The job ain't finished till the paperwork's done?

It's been a fairly quiet week in the cabinet, and all my birthday books have arrived including the latest (2nd) edition of the European Science Editors' Handbook. It's a unique compendium of scientific and publishing information, so I've been doing a little reading in between some admin tasks, and pondering its various chapters on taxonomy, a subject that I haven't considered per se for, ooh, nigh on thirty years. So, when Ross Mounce's tweet bounced into my feed earlier in the week, my mind was particularly prepared to dive into what may be the last storm before the final triumph of the web.

.@BioMedCentral & @PLOS folks might want to read this new @Zootaxa paper: http://t.co/SNRr4hUH0n Seems to take issue w/ "online periodicals"
— Ross Mounce (@rmounce) November 13, 2013

Ross was drawing attention to a 94-page article in ZooTaxa from a group of eminent taxonomists whose point of view basically seems to be that if it's not published on paper, then it doesn't exist, at least for the purposes of establishing precedence. Convention required, until the rules were amended in 2012, that at least five paper copies of any article be lodged in five separate reference libraries. Now, on first reflection this position seems somewhat dinosaur-ish, but Dubois et al's meticulously documented critique of the slippery nature of online publishing should give web triumphalists pause for thought.

As I understand them, Bubois et al's view is that an insistence on a paper publication forces all concerned to fix upon a canonical version of an article that exists and is publicly available for sale or by request at a certain date. Precedence is sacrèd in taxonomy because the winner gets to name the newly discovered lifeform, immortalizing a hero along the way, and the discoverer is then cited as the 'authority' responsible thereafter. With the prize of immortal memory at stake--not quite as good as having an SI unit named for you, but close--a legalistic rule book has developed over the years to ensure justice is done.

Dubois et al. are particularly scathing of electronic publishing practices which change articles without updating the publication date and reference information. Taking the long view—many 18th century works of taxonomy are apparently still in current usage—they criticise the electronic publishing community in general and BioMedCentral in particular, for playing fast and loose with traditions and systems that have accreted over literally centuries. As the linkrot rate, even in scholarly publishing, reportedly approaches 40% about five years after publication, the traditionalists certainly have a point, and everyone concerned with scientific communication would benefit from reflecting on Dubois et al's justified criticisms, and considering what may be done to address them.

Paradoxically of course open access is part of the solution—lots of copies keeps stuff safe, and all that, but there is still, in my view, a need to force all concerned into producing a canonical version of an article, and the moment when a file is fixed for the presses to roll would be a pretty good time for that. Then there needs to be some sort of digital service that provides assurances that we're dealing with files that have integrity. All the technical problems for this are already solved in the software world, but it will be a while yet before the necessary technical changes have fully permeated into non-technical scholarly areas. So I'm sure there'll be some space for boutique paper publishers for some time to come.

Update 1830h: I had to rush out to pick up the boy from school moments after completing the first draft of this blog at 1630h, so it seems a fitting homage to Prof Dubois to tweak it a bit now I've got a moment, but leave all the publishing metadata essentially unchanged. (!)
Update 17/11/2013 1310h: 1) My own response to Ross' tl;dr plea, after the briefest of flicks through Dubois et al's PDF, was admirably on target, though I say it myself:

@rmounce But they do have a point that "an electronic document ... modified while keeping the same DOI and publication date" = chaos

— Juliuz Beezer (@JuliuzBeezer) November 13, 2013

2) Dubois et al's article really should have been better edited. A document of 94 pages begins to demand either a table of contents, an index, or preferably both, for sparing yourself this effort wastes everybody else's time. The unwieldy nature of the article undoubtèdly undermines its rhetorical effectiveness. ("Sorry for this long article, I didn't have time to write you a short one."--> But then, if you're ranting for the canon of the centuries, perhaps this is not an excuse you can honourably pull. 3) Also, if it was proofread by a native English speaker, s/he missed a few Franglicisms, deep down the page, none grave, but still...

Bayesian limits to screening populations for rarities e.g. "being a terrorist"

