of trip-wires and high-speed cameras, he was able to capture a sequence that settled the point. They do.

      Muybridge's horses

      It was a breakthrough that ultimately convinced the artistic community to change their ways. The previous tradition of rendering horses with a rocking horse gait (fore and hind legs stretched out) was abandoned. Curiously, there was initial resistance because Muybridge’s images differed from the perceived reality (probably largely based on paintings); only after he had assembled a moving image from his sequence of stills to re-create the familiar running motion of a horse were people convinced that the camera had not been lying.

      These days with a digital camera, it is quite easy to replicate this technique. I got my daughter to film me in motion and this is the sequence that it produces. It reveals that even with my leaden step, there is one instant at which both feet are off the ground:

      Stephen runs - panels1

      Muybridge went on to apply his technique to other animals, and to men and women, mostly scantily clad (his interests were prurient as well as scientific). But although his technique captures the elements of motion, it loses the dynamic. The movement is broken apart and his images are strangely static. The eye does a poor job of re-creating the motion in the mind.

      A different approach and one that is more visually appealing was developed by the French photographer Etienne Jules Marey who worked out how to capture a sequence of stills on a single image. He did this using cameras with high speed shutters. Marey’s images retain a sense of dynamism and are immediately more… arresting. He photographed runners and jumpers and even birds in flight. The latter impressed him so much he commissioned an artist to render the bird in a statute that is on show at the gallery.

      In later work—some of it funded by the French military in the hope that the analysis of motion might help to devise better training regimes for their troops—Marey sought to abstract the movement into its elements. He would dress his subjects in black but affix bright white strips to their arms and legs. There resulting images have faded somewhat but retain an mathematical beauty, swathed in curves that connect the swinging lines; they are like spirographs partly unwound.

      Marey's lines
      Marey’s ‘lineograph’?

      Marey’s chronophotographs, as he dubbed them, were artistic in themselves but clearly inspired artists such as Giancomo Balla to try to capture the dynamism of motion in paintings, as here below in The Hand of the Violinist. I have to say, I prefer Marey’s photos.

      Violinist by Balla
      The hand of the violinist (Balla)

      In the 1920s the baton was passed back to the US where an MIT engineer, Harold Eugene Edgerton, improved on Marey’s technique by incorporating multiflash or strobe lighting. The regular bright pulses of light gave much better illumination of the subject and, along with faster emulsions, yielded crisper images. Edgerton also worked on high speed photography and was responsible for iconic images of splashing milk drops and bullets smashing through fruit that many of you will already know (though none are represented in the exhibition).

      Though an avowed engineer (“I am after the facts. Only the facts.”), Edgerton collaborated with the Italian photographic artist Gjon Mili whose pictures are among the most memorable of the exhibition. Using a creative combination of lights attached to his subject and bright flashes, Mili conjured some brilliant images. A particular favourite of mine was his picture of a violinist in action. To me this is more evocative of the music and the musician’s artistry than Bella’s painting.

      Violinist by Mili
      Mili’s violonist

      I’ll say little more – this is only meant to be a taster. It’s not a very large exhibition but I found it absolutely fascinating; there is an eclectic collection of images and objects. Miller, for all his bombast, was not too stuffy to include cartoons images of Billy Whizz from The Beano, arms multiplied as he threw snowballs, that made me smile in recollection. But more eloquent and more moving was a sculpture of fluid beauty inspired by the wing-beats of a dove taking to the air:

      Dove in flight
      Poetry in motion.

      Stirred by the exhibition I made my own homage to Marey and Mili. I will leave it to the reader to judge whether this constitutes any kind of poetry in motion. I fear not.

      Stephen running - panel2
      Prose in motion?

      Which brings me back to running. The images from the exhibition each sought to extract an instant of stillness from the moving subject, whether runner or musician or horse. In my own running I am also seeking a kind of stillness – a moment of peace, an escape from turmoil.

