Over the past few months, as the available time could be found, I have slowly been assembling a set of PHP classes for retrieving data from PubMed, and set a tools for doing cool things with it. You can find what I have so far achieved here. The exact details of each tool can wait for another day, when they have been further developed. Each of the tools is, however, stable enough for you to have a play around with, should you wish.

The reason for this post is, however, to make a few comments on the results of a tool that I put together this afternoon.¹ The tool is currently called "TiPS", for want of anything better, and it turnsPubMed search terms into graphs showing historical trends for that term on a monthly or yearly basis. For my test terms, I chose to search PubMed's affiliation field for a number of countries. This was the result:

There are some interesting observations to be made here. A couple that caught my eye:

Firstly, I noted that the biomedical publication output of China appears to double between 2001 to 2002. I imagine the numbers could be skewed, e.g. byPubMed adding a number of Chinese journals to its index in 2002, but it's still an observation worth noting.

The second observation worth noting is that, not only will China overtake Japan in publication output this year, it is entirely plausible that China will also overtake the UK. At the time of writing, and with less than two months of the year left, British-based biomedical scientists have published 36,558 papers, to 36,443 from China. Breaking the results down by month reveals that China's output has been greater than the UK's every month since July.

¹ With the library of classes in place, I can now throw these things together in one evening.

This week, I am mostly clearing my Google Docs of old half-written blog posts which I never got around to publishing...

From the discussions in the publishing/OA blogosphere, one would get the impression that the "citation advantage" gained by open-access publishing is an important issue. Peter Suber collects links to recent items on the question of whether open-access papers are cited more often than equivalent closed-access articles here. There evidence so far is mixed: some studies show the effect, some do not.

So what? Sorry, that may sound flippant, and all to easy for somebody who has no need to gratify grant agencies or tenure comities to say. But I have yet to find anybody in either publishing or academia who finds journal citation rates a satisfactory metric for anything at all, and I'm not convinced that it is of any use in this case either. Are we advocates of open access because we want more citations flying back and forth? Pffft. Open access is about doing cool things (reading, mining, building, using) with information that rightfully belongs to humanity. No "advantage" shown for single outdated measure of "use"? Who cares?

Photographs from London's Big Busk are here.

This totally really happened to me. Exactly like this. In a dream that I had this morning.

I was raised in the hamlet of Frunchbridge Henklecombe, Gloucestershire, around ten miles north of the city of Bristol in the south west of England. Small, quiet, triangular in shape and agrarian in nature, the village lists as its distinguishing features an 18th century church tower and an impressive 16th century manor house. The unassuming tower could be mistaken for those in any other English village; the manor house, meanwhile, really is in another village, situated as it is, three miles away in the village of Plunk.

I can hardly call myself a Frunchbridgian after the years I have been away from the West country. But the village and I have never become entirely estranged, despite our first parting ways nearly forty five years ago. Indeed, my last visit but one was twelve years ago to the day.

At the last census, the population of the parish of Frunchbridge was put at four-hundred and eighty-six: just enough to sustain a halt for the stopping trains on the Bristol to Gloucester railway. The village itself is nestled under the scarp face of the Cotswold Hills, some half mile from the station, and, with a largely retired populace, few trains are actually called upon to stop here. Nevertheless, residents fiercely defend their right to stop a train at Frunchbridge should they one day wish to do so.

And so, at three in the afternoon of September 27, 1996, I found myself alone on the featureless down platform of Frunchbridge station, twenty-five minutes early for the stopping train to Bristol Temple Meads. The today of twelve years ago in Frunchbridge was, like the today of 2008 in London, a warm and sunny day with a hint of early autumn in the air. As I negotiate the station's small green picket gate, the last of the seasonal arthropods form one last frantic cloud, while cows in a balding field tangle themselves in fence wire as they rip long grass from the cracked station platform, and the tall trees of the railway cutting rain a colourful rain through the dusty afternoon light.

Continue reading under the fold...

