According to the New Testament account, after the crucifixion Thomas insists on seeing and touching the wounds of Jesus before he will believe in the resurrection. Jesus shows Thomas but gently upbraids him: "Because you have seen me, you have believed; blessed are those who have not seen and yet have believed."

Which is fine, as a basis for faith. If that is your response to the ineffable mystery of existence.

Caravaggio’s “The incredulity of St Thomas” (from Wikipedia)

But not when it comes to science or medicine. Or government policy.

In science, our instinct is to side with Thomas: the only acceptable basis for belief is seeing. Show us the data is our mantra. Show us the evidence. No substitutes or alternatives are acceptable. Now and then we might argue about the data and what it means. We might not even properly understand it. But that’s OK, because science tackles hard questions. By talking, debating, turning the problem over and over to see it from all sides and using the power of imagination as best we can, we construct new ideas about how the natural world works. And then put them to the test. To generate more evidence. And so it goes.

This sceptical, exploratory, testing method is the true glory of science. Our experience is that this system has profoundly altered our understanding of the world around us and shaped our influence over it. Through the 19th and 20th centuries, the same interrogative approach has been applied to medicine. The method is imperfect and our understanding far from complete, but the advances in antibiotics, vaccines, organ transplants and fertility treatment are a lasting testament to its success.

And yet there are many who would demur, who cling to fanciful notions generated when medicine was in its infancy, notions that have seen little or no development since that time and are—if anything—a little shy when it comes to rigorous investigation. Fancies such as homeopathy and chiropractic. So-called alternative medicines.

You might think that science could easily bat away such interlopers, who like borrow the vocabulary of science and medicine but are nevertheless easy to spot because, like a tourist on a package holiday, the accent is all wrong. But they defend themselves with vigour, even if it is sometimes with comedic effect.

On Wednesday 25th November the UK Parliamentary Select Committee on Science and Technology will examine the evidence for homeopathy. This is called an Evidence Check and the committee will hear submission from both sides. It promises to be a truly fascinating encounter (details here; catch it on parliament TV ). 

But the homeopaths are nervous and are trying to respond to this unwanted investigation in the only way they know how — with more woo. Gimpy’s blog reported last week that there is a homeopathic plan to interfere with the committee’s hearing using… mind tricks! On the morning of the Committee meeting, between 9:05 and 9:15 they have asked supporters to participate in an Intention Experiment to sway the honourable members by focussing en masse on the following statement:

We intend the outcome for the UK homeopathy evidence check to be wholly and fully in favour of homeopathy. We intend for the vast and thorough body of scientific data supporting the efficacy of homeopathy to be seen, heard and recognised as valid, solid and scientific. This is so, and it is done.

Yoda would have been so proud!

I’m not making this stuff up. But clearly the homeopaths are.

This sort of voodoo is all of a piece with a world view that is so strangely unworldly. There was another taste of it last week from one of homeopathy’s most enthusiastic proponents, Richard L Milgrom (Ph.D., F.R.S.C., M.A.R.H.) in an article in the Journal of Complementary and Applied Medicine in which he tried to reconcile homeopathy and biomedicine. Permit me to quote from the abstract:

Based on known observables, a rudimentary fractal model of the universe is proposed consisting of a series of self-similar integrated levels of reality, or “wholes” contained one within another like a set of Russian dolls. This model suggests possible contextualization of homeopathy and biomedicine’s observational stances.

The fractal model bears compelling similarities to the ancient Hermetic tradition encapsulated in the phrase, “As above; so below.” In the context of this model, homeopathy’s observational stance includes a multidimensional range of symptoms from across several “levels of wholeness.” In contrast, biomedicine’s stance corresponds to exclusive observation of separate symptoms, each originating from one physical level of reality.

If anyone thinks they know how to explain what this means, please don’t bother to get in touch.

It is easy to laugh (and some would argue that is the only approach to take with these outlandish people) but there is a sober side to all this. In England and Wales, the freedom of the sceptic to poke fun or, more seriously, an inquiring finger is limited by our libel laws. Few here can be unaware of the case brought by the BCA against Simon Singh when he wrote to challenge the evidence for the therapeutic reach of chiropractic. 