Silicon valley software engineer Ben Adida (36) certainly doesn't hesitate to grovel before his president in his recent blog post concerning the recent revelations of US state surveillance of the internet: ["...I’m no stubborn idealist... I know you cannot steer a ship as big as the United States as quickly as some would like. I know tough compromises are the inevitable path to progress... The responsibility you feel, the level of detail you understand, must make prior principles sometimes feel quaint. I cannot imagine what it’s like to be in your shoes..."] Yuk! The ship of state, with its concomitant all-powerful captain fully implied. Yuk, and yuk again, puke! But M. Adida does make a good point about the unintuitive statistical operation of true and false positives in population screening programmes, be they medical or criminological. The explanation he offers on his blog is correct, but lacks detail. More seriously, for anyone who'd like to know more, a couple of keywords needed to construct a quality search are missing. These were "false positive" AND "Bayes", so I decided to post a wee comment mentioning that, and a link to the best explanation I found. Perhaps M. Adida has just had enough of blog spam, but he seems to accept comments only very selectively on his blog: and mine was not one. Ho hum! Anyway, he's quite right to point out that even a good (say 99% accurate) test for a rare condition (e.g. being a terrorist) applied to a large, mostly innocent population will generate WAY MORE false positives than true positives. This has two bad effects: 1) innocent people are wrongly suspected and subjected to further unjustified intrusion and harassment; and 2) law enforcement time is wasted. You might suppose that intelligences sufficient to build data centres capable of archiving the whole internet would also be fully conversant with Bayes' Theorem. But with no meaningful oversight, how can we be sure? Idiocy is common; and mission creep happens all the time. Just like the Hackney wide boys who can't resist trying out their guns over the back hedge once they've bought them, the temptation to mine all that data must be well-nigh irresistible--but wrong.

Cycle apartheid enthusiast rejects effusion

There's a man called David Hembrow, a resident of the Netherlands, who enthuses about the virtues of the Dutch policy of taking cyclists round the back of every bus stop here. It seems he doesn't really like having his ideas questioned, nor in hosting an honest debate on the issues he raises, which would explain how his views have become so misguided. Ho hum! Here's my comment on his recent post anyway, which M. Hembrow had hoped to moderate out of existence:

These 'cycle paths' round the back of bus stops are exceptionally irritating: I've been negotiating the recently installed series on Brighton's Lewes Road in both directions this summer, and I don't like them one bit. Firstly: why does the cyclist go the long way round? In other words, why should the cyclist negotiate two additional bends and ride some extra metres at each bus stop on each journey? Then, as you mention, there's the usually inferior surface on the 'cycle path' to contend with, the kerbs, the bollards, the additional signage. But now, when I wisely ignore this evidence of local government idiocy, I get hoots and shouts from motorists for being in "their" space. I have no words for this publishable on a family blog such as this one! NO!

Plus: human factors: bus stop users expect traffic in front of them on the carriageway, but not necessarily behind them while waiting, or crossing the 'cycle lane' to the bus stop. So the prudent cyclist using such a 'facility' seeing people in the vicinity of the stop ***inevitably has to slow down.*** Meanwhile public transport users get to occupy a space with traffic whizzing by them on both sides: not good for parents of young children waiting at the bus stop.

Meanwhile, the real users of the road environment, the important people, the people who it's all for: the private motorists, continue on their sweet way, untrammelled by any consideration of users of other modes.

Proponents of these "dif-facilities" are misguided apologists for the triumph of the motor car, in Holland as much as anywhere else. Why else would they be so keen to place obstacles in the way of the cyclist, while removing cyclists' right to follow the ancient desire lines across the land established in antiquity?
If you must insist on modal separation on wider roads, then a 4-metre+ (i.e. generously wide) bus and cycle lane, which leaves pedestrians/public transport users on the pavement, and where the cyclist, enjoying a luxurious and tyre-swept lane whose only other occupants are accountable, professional drivers, has room to overtake stationary buses without changing lanes.

Naturally I keeps a backup copy of every comment I submit, for precisely these occasions: it's the comments that the blogger refuses to publish that are most worthy of heightened attention...

Update 21/4/17: Here's a good example of the kind of annoyance this arrangement generates for pedestrians (and any cyclist accepting the local authority's invitation to ride on the sidewalk) (via road.cc). (A bit sweary, your maiden aunt may appreciate you listening on headphones, if she's within earshot):

And here's a picture of the classic Dutch "round the back of the garage" arrangement (mustn't obstruct petrol sales now, must we?). Note the sharp blind curve it creates:

Why I write comments (and where you can find them)

When I decided, in 2009, to re-establish an online presence after a couple of years off, I made a couple of decisions whose effects persist to this day. Firstly, I decided to play with being anonymous, and Julius Beezer was the character I invented to represent me on the internet.§ As does happen, this representation has now spilled over into real life: my modest translation and editing business is entitled "Cabinet Beezer," and I write this from my cabinet, a real place, for which I pay rent.
To pay the rent I accept translation and editing tasks that fit with my interests, but much of the time I find myself on what I call "general internet patrol": engaging with my longstanding interest in the medium of internet communication generally, and specifically free software and open access scholarly publishing. Although my degree was in medicine, and I practised for many years as a GP in east London, my translation activity has pulled my centre of interest into the humanities: languages, belles lettres, philosophy, and history. I consider myself fortunate that my interest in these subjects has developed in the age of the internet.