At the age of ten, nearing the end of the final year of primary school, we, the class, were sent for a week to Brenscombe Farm, near Poole Harbour, on the coast of Dorset. One of the days was devoted to games on the harbour. We went canoeing, and ended up on one of the small islands which dot the shallow estuary. Accompanying the dozen of us were two or three instructors from the farm, who, with hindsight, I guess were under twenty -- gap year students, perhaps -- but to a ten year old represented the adult race.

On the island -- wooded, and populated by heather and gorse -- the instructors organised for us a game. We were to run around a clearing with one oar each and, on their signal, drop the oar in the grass and run back to them. Then, with our backs turned, one of the instructors would remove an oar from the collection, before we were all set running back, scurrying for an oar. The oarless individual at the end of the round would be the "loser", and barred from participating in the next.

It occurred to me very early on the game that the odds were against me, and that victory would require tactics. Rather than just drop my oar somewhere random, I placed mine towards the far side of the clearing, where the growth was a little thicker, and I kicked up the heather in front of it. The hypothesis was that, while the fast runners were fighting over the easy pickings, I could dawdle past to the the unnoticed cache.

The plan failed. Imagine my surprise when, on the first test of the hypothesis, the least conspicuous oar in the pack was the oar which had been taken out of play. Or rather, it was an oar which had been taken out of play. There were two losers in that round, and one was a dishonourable exit from the game. Apparently, somebody had been cheating. The punishment for cheating was a seaweed wig.

The moral of the story? The winner runs fastest, and pushes his weight around in the struggle. One loses at the whim of those in control, who can pick which paddle to remove. But to approach this problem with logic and reason is cheating.

It took eight years to unlearn that lesson.

There are differing opinions in the blogosphere over the merits of calling out bullshit. Does one feed the troll? Is it ever acceptable to sink to ad hominin attacks?

I try to stay civil, and I try to resist commenting on every bad article and news report. But I make no apologies when it comes to this:

A teenage girl in central India killed herself after being traumatised by media reports that a 'Big Bang' experiment in Europe could bring about the end of the world, her father said.

Oh. Well done, media.

The Daily Mail, of course, has been trolling the country since before "trolling" was even coined. The readers' comments are performing as usual:

How devastating for this girl's family. However, I am surprised that there has only been one reported case like this. Whoever is responsible (or should I say, irresponsible) for allowing this circus to continue should hang their heads in shame.

What a fine, democratic world we live in, where secret experiments costing billions and endangering humanity can be allowed to be devised with absolutely no consultation of the public whatsoever.

- Sara, Paris, France, 11/9/2008 9:40

Secret experiment? What kind of fucktard are you, Sara? Other than that, you make an excellent point here: the writers of the Daily Mail, and other irresponsible elements in the media, should hang their heads.

This was just the start of the trial and by no means the BIG BANG. This will come in a few weeks time when the huge explosion actually occurs--not to mention the after effects of the black hole atoms reproducing at an alarming rate which will effect us in a few years time. God bless her.

- Jane, SPAIN, 11/9/2008 9:04

Hi, Jane! If I were you, I'd be more worried about your immense density attracting celestial objects or knocking the Earth out of its orbit. Perhaps CERN's scientists could be profitably employed investigating how it affects the curvature of space-time?

I don't want to dwell on this. I'm repulsing myself by participating in this point-scoring match over one person's personal tragic tale. Which is perhaps why I find this foul attempt at smearing science so outrageous.

It's a right good science fest on Radio 4 at the moment. If you missed it, you must listen to Physics Rocks (available until 17/9). It's Brian Cox talking to comedians about their enthusiasm for science. It's a great antidote to some of the neurocidal drivel written by proudly illiterate twats (Brian Cox's word, not mine) in the less reputable members of our gutter press.

They managed to get several of our favourite themes in the programme, and seemed to be channeling the spirit of Carl Sagan. In a conversation with Alan Alda, the question "what's the point of the LHC?" was addressed—if the beauty of the universe isn't enough for you:

We can drive a car without knowing how to take it apart and put it together again. But somebody better know how to put a car together, otherwise we'll all be back on foot again. Every time we have figured out something basic about nature—discovering the electron, figuring out how radio waves work -- we got an advance that has improved life on the planet immeasurably.