That law suit is rightly mentioned in a report published on November 10th by The Libel Reform Campaign. The campaign, sponsored primarily by English PEN and the Index on Censorship, has attracted a broad church of support and is striving to bring this country’s libel law up to international standards. Science and public health matters feature prominently among the recent cases used in the report to illustrate the way that the current law is too easily deployed to silence critics. 

There is a concise and very readable executive summary which enunciates a clear plan of reform. I can also recommend to you the succinct dissections of the report presented by Jack of Kent and Simon Singh himself, so I won’t go into much further detail.

The report is lucid and level headed. There are no strident calls for special pleading for science or any other sphere of human endeavour. There is a frank acknowledgement that protection from baseless defamation should certainly be enshrined in law. But the argument that the current defective libel law cedes too much censorious potential to powerful organisations and individuals is built of solid data. It’s not just Simon Singh who has been threatened. The dreadful impact of the libel law on critics of alternative medicine (such as Andy Lewis of the Quackometer) or those who challenge medical or pharmaceutical companies (such as Peter Wilmhurst) are particularly relevant to anyone who cares about having the freedom to debate and discuss the evidence.

In common with many scientists, I don’t see myself as particularly at risk under the present libel regime (as long as I am careful). My research is mostly of a fundamental nature and I am not likely to come into conflict with powerful vested interests. But I don’t see that as an excuse for inaction. As scientists we are particularly aware of the nuance and sophistication of our art, and of the contingent and incomplete nature of our understanding of the world. The necessity of being able to interrogate ideas remorselessly is so engrained in our scientific bones that we may sometimes forget it is there. But that freedom of interrogation — so prized by science — it is not something that we can take for granted, especially when our work rubs up against powerful commercial and political interests.

So I would urge you to act. Proselytise for science and the scientific method at every opportunity. And, if you have not already done so, please sign the petition organised by Sense about Science to keep the libel laws out of science. The wider campaign for libel reform is no less important and appears to be gathering important momentum from across the political spectrum. There are statements of support from Jack Straw (the Labour government’s Justice Secretatry), Joanne Cash (Conservative) and the tireless Dr Evan Harris (Lib Dem).

Evan Harris, who is a member of the of the parliamentary Science and Technology committee will, I hope, play a leading role in the interrogation of the evidence on homeopathy this coming Wednesday. He has a very clear understanding of the value of scientific evidence and supports not only Simon Singh but also Professor David Nutt, the recently departed independent scientific adviser, who’s pronouncements on the relative risks of different drugs have so challenged two Home Secretaries.

Preaching or teaching?

Harris and Nutt both spoke at the second Westminster Sceptics in the Pub (SITP) meeting in The Barley Mow last Monday. It was an excellent meeting (as already reported by @jourdemayne and @doctorblogs): vibrant, thoughtful and good humoured. Nutt and Harris provided fascinating insights into the facts about drug risks and the sometimes unbelievable difficulties in having a logical discussion on these contentious matters with government ministers. The Q&A session, deftly chaired by Jack of Kent, lasted a good hour and gave the audience a welcome chance to dig deeper. All of it lubricated — a delightful irony pointed out by @doctorblogs — with plenty of beer, one of the more harmful drugs on Prof. Nutt’s list.

Were they preaching to the converted? Probably, but the ‘sermons’ were nonetheless invigorating and inspiring. And provided us with some of the ammunition that we, the apostles of science need to take with us if we are to act in the world and make a difference.

The Westminster sceptics are gathering again on Tuesday to discuss “What Next For Science Activism in the New Media?”.

It should be a good meeting, brothers and sisters.

Last month I gave a talk to a group of Imperial College Alumni, all of whom had made a generous donation to the university and still take an interest in what goes on there.

An interest keen enough to drag them to a lecture theatre on a grey October evening to hear one of the College’s researchers give an account of their latest work. On this occasion the task fell to me and I opted to tell the tale of our quest to determine the structure of the 3C protease from foot-and-mouth disease virus (a topic we’ve published on just recently).

I do enjoy this kind of challenge — though it takes a good deal of preparation — and sought to make the story accessible to a general audience by giving an account not only of the scientific results but also of our travails in the laboratory and in our search for funding. Having recently completed the biography of Thomas Henry Huxley, who has a strong connection with the College, I also wanted to weave some of my late-found admiration for that great 19th century scientist into the tapestry.

iLecture to Alumni.

