Tuesday 30 April 2013

Not shrimps, the legionnaires

Today is the 150th anniversary of the "Battle" of Camaron in Mexico, a long day for a small detachment of 65 members of the French Legion etranger who held off an army of at least 2000 Mexicans during the French Intervention in Mexico.  Captain Jean Danjou, the French commander, died in the process along with 2/3rds of his men.  Only two unwounded soldiers remained at the end of the day and they refused to surrender unless they could keep their arms and escort the body of their Capitain off the battle-field. It was an iconic moment in the history of the Foreign Legion and is celebrated by them each year on this day.  Two peculiarities attend the ceremonies.  The officers make coffee for the ranks because in 1863 the soldiers were interrupted by the Mexicans just as they were about to have theirs and spent the whole day without water, let alone coffee.  The Hand of Danjou is also reverenced.  Captain Danjou, a career soldier and graduate of St Cyr had blown off his left hand in an accident in 1853 and sported a wooden prosthesis painted to look like a gloved hand.  This was discovered after the battle and found its way back to the Legion's head office in France.

The French Intervention was an abortive example of Imperialist politics which seems appropriate to celebrate the day before MayDay.  A group of Mexican monarchists came to Europe looking for any member of any royal family for hire and offered the crown to Maximillian: a rather bright, fairly liberal nephew of the Hapsburg Emperor Leopold I. 
Maximillian declined, preferring to go to Brazil botanising - he was an accomplished scientist as well as being fluent in at least six languages. But when Napoleon III of France (just possibly Maximillian's genetic half-brother) started the Mexican adventure,  Maximillian was blagged into taking up the post as titular head of the Mexican 'empire'.  He was deposed and executed a mere three years later.  The event being 'recorded' back in Paris by Manet in the famous picture which seems more designed to fit on a commemorative postage stamp than a realistic depiction of death by firing squad - if it happened as represented, Max's shirt would be in flames.

So today, if you refuse to eat blood pudding at least sing a few lines of Le Boudin the legionnaire's anthem. Don't know the words?  Try: Tiens, voilà du boudin, voilà du boudin, voilà du boudin Pour les Alsaciens, les Suisses et les Lorrains, pour les Belges y en a plus, ce sont des tireurs au cul. . .Au Tonkin, la Légion immortelle / À Tuyen-Quang illustra notre drapeau / Héros de Camerone et frères modèles /Dormez en paix dans vos tombeaux.Don't know the tune?  Listen: Le BoudinStirring stuff for chaps with a Y chromosome and/or a HUGE beard.

Unexpected books

I confess: I've bought books through Amazon.  Accordingly, I get info-mails from them - today "New books for May", pushing a score of books that I might think of buying.  As I've also bought books through Amazon for my creditless teenage daughters, there's some diversity there.  But not half enough as 20 books is about 1/1000th of the publishing output for the month, from Britain alone.  Google tailors its searches according to the IP number of the computer asking, Amazon tailors its recommendations according to previous buying habits, so we are sheltered from the unexpected. I'm sure this makes for more efficiency most of the time but I do feel sometimes as if I'm already back in diapers.

I used to work on Trinity College Dublin. It has the distinction of being one of half a dozen Copyright Libraries in the British Isles, authorised to request a copy of any and every book published in these islands.  That's a LOT of books: about 200,000 each year. And the sad truth is that the Library doesn't chase up all the books to which it is entitled. In the basement of the TCD Library is a section where the books which have been acquired under the rules of copyright are stored after being catalogued but before they’re shipped out to wait-for-readers in a warehouse out by the Airport.  They are shelved by accession number - as they came in – rather than by author or subject.  It’s wonderful down there: an Al-Addin’s cave of treasure peppered through the dross of hydrodynamics, Hogwarts, and history.  I often used to dive down there to choose my weekend reading and always surfaced with an oyster and occasionally a pearl.

I've written before about the increasingly finite Universe of the internet as mediated by Google and Wikipedia for our convenience. If I'm not given more windows to the outside of my internet bubble, I may burst out and go on a merry dance through the dangerous but colourful jungle of the unknown.