      Curiously, as I headed out the door on Saturday to take the train up to London I grabbed my old copy of John Updike’s Rabbit, Run. I suppose this blogpost on running was on my mind and triggered a memory of the title. The book is the poignant and painful story—written in Updike’s trademark exquisite prose—of Harry ‘Rabbit’ Angstrom for whom the American dream is not working out and yet he can’t figure out why. His solution is to keep running away but he can never seem to outrun his misery.

      Updike book

      The cover refers to the book’s opening which has Angstrom dallying in a side-street on his way home from work, watching some kids playing basketball. He is reminded of his own youthful prowess at the sport; he tries to join in, to recapture something he knows he has lost.

      I don’t want to overload this piece with symbolic weight. I am not the tragic figure of Rabbit Angstrom, though my own recourse to running is a kind of escape. I thought I might be able to use the book to make a connection. There was one, but it turned out to be astonishingly coincidental.

      As I mulled and turned the book over in my hand I read that the photograph on the front cover of young Americans playing basketball had been taken by Gjon Mili.

    • Science and Politics Mix

      Wednesday, 13 Jan 2010

      Tonight I attended a science policy debate organised by CaSE at the Institution of Engineering and Technology on London’s Embankment. Chaired by Roger Highfield, the editor of New Scientist, the debate featured the science spokesmen from the three main UK political parties, Lord Paul Drayson (Lab), the currrent Minister of State for Science, Adam Afriyie (Con) and Dr Evan Harris (Lib Dem).

      Science Policy Debate
      Ready for action

      As in Question Time, the audience had been invited to submit questions for the three panelists and these were used to drive the discussion. The debate, which you can watch online, ranged over a variety of topics with the overall aim of teasing out the positions that are likely to be adopted by the different parties in the upcoming general election. These included science funding, the impact of ‘impact’, science education policy, the role of charitable and private funding of science, the role of scientific advisers and last, but by no means least (and well done to Sile Lane of Sense about Science who raised the question), the partys’ plans for libel reform.

      The answers of all three contained no great surprises. Roger Highfield did a pretty good job of keeping the minister and the MPs on topic but there was only one point at which the audience was offered the chance to ask follow-up questions. This meant that some rather slippery statements were made without much of a challenge and I’m glad Evan Harris was there because he did a good job of taking the other two to task when this happened. He managed to get Drayson to concede that ‘efficiency savings’ were synonymous with cuts (the minister had stunningly opened his remarks with the contention that there had been no cuts – contrary to reports in the press or the recent experience of anyone funded by the STFC). He also pulled Afriye up on his rather gelatinous point that David Cameron’s ‘zeitgeist’ would suffice to stimulate stronger social cohesion and thereby induce private individuals to donate more to medical research charities!

      I was particularly interested to hear what the panelists had to say about the government’s recent preoccupation with the economic ‘impact’ of the science that it funds. Drayson was fairly unequivocal about the role that science has to play in helping to generate the new businesses and industries needed to help drag the country out of a global recession inflicted by the systemic failure of the financial system. This is certainly an important point, but I fear that the focus is too much on immediate short-term returns and didn’t hear anything from him to allay that perception. Harris was unequivocal on the point that economic impact should have no play in the decisions to determine which grant applications get funded. Amazingly, Afriyie echoed this point quite strongly. But he then went on to say that it was not unreasonable for Research Councils to ask scientists to outline the likely impact of their work in grant applications; not for the purpose of deciding funding but to enable the RC’s to assess impact ‘retrospectively’. I’m not at all clear on what he meant by this or how that would work. You can make a retrospective assessment (no bad thing in itself) without burdening scientists with the additional pen-pushing at the grant-writing stage.

      Having said all that, it was certainly a good thing that the debate was held at all. The three participants have already had one debate in Cambridge last year and are due to hold another one in the House of Commons in March, so there is still a chance to go along (assuming there isn’t a snap election in the next 4 weeks). Let’s not kid ourselves that science is at the top of any political agenda but I can’t remember it being higher.