Thanks to the College’s burgeoning audio-visual department, you too can attend the lecture. A video was recorded and last weekend I spent a few hours inter-cutting the slides that I showed on the night, hoping to make the package a bit more digestible.

It does go on just a wee bit (I couldn’t help warming to my theme!) so I have few illusions about people sitting through the whole lot. There’s an introduction by the rector and I get started at about 8:20 with an historical introduction, mostly devoted to Huxley. The description of foot-and-mouth disease and the virus that causes it begins at 17:00 and I finally start on describing the work that we have done at about 34:30. These times are min:sec, not hr:min!

Anyway… for those who may be interested, you can catch the video within your browser on my web-site. Alternatively, the College* also has a web-page on the lecture that provides a RealPlayer version. Or, and I am inexplicably and disporportionately chuffed by this, you can even download it via iTunes!

You wouldn’t think from the video that I had to take myself outside and walk around the block in the fresh air just before the lecture to steady my nerves. Speaking to the public is much harder than speaking to other scientists – but also much more fun, once you get going.

*For reasons that I’m afraid don’t properly understand, the College versions have a slighlty squashed aspect ratio. However, this has the advantage of making me look a bit thinner!

Without quite meaning to I realise that I have been generating a series of blogposts about the publication process.

Initially I wrote about my struggles to finesse the figures needed to show off the important aspects of our structure of the complex of the 3C protease with a peptide substrate. After we had submitted the manuscript, I discussed the issues surrounding our use of language that had been raised by one of the reviewers.

Then Richard weighed in and kicked off an interesting discussion on the costs of Open Access publishing. There is a fair amount of enthusiasm for this dissemination innovation among many scientists — it chimes with our amateur ethos — but in these straitened times the costs to authors are starting to bite.

When our paper was accepted by the Journal of Molecular Biology last month I had to decide whether or not to shell out the $3000 charge that the publisher levies to make the final, edited and prettified version of the paper freely available via PubMed Central.

The work reported in our paper was funded by the BBSRC on a grant that started before 2006 and has now finished. That meant that, although the BBSRC encourages OA publishing, we were not required to deposit the paper with PubMed Central. If we opted to go down that route, we would have to stump up the OA fee.

However, it is still possible to make the article freely available. According to Elsevier (the publisher of J. Mol. Biol.), authors retain

the right to to post a revised personal version of the text of the final journal article on the author’s personal or institutional web site or server, incorporating the complete citation and with a link to the Digital Object Identifier (DOI) of the article.

Now, I am well aware that this is a second best solution since anyone searching for the paper within Pubmed will not automatically be presented with a link to the OA version of our paper. But $3000 is $3000.

Moreover, I am not permitted to upload the final, journal-polished version of the paper on my web-site. But it did occur to me that I could, without too much difficultly, convert my double-spaced manuscript into something more akin to the look and feel of a published paper. Our manuscript was written in Microsoft Word, a necessary medium since it is used by all the co-authors and integrates with Endnote, but I turned to Apple’s Pages program to prepare the pre-print because this made it easy to integrate the figures and tables within the body of the text.

Publish with polish?

 

With an hour or so of fiddling and formatting I had what I thought was a passable imitation of a published article, double-columned with inlaid figures and figure legends. On top of that, given the noises I made recently about the frustrating fragmentation of supplementary information, I had the opportunity to show how I would like it to be done.

The final document is a single file integrates the text, figures, tables and Supplementary Information as an openly accessible bolus of information. You can download the PDF from my web-site to guage for yourself how digestible it is. No purchase necessary. If still not completely sated, you may even wish to have a gander at the morph animation (with commentary) that was made to accompany the paper.

I was pleased to discover how relatively quick and easy it was to re-format the manuscript. So open access pre-prints don’t have to be the cumbersome files that we often handle as reviewers. And, if this science gig doesn’t work out, maybe I can forge a new career in desktop publishing.

Last week, the engine on NASA’s brand new Ares 1-X flamed into life and the oddly thin white tube slowly raised itself from the launchpad. It accelerated impressively quickly and arced into the blue Florida sky. Within about two minutes it was travelling at almost five times the speed of sound.

Aiming high (picture courtesy of NASA).

Right on cue, explosive bolts fired to initiate stage separation. But that’s when things began to go wrong. The booster and payload stages unexpectedly started a slow tumble as they lost speed and fell to earth. Then, on its descent, only one of the three parachutes deployed properly and the booster was badly dented as it smacked into the Atlantic ocean.