Monday 29 April 2013

Happy BirthDay-Lewis

Happy Birthday - Daniel Day-Lewis.  I mentioned him in passing because one of the parts he has played in film - Abraham Lincoln - shared a birthday with Charles Darwin. It's not for lack of commitment that he won an unprecedented 3rd Best Actor Oscar for the part: he is famous for taking method acting to extremes - learning Czech, skinning a deer and contracting pneumonia for his craft. It is said that he even saw the ghost of his own father while playing Hamlet, blew a psychic gasket and hasn't appeared on stage since.  We have a neighborly connexion in that the same (ghostly) father was born near Stradbally, Queen's County while my grandfather was born across the border near Birr, King's County.  There's hardly anyone left alive who would care enough about their Anglo-Irish roots to affect to deny the existence of Offaly and Laois. I don't know if DDL cares a button one way or the other.
I haven't seen Lincoln yet, and am not in a tearing hurry to do so but still have strange dreams about DDL's buckskin-clad thighs pumping up and down as they leap through the woods in the steps of Chingachgook (or was it Queequeg? or Umslopogaas? I forget)

Saturday 27 April 2013

The end of the line

DauII and I arrived in England by plane this morning, having left home at 0230hrs.  We went down to visit my mother, who was born in Dover in 1920.  Her mother had been born in Limerick in 1893 and was living in Dover in July 1909 when Louis Bleriot landed on the cliffs of Dover having completed the first aerial crossing of the English Channel; she lived to see, albeit on the the telly rather than in person, Neil Armstrong take his own giant step 60 years later.  Some progress in her lifetime, no?

In the late 1950s, my mother was living, with three small children, in a house in Norwood, South London.  Her husband, serving since the age of 14 in the Royal Navy, had secured a rare home posting and was working in Whitehall on a joint defense staff committee.  It was at height of the Cold War and things could get a little jittery.  Some politico would point to a map of the world and ask. innocently enough, what would happen if the Russians turned up here.  The Da and his committee would turn to and find out what was available in the way of Avro Vulcan bombers in Cyprus, associated army units on the same island, surface ships and submarines in the Eastern Med  and work out how quickly they could get enough oil-tankers to Malta to fuel up the rag-tag armada that would keep the world safe for democracy.  Nobody wanted to get caught with their pants down, so they put in the hours; frequently working late into the night.  No overtime.

One night, after a few weeks of this rigmarole had worn everyone to a frazzle, my mother was woken at 2.30 AM by The Da. 
"I'm really sorry, but could you pick me up from Elmer's End?  I caught the last train South from Charing Cross."
"Okay," she replied, "where is Elmer's End?"
"I don't know."
In the middle of the night, in a strange metropolis, my mother abandoned her sleeping children (you could do that in those days) and set off  in the Austin to repatriate her bloke.  Nowadays it would be no problem: Gmaps and GPS would sort everything and indicate the quickest route for reuniting them.  They were well 'ard in them days.

Friday 26 April 2013


. . . it's a horse.  My cousin Evan has been mad about de nags since he was in short pants, but it's an alien world for me.  It transpires that there has been a local triumph - in Japan!  Blackstairmountain just won the biggest prize in global horse racing by coming in first in the Nakayama Grand Jump.  The prize is $1.5m, and I'm sure that the owner, trainer, jockey, groomer, fetlock-currier, dung-barrower, have all done handsomely at the bookie because he came in at 25/1.  That's a pony for every quid you plunge mate, to use the technical jargon of the turf.  That's pretty cool as B's home is just down the road in Bagenalstown.  I hope that some local bard will compose a song to displace Dawn Run famous in song and story and another really local nag from 30 years ago.  Actually, I should say reprise Dawn Run because her trainer was the father of B's.


7up MAYBE causes diabetes

After a hard day at The Institute, I was presented last night, appropriately at dinner, with the fact that "an extra fizzy drink a day will increase your chance of diabetes by 20%" - as The Beloved heard it on the radio.  The ould skepticism alarm [DRRRRRANG!] went off immediately.  So it's taken me a little (company) time to track down the study which is is commendably available on line,(see the In The News section there about Consumption of sweet beverages and type 2 diabetes incidence in European adults: results from EPIC-InterAct by The InterAct consortium). As I suspected, it's a little less black and white when you read the research paper let alone with access to the actual data.  The study is noisy: it's a meta-analysis of 12 separate studies from 8 European countries; but it's also chunky: more than 15000 individuals have been included in the study.  As a tiny example of the issues of integrating such disparate data, the paper reports that all the study-centres measured the height and weight of their subjects except those in Oxford and France who just asked their people how much they weighed.