      To add to the good cheer, there was some indication of emerging clarity on the standards that need to be applied in the treatment by government of its independent scientific advisers. Afriyie was a tad erratic on this, claiming ministers should have the right to sack them for any reason, but was immediately rounded on by Drayson and Harris. The consultation on the principles that should be applied to scientific advisers (now being re-drafted in the wake of the sacking of Prof David Nutt) is still ongoing; you can register your view here.

      Finally, there was unanimity from the panel on the absolute requirement for scientific debates to be unfettered by the libel laws and clear backing from all three for the reform campaign. Harris’s record on this issue speaks for itself but it was heartening to hear strong support from the Labour and Conservative representatives. With luck, that is a program for change that should be independent of the political colour of the next UK government.

    • I have discovered Jupiter

      Saturday, 02 Jan 2010

      I am 46 years of age and I have just discovered Jupiter.

      This is a surprising revelation, even to me. I have strong memories of being a child besotted with things astronomical. Looking back now, however, I have to wonder at the superficiality of my interests.

      I was certainly a devotee of space and space rockets. Though too young to properly comprehend the significance of the Apollo 11 moon landing, I soon caught up with later missions and have since kept at least one eye on our forays into space. I remember scouring the library for titbits on the planets of our solar system and the stars and galaxies beyond. But my familiarity was almost entirely bookish. Perhaps it was effect of the near permanent grey skies of my youth in Northern Ireland, but I never really thought to look up. 

      The trajectory of my childhood interests carried me effortlessly to Imperial to study for a degree in physics. There I learned the maths of Kepler’s laws governing the motion of the planets and of the gravity that slings them around the sun, once even measuring G, the gravitational constant, in a laboratory practical using apparatus that conformed closely to Cavendish’s original design. I also delved into the nuclear reactions that power the stars. But despite increasing my comprehension of celestial mechanics, the planets and stars remained distant, not just in space but also in my imagination. It’s a puzzle to me that this separation was not bridged sooner: I could see things in fantastic detail on the page but was still not connecting with reality.

      Later I found myself lecturing at the same physics department but by then had hitched my star to the life sciences and ended up teaching molecular biophysics in a timetable slot shared with cosmology.  I used to start my lectures by congratulating my students on the tremendous sagacity of their choice. Cosmology was all very well, I declared, but it was a subject concerned with the investigation of a universe that was largely invisible, being mostly composed of dark matter. Even those parts that could be perceived were too far away to see in any detail. Far better, I opined, to focus our attention on the one corner of the universe where something really interesting was actually going on — by which I meant the superabundance of life on planet Earth. The media frenzy whipped up by by NASA at the discovery of the tiniest particle of water on some distant planet or satellite, I noted, was an inadvertent admission that life—or even the merest possibility of life—was the topic that excited humankind’s most passionate interests.

      Although I was only practising my jaundiced cosmological eye as a piece of rhetorical trickery, I suppose it may have had the effect of distracting me still further from my latent interest in astronomy. (Perhaps I was also partly motivated by envy: cosmology was always a more popular course among the physics students.)

      Blue Moon - 31-Dec-2009

      And then in the past several months an unusual conjunction of events conspired to reignite my enthusiasm. In September astronomer Alyssa Gilbert popped up on Nature Network, clearly determined to tell the world about the wonders of her subject. At about the same time my daughter joined an astronomy after-school club led by one of her more enthusiastic science teachers so the topic started to come up at home. I realised then that, despite my own long-standing interests, I had never in my life peered at the heavens through a telescope. That was something I wanted to change.

      Thanks to Alyssa and NN’s very own Londonista, Matt Brown, I found out about the public observing evenings held at the Greenwich Royal Observatory and promptly booked tickets for myself and my son and daughter for a moon viewing in late October.