In a conversation with Eddie Izzard, the fascinating topic of multiverses came up. Cox suggested that there is a good chance that, while it may not be multiverses, the results of the LHC's experiments will cast light on something revolutionary—of Copernican proportions. I can see the next chapter in the shrinking-pains of the God-of-the-gaps on the horizon...

In a conversation with Dara O'Brien, the topic somehow turned to CAM:

O'Brien: ... cos unlike Deepak Chopra, I know what "quantum" means... it does actually mean something. It doesn't mean like ... 'I'm not sure where my life is going'.

Cox: Ancient wisdom! It would help me build a better mobile phone!

O'Brien: Oooh. Ancient wisdom, my arse. Stop it, it's awful... Ancient herbal medicines: we tested them! The ones that worked became just "medicine". The rest is just a nice bowl of soup and some potpourri... CERN isn't going to help that either. It's not like you're going to find some neat way that it [homeopathy] will -- there's no bow that goes on top of 120 particles to make it all just, you know...

There were two more quotes I just had to share:

• Cox: The LHC will be a candle in the dark, lighting the way to a new and more profound understanding of the universe.
• O'Brien: Physics does not rock. Physics does not have to rock. Physics underpins the very nature of the universe and our understanding of where we are. Just tiny bits of flotsam floating in a much bigger picture

But, really, listen to the whole thing.

I am satisfied with the mystery of life's eternity and with a knowledge, a sense, of the marvelous structure of existence - as well as the humble attempt to understand even a tiny portion of the Reason that manifests itself in nature.

- Albert Einstein, The World As I See It (1949)

Oh my. I stumbled upon this:

But we are not satisfied with answers, because there are always more questions: we are satisfied with mystery.^[1]

How appalling. Such a depressing philosophy. People celebrate such a ghastly concept? People really believe that an unknowable world would be a good one to live in?

How thoroughly appalling. Is it comforting to be incurious? Is it safe being dull? Do you declare with pride your wilful ignorance?

Of course every new answer raises new questions — questions that were always there, but which we never knew to ask. The appreciation of beautiful mysteries is (alongside the appreciation of beautiful answers) exactly what drives scientists. Science is all about the explorer surveying exotic lands, full of strange phenomena, unfamiliar languages, bizarre biota, and even the occasional monster. Science is exploration at the frontiers: it is the very definition of curiosity; something to be nurtured in every child.

How absolutely appalling then, that somebody would celebrate the opposite. The child dulled; the explorer settled; the constant familiar; Einstein, satisfied just with marvelling at mystery, no interest in understanding his portion of it. Or worse — Carl Sagan's truly unknowable and mysterious word, where events are random.

But wait one moment.

Who here is really trying to explain away mystery? Is science alone in trying to supply answers? Who is constantly trying to fill any (perceived) mysteries — lets call them gaps — that science has yet to succeed in exploring?

Oh wait, that's right. Religion.

Religion is about being satisfied with mystery?         . Religion is about being satisfied with an unsatisfactory answer.

Continue reading under the fold...

This was written on Sunday afternoon, but I have only just been able to get the blog back up -- this is in part related to the issues raised in Scott's "motivation" session.

It was great to meet everybody at the London Science Blogging Conference. Before my dissection of what I thought were the important themes, I should just apologise for the accident with my facial hair -- it was only this morning that I noticed just how bad it was, and it pains me to know that there are now dozens of cool people who, whenever I meet them online, will believe that I routinely leave the house looking like that.

