Sunday, 31 March 2013

Will work for chocolate

In any family, you can make your own traditions. You can, of course. take the ‘standard’ traditions of whatever culture you were born or migrated into or you can modify them to better suit the true selves of the people with whom you share living space.  Insofar as the standard trads have been shunted aside by Hallmark and Toys’R’Us, modification may be closer to The Old Ways. We’ve been blessed with two families: a single boy when we were very young and foolish and then two girls after a gap of 18 years.  So we’ve had our own children in the house for the best part of 4 decades.  That’s at least 3 dozen Easters to develop a Paschal tradition. 

Easter is derived from Eostre the Saxon goddess of the radiant dawn and is redolent of Spring, fertility and regeneration – as symbolised by the eggs and bunnies which you can buy from Supavalu in the run up.  So it’s entirely appropriate to honour the childer on that day – they are after all the product of all that fertility.
There is a thread of the Protestant tradition in our family that values the work-ethic and feels it is no honour to hand the monstrous eggs, the Kinderüberraschungen, and the straight-up slabs of chocolate to children on a plate.  So for almost all the years since about 1980  I’ve gotten up bright and early (with Eostre indeed) and set out a treasure hunt designed to mak t’buggers work for their hyperglycaemic fix. For youngsters it’s been a straight enough hide and find, but, as they grew, the egg-hunts became more cryptic – my mother taught me the conventions of cryptic crosswords from the English broadsheets almost as soon as I could read, so weaselly reasoning is rather ingrained.  Less admirably perhaps the clues have also acquired a lot of doggerel:
currants, then raspberries,
a fence and a row
of thorny ould sciachs
to the middle one GO
One year we were off site and all I had to work with was 3 six-year-olds and a haggard full of rocks and machinery.  In the mess of agricultural detritus, I found a 5m length of baler-twine and tied a loop in each end.  The instructions were that there was an egg at each end of the rope.  So the kids had to cooperate – one to hold an end over the last egg, another to swing the string in an arc until pay-dirt was hit.  That year it was a wonderful brilliant sunny morning, a looping barn-dance “swing yer pardner by the hand” around the perimeter and through the middle and back to the kitchen for breakfast.
Another year, we had a hunt which required pulling individual letters from the Encyclopaedia Britannica to spell out clues to locations outside.  When I finally gave up on overhead-projection acetates and started using powerpoint as teaching aid, I made a whole hunt using that medium and no words.  When we bought a farmlet with 7 hectares of fields and ditches and hedgerows, we could really get out for some exercise climbing trees and getting wet in the river.  When the Boy returned home with his francophone Swiss girlfriend, we had une chasse au trésor in franglais.  I based it one year on playing cards using the suit of hearts which forced a convenient 12 clue limit with a larger egg at the Ace.  Looking back on previous years, I am amazed at my presumption in putting the kids through such antics and regard a lot of the clues as an elaborate game of “Isn’t Uncle Bob Clever”.  But they have risen to the challenge year after year and learned something about how to reason, how to free-associate and how the rewards of not giving up are more than 15g of chocolate.
But now I’ve run out of steam, the youngest child is learning to drive, and it seemed sensible to modify tradition yet again to No Egg Hunt This Year (sorry).  Except that the Boy is home with his own small child and he’s taken the hunt-baton on and up the mountain behind the house.  So we’ll really have to work (boots, binoculars, compass, Kendal mintcake, maybe even crampons) for chocolate this year.  Looking forward, me: a rough 3 hr hike through the heather will seem like a holiday.

Saturday, 30 March 2013

On Singing Together

This is one of the great celebratory weekends of the Irish year.  So it's time to celebrate something inherently celebratory, like singing.

Everyone can sing!  But most of us don’t do so half enough.  I have recently come to believe that singing together is a defining attribute of the human condition and if you fail to do it often enough you become something less than human.  It might be closely related to laughter.  Recent research has shown that laughter is an essential social lubricant; that it is difficult to laugh if you are alone in the room; that endorphins are released when we laugh together.  Everyone knows that it is impossible to tickle yourself.