      But alas, an evening that I was almost surprised to find myself looking forward to with bubbling excitement turned to sour disappointment when the cloudy skies stubbornly refused to break for the entirety of our session. At the observatory they didn’t even bother to remove the lens cap from their magnificent 28-inch refractor telescope. I was forced to swallow a second bolus of dismay when one of their resident astronomers (@Skyponderer) posted a beautiful picture of the moon on Twitter, taken by just holding his iPhone to the telescope eyepiece the following evening!

      I was gutted.

      And faced with a dilemma. I could try to book for another night hoping for clearer skies; but the tickets weren’t exactly cheap and the risk of another disappointment was palpable. This fear, and the remark by one of the Observatory’s speakers that a modern amateur telescope would produce images almost as good as their huge but elderly refractor, triggered a thought about buying a telescope of my own.

      And so it came to pass that on Christmas night I was out on the patio fiddling with the optics of a Sky-Watcher Explorer-130P SupaTrak Auto, a motorised Newtonian reflector with a 130mm diameter mirror. It was a clear night and bitingly cold. For a first session I set my sights on looking at the moon which hung luminously, three-quarters full, in the night sky. But the practicalities of setting my sights proved a little tricky since the spot-finder, an accessory fixed to the barrel of the reflector that conveniently places a red dot wherever the telescope is pointed, had yet to be properly aligned. I swung the telescope around to put the red dot in the centre of the moon and squinted into the eyepiece.

      All I could see was a blurry glow which leapt and wobbled as my numbing fingers twisted the focus knob. But no amount of adjustment seem to sharpen the image. I then realised that since the spot-finder had yet to be calibrated, the telescope was not actually pointed at the moon, though it must have been close. Grabbing the controller I nudged the telescope barrel towards the glow and was immediately rewarded as the bright disk of the lunar surface slid into view. For the first time in my life I gazed at the crated, pitted surface of our silent satellite, thrown into sharp relief along its shadowed edge. No amount of reading or studying, I suddenly discovered, had prepared me for the amazing intimacy of that encounter. I called my children to come outside and share in the lunar glory.

      A couple of nights later I was out again – just looking. I haven’t yet made much effort to read up on the ins and outs of star-gazing, to navigate my way across the night sky. It was my brother-in-law who reminded me that the ecliptic—the plane that, give or take the odd deviation, contains the orbits of the moon and planets—would be defined by the path of the sun (well, duh). For now, I am content just to explore.

      Spotting a bright star low in the sky over towards the west I marked it with the red-dot—now correctly aligned—and was pleased to see this, a pale disk flanked by points of light:

      Jupiter Sketch 1

      Keen eyed readers will have noticed the similarity between my drawing (I hadn’t yet acquired a bracket for my camera at that point) and one produced some centuries earlier by Galileo Galilei:


      From Galileo’s book, ‘The Starry Messenger’; image hosted at www.lettherebenight.com

      Galileo’s observation of Jupiter, and what he correctly interpreted to be its moons, were a vital part of the observational evidence that not everything in the visible universe orbited the Earth. It was these observations that initiated his collision course with the Catholic church.

      I claim no affiliation with Senor Galilei, a far greater scientist than I will ever be, but as I gazed with my own eyes at Jupiter aligned with its satellites that night, I could nevertheless sense something of the transformative power of seeing things for the first time. What an incredible moment that must have been for him, as the carapace of stars was punctured by the moons of Jupiter.

      Tonight I was out again and, turning my view towards Jupiter once more, was thrilled to see that in the four days since I’d last looked the moons had changed position:

      Jupiter Sketch 2

      There is nothing original or new in this. But for me, it means that the universe has come alive and I am attuning to its rhythms. There is something wonderfully fresh and vital about the night sky that I had simply—shamefully—been ignoring.

      Last night, though the cloud cover prevented me from sighting Jupiter, I managed to catch the glorious “blue” moon, the second full moon of the month of December. I was able to try out the camera attachment that I purchased hastily this week and took the photograph above, that hovers serenely, anciently, over the mess of text.

