I’ve been stuck at my desk for weeks now, analyzing data and working on manuscripts in preparation. The lab is just around the corner from my office, close enough to hear the laughter and banter of all my colleagues as they perform their experiments.

This reminds me of being a little kid again — it’s a long, summer evening, and Mom and Dad have just dictated that it’s too late to go out and play. But I can hear all the other neighborhood children running around and shrieking in the dark as I sit indoors in resentful silence.

No fair.

The Research Assessment Exercise (RAE) was the late, unlamented process by which the UK government decided on the allocation of billions of pounds of research funding. It worked with the kind of blistering, quicksilver efficiency that one would expect of an organization with 15 main panels overseeing 67 ‘units of assessment’ and ‘sub-panels’. Departments spent untold hours preparing their RAE return, trying to figure out how best to divvy up their published papers among their academics, in order to maximize each person’s personal impact factor.

To say the RAE was reviled is putting it mildly. It was also criticized for being obsessed with things like journals’ impact factors. It’s well known by now that these are imperfect measures of scientific prowess, and they vary hugely across fields. In medicine, impact factors are typically very large, but in a more niche market like parasitology, they are low. This is not the fault of parasitologists, whose work is of enormous importance to people who suffer from parasitic diseases. But those people tend not to live in places like the USA, or Europe, or have lots of money to spend on drugs. This may go some way to explaining why work on diseases that kill a few hundred Americans tends to get cited more than research on diseases which kill a few tens or hundreds of thousands of Africans.

But enough bitching there. The RAE is dead. So what is going to replace it? Step forward the Research Excellence Framework! With the REF, the name has been updated, removing any suggestion that research is being assessed, and trendily combining words in ways which make little grammatical sense. What is an excellence framework? A framework for excellence I can just about understand, and an excellent framework as well, but not this combination.

It reminds me of a conversation I had with a senior anaesthetist some time ago. “Everybody bangs on about ‘Centres of Excellence’” he said gloomily. “I don’t know about you, but I’d settle for Centres of Adequacy”.

So how is the new system going to change things? Er, not very much at all. Those panels are up for a cull, with the number of main panels being reduced to 4 and more than half of the sub panels being cut in a way which will look good when somebody shows up to ask HEFCE what they did in the great public funding squeeze of 2009, but other than that it looks like business as usual. There has been a suggestion that rather than simply looking at journal impact factors, scientists should be assessed by asking how many times their work gets cited, rather than the average of all papers published in the journal in question. Metrics like the H index, which is the number of papers you have which have been cited at least that many times or more. So if your H index is 25, you have published 25 papers, each of which have been cited 25 times or more.

But no, apparently citation data will ‘supplement and inform’ the decisions and er.. that’s it. It’s still early days as the inevitable consultation exercise kicks off today, but it looks like those of us hoping for a transparent, open and equitable system will have to hold our breath a bit longer.

Richard Holmes’ book “The Age of Wonder” was last week announced as the winner of the Royal Society Prize for Science books, beating such luminaries as Ben Goldacre (for “Bad Science”) and Neil Shubin (for “Your Inner Fish”) to the podium. I’m delighted. I’m half way through it, and was whooping with joy already at the end of the first section, which deals with the rise of Joseph Banks – explorer with Captain Cook, consort of Tahitian maidens, and the Royal Society’s longest serving president. Holmes is particularly good at examining science within the context of its time, and since this was the romantic age, the scientists are given to awe and the romantic poets quite open to the beauty of science. The classic example of this is Keats’ “On first looking into Chapman’s Homer”. This poem contains the often quoted lines

“Then felt I like some watcher of the skies
When a new planet swims into his ken;
Or like stout Cortez when with wond’ring eyes*
He star’d at the Pacific — and all his men
Look’d at each other with a wild surmise —
Silent, upon a peak in Darien.”

The watcher of the skies in question is William Herschel, whose discovery of Uranus had recently stunned the world by suggesting how much there might be about the universe we had neither known nor suspected. Nor is this the only link with science; when he wrote this Keats was actually a medical student (I will leave the argument about how scientific medicine was at the time for another day).

Holmes is magnificently dismissive of the notion that already, at this stage, there were any traces of the ‘two cultures’ debate which bedevils science in our age. He is himself primarily a biographer of the romantic poets, in particular known for work on Coleridge. Yet this in no way prevents him conveying the scientific ideas which were important at the time – some of them stunning in their prescience – and their thrilling significance to a society convulsing itself around the first of the great political revolutions.

Living as I do in the 21^st rather than 18^th century, it is impossible to not wonder where things changed. Is it the professionalization of science? Or is it the complexity of work at the cutting edge? Whichever, Holmes reminds us that Science and Literature can make very good companions. Lablit indeed.