In recent years my pal Lulu has organised singing weekends led by Sian Croose at the Camphill Community in Ballytobin, Co Kilkenny.  Not being a religious fellow, I haven’t been to every session, but I have, on a few occasions, found myself being transported to another space.  The suffering of being an Intellectual is that it is difficult to leave that tick-tick-whirr aside and let yourself GO.  Sian typically allows people to decide their own pitch and assemble into sections, she then teaches, by ear and repeat, each section its part.  That can be a teensy bit draggy sometimes, but eventually everyone knows their bit and Sian starts one section going on their own.  After all the rehearsal, it sounds good.  Then she brings in another part which, by accentuating and complementing the first, sounds much richer.  When she adds a third part, your first thought is “it can’t get better than this – this is really fine”.  But there are two more parts to be woven in…!  If the conditions are right it can be remarkably affecting.  Indeed, there have been times when I’ve had to concentrate really hard on just singing my own small bit because if I listened to The Whole, I knew I wouldn’t be able to continue: I would be, as the Victorians had it, unmanned.
A tuthree years ago, I saw a familiar figure across the car-park at one of these workshops and bounded across the intervening space crying “SenSei, SenSei” because Sinead O’Brien my old djembe teacher had come to sing.  Religiously (you see I used to be religious), I went to her “drum, dance and body-percussion” classes every Tuesday night for about four years at the end of the last century.  It took forever for me to stop thinking and just drum.  It was, for example, fatal to look at my hands because their response was “oh ho, brain taking over, flub”.  Sinead reminded me about the time when at last, I managed a simple variation of ‘elephant walk’ called ‘fumé-fumé’ and the light came on across my face.  To drum together, like to sing together, you’ve just got to leave yourself (and all those quotidian worries) at the door and listen to the heart beat (the name of another simple drumming exercise).  There was a time in Sinead’s classes when she was busy as people drifted in from work and took their seats.  Someone started an idle riff on his drum, and his neighbour took it up, and that seemed good to another person in the circle and they embellished the rhythm and … soon we were all jamming away and Sinead left her paperwork and took up a spare drum (or two!).  40 minutes later we're still all up to ninety and class hadn’t even started.  Another week, half an hour before class was due to finish, Sinead stopped abruptly and said: “that’s it, who’s for a drink?”.  And we all heaved a sigh of relief because that night it was all work and no reward and we were going nowhere. Who knows how these group dynamics work?  Is it pheromones?  Is it so deeply embedded in our psychology that we have collective emotions?
A few years ago at the annual home educators gathering,  I sat in on one of Raj Padam’s drum circles.  Our group was heavy on the adults, so Raj spent rather along time lecturing us about the virtues of drumming with small-small children before he go t on down to just drumming.  There were several in the group who, like me, had been drumming before, and a lot of them, like me, were in trouble because they were thinking about it far too much.  On the collective lap, however, there were three toddlers, who were drumming much better that me and the other thinking reeds.  We never lose our sense of rhythm but, like learning languages, it’s a lot easier to acquire skill if we do it early.  Drums cost money, but if we all sang together we’d have a better idea of our place in the world.

Thursday, 28 March 2013

Package to packet to package

I've been in the internet business longer than most.  I sent my first trans-Atlantic e-mail in 1983, I marketed a book on the internet in 1985, I wrote one of the first web-pages in Ireland in late 1994.  

 In 1991 work was analyzing DNA sequences, so we used regularly to receive a copy of GenBank, the database of all the DNA sequences known to science, on a 2400 ft magnetic tape.  This was the size of an inch-thick dinner plate and arrived in a padded envelope from France.  After downloading the data, the tape itself was sent on to Indiana, then Houston and finally back to Lyon.  By mid 1992, we had left 19th century communication behind and were downloading GenBank over the internet.  The whole database then was only about 200 Megabytes in size (say, three MP4 TED talks in today’s e-currency) – it’s 1000x bigger now – but the connexion  was slow (overnight at least) and unreliable.  Traffic was lighter and the connexion accordingly faster and more certain at weekends. All too often, however, I’d come in on Monday morning to find that only a fragment of the database had arrived together with a laconic “BROKEN PIPE” error message – which evoked an image of packets (technical term for an aliquot of data) of As Ts Cs and Gs spewing out across the Atlantic seabed.  So I took to going into town on Saturday or Sunday to check progress and start it all again if the process had failed.  This was conscientious but tedious, and I was delighted when, foraging about in the basement at work, I found an acoustic coupler and brought it home.  You could plug the coupler into a computer and telephone at home and send commands to the server at work albeit at less than the speed of light – maximum 300 bytes/sec.  The phone handset sat into a foam-rubber surround to minimize noise and maximize signal but you could still hear it fizzing and clicking.  With that appropriate technology, from home I was able to . . . C H E C K  P R O G R E S S  at work and R E S T A R T   J O B  if necessary.  This was – marginally – quicker than making a 25km round trip on my bike.   