The bittersweet outcome of this test firing reminded me of Oscar Wilde’s famous saying: “We are all in the gutter, but some of us are looking at the stars”.

The scientists and engineers at NASA may draw some consolation from this as they examine their precious but damaged booster and wait, breath bated, for the US government to decide just how committed it is to the Ares program.

But such intimate mixtures of success and failure, it struck me, are part and parcel of a life in science. Our sense of achievement does not endure very long.

Or maybe it’s just me? I recently basked momentarily in the glow of the news that our latest paper had been accepted for publication. It was a great result — a new structure of a viral protease-peptide complex — and one that my group has worked hard to achieve and is justly proud of. But before I had even received the proofs I could already see the dark lineaments of looming deadlines and hear them growling for my attention. They are relentless. I have lectures to prepare, references to compose, accounts to manage, manuscripts to review, grant applications to get sorted, more papers to write. The buzz of our success was quickly dulled, in my mind at least. All I could think of this week were the jobs not done, the targets not met, and the time that I don’t have available to do the things that I usually love about this job. I felt dented, out of shape.

And so, blinded by the minutiae of everyday preoccupations as I was rushing from lecture theatre to undergraduate office last Wednesday, I was arrested briefly by the sight of a poster announcing that 4th November was National Stress Awareness Day.

“Don’t miss out!” trumpeted the cheery but bizarre tagline across the bottom of the notice.

Don’t worry friend, I told myself grimly, I’m getting my share.

But then I thought, why am I subjecting myself to this? Being grumpy about my job is just an attitude of mind. Isn’t it?

This line of thought may have been triggered by a video of a TED talk that I saw recently given by the designer Stefan Sagmeister. Sagmeister seems to have developed a much healthier attitude to work than the one that assaulted me this past week. His presentation is called “The Power of Time Off” and I thought it fascinating. The first 4 mins or so are the highlight and deliver the central message, which is that time away from work can be enormously re-energising. (But if you ’re the least bit interested in design the rest of the video is also worth a look.)

Sagemeiter on stage.

 
Now all I have to do is figure out a way to reach escape velocity.

Yesterday, I had a new experience that tested my scientific mettle to the limit: I got stuck in a lift.

There I was, dropping smoothly from the 7th floor of the Huxley building on my way to a student viva, when the lift suddenly jerked to a halt. The metal box then announced, in soothing female — almost Adamsian — tones, “This lift is out of service.”

She wasn’t wrong. The doors remained clamped shut and the lift did not respond when I jabbed at the buttons. I guessed I’d only got about as far as the 6th floor but clearly I wasn’t going any further.

Time to raise the alarm, I told myself. The instructions beneath the alarm button said, “Press for 3 seconds.”

I pushed the button and flinched as a loud bell clanged in the lobby outside. My natural instinct for not drawing attention to myself kicked in and made me let go.

Ah, silence.

But no assistance. So I gritted my teeth and pressed the button again, holding it for the full three seconds until the little yellow alarm light came on and a voice spoke from the intercom: “Yeah?”

I gave my location and the disembodied voice said, “OK, I’ll send a couple of guys.”

The intercom went dead again.

I looked around and considered my situation. I tried to be rational.

Don’t panic, I told myself.

First off, I put the papers I was carrying on the floor. No sense in needlessly wasting energy.

I briefly considered what would be the best position to adopt should the lift suddenly plunge. I know enough physics to discount the ‘jump up just before impact’ fallacy. In the first place, judging the time of impact would be impossible in a windowless box. And secondly, the relative upward motion would only have taken the the tiniest smidgen off my downward momentum, soon to be imparted to the planet.

I figured the chances of surviving such an impact would be miniscule but wondered if spreading myself on the floor of the lift, head cushioned by my arms, would have brought me closest to surviving the fatal drop.

But in any case, I told myself, that’s ridiculous. These lifts have fail-safe mechanisms. Even if the cable were to be severed, there must be a braking system of some kind. Right? People only plunge to their deaths in lifts in the movies. But this isn’t The Towering Inferno or The Omen or Speed. No wait, in Speed Keanu Reeves and Jeff Daniels turn up to rescue the terrified elevator occupants.