Outputs

Although I maintain several blogs in the spirit that rights that are not exercised are lost, and do indeed use them as a convenient place to publish a bit of text when the moment strikes,* I no longer primarily consider myself as a "blogger"; indeed, I find the term in contradiction with my longing for the overturn of Gramsci's observation that "all men are intellectuals but not all men have the public function of intellectuals." In other words, everyone should blog, when they feel like it, and hopefully that'll be helpful.
But what I really want to do is change peoples' minds. Whatever I write, I write primarily for the satisfaction of being able to reread it and say "Yep, that guy's nailed it. At least there's someone on the planet I totally agree with!" It struck me that one of the conventions of blogging—the replies function—is undervalued, and I decided to explore it as a participant-observer.  I've enjoyed reading reading blog comments since the early days of Slashdot, and the BMJ's rapid responses, back in the day when it was unpaywalled: there's a new kind of truth there that wasn't possible before. And new problems of course.
I found, when I looked recently, for example, that I have left 72k words at the Guardian's 'Comment is Free' site over the last four years.† But the Guardian is unsatisfying for several reasons, and now that I have a well-populated RSS stream, I prefer the roads less travelled away from the mainstream.
I collate this activity as a set of public bookmarks along the way, which enables a chronological listing of the comments as I left with them, using two tags dccomments and jbcomments. I also maintain a list of tagged bookmarks relating to the activity of commenting itself.
All this was just by way of diving in. But my theoretical knowledge is growing, and maybe one day I'll write something solid about commenting, and attention, and democracy, and the internet, but in the meantime, I'll just have to leave it to your imaginations and this lousy blogpost.
---
[update: 27/8/14] *Particularly, it must be noted, when a comment composed for another online venue is rejected. Examples: twitterblocking, cycle apartheid, France24 rejection, screening for terrorists, HuffPo atheists.]
[update: 30/11/15] §This conceit was formally abandoned on 28/06/14
[update: 22/01/16] †Fixed busted link to juliuzbeezer public profile at The Guardian's site. That word count is out of date now, though I effuse there much less frequently than I once did.

Outrage to freedom of expression in a British university

Life as supportive spouse and father takes up most of my time on campus, so I haven't really paid too much attention to the Sussex University occupation protesting the privatisation of campus services, now in its fifth week. I broadly support their aims though, and the other day a gap in my schedule between talk and pre-school pickup coincided with a loudhailer call from on-high to come up and look at their art show. How could I resist?
The upshot of the conversations I had at the show was that news of the occupation of the ZAD in Nantes would be of interest to the Sussex occupiers, so we agreed I'd put together a talk about this for the following Tuesday.
That Tuesday has now arrived, but my talk has not! I spent the afternoon scrabbling images off the net with complete abandon for copyright (so I won't post the slides), and toddled up to the 3rd floor conference room to check in with the collective about 18h, check the projection facilities and so on. This was no problem, but when I returned just before the invited hour of 20h to actually give my talk, two very large black-clad men with sinister armbands physically barred my entry to the room, and demanded my student ID.
This is something I don't have. Nor, in my view, should I need to. If the students wish to invite a speaker of an evening, that is their absolute right to freedom of association and expression, and I took a very dim view of them obstructing me in this. I was forced to retreat to the ground floor and find a likely looking student to assist me in contacting the occupiers, who were then able to emerge and negotiate. Eventually the hired temporary security, who, of course, "were only following orders," yielded to the permanent university security guard who arrived, and I was admitted. But the stairs are now blocked, there have been shouts and argy-bargy, and any student arriving to hear what I have to say cannot do so.
It appears this policy reflects a hardening of management attitudes, frustrated at the slow pace of the partial siege. Somewhat stressed at this unexpectedly difficult accueil, I calmed down by suggesting the students research the Greek laws on freedom of entry and egress to universities, laws passed following the oppression of the Universities from 1967-1974 under the military junta.
The university seem to be shooting themselves in the foot here: my right to give my talk is a lot more interesting that its actual content. I am genuinely outraged. I bet that Will Self didn't get all this hassle!
This evening's cultural reference: The Clash.

Update: 0258h, 20/03/13: After all the fuss, I was eventually able to give my talk, starting at 2225h. There was a good discussion after, and I left at 0015h, having sung Happy Birthday to one of the lovely occupiers, and admired an exposition of excellent hula hoop technique. I found them a pleasant and thoughtful group, and morale seems high.
Back at the flat, I find my head out of the frame much of the time in my attempt to video myself, but the audio is good, so I might get round to transcribing it. Note to self: in future, offer the audience a small cash prize for each utterance of the words "you know," or "the fact of the matter is." Verbal ticcing aside, I think I did succeed in conveying something of what it might mean to be in a successful occupation, though circumstances are very different, if the signals observed by Élysée-watchers are to be believed.