So the media-fact that has been abstracted from this huge study is a convenient soundbyte "The HR of diabetes per 12oz increase in sugar-sweetened soft-drink consumption was 1.22 (95% CI 1.09, 1.38)". Which I've put in bold so that reporters from Nauru (where the incidence of diabetes is a frightening +40%) don't need to read the small print.  HR is hazard ratio and CI is confidence interval: here 1.09-1.38. If the lower CI value is less than one ( <1.00) the association is not significant.  Now get this.  In the same paragraph as the soundbyte the paper reports that the "HR . . . for artificially sweetened soft drinks was 1.52 (95% CI 1.26, 1.83".  A much "better" result than a 22% increase, surely, except that when BMI (body mass index was calculated for everyone in the study along with a raft of other data as well as soda-consumption) was factored into the equation, the Hazard Ratio evaporated to zero.  And am I alone in my Eurochauvinism in objecting to "12oz" appearing in a scientific report compiled by a European consortium: jakers! even the Brits and Irish have embraced {ml, kg, km} these last 20 years and more.

Maybe soft-drinks contribute to diabetes, and maybe I'd like to see them banned (easy for us because we don't have 'em in the house), but I wish RTE would be a little more discursive and critical in their presentation of information that may impinge on a) dialysis rates in Galway b) peripheral blood circulation problems, gangrene and amputation in Donegal c) blindness in Wexford and d) jobs in Atlanta.  The way the report is received in an average math-anxious Irish kitchen where a family of 5 is washing down dinner with Fanta (and why shouldn't they?) is that one of them is done for (but that the rest will be all right).  
But if they are all within the normal range of waist, they're probably ALL going avoid diabetes.

The Guv'nor

Another scoop for The Institute.  Just two weeks after a talk by a Certain State Pathologist we were invited yesterday to hear John Lonergan speak to the law students.  A fair turn out, but I guess not everybody is a scalp-hunting celeb-groupie like me.  We've often heard Lonergan on the wireless in Ireland because he is articulate and has a particular view of the failure of the state to notice, let alone cherish the dispossessed.  As Governor of Mountjoy Prison, he tried to skip the 20th century and bring the Victorian prison system (slopping out, banging up, a little light sodomy) into something that was more modern, more compassion and more effective.  He has acknowledged that the heart of legislators may be in the right place but their purse is in the other room.  It's all very well to insist that each prisoner should have his own cell, but if you send arbitrary numbers from the court to chokey (arriving often in the middle of the night), you inevitably have 'doubling-up'.  I think he was on the button in elaborating that this might mean sharing a few cubic meters with an incessant talker for 17 hours every day: abuse and oppression doesn't have to employ the lash ... or sodomy.

Another refreshing aspect of his talk was that he just stood up in his tweed jacket and talked.  No powerpoint, no notes, just a capella.  But this did not mean a rambling anecdotal discourse.  It was data-heavy on the exponential rise in prisoners, the percent recidivism, the statistics of overcrowding.  I'll now have to get to the CSO to confirm my notes: can it really be that there were only 600 prisoners in Ireland when Lonergan started work in 1968 and 6000 now??  And it's a wake-up (he knows his theatre, this feller) to hear an elderly man in a suit and tie channeling his young charges to utter the great taboo  "Fuck Off" in a public forum.

I had to leave before he had quite finished questions (places to go, classes to teach) but mine would have been "What can we do, now, to most effectively erase this blot on the landscape of our compassion?"

Tuesday 23 April 2013


Years ago, when I was teaching bioinformatics, I clagged together a page of queries that 'one' could sic on biological databases for a bit of light relief.  But it was also designed to point out that all data, even that published by reputable authorities (Youtube, Harvard, Reddit, CSIRO, Wikipedia, Friendface) should be approached with caution.  We all mek spelinge errurs.  That original page died with the end of INCBI but it has been cloned

Today, St George's Day, is traditionally associated with the birth of William Shakespeare, because a) he was baptised on 26th April b) he died on the 23rd April c) the English would like to consolidate the connexion between their patron saint and their patron bard.  So who was William Shakespeare?  There is controversy about whether the works of Shakespeare were written by him or by another fellow of the same name, but clearly the poor chap was confused in himself.  Scholars have agreed that there are six extant authentic signatures and none of them agree:

Willm Shakp
William Shaksper
Wm Shakspe
William Shakspere
Willm Shakspere
William Shakspeare
But these guys from the Arts Block are clearly on shakey ground (a joke may have just slipped past you there) because the data show:
that WS was really the comic duo William & Zhubstic - the former a rather slow straightman, the latter a zany Russian with extravagant orange tufts for hair and enormous shoes. Their schtick was later adapted by Matt Groening for the Simpsons.  But if the man himself(s) wasn't sure how to spell his own name, it's open season for the rest of us.  At least the following alphabetical list has been attested at some place and time to refer to him:
Saxpere,  Shagsper,  Shakees Pear,  Shakespear,  Shakespeare,  Shake-speare,  Shakespeart,  Shakespehar, Shakpear,  Shakspere,  Shaxper.
What to do?  The Oracle of Wikipedia has it “William_Shakespeare  so take note and obey, that is the New Normal as they have it nowadays on the Danske Bank ads on the wireless.

Beer, bread - simplify, simplify

497 years of simplicity in German beer.

On the this day in 1516, the first Reinheitsgebot (purity order) was published in Ingolstadt in Bavaria.  By uncritically re-churning the idea, over the last many years, that German beer is composed of only four ingredients, I have been guilt of gross (33%) exaggeration.  A bit of research shows that in the original order only barley, water and hops are allowed. Everything else is streng verboten. In 1516 Pasteur was 300 years in the future, spontaneous generation (geese from barnacles, and so on) was universally accepted and yeast may not have been recognisable as an ingredient. 
I’ve extended my misapprehension to insist on only four ingredients for bread (flour, water, yeast, salt) and I stick by that.  Next time you buy one of those dreaded sliced-pans check out the (>4) excess on the table of contents.  If that gives you pause, join me in baking your own bread at home.  Actually, I’ve been on a bit of a sourdough jag recently which gets me back into Reinheitsgebod territory: flour, water,  salt . . . and a bit of stuff from the last batch (which didn’t and doesn't count).
The mention of bread is relevant here, and not only because bread and beer are the two great products of fermentation by Saccharomyces cerevisiae.  The original Reinheitsgebod was brought in, at least partly, to manipulate the market to ensure the availability of cheap bread by preventing the brewers from making mere booze from wheat or rye, and diverting those staples from Pudding Lane.
The effect of the Gebot was to homogenise the sorts of beers available so that every shaggin’ bierstube served essentially the same lager – an early-modern example of macdonaldfication.  So it made the world more boring, but as the previously used ‘preservative’ ingredients included out-there hallucinogens like fly-agaric mushrooms Amanita muscaria and henbane Hyoscyamus niger, not to mention soot and twigs, it was safer too.

Modern beer is, of course, completely safe – except insofar as it makes you foolishly try to txt while driving – but so gypped about with additives and processing as to warrant the phrase “tis a long way from food that was rared”, and that goes for shop-bought bread too - yes, even the 'baguettes', 'ciabatta' and 'chapattis'.

Sunday 21 April 2013


AUC 21st April 753 BCE
In this post our own James Ussher, Primate of All Ireland meets Marcus Terentius Varro, a contemporary of Caesar adsum iam forte as well as Pompey aderat (for those who never had Latin at school, it will help if you say the italicised phrases aloud to appreciate the joke).  The connexion is that they were both accomplished calendarists, albeit separated by 1800 years.

Varro is sometimes know as Varro Raetinus because he came from the town now known as Rieti which is close enough to being the geographic centre of Italy. He is responsible for deciding that what we call 753 BCE was Ab Urbe Condita (from the foundation of the city) from which Romans counted their years. He was a gentleman and a scholar, who fought on the wrong side in the civil wars, was pardoned and so given time to fossick through the incomplete records listing the Roman consuls, interpolate between equivocal data points, make an informed guess about the really ragged gaps and come up with a date for when Romulus and Remus had their spat and the winner built a city.  That date is today - 21st April; insofar as you can match dates then with dates now, having had the Julian and Gregorian ("gives us back our eleven days ... ye baastids" etc etc) calendar reforms in the interim.