Over the next few months and years it got easier - the wires got fatter, connexions more reliable.  Perhaps more importantly, Genbank got too big to download locally at about the same pace at which it became possible to do all the necessary analysis off site on what we were still years from calling The Cloud.  It became possible because capable graduate students and tech-savvy post-docs across the globe were writing code to abstract particular sequences from the database and analyse them in particular, and even peculiar, ways.  Of course HTML, WWW and HTTP made it all so much easier to produce functional procedures than the primitive comms we'd used before.

Now here's the weird, I was in the pub before Christmas last year talking to a couple of the young effectives in our world of bioinformatics.  One of them said that he was routinely communicating with his US collaborators by FedExing a terabyte external hard-drive back and forth across the Atlantic. Parkinson's_law states that "work expands to fill the time available for its completion".  If there isn't already a similar law like "data proliferates to fill to capacity the conveniently accessible means for storing it" then I hereby claim/name it as Bob's Law of the Data Packet.

Was it the Red Queen or Madame de Pompadour who quipped about surfing the deluge to keep abreast of it?  I forget.  "Apres nous la brioche" was it?  "Surfing’s the source code man . . . swear to God"  Now that was Bodhi in Point Break.

Home is where the heart of education is

My older Blogging-for-Ireland daughter returned home from England yesterday and as we were driving the 25km home from the bus-stop (we live that rural, yes) she mentioned that one of her English pals had been sacked from his job for shop-lifting (from the place where he worked!).  At dinner that night The Beloved asked
"What's Jack doing?"
"Time", I quipped before B4I could answer.

Friends of ours, from the other end of the county, are also up before the beak. Their crime?  Failing to register to educate their children at home.  It's reported today in the Irish Times (
In Ireland we have a written Constitution and article 42 (full text of article here which states
"Parents shall be free to provide this education in their homes or in private schools or in schools recognised or established by the State.
The State shall not oblige parents in violation of their conscience and lawful preference to send their children to schools established by the State, or to any particular type of school designated by the State.
The State shall, however, as guardian of the common good, require in view of actual conditions that the children receive a certain minimum education, moral, intellectual and social."
Monica and Eddie have chosen to emphasize the first of the three paragraphs above and feel that, as a constitutional right, they don't need permission from the state to educate their children at home.  The National Education Welfare Board (NEWB) was set up about ten years ago to vindicate the last paragraph above.  This is accordingly a great legal issue: if it was all black Monica and Eddie would be banged up in chokey ek dum; if it was all white the NEWB wouldn't have a place to stand.  As you can read in the Irish Times article and from a youtube video called Homegrown Knowledge it's clear to me that O'Neill/O'Connor clan are getting rather more and rather better than a certain minimum education. 
It would be easier for everyone if Monica and Eddie would just fill in the form, have the visit from the fonctionaire from the NEWB, let him see the projects, the portfolios, and the art-work, listen to the music, eat a cookie put together and baked by the four-year old (and know that the maths would be okay there) . . . get registered and get on with letting the kids grow up as useful members of their community and happy in their own skins.
As the state continues to regulate our lives for our own or for the common good, it's easier if we all go along. But regulation compels us all to be more like each other.  In this case regulation is forcing us, even if we don't chose to send our children to school, to accede to someone else's concept of what (a certain minimal) education is. As most of the officers of the NEWB are ex-teachers or ex-school inspectors and ALL of them were educated in school, they are going to have a defined and school-based view of the matter.  So Monica and Eddie are implicitly asking us to rein in our gallop of assumptions and reflect on how we deal with difference in our society.  We need to embrace and celebrate rather than tolerate diversity and get behind the mirror: there could be a wonderland of new ideas there.