The first theme, then, was communicating science to the public, which mostly involved criticising professional writers. Certainly, the poor quality of much of the mainstream media presentation of science is a major motivation for most science bloggers. Ben Goldacre started the ball rolling by claiming that we need less science writers and more editors who can work with real scientists -- a reasonable enough comment (actually, I'd say we need more of both professions, and less science-illiterate writers trying to write the science pages). Others were not so reasonable, dismissing professional science writing altogether. I like to bitch about poor science writing as much as the next blogger, but most of the attendees seemed to have forgotten that are good professional science writers too! Indeed, of those science writers that I know, many were themselves motivated to join the profession because of their own concerns regarding science communication.

The second theme was communicating science to other scientists. On this subject, there seemed to be widespread agreement that blogging is just a part of a larger ongoing revolution, which also includes journal publishing and peer-review, and even the structure of academia itself:

• There was an awful lot of dissatisfaction all round -- both from the academics and from the publishers -- with the old fashioned methods of communication and publishing. It was great to attend an event where a dozen different people will independently start a rant about impact factors over a pint, each with a different perspective, but all with the same fundamental hatred of them.
• Some people called for more formal acceptance of blogs in academia. Richard Grant's institution were progressive enough to waste spend money on sending him all of the way from Sydney to attend, but GrrlScientist pointed out that many bloggers still have to maintain anonymity because their seniors do not see blogging as a constructive use of time.
• Methods of formally measuring and acknowledging the impact of blogs were then mentioned -- Google pageranks, Technorati, and so on. But, fresh from ranting about impact factors, everyone was skeptical about how helpful these can be -- after all, how do you make a fair impact comparison between a blogger who writes fifty short items about religion each week, and a blogger who writes a single thoroughly researched item about their field each week?



Peter Murray Rust, seen here writing a paper with an invisible floating keyboard.

• When it was suggested that blogs should feed back on individuals' careers and even the prestige of the old-fashioned journals that are cited in them,^[1] Nature editor Henry Gee pointed out that blogs are just a place for half-baked ideas. Everybody else retorted that so is Nature are journals! Science is never complete, and peer-review is not a rubber stamp of truth.

"Open lab notebooks" were also considered to be part of the conference's remit, with a talk from Jean-Claude Bradley. Under my own definition of "blog", I'm not sure I'd classify open notebooks as blogs -- as far as I'm concerned, what makes a blog a blog is about more than just the software it's published on (which is why I would exclude most corporate "blogs" from the definition). That's not to say that I didn't think the issues raised were not interesting. But I was rather surprised by how underdeveloped the software was -- just a standard free blogging platform and a wiki, no integration or lab notebook specific features -- and how underdeveloped support for it was. I think I overheard a couple ofBadScienceBloggers mumbling about "asking scientists to give away their work to their competitors". Guys: this is why we need a revolution in how we evaluate academic careers. People need to be given credit for having fantastic creative ideas and/or competent experimental skills; people do not need to be given credit based on the average number of citations made to other people's work.

Finally, a couple of random observations:

I have to disagree slightly (and only slightly) with Ben Goldacre when he defends Andrew Wakefield. Ben raised three ideas, which I don't think are entirely compatible:

1. Scientists should be free to have bad ideas
2. The media is to blame for the MMR-autism fiasco
3. Scientists should take a more direct role in communicating science

The modifier that I would add to make the three work together is that scientists must act responsibly when communicating their ideas to those who may not have access to the skills or literature required to independently evaluate the ideas being presented ("the public"), and, even if they feel strongly about a subject, avoid making claims that they can not substantiate. I would therefore suggest that one should be free to share one's bad ideas with colleagues, in journals, and at conferences, but that one should avoid giving the world advice in a press conference.

I don't think that anybody ever thought to try to define "blog" when discussing them. As previously mentioned, I think that a record of experiments is a lab notebook, whether it's written in a hardback book of square ruled paper, or on a freely accessible blogspot page. A corporate "blog" which announces with delight the company's exciting new venture each morning is not, in my opinion, a blog. When it was asked what the top 10 science blogs were, the instant reaction of everybody in attendance was "they can't be ranked like that!" The reason of course, is that there is such variation: the lighthearted, the serious-but-chatty, the campaign blog, the popular science writer, the collection of work-related notes and links, and the pure technical science^[2]. The reason that I mention this is that I think that acknowledging this variation will be important when taking action on the other issues raised in the conference, such as persuading institutions that blogging is a constructive use of time, or persuading our favourite Nobelists to get a blog.