Steve Reich in the afternoon

from the somewhat-testy-new-york-composers dept.

Composer Steve Reich passed through this afternoon, to give the Eighth Tony Dummett memorial lecture. In fact, it was more of chatshow appearance than a lecture. After an encomium from a member of the University of Sussex's music department, the 75 year old Reich—very chipper in a jaunty peaked cap—reminisced down the front, prompted by some bod from the London Sinfonietta.
We learned that Reich was born and bred in New York, and his family home was four blocks from the World Trade Centre, so the events of the 11 September 2001 affected him personally. He and his wife were in his country place in Vermont at the time, but his son, daughter-in-law, and grandchild were trapped in the chaos. An army line outside his place meant that the family couldn't return home for a month afterwards. It would nevertheless be eight years before he began work on a reaction to these events, entitled 9/11 WTC, following a commission from the Kronos Quartet. A recording of the piece was played. It was not my cup of tea. I am none the wiser as to his political reaction to the event, and am left with the suspicion one does not remain "America's greatest living composer" by emitting anything other than the anodyne and obvious. Ho hum!
But he was an interesting raconteur, and generous in sharing his compositional methods (MacBook Pro, Sibelius, Reason, Granular Synthesis). Then he took questions from the assembled audience. These he answered fairly, though it was perhaps an irony that the founder of minimalism gave very short shrift to questioners whom he felt were trying to get him to repeat himself. He positively beamed at a drummer who had tried to reconstruct his phasing technique and found it impossible. Reich agreed it was very difficult—when he first devised the technique he always played against a tape and didn't know if it would be possible with another human being. Then he and fellow Juillard student Arthur, both having practised against tape, managed to find a pair of pianos and a method. (One musician must remain absolutely steady, one move).

Abby's* question:

Q. As a composer who also leads a live ensemble to play your work, what is your attitude to mistakes?
A. [a kind smile] Mistakes happen, always have happened, and always will happen. What I will say is that recording is a crash course on the piece. We record something, then we go into the box and all the musicians listen to it, some wincing, and then we do it again, and they do it better. And that improvement stays with you into future performances. Also, Glenn Gould is mocked for playing music just as it was written, but I think he's a genius, and I think it's very interesting to produce a version that the composer would have been very happy with.
[Related quotes: "I'm not a great improviser. I greatly admire those who are, but it is important to understand that improvisers are always improvising from some underlying structure—in be-bop, it's a chord progression, in Indian music, a raga, in African music, a rhythmic pattern laid down by the master drummer and so on..."]
--
*Abby's childcare fell through so she couldn't go, so she primed me to ask this question on her behalf. It's probably a good thing I was steered away from Palestine...
§This blogpost's title is shamelessly lifted from Mike Powell's chiste on Abby's Facebook page.

Interesting typo in The Argus

No sooner do we arrive at the University of Sussex than revolution breaks out. In a heroic historical reenactment, a band of radical students have occupied the 3rd floor conference centre here in protest at plans to privatise some campus services.
I remain aloof from proceedings, for several reasons, not least that as a "campus spouse" I have no formal relation to the university, nor indeed any particular affection for it. That England can no longer afford to educate its young people without burdening them with a massive millstone of debt seems to me tragic and unjust, but that battle has already been lost, and occupying a poxy carpeted meeting room which is above the eyeline of every passing student, never mind the general public, is hardly going to change that.

Still, they've managed to pull some high profile speakers to the now fetid atmosphere up there, and I finally yielded to the temptation of wandering along to catch David Graeber's talk in person. His book Debt: the first 5000 years is wonderful, particularly its demolition of the notion of "barter" as the primeval mode of exchange (chapter 2), and I was happy to pass him a fan letter. He is, of course, a very "out" anarchist, and the next day, as I got some cash, I observed that the occupiers had been so inspired by his presence as to publish a list of demands on an A4 flyer on the wall beside the cashpoint. The main entrance at the library was similarly adorned. And here it is, faithfully reproduced in the Argus, which still sells 18,000 copies/day.

Oops. 

So it is unfortunate indeed that demand 2) for "a comission [sic] of students, staff and lecturers" was in error. Firstly, these students are supposedly the cream of England's crop with regard to competitive A-level results etc., so if they can't spell, who can? Secondly, even if you can't spell (and I have more sympathy with you now that I grapple with French) you could at least run a spellchecker. But what is even sadder than this basic incompetence is the political failure that it demonstrates: if this document had been the issue of any kind of democratic process, this error would surely not have survived through into the final draft. I commend Jo Freeman's The tyranny of structurelessness to you all.