Thinking of movies caused me to look up. Surely there had to be a hatch in the ceiling though which, if push came to shove, I could clamber to safety? In the movies, there’s always such a hatch. Always.

But there wasn’t one. The ceiling was composed of two sections joined by a metal strip. It looked fairly immovable. If I needed to, I figured, I could try to climb onto the hand rail to see if I could dislodge it. But what then? I have no head for heights and wouldn’t want to ruin my jacket on an oily cable.

“Hello? Hello?”

The voice came from outside. Slowly the doors were prised open revealing the floor of level 6 at about one metre above my feet. I tossed my papers through the gap and clambered out to the two engineers who had come to my rescue. Neither of them looked remotely like Keanu Reeves or Jeff Daniels.

But I guess that was a relief. The real world is more prosaic but also more lawful than in the movies.

I’m beginning to recognise the signs. Have you seen them too? The mercury is holding steady but there’s a sudden and unexpected stiffening of the breeze. And a darkening tint to the clouded sky. Yes — there can be no doubt — there’s a storm coming.

A Twitter-storm.

We’ve not had much of this kind of thing in the past but these squalls seem to be becoming more frequent. They are a very interesting phenomenon; the kind of climate change that I might welcome.

I don’t think anyone expected this sort of impact from Twitter. Maybe it’s illusory? The past two weeks have been so blustery that my head is still reeling. But things are calmer today so I have a moment to take stock.

I first noticed a change in the air when, on the night of Monday 12th October, Jack of Kent wrote a carefully worded post about an equally “carefully worded” article in The Guardian revealing that the paper had been prevented on legal grounds from reporting an item of parliamentary business. Within a few minutes news of the Guardian’s gag had spread around Twitter and the involvement of Trafigura and their attempts to keep secret their report on the dumping of toxic waste in the Ivory Coast came tumbling out. At the end of his post, Jack of Kent raised a quizzical eyebrow and wondered if the newspaper might have acted in a calculated fashion by placing enough cryptic clues in its article to let the twitterati solve the puzzle.

On Wednesday of that the week Twitter, or at least that tiny segment that I choose to keep an eye on, was alive with the unexpected news that Simon Singh had been granted leave to appeal Justice Eady’s ruling on the meaning of the word ‘bogus’ in the libel suit being brought against him by the British Chiropractic Association (BCA). At the Wesminster Skeptics in the Pub meeting the previous night where Singh and others had spoken out against the dis-empowering effect of the English libel laws, the mood had been feisty but resigned. So there was an eruption of delight buzzing across the net as soon as those attending the appeal hearing had managed to rush outside and reconnect with it.

The news of the appeal, and perhaps also the effusive response from Singh’s supporters, elicited a hasty press release from the BCA. The organisation affirmed it would continue to press its case because it felt it had been “maliciously attacked by Dr Singh in the Guardian newspaper” (my italics).

That careless adverb was seized upon immediately. Word went out on Twitter asking people to download or cache the BCA statement because it represented a serious mis-step by the organisation. They appeared to realise this themselves since the press release was quickly reworded to remove the offending term. But that was of course too late. As Jack of Kent explained in a post that evening, in attributing malice to Singh, the BCA had defamed him and the author may now be in a position to counter-sue. Whether he will do so remains to be seen but it was a moment of delightful irony. One that was shared by hundreds, probably thousands of witnesses, on Twitter.

The Trafigura and Singh cases came together on Wednesday of this past week in a parliamentary debate organised by Evan Harris (Liberal Democrat MP for Oxford West and Abingdon). Thanks to notification on Twitter I discovered it was being shown live on the web and managed to catch Harris’s impressive speech outlining the threats posed to open debate in this country by our laws on injunctions and libel. (You can watch it here or read the Hansard Report).

Evan Harris waxes lyrical

I suspect the audience for this debate was one of the largest they’ve had in a long time on Parliament TV. For me, who had never tuned in to a debate before, the revelation of this level of access was an impressive demonstration of the transparency of our parliamentary procedures, a window across which Trafigura had sought to draw a heavy curtain. I have them, and Carter-Ruck and all the good folk on Twitter to thank for bringing it to my attention.