In conclusion, we are all agreed that blogs are fantastic, that much is wrong with the world, and with science communication in particular, and that blogging is the solution, if only everybody else would wake up and realise this!

References

1. ^  Ohes Noes! Please, think before you implement this! Imagine the number of ways you could cheat under such a system.
2. ^  Sadly, I couldn't actually find a pure technical science blog by a conference attendee, so had to pick one from myblogroll instead -- please let me know if I missed one!

Oh. Wow. Currently lead item on the Daily Mail Sci & Tech pages:

This is a repost of something which was lost in the server move...

In The Family That Couldn't Sleep, D.T. Max states that

Prion diseases are a fascinating medical mystery because they appear to be the only disease that takes on those three forms: genetic, infectious, and accidental ("sporadic").^[1]

What a bizarre thing to say. Bizarre in part because prion "diseases", as the plural suggest, is a category of diseases rather than a single disease, and there is a near infinite set of categories that one could devise for diseases, based on molecular, cellular, genetic, physiological, anatomical, epidemiological and clinical variables. A great many of these categories will, of course, include individual diseases of each form. Max surely knows this: he himself introduces another disease category in the book -- Transmissible Spongiform Encephalopathies (TSEs). The TSE category overlaps with the prion disease category, but, as the name suggests, the TSEs are transmissible.

But bizarre, mostly, because the lack of truth in the statement stares one in the face.

The obvious example here is the disease category "cancer". We could call them "cell-cycle regulator diseases" if we wanted to illustrate that this category is based on similar molecular level criteria as prion diseases are. Cancers are clearly hereditary, familial ("genetic" is too simplistic^[2]), and sporadic. But they can also fit into the "infectious" category, either in the form of viral oncogenesis (e.g. with HPV, famous for its role in cervical cancers), or in fully transmissible cancers, of which there are two known examples. One of these, Devil Facial Tumour Disease, was blogged about here.

But, to complicate things further, most instances of cancer can not even be neatly filed as genetic, sporadic, or transmissible. Indeed, few disease aetiologies can be pinned down so precisely. Rather, for every disease, a number of variables are interacting and playing a role. The cancer may have a familial trend, but it would not have occurred had the individual led a different lifestyle. You may live with HPV, but be deficient in the other variables that are required for cancer development. The Tasmanian Devil may even have a chance mutation in its major histocompatibility complex (the set of genes which raise flags to the immune system to inform it that the cell is a friendly one which should not be destroyed) which allows the immune system to recognise and combat the transmissible tumour.

Max is aware of this fact too, but I think he fails to pick up on its importance. In the book, he mentions that the incidence of variant CJD (the novel human prion disease thought to be caused by eating beef containing BSE prions) rose from three in 1995 to 27 in 2000, and then began falling again.^[3] Rather than the numbers growing rapidly and continuously for many years, as initially projected, there were only a small number of deaths relative to the population of British meat-eaters. The reason? Most of those who died carried mutations which pre-disposed them to developing vCJD (the beef simply tipped them over the edge).^[4] Of course, a vCJD epidemic has not yet been ruled out -- perhaps those who are not so pre-disposed merely have longer incubation times for the disease. If this turns out to be the case, how should be categorise vCJD? As a single disease caused by contaminated beef, or as two different diseases, classified according to genetics? Either way, to call it (and other "transmissible spongiform encephalopathies") transmissible, is an oversimplification.

Why do I labour this point so? Because I think it is another example of faulty "nature versus nurture" thinking: this prion disease is genetic; that prion disease was caused by contaminated food. There's just no need to categorise everything as one-or-the-other.