      It’s by no means a great picture of the moon — it could be sharper and there is a rim of chromatic aberration along the top edge. But I am utterly delighted with it.

    • Singh at Imperial

      Tuesday, 15 Dec 2009

      This’ll be brief. It’s late. Tonight Simon Singh returned to his undergraduate alma mater to speak to students and staff at Imperial College about his adventures in science and his battles with libel.

      With good humour but serious intent he warned the audience – a full house in Blackettt Laboratory Lecture Theatre 1* – to be on their skeptical guard about nonsense in the world. Nonsense such as The Bible Code, debunking of which led to the revelation that predictions of the death of Princess Diana could be found encoded in the dense text of Melville’s Moby Dick!

      Simon Singh speaking at Imperial
      Simon Singh speaking about libel chill – definitely not treatable with chiropractic

      But the humour largely dissipated as he recounted the sorry tale of the libel suit brought against him by the British Chiropractic Association, facilitated by the slack and outdated libel laws of this country.

      The audience, many of them hearing the story for the first time, was rapt, absorbed. At the end they probed and examined with serious questions – some evidently astounded at the over-reach of chiropractic, some by the cold grip of current libel legislation, and others testing his journalistic mettle.

      He was sure to remind those present that more information can be found at the www.libelreform.org web-site, where I hope that not of few of them will be heading to sign the petition in support.

      Naturally, I trust that many of you will follow suit.

       
      *Thanks to Felix editor, Dan Wan, and RCSU president, Katya-yani Vyas, for organising such a great event.

    • Ego Tripping At The Gates Of Hell

      Sunday, 13 Dec 2009

      On Friday evening the structural biologists of Imperial College and the friends of the structural biologists of Imperial College gathered together for a screening of the film, Naturally Obsessed.

      Filmed over three years, this hour-long documentary tracks the lives of graduate students Rob, Kil and Gabe, as they battle the recondite mysteries of protein crystallography in their quest to become scientists.

      Naturally Obsessed
      Larry and Rob talk science

       

      Our screening was quite timely, following hard on the heels of a day that had seen the best and worst of crystallography, confirming it as a tortuous vocation that offers huge rewards but only at the price of severely stressing its adherents. On Thursday the Nobel prize for chemistry was presented to Ramakrishnan, Steitz and Yonath for determining the crystal structure of the ribosome, and another potentially prize-winning structure appeared on the cover of Nature. But that day also brought news of that no fewer than twelve crystal structures published by H.M. Krishna Murthy of the University of Alabama Birmingham were to be withdrawn from the protein data bank and the associated papers retracted because the university had a ‘preponderance of evidence’ that the structures had been fabricated. This was a truly shocking revelation, one that the community is struggling to absorb. It will no doubt play out in full over the coming weeks.

      In the film we watched Rob, Kil and Gabe, their eyes very much fixed on the prize of growing crystals that will scatter X-rays to high resolution and open the door to a future career in science. But much of the action was inaction as the three graduate students dealt in their various ways with the ever-present strains of failure.

      Presiding over the lab was PI Larry Shapiro, the grinning guru, who stroked and joked with his charges but nevertheless spoke with great feeling about his passion for science, and his determination to become the scientist of his dreams.

      The film deals frankly with the failure, that perennial accompaniment of experimentation, giving the three young scientists space to share their experiences of life in the cramped, equipment-packed lab. There were plenty of moments of resonance for our audience of structural biologists, as we watched the nigh eternal cycle of new plasmid construction, protein preps and failed crystallisation trials. The film was really quite poignant at times; I am thinking of Kil’s fixed stare at the road ahead as he drove back from yet another disappointing synchrotron trip, the consoling words of his mentor clearly not having any impact; and of Larry’s own dreadful revelation of the tragic circumstances surrounding the publication of his first Nature paper.