But that’s not all. On Friday 17th October, just a couple of days after Singh’s success in the court of appeal, another storm thundered and flashed across Twitter as people reacted to Jan Moir’s now infamous Daily Mail article on the death of the Boyzone singer Stephen Gately. Without bringing any new information to bear on the case Ms Moir felt able to flatly contradict the cornoner’s finding of “death by natural causes”, link Gately’s death to the recent unrelated demise of Matt Lucas’s former partner and wax unlyrically about this being “another blow to the happy-ever-after myth of civil partnerships.” The article was grossly insensitive and struck many, including myself, as tapping into a homophobic vein. To add further insult, it appeared in the paper the day before Gately’s family were due to bury their beloved son. The reaction on Twitter was exponential; a few drops of rain in the morning turned into a crashing downpour by lunchtime.

Later that day Charlie Brooker fired off a characteristically caustic Comment is Free article in The Guardian that gave voice to many people’s anger at the insensitivity of Moir’s article. Helpfully, he detailed which aspects of the press code of conduct might have been breached. He also provided links to the Press Complaints Commission (PCC), information that was rapidly disseminated, 140 characters at a time.

As so, because I was appalled at the article and — crucially — had ready access to the means to do so, I logged on to the PCC web-site and, for the first time in my life, complained about a newspaper article. It took a little while to get connected; I think they were having trouble with the volume of traffic. Once I got through I saw that the PCC had obligingly put up a special link for those wishing to complain about Moir’s article.

Moir saw in all this an “orchestrated campaign”. I suspect that is probably what it feels like when over 20,000 people complain about your obnoxious journalism but there was nothing terribly orchestrated about it. Nobody told me what to do and I like to think that, in common with most other people, I have a mind of my own. But — as with Trafigura and the reports on the Singh-BCA case — there was instant access to information on Twitter and elsewhere on the web and to modes of action. And it was exciting be be able to be involved.

Finally in this past week great interest was excited by the appearance of Nick Griffin, the leader of the British National Party, on the BBC’s Question Time program. Griffin, an odious little-Englander racist who has denied the holocaust, faced a largely hostile audience in the studio. But there was an even larger audience watching at home and many of them were simultaneously bombarding Twitter with comments. It was a strange new experience to be watching TV in the company of this vociferous online audience. Thrilling even.

So I joined in.

I’m not sure if anything so very insightful was said in these comments. It felt much like shouting at the screen as you might do while watching football. But not entirely the same. Occasionally, because our society is thankfully not as homogenous as some might like it to be, there would be a dissenting or sparky view. One person wondered about the true value of all the self-righteous Griffin bashing. The comedian Peter Serafinowicz, observing those in the studio audience with their arms raised to catch the Chairman’s attention, made me laugh out loud by commenting “Surprising amount of people ‘sieg-heiling’ between questions.”

There have been lengthy and knowledgeable debates elsewhere on the rights and wrongs of the BBC’s invitation to the BNP’s elected representative. I won’t rehearse them here except to say that I favoured allowing Griffin to appear on Question Time. If freedom of speech is to mean anything, it must include allowing those whose views we despise to be heard. Anyone wishing to oppose Griffin and the BNP should have enough respect for the electorate to try to win the argument with facts and logic and a sense of natural justice (resources that Griffin so clearly lacks). We need to have some faith in our democratic institutions.

In Twitter, especially in these past two weeks, I think I detect the emergence of a new pillar to support our democracy, simply because it has provided a new way of bolstering of our freedoms of speech and information.

Now I have no doubt that there’s a mob element to much of the activity on Twitter. The re-tweet (RT), which simply re-broadcasts a comment that you have seen to all your followers probably makes it too easy for news to travel without the intervention of thought (though Ian Hopkinson suggested aninteresting possible counter-measure). And there’s certainly something primal about being part of the crowd – even when you’re not in close physical proximity to those baying around you.

But I would contend that it isn’t simply mobbishness. Perhaps it’s just from the people that I happen to follow on Twitter but there is a reflective thread running through all this commentary and activity. In the aftermath of the Moir shitstorm and his own foot-in-mouth episode with the people of Poland, Stephen Fry wrote a wonderfully thoughtful piece musing his own foibles, the accusation that he has a disproportionate influence as a result of his prominence on Twitter (at the time of writing he has nearly 900,000 followers) and, most interestingly, on the possible broader role of this new medium.

Of course I re-tweeted it as soon as I’d finished reading. (It is well worth a look.)