Scientists of the less tolerant variety snicker at Ussher for having given the biblical fundamentalists a certainty about when their god started making the world.  But he also was a gentleman and a scholar and knew his literature a lot better than a great many scientists know their.  He also lived through a civil war, and I like him for being sensitive enough to faint while watching the execution of Charles I.  His chronology required considerable expertise, multilingual skills and years of dogged research.  Those who know credit him with considerable accuracy where there were data (astronomical, historical, archaeological) to cross-reference .  But when he was forced to rely exclusively on the bible and its internal inconsistencies, the accumulation of error got him into the fix of pronouncing that god's second task (immediately after the Fiat Lux! business) of "separating the light from the darkness" happened in the evening before 23rd October 4004 BCE.  And, in fairness, the title of Ussher's magnum opus is  Annales veteris testamenti, a prima mundi origine deducti - he was only trying to sort out the annals of the old testament, which as I say were in rag order because the primary data were inconsistent.  He was conscious of his own special pleading in setting the creation exactly 4000 years before the birth of our lord; and also the foundation of the temple exactly 3000 years later - it helped fulfill the prophecies.

And everybode kno that the first attempt at pegging the year of the birth of Jesus (1 AD - because Unix hadn't been invented, they weren't used to doing their counting from 0) was out by a few years and that the delightfully named Dionysius Exiguus (Dennis the Short) sorted it out so that it was consistent with Roman history in around 500 CE.


When I were a nipper (that's before the First War), I used to browse the Encyclopedia Britannica in the school library.  I'd be there for a reason - possibly consulting the biography of a 19th century general, or a technical article on pistons - and a phrase or word would give me pause . . . and I'd be off down the rabbit hole.  A hour later, I'd surface like a desperate whale gasping for air and wonder just how I'd got from General McClellan (the American Civil War general with the least facial hair) to the Northamptonshire boot industry.  It's easier nowadays, and so more time-consuming, since they invented the hypertext link but you don't get the exercise of hefting 2.5kg books off shelves.

So I was resting on my oars in the blogosphere waiting for something to happen when over the horizon loomed a (British) Independent link to a compendium of fact(oid)s about 42.  Facts like: "The atomic bomb that devastated Nagasaki, Japan, contained the destructive power of 42 million sticks of dynamite."  That made me reasonably confident that Fat Man released energy equivalent to either 42 or more likely 21 kilotons of TNT (this is the standard comparative measure of explosive power) and the usual sources revealed this to be so.  The same train of reasoning circled on the fact that a stick of dynamite weighs a kilogram or more likely 500g.

But this confidence hinged significantly on the assumption that the journo who wrote the article had been educated in the Arts Block.  Because TNT isn't the same as dynamite.  It's much less powerful: 2.8 megajoules/kilogram compared to dynamite's 7.5MJ/kg. What he should have said was "...destructive power of 14 million sticks..." and then gone off back to google to find a different 42-fact because the Nagasaki line was a bust.

So TNT (tri-nitro-toluene) is interesting. Its chemical formula
C7H5N3Oshows that it has proportionately much less oxygen than the related compound tri-nitroxy-propane C3H5N3O9 aka nitroglycerine which is the active principle in dynamite.  This means that combustion is less efficient - hence its lower MJ/kg.  Chemical reactions are usually complex but chemists like to summarise them with formulae - and insist that budding chemists add up the atoms on each side of the arrow to ensure they have accounted for everything. Here's what they think happens when TNT goes up:
2 C7H5N3O6 → 3 N2 + 5 H2O + 7 CO + 7 C and/or
2 C7H5N3O6 → 3 N2 + 5 H2 + 12 CO + 2 C
Note all the surplus carbon on the right-hand, result, side of the equation: that's the enormous cloud of sooty black smoke that is characteristic of TNT explosions.  Here's a video from Operation Sailor Hat - a cunning plan by the US navy to simulate the effect of a massive blast on their ships.  They commandeered Kaho'olawe, the smallest Hawaiian island, built a stack of TNT weighing 500 tons (that's 300 cu.m. - just about the size of our modest house); moored some surplus-to-requirements ships and ... baDOOM.  As well as sending a dirty black plume up into the air (three times in the Spring of 1965), and knocking chunks off their floating Tonka-toys, the USN created the only non-volcanic crater in the state of Hawaii.  Kaho'olawe hasn't had any surface water since shortly after the Hawaiians arrived around 1000CE and stripped off the forest. But Operation Sailor Hat has created a brackish anchialine pool - a landlocked body of water connected to the ocean by a subterranean passage - which is home to some unique shrimps.

Thar she blows!!  One minute you're safe in a warm bath of truthiness on a Douglas Adams tribute site and an hour later you bob up with hearing loss in a remote pond in Hawaii wondering if Halocaridina rubra is edible.