*Keats changed ‘wond’ring’ to ‘eagle’ in later versions. I prefer the original. It seems more in keeping with the scientific part of the poem’s inspiration. Oh, and he got the Cortez bit wrong, it was actually de Balboa. But heck, this is poetry, not history.

We’re just putting the finishing touches on Richard’s review of ‘Creation’, the new film about Charles Darwin (to be published tomorrow on the main site). LabLit was lucky enough to get a few invites to the private screening this past Wednesday at the Science Museum. Despite a competing bitch-fest event over at the Ri with Ben Goldacre and Lord Drayson, the luminaries were out in force in Exhibition Road, including David Attenborough and scores of other sci/art/media luvvies.

Decent wine, root-vegetable snacks indistinguishable from potpourri, and a seriously weepy flick – what more could a girl want?

Ben Goldacre is debating the science minister Lord Drayson tonight on science and the media at the Royal Institution. I’d love to go, but have, ahem, another engagement. I did catch an opening skirmish on the Today Programme this morning, in which Goldacre complained about the media and Drayson gave the impression everything was grand and we are living in a golden age of science reporting.

Bullshit. Every single national newspaper, including Goldacre’s Guardian is guilty of huge and sustained science abuse. The vast majority of journalists charged with reporting science have only mastered the copy and paste function necessary to crib their articles from the helpful press release.

And when you complain, you get some patronising fool whose ignorance is matched only by his self regard banging on about “the 24 hour news cycle” and its demands. Well, I apologise if I sound blunt, but nature knows nothing of the 24 hour news cycle, and MMR will still work, swine flu may (or may not) kill millions and the whole planet is quite capable of shrugging us off in favour of some less polluting life form like the cockroach with no input whatsoever from the 24 hour news cycle and the dingbats who drive it. And anyone who cannot see that is not fit to use the toilet on their own let alone spout their factual inaccuracies at their fellow citizens.

You can follow the debate live here, and a recording should be up tomorrow.

Someone, almost certainly Jenny, is going to immediately start claiming I am biased on this, but I think Uefa made the correct decision in rescinding their 2 game ban on the Arsenal striker Eduardo for his alleged dive in the recent home game against Celtic.

Now I don’t like diving any more than the next fan, and I certainly feel for Celtic goalkeeper Artur Boruc who showed remarkable reactions in trying to get his arms away from the oncoming striker. While it can’t strictly be described as a dive I feel queasy when I think a player is falling before contact is made. For another example see Wayne Rooney’s successful penalty claim against Arsenal the following weekend. But crucially, in the case of Eduardo (and Rooney) I do think contact was made. As it happens I think both fall into the ‘could be given’ category, and the question as to whether they should depends on whether the ball was under control. As an example of a blatant dive I cite Rooney’s other successful penalty claim against Arsenal a few years ago when he jumped over Sol Campbell’s leg. This from a man who ‘doesn’t dive’. Doesn’t dive my arse.

The scientist in me also comes to the defence of Eduardo (and even Shrek) when wondering what happens in the mind of a player approaching a challenge. In video replays, these milliseconds get stretched out to an extent which it is absurd to expect a referee to be able to detect, but also to a point which may not be accurate when judging a player’s intent. I play football. Badly I might add. In fact appallingly. But I am less appalling as a forward than a defender so that is where I tend to play. I have never had the benefit of a replay of myself confronting an oncoming player at speed, and I have never consciously dived. But would I start to fall before the contact is made? Is that what I recall? If not, is that a false memory, or is it simply that anticipating contact, a player’s body reacts in the same way that a fighter rolls with the punches?

What I am saying is firstly, we cannot read minds, and secondly, we tend to see replays of controversial incidents vastly more than others, this biasing our sample. Anyone know how often players show signs of falling before contact, and the extent to which it happens more in the penalty area? I would be surprised if no one has looked into this.

In fact, they have. Paul Morris of the University of Portsmouth has recently published a paper claiming to accurately diagnose diving. It’s pretty interesting stuff, standing alongside his previous work “Survival of the cutest: who’s responsible for the evolution of the teddy bear?”. His conclusions do not rely on when players start to fall, but a characteristic “archer’s bow” shape made by the falling player which is wholly unnatural.

Interesting stuff, though I can’t figure out how the research measures intent. Indeed, it involved showing taped incidents to a sample of people, who showed extensive agreement on which were dives and which were ambiguous. But this only tells you that there is widespread agreement on what a dive ‘should’ look like. If it really is so easy, why are referees the world over so easily conned?

Thinking more about it, I am pretty sure that any experiment to test the behaviour of a diving footballer will be flawed by the fact that the experiment has to be staged and controlled – in other words artificial. By interacting with the experiment, we could alter the conclusion.