I get the sense that tools like Twitter are switching people on. It has certainly affected me. I noticed it first when Twitter became my primary source for news of the protests that erupted in Iran in the aftermath of their presidential election in June. In that case I was able to keep informed and to pass on information, reports of attacks by the security forces and links to photos and videos. It didn’t, I have to say, lead to much action beyond that on my part.

But these latest episodes — more home-grown — have been different. I have never felt more engaged in society than in these past two weeks. This has happened because I have better, faster access to the information about what is going on and because I have tools at my disposal, either through blogging or tweeting or writing to the PCC, to do something, even if it is just to make my voice heard.

I know just enough about human history not to get too carried away with the promise of a bright new future. But I cannot help being at least slightly optimistic that some of the energy humming around the internet might, just might, do some good.

Then again, perhaps it is just a local shower and will pass.

The twitterverse has been alive this morning with the wonderful news that Simon Singh has been granted leave to appeal Justice Eady’s ruling in the libel case that the British Chiropractic Association had brought against the popular science author. See here and here for some background to the case.

The news is all the more wonderful because it was so unexpected. The first synopsis of this morning’s court ruling has appeared on arch-skeptic Crispian Jago’s excellent blog. He has done a great job of rendering the very brief legal proceedings in lay terms!

The news will also be a great boost for the Sense About Science campaign to Keep the Libel Laws out of Science

That’s all for now (work beckons). To keep abreast of developments and further blogs on this issue, follow the hashtag #singhBCA on Twitter.

When it comes to language, I am a lover and a fighter. I’m no great expert but I know what I like and do try to take a bit of care every time I lay out my little handkerchief of prose here on Nature Network.

So today, when I spotted that The Guardian’s report on the award of the Nobel prize for Chemistry to the three crystallographers who determined the structure of the ‘rhibosome’ (I kid you not), I fired off a tweet of correction. This weird mis-spelling of ‘ribosome’ didn’t look like a forgivable typo. No, the deformity rankled as a bad guess.

But last week I was myself pulled up for offences against the English language. This occurred when I received an email from an editor at the Journal of Molecular Biology inviting me to revise our recently submitted manuscript (on the structure of a protease-peptide complex) “in the light of the referees’ comments”.

Now my first reaction was one of delight since, if past experience is anything to go by, this circumlocution means the paper should be accepted subject to minor revisions. I was also pleased because this means we will probably have a paper in JMB in the year that this venerable publication celebrates its 50th anniversary.

Then I turned my attention to the requested revisions, three of which referred to my use of language.

To the first charge, the use of ‘apoenzyme’ to refer to the unliganded form of an enzyme, I have to plead guilty. That was sloppy of me. An aopenzyme is, of course, a protein catalyst without its co-factor.

In the case of the other two charges, however, I think I will fight my corner. The referee claims that ‘complex’ is not a verb in English. But it seems to me to be in common parlance, at least among crystallographers. We had written ‘prior to crystallisation we complexed the peptide with the protease’. I was relieved to find that ‘complex’ is indeed defined as a verb in the dictionary on my computer, and one of my co-authors found it in the Merriam-Webster online dictionary. Case closed, I think.

Finally, and most surprisingly of all to me, we were taken to task for using the term ‘protein expression’ to refer to the synthesis of our protein in bacteria. The reviewer pointed out that genes may be expressed but not proteins (!) and went on to bemoan the deterioration of accuracy in scientific language. Well that was a first for me. I can see where the reviewer is coming from but is there really any ambiguity in ‘protein expression’? It is a phrase I have used and heard used without confusion for nigh on 20 years.

Now I don’t want to row with the reviewer. (By which I mean don’t want to argue, not that I am averse to taking a trip with him or her in a boat equipped with oars. My goodness, this English language is a slippery thing. Look at the stacks of alternative meanings building up for just one little word, row upon row… but I digress). After all, this person has done me a great service by reading our manuscript very closely and politely suggesting improvements. But I have to dissent from their rather static view of language.

When it comes to the ways that we create meaning with words I am bound to say that I am firmly in Stephen Fry’s camp. Language is a living, breathing thing. It grows and develops. And, as long as meaning is not obscured, anything goes.

That’s what makes writing fun. Innit?

At the Diamond synchrotron last week, Jamie Oliver would have been proud of us.