      But there were plenty of laughs too: crystallographers may have to be a steely bunch but they are also strange creatures with bitter humour who sometimes need the juju of pickle juice or the gentle melodies of “Yoshimi Battles Pink Robots” by the Flaming Lips to tickle their proteins into crystallisation.

      The particular projects undertaken by Rob, Kil and Gabe are hardly explained as the film concentrates on their day-to-day experiences. I suspect it therefore appeals mostly to crystallographers who will most readily connect with the various tasks that were depicted, both in the lab and at the synchrotron. It certainly chimed with our audience of structural biologists at Imperial – and I enjoyed the film much more at the screening than I had in a sneak private preview. I suspect it may reverberate less powerfully with non-crystallographers and less still with non-scientists, who will certainly see and feel the students’ frustrations and joys (either through success or self-revelation) but may to not fully understand their origin.

      But I thought the movie was fascinating. It was most definitely an experiment worth trying. I hope that the film (which, by the way, has already been nicely reviewed here on NN, at LabLit and on the P212121 blog) gets the wider audience it deserves, and may perhaps inspire scientists in other fields to open their laboratory doors to the all-seeing eye of the camera.

    • Libel Reform Campaign Reform

      Thursday, 10 Dec 2009

      The prospects for much-needed changes to the outdated libel laws of England and Wales received a fresh impulse in the past couple of days as Sense about Science, the Index on Censorship and English PEN joined together to lobby as the Coalition for Libel Reform.

      The coalition has just re-launched the campaign for reform with a flurry of publicity to ensure that the laws are reset to maintain protection from defamation but without placing any disproportionate burden of proof on defendents. (I was fortunate to be invited to Wednesday’s celeb-packed launch but synchrotron duty, alas, prevented me from attending!)

      Free-speech
      The campaign for libel reform

       

      As we have seen, reform is necessary to release scientific discourse from the deadening effect of libel laws that make it too easy for wealthy individuals and organisations to silence critics with the mere threat of a libel suit. I’ve been banging on about this recently. And Nature has also lent support to the campaign for change.

      The celebrated case of the science writer Simon Singh, who is being sued for libel for an article in the Guardian, sparked Sense About Science’s campaign for scientific and academic freedom from libel threats. Impressively, that campaign has racked up nearly 20,000 supporters, including scientists, authors, broadcasters and lawyers.

      But now the push for libel reform is stepping up a gear and will be working to develop a much broader base of support. The new coalition aims to reach 100,000 or more signatories to ensure that politicians truly understand the level of public support for a change in the law. There are already encouraging signs of sympathetic responses from members of the three leading parties but the new campaign is determined to convert that initial momentum into a powerful political imperative for reform.

      One immediate step that those in the UK can take is to sign the new petition (even if you have already put your mark to the earlier Sense about Science petition!). I’ve already done so and would urge you to do the same.

      And, if you can locate pen, paper, envelope and a stamp, write to your MP to impress on them the need for reform. The petition web-site will allow you to email a form letter to your MP but I think that the more personal you can make your case, the more impact it is likely to have with your parliamentary representative. The campaign launched with lobbying of parliament today by academics, medical and science editors, human rights activists and writers, but that will only be the beginning.

      And that’s not all. Those of us with a university affiliation can spread the word at work to raise support for the campaign. I was pleased to see that Malcolm Grant, the Provost of UCL has declared his support. I want to see if my own institution, Imperial College, will also give its backing to the campaign.

      This won’t be my last word on the matter. Check out blog posts by JackofKent for a more legal insight into proceedings, or follow the hashtag #libelreform on Twitter to keep up with the campaign.

    • My Nobel prize acceptance speech, 2010

      Saturday, 28 Nov 2009

      Your royal Highness, members of the Academy, esteemed colleagues, ladies and gentlemen, it is a great and singular honour for me to accept the Nobel prizes for physics, chemistry and medicine.

      In my speech this evening I would like to present a brief account of the thought processes that gave rise to my revolutionary (and prize-winning!) Theory of the Tangential Universe and to show how it finally solved one of the most enduring problems of modern science and medicine, the existence of the strange phenomenon known as the homeopath.