References

1. ^   D.T. Max, 2006. The Family That Couldn't Sleep: A Medical Mystery. Random House.
2. ^  There is an introduction to the differences here.
3. ^  Azra C Ghani, Christl A Donnelly, Neil M Ferguson and Roy M Anderson: Updated projections of future vCJD deaths in the UK. BMC Infectious Diseases 2003, 3:4 doi
4. ^  e.g. Cathepsin D -- Matthew T Bishop, Gabor G Kovacs, Pascual Sanchez-Juan and Richard SG Knight: Cathepsin D SNP associated with increased risk of variant Creutzfeldt-Jakob disease. BMC Medical Genetics 2008, 9:31 doi

The psychologist Oliver James was on The Late Edition a couple of weeks ago.^[1] His argument was unconvincing and his behaviour unimpressive. So I took a quick look at his website. He offers for download a Radio 3 Nightwaves debate on "nature versus nurture" with James, Steven Pinker, Hilary Rose and John Gray from 2002. Always at the cutting edge, I thought I'd take a listen.

What an utter waste of airtime.^[2] Anybody who knows a good chunk of background on the subject would just have heard some people sitting around having an over-the-top argument over trivial matters. But if you don't know the background, you could very easily get the impression that the argument was over something fundamental — especially considering all of the appeals to consequences that were flying back-and-forth. One camp arguing fiercely for nature and the other arguing fiercely for nurture. The root of the problem? Nobody thought to explain that they were arguing about the cause of variation in behaviour, not the cause of the behaviours themselves. Nobody ever seems to do that when discussing "nature versus nurture," yet these four academics must be aware of the difference, and how misleading it is to conflate them. Pinker stated that genetic determinism is a myth, while Rose pointed out that nobody has believed in the "blank slate" for a century. But this was as close as they got to acknowledging the true nature of development. I know that Pinker did eventually make the point in The Blank Slate, the book he was promoting at the time of the debate, but it was buried somewhere near the end.

Perhaps if every discussion of the topic came with some sort of disclaimer, or started with a basic introduction, a lot of misunderstanding and unnecessary shouting would be avoided. Here's my proposal for it: there is no nature versus nurture problem. All traits — physical and behavioural — require a certain set of genetic and environmental conditions. All characteristics have many diverse and variable influences. All personality quirks, preferences, and even diseases require just the right nature and nurture in order to develop. Even when things go wrong, our biology is contributing something: if (contracted(disease)) die;.

When people argue over nature and nurture, the argument is over which is behind any between-individual (or between-population) variation in the trait in question. Sometimes we can agree that one-or-other factors is trivial — the death certificate of a traffic-accident victim will never list "lack of hard-exoskeleton" as cause-of-death — because there is no significant or relevant variation in it. But in more cases than you might imagine, it is important to consider both sets of conditions.

Lets illustrate this to the point of absurdity. We'll compare HIV/AIDS and severe combined immunodeficiency (SCID).^[3] When comparing the immune systems of healthy and HIV positive individuals, the variation has a clear causal relationship with environmental variation; when comparing the immune systems of healthy andSCID individuals, the causal relationship is with a genetic variation. So is immunity genetically determined, or environmentally determined?

But SCID has an environmental component! It is only in the context of pathogens that people die from SCID. And HIV has a clear genetic component! HIV can wreak havoc only in the context of human biochemistry and cell biology. But stop the presses! We already know of some people who are naturally more resistant to HIV. In areas with little medical intervention, genetic variants conferring resistance to HIV are almost certainly at a selective advantage and will increase their frequency in such populations. Suppose that one day 999 in 1,000 people have inherent resistance to HIV — carrying and transmitting the virus, but living perfectly healthy lives with no need for medical intervention. How do we then categorise HIV/AIDS on the nature-nurture dichotomy?

These diseases are, of course, extreme examples which are far removed from normal developmental processes, but they illustrate how a great many variables affect each phenotype — and that's just when things go wrong. Unfortunately, so long as people continue to believe that this argument has consequences, they will continue arguing vociferously. From "gay genes" to "god genes", too many people are convinced that nature versus nurture is an important debate.