Amar and I pitched up last Thursday afternoon at the great gleaming doughnut in the Oxfordshire countryside with the latest batch of Amar’s crystals, packed carefully into a dry nitrogen dewar to keep the little jewels frozen at a chilly 80K. Because we were sharing the beamtime with other users from Imperial our slot didn’t start until about 8.30 in the evening. Amar had plenty of time to transfer the crystals — under liquid nitrogen — to the pucks that would eventually be loaded into the mounting robot. There was even time to stroll over to the cafeteria for a leisurely dinner.

But as soon as we got going with our experiments it was clear that something was not quite right with the samples. Each crystal was mounted in a tiny nylon loop stuck on the end of a thin metal pin. Plucked from liquid nitrogen by the robotic arm, they were kept frozen on the X-ray camera by a steady stream of nitrogen gas at about 100K. But rather than glinting in the fluorescent lights, the crystals looked opaque and rather ragged in outline.

That could mean only one thing: ice.

The diagnosis was confirmed as soon as the crystal was exposed to just half a second of the intense X-ray beam:

The concentric circular rings on the diffraction pattern, partially and annoyingly obscuring the lattice of spots that we needed to measure, were due to the presence of randomly oriented ice crystals, either within or on the surface of our protein crystal. Before freezing, protein crystals are usually soaked in a solution containing a cryo-protectant — or anti-freeze — such as glycerol. The cryo-protectant prevents the water within the solvent channels of the protein crystal from turning into crystalline ice. Instead it should form a glassy solid that only scatters X-rays diffusely and doesn’t seriously interfere with the diffraction pattern.

When you see ice rings it sometimes helps to “re-anneal” the crystal. You do this by blocking the cooling nitrogen stream for a few seconds, usually with a handy credit card, to allow the liquid surrounding the crystal to thaw and then quickly re-freeze it again.

Well we tried that. It didn’t work.

And then Jeremy, a colleague from Imperial, popped into the station and mentioned that Juan, the Diamond beamline scientist, had suggested ‘washing’ crystals with liquid nitrogen to get rid of ice.

By this time we’d been through several samples and were certainly open to suggestions. So with a long 25 mL plastic pipette dipped briefly into liquid nitrogen we quickly drizzled a few drops of the slick colourless fluid over the crystal mounted on the camera.

The effect was immediate. Already on the video screen the appearance of the crystal changed considerably. Gone were the ragged edges and out of the obscurity emerged a gleam of shining light.

Better still, when the crystal was exposed to X-rays the rings were gone. Completely.

And we could see that the crystals diffracted to about 1.5 Å. I’ve mentioned before what a rich treasure-tove of structural detail such data can reveal. Thanks to that timely tip-off from Jeremy and Juan, we were able to get stuck into several hours of solid, rewarding work. We were cooking, if you’ll pardon the pun.

When I got back to Imperial there was the usual round of inquiries as to how the trip had gone. It’s always good to be able to report that you got some data. But this time I was more interested in recounting the impressive effect of the liquid nitrogen wash – to spread the good news, so to speak. And I found plenty of eager ears.

And that’s what I’m doing here I guess. The title of this blog is Reciprocal Space, after all. Every so often I feel duty-bound to make some mention of X-ray crystallography and the joy it can bring.

Thanks to the very good offices of Matt Brown, who knows everything about everything happening in London, I found myself at the Smithfield Gallery last night. Jenny, Richard and myself joined Matt there to gaze at Luke Jerram’s artful glassy virus sculptures.

Matt has already blogged about the evening so I will leave it to him to tell you more about the exhibition (which may also get a mention on Lablit before too long). I want to go in a slightly different direction.

You will also see some beautiful photos on Matt’s post, but when I dug out my iPhone to snap a picture of one of the sculptures displayed on a light table, this is what I got:

Strip-lit sculpture?

Jenny asked me why the background was ribbed in the photo since no stripes were evident to our eyes – or in Matt’s or Richard’s pictures, taken on ‘real’ cameras. I had to confess that, despite being in possession of a degree in physics, I was stumped.

However, I guess the question must have been gnawing away at me in the background because this afternoon, whilst traipsing back-and-forth between my office and the laser printer, I stumbled across a solution. Or, at least, I think I did.

But before we get to that – would anyone else care to puzzle it out?