      The key moment came on 25th November last year as I was watching the Science and Technology Committee of the UK Parliament perform an evidence check on homeopathy by quizzing scientists, pharmacists, health administrators and homeopaths. As I listened — in open-mouthed wonderment — to the latter group speaking, I struggled to fathom the source of their incredible pronouncements. What infinite dilution of critical faculties, I asked myself, could have led them to utter such utter nonsense with straight faces? (Pause for laughter)

      In a moment of blinding insight, I realised that the answer to my question was embedded within it. As I tried then to empty my own mind of thought, to shed from it the clutter of the scientific insights that have accrued and evolved over centuries, I was suddenly gripped by a powerful vision. It was a Eureka moment such as must have been shared by many who have graced this platform down through the years.

      There must be a “Tangential Universe”, I hypothesised, to which the homeopaths — uniquely until now — have had access. I gave it this name both to distinguish it from parallel universe theory (whose proponents might one day find themselves here in Stockholm) but also to highlight the very different laws of physics that obtain there.

      By unshackling myself from thought I found a way to gain access to this tangential universe and began to codify the wondrous phenomena that occur there, not the least of which is homeopathy.

      Within a few weeks of feverish work I had shown that none of the zeroth, 1st, 2nd or 3rd laws of thermodynamics operate in the tangential universe but was able to formulate the 4th, 5th, 6th, 7th, 8th, 9th and 10th* laws which do. From there it was a short step to the formulation of my general and special theories of unintelligibility, my development of bunkum mechanics and, my crowning achievement, the discovery of the querk. (Pause for applause)

      This new system of physics, which has remained hidden for so long because of course its laws have no purchase in our own universe, immediately solved the riddle of why homeopaths exist and why they appear to talk in such mysterious terms. In the Tangential Universe all of the following statements are right and proper:

      • Water has memory. (Pause for laugher)
      • “It may yet happen…” that a Nobel prize will be awarded to the person who discovers the mechanism of action of homeopathic preparations**
        Dr Peter Fisher, Director of Research, Royal London Homeopathic Hospital
      • “there are significant numbers of homeopathic medicines that are not diluted to the point where the molecular content is uncertain”
        Dr Robert Mathie, Research Development Adviser, British Homeopathic Association
        (This is the cake-and-eat-it conundrum where one simultaneously holds two contradictory positions, in this case “active molecules are not necessary, because water has memory” (see above) — and “active molecules are necessary”).
      • “One plausible hypothesis is that such instability points act as local dynamic attractors of the system. These necessarily exist in such microscopic form, it requires a novel quantum description that predicts effects at the macroscopic level, with consequences not dissimilar to those of superconductors and super-fluids in low temperature physics. The model is applicable to several systems of complementary medicine, including homeopathy.”
        Dr Lionel R Milgrom (written submission HO 04 to the committee)

      (Intriguingly and parenthetically, Milgrom’s prose has a potency that is as yet undetected in any homeopathic preparation made in this universe. Just a couple of sentences of his apparently randomly assembled buzzwords are sufficient to stun temporarily even the most robust of intellects.)

      My future work will concentrate on the more practical problem of developing a means of transport that will grant physical (not just mental) access to the Tangential Universe. This will enable the homeopaths to return to their natural habitat.

      In closing I simply want to thank the Academy again for the embarrassment of riches that they have showered upon me. My heart goes out to the wonderful men and women at the LHC in CERN whose discovery of the Higgs Boson would, in any other year, have guaranteed them the prize. I hope and trust they will be honoured next year.

      Thank you very much for your attention.


       
      * unfinished
      ** This used to be true but I fear I may have scooped them.

      P.S. For similarly accurate but perhaps more serious accounts of the Committee’s proceedings, check out the reports from Ben Goldacre, Majikthyse and Skeptikat.


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