In summary: if I were Oliver James, I wouldn't be advertising the debate at all. Leaving aside the general pointlessness of it, he comes over as an even bigger arse than he did on The Late Edition. The fact that he confuses The Selfish Gene with evolutionary psychology sums up the value of his argument.

Footnotes

1. ^  Yes. Yes, I did start writing this post in early March. Yes, it has taken me nearly six months to get around to writing the second half and publishing it. Whatever.
2. ^  I know, what was I expecting from a programme featuring Hilary Rose?
3. ^  I know, I know, these do not reflect normal development, and are only superficially comparable diseases. It's just that normal development is so much more subtle: when I needed a crass example that spelled things out, this was the first that came to mind.

Discussions about Open Access publishing are constantly flaring up in the blogosphere. There is a lot of re-treading old ground as some struggle to catch up. This is particularly the case with criticisms of the author-pays or "article processing charge" (APC) publishing model. Under this model, rather than a library paying £30,000 for a year's subscription to a journal, academics pay around £1,000 upon acceptance of their paper for publication.

Members of the blogosphere tend to be quite young, many think that "open access" is a synonym for PLoS, and most are in real science, rather than publishing. What I am trying to say is that not all that many of them have actually followed the history of open access very closely — myself included, until around a year ago. So it was with great enjoyment that I read the summaries of this discussion from 2001, when this publishing model was first proposed:

Free access - who pays?

Seven years ago, even open-access evangelists were sceptical that it could be done. Now, even at three times the rather optimistic estimates (who said $50 would be enough to break even?), it's very firmly established. The pioneer in the field is running at a profit ("BMC hasn't yet reached the stature to impose fees."), the biggest funding agencies in the world have made it mandatory, and, in the meantime, the PLoS journals have come from nowhere to become one of the biggest brands in the industry.

Now, blogosphere, would you like to take a step back and reconsider some of those statements you've been making?

A few thoughts on Peer Review In The Dock (this evening, Radio 4) [Note: posted late due to ongoing database issues -- will move to a new host when I get the time.]

1. Nobody has ever questioned whether peer review is really needed: wrong. A lot of people have questioned this, and many experiments have been tried. The most prominent recent example is probably PLoS ONE (no reference to this in the programme). They very rapidly discovered that, yes, a minimum standard is peer review is required when running a journal. Perhaps moving to a non-review model is like communism: you need to have world revolution for it to have any chance of working; going it alone will just lead to your own collapse.
2. Peer-reviewers aren't trained: somewhat misleading. Reviewers, at least in the publishing model that I am familiar with, are actively publishing research scientists of at least medium seniority. Most will, while pursuing their doctorates, have participated in "journal clubs" (where the grad students get together to shred a published paper), and many will also have co-reviewed manuscripts alongside their supervisors (not strictly allowed, but very widespread). What all students certainly are trained to do, even at undergraduate level, is not to take the truth of published work for granted, and to watch for potential flaws. To teach science is to teach scepticism. Which brings me on to the next point...
3. Reviewers aren't all that great at spotting errors: so what? Academics and publishers know this. The system is designed this way. Review is supposed to be a basic filter for sanity and competence; it is only journalists who hear "peer-reviewed" and think it is the definitive stamp of authenticity. Like democracy and trial-by-jury, it is not used because it works, but because it fails less disastrously than the alternatives. (Incidentally, their example of introducing deliberate errors to a paper and seeing who notices them is not entirely fair: most papers are not only reviewed by the journals reviewers, but by the authors' colleagues before they submit the manuscript, and by editors before review.)
4. The last part of the programme was devoted to publication bias. Publication bias is a big problem. But it has little, if anything, to do with peer-review, and everything to do with publisher policies and author dishonesty. The only conceivable connection it has with peer-review is that some people still mistakenly believe that negative results aren't worth publishing at all -- something that journals like BMC Research Notes and PLoS ONE, and initiatives like trial registration are explicitly tackling.