Which means this may be the first time Wayne Rooney and the collapse of the wave function have appeared in the same sentence.

A friend once told me about his rotation while a junior doctor, with a consultant who could only be described as blunt. They were discussing a teenage case of gynecomastia – in which males develop noticeable breasts, a somewhat unexpected and surely disturbing event for the young man in question. A quick look at the karyotype had shown the underlying cause was Klinefelter’s syndrome: an extra X chromosome. He was XXY rather than XY.

While considering the case, it was emphasized that explaining this to a teenage boy is something must be done with care. Apart from anything else, the patient’s fertility would be greatly reduced and Klinefelter’s carries an increased risk of several tumours. Having discussed the need for delicacy, the consultant invited the boy and his mother to join him in his office with my friend, cleared his throat, and kicked off as follows.

“Now you know that there are men, and there are women? Well you are somewhere in between.”

Now it’s just a guess, but I imagine the consultant in question might have had a glittering career with the International Association of Athletics Federations (IAAF), the governing body of world athletics, which has in the last month or so done its utmost to torment the young South African middle distance runner Caster Semenya.

To recap, very briefly, in case you have just arrived from a parallel dimension in which this has not happened, Semenya has emerged with stunning swiftness (literally) as a new force in women’s middle distance running. Only 18, she won gold in the 800m at the 12^th World Championships in Berlin without looking as if she was really trying. But already there were whispers that Semenya had an unfair advantage. At first this was simply due to her, to be fair, strikingly masculine appearance. Then the day before the 800m final, it was announced that she was to be investigated by the IAAF to determine her gender. I should not need to comment on how bizarre and cruel this is, not least because this is not a question of deliberate doping. Were Semenya suspected of cheating through taking banned substances, she would be subjected to less humiliating scrutiny than she has through an accusation for which, even if upheld, she bears no blame for whatsoever.

And to compound this, leaked stories are prejudging the results of the examination. It must be said that it does seem that Semenya has abnormally high levels of testosterone for a woman (though still low for a man) and will probably be barred from further competition as a result.

It would take a heart of stone, or failing that, an IAAF official to not be moved by this. Questions of gender go to the core of our identity and whatever the results of the investigation Semenya will certainly be scarred by the experience. Whatever teasing she endured as a child through her appearance could be put aside as she discovered her gift for running. Now it seems that gift is worthless.

Having said that, her case makes me wonder about sport in general. What is it intended to celebrate? The person who has worked the hardest to develop themselves, or the most naturally gifted? Semenya is undeniably naturally gifted, and yet to judge her by the standards of others without those gifts can seem unfair on them. On the other hand, is it any more so than expecting human beings without Usain Bolt’s combination of physique and fast twitch muscle fibres to compete with him?

I wonder if, at some point in the future, our understanding of sports physiology will be such that following genomic analysis, we can crudely group humans into classes in terms of their athletic potential, and then allow them to compete against each other. Boxing is a sport in which it has already been recognized that competition can be maintained only by weight classes. Admittedly, the athletic class I would personally fall into would not be one which anyone would pay to see, but then it would have been something of a relief to be able to recognize the limits of my aspirations. Maybe this sounds too much like GATTACA, but it would at least offer a world in which people like Caster Semanya would be recognized for their gifts, rather than penalized for them.

From the Provost’s Newsletter, which has a bit of a cult following round these parts:

“I am grateful to those who noted an error in the very first sentence of the last Newsletter. They pointed out that a Newsletter cannot come out of summer hibernation. That is a winter-only phenomenon, so my usage was oxymoronic. The summer equivalent is aestivation.”

Are we all clear on that point?

Good. As you were.

It might be a bit too early on a Monday morning to be irreverent, but when I was walking through the Quad this morning, I noticed a sorry-looking creature on one of the benches. She had disheveled hair and clothing, and a bag stuffed to the brim with paper.

I was surprised: the university staff are usually quite brisk about politely but firmly moving the homeless on. But then I thought, it’s graduation ceremony time and the Quad has been absolutely heaving with strangers, albeit much more smartly turned out ones.

It was only then I got close enough to realize that the person on the bench was actually a respected professor.

Time for that second cup of coffee, I think.

I promised labliterate photos, but all I could come up with was this cheap gag.

water with a hint of yeast

Fnarrr. So far as I am aware, candida means ‘candid’ in Italian, which is still a pretty strange name for bottled water. There was also a whole shelf in the supermarket of canine food marketed under the name “Randy Dog!”

Sardinia is a beautiful place with fascinating geology. At some point I’ll write something about the fantastically preserved stone age dwellings, the Nuraghi, which are scattered over the landscape. But for now, here’s a photo of Li Longhi, a well preserved grave site in the north of the island.

The central stone at the Li Longhi grave site, under a balmy mediterranean sky