The programme explored what is an interesting issue in academic publishing at the moment (there are more interesting issues, of course), but, I think, from the wrong perspective. While it discussed many very real problems with the system, these problems are all well known and acknowledged; for decades people have explored solutions, and there are many interesting current developments. The makers of the programme seemed mostly unaware of these.

This is, of course, the limitation of having a half-hour national radio programme about a topic like academic publishing.

Weston-super-Mare Grand Pier was destroyed by fire this morning.

BBC News

So, the following video was brought to my attention, and I was so impressed that I had to share. Admittedly, it took me some time to getting around to the sharing bit: it's difficult to find the motivation for an argument as patently absurd as that over gun ownership.

This is truly the most marvelous case study in rhetoric that I've seen all year. For those Americans who are unfamiliar with contemporary (and recent historical) British politics and society, allow me to dissect for you some of the more remarkable examples.

The video starts with Britain's "largest peacetime protest" (the untruth in this statement is only trivial). Primed with a title containing the word "guns", American viewers could be forgiven for assuming this protest had something to do with guns. It did not. The law was about hunting with dogs.

"Many are asking: where were these voices six years ago, when there was an outright ban on handguns?" Indeed. The fox hunters were largely apathetic towards a ban on handguns because you don't hunt foxes with handguns; but they got upset about the ban on hunting with dogs because they like hunting with dogs. Hence the protest regarding hunting with dogs, and the absence of the protest about owning handguns. Do you see?

But why was there so little opposition to the tightening of laws on handgun ownership? Because they came in the wake of the mass-murder of children with legally owned handguns. You can argue that this was an irrational reason to ban handguns, but it's the answer you're looking for.

"There has been a forty percent increase in gun crime since the law was introduced..." Wow. Crime statistics rise when something goes from being legal to illegal. I guess the ban on smoking in pubs and restaurants has similarly failed, since we've seen an increase in illegal smoking. This factoid is mediocre and meaningless: what do the real outcomes look like?

"The use of weapons in crime has risen dramatically," says Frank Cook MP. Actually, lets listen to that that again: "The use of weapons in crime has risen dramatically" (his emphasis, not mine). That presumably includes knife crime, the big one as far as popular discourse in the UK is concerned (though that too is largely a media fabrication, and the data demonstrate a falling rate of violent crime). I've no idea what Frank Cook's views on handgun ownership are, so I quickly searchedTheyWorkForYou .com for Frank+Cook+gun and, so far as I can tell, he has mentioned guns once in parliament during the timeTheyWorkForYou.com has been tracking debates. In a November 2005 session, Cook mentioned, as an aside, that the post-Dunblaine restrictions on gun ownership were knee-jerk. And he's right. But it doesn't paint a picture of a man tirelessly crusading for a fundamental right on which our safety and liberty depends.

More soundbites: police morale is "at an all time low." Wow. I didn't even know there was an objective rolling record of police "morale"! Police morale has been a little low lately: they have a pay dispute. Not a gun dispute, you understand. A pay dispute. Police safety^[1] is an empirical question which is not measured in "morale".

Next it's over to Tony Martin -- the poor defenceless old farmer who shot violent intruders in self-defence. Er... yeah. Not the Tony Martin with paranoid personality disorder who shot a fleeing teenager dead, hid the weapon, and went to the pub, then? Tony Martin is not a good poster boy for the right to bear arms.

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I don't think we saw a single datum in the video. There were a lot of anecdotes and soundbites, a lot of selective footage and an absurdly crude misrepresentation of the situation in the UK. But the issue surely just rests on empirical questions? Where are the data on this issue? Well, so far as I have been able to ascertain -- and it's difficult to be sure of anything on the topic when there are two polarised dogmas desperate to make the loudest and most preposterous noise -- neither side have much going for them. Being armed does nothing to make you measurably safer; but then, neither does a gun ban or amnesty. Arguments on this issue tend to be about simple solutions to complex social problems, and each side seem quite content to defend their positions with arguments as flawed as those above. They're the best arguments they've got.

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