Hats off, gentlemen!

Monday, 25 March 2013

Shuttle safety record - not so bad

After casting asparagus last night at NASA for the safety record of their Shuttle program, I realised in the cold light of day that I had been a bit unfair.  In particular, I may have fallen into a well known psychological trap of risk-analysis - we tend to pay attention to spectacular accidents and this affects our behaviour in counter-productive ways.  Gerd Gigerenzer, a risk expert, estimated that, in addition to the 3,000 Shanksville, PA, World Trade Centre and Pentagon deaths, an extra 1,500 people died in cars (inherently dangerous) because they were illogically leery of flying (fundamentally safe) in the months after 9/11.

On reflection, I thought that a better statistic might be deaths per vehicle mile.  The Shuttle program cumulatively clocked up a pretty impressive mileage in 135 missions for a total of 21,158 orbits of the Earth.  As the Earth is, by definition, 40,000km in circumference, that totals about 850 million kilometers, resulting in 14 deaths, no serious injuries.  That's about 1 death per 60,000,000 km travelled.

In Ireland, there are about 1.5 million private cars.  The average annual distance travelled by each personal-stereo-on-wheels is supposed to be 10,000km.  The Irish Road Safety Authority struggles to keep the annual road death toll under 200.  Curiously, the injuries (minor, disabling, serious), which probably cost society more than the deaths are rarely remarked let alone weighed in the balance.  ANNway, the figures just enumerated indicate that the death rate on Irish roads is about 1 per 75,000,000 km travelled.

So I stand by my recommendation to travel by bus, but retract my implication that the Shuttle was outrageously more dangerous than other modes of transport.

When 200 = 100,000

Last night I was watching The Challenger, a BBC docudrama starring William Hurt as Richard Feynman on the Presidential Commission that investigated the first Space Shuttle disaster in 1986.  That's the one that blew up a minute after launch because a huge rubber washer failed to keep hot gas where it should be.  Feynman, according to the story/legend/record, is the only one who really wants to find out what happened - so that it won't ever happen again but also for the pleasure of finding out.  As a scientist he talks almost the same language as the engineers who designed the Shuttle and as a transparently honest person he has little time for the NASA spokesmen who seem bent (sic) on laundering the story so that they and their institution come out squeaky clean. There are two interesting aspects of the story as portrayed by the Beeb. 

Firstly, Feynman found other faults in the technical design of the spaceship apart from the famous O-rings.  He discovers metal fatigue in the blades of the turbines and there is a nod to the future (specifically the next Shuttle disaster) when Feynman runs his hand over the heat-shield tiles which failed to protect Columbia in 2003.  So some of the complexity of the design, the engineering, and solving the cause of the disaster is addressed.  If not the O-rings something else could have failed.

Secondly, the drama focuses on the disconnect between what the engineers at NASA and its sub-contractors were saying about safety and reliability and what the NASA management was hearing them say about safety and reliability.  The engineers conclude that the Shuttle is going to work as specified 99.6% of the time, which being interpreted means that it's going to fail about 1 time in 200.  The management OTOH maintain during the public raree-show for the media that their estimate of failure is about 1:10^5 which being interpreted means that it's going to fail about 1 time in 100,000.  To most of us 99.6% reliable sounds pretty darned reliable and 99.999% reliable is a little bit better. 

Feynman was charismatically famous, as only the very best scientists are, for being able to explain complex issues to ordinary folks. His rhetorical question to the management graphically exposes the absurdity of their position "So you're saying that NASA can launch a Shuttle every day for 300 years and not expect it to go wrong?"

Unfortunately for the astronauts and their families, even the famously pragmatic engineers were optimistic about the safety and reliability of their baby and its 2.5 million components.  The Shuttle lumbered along for 30 years from 1981-2011, had 135 launches and fucked-up twice.  Failure rate 1 in 70, reliability 98.5%.  Take the bus?

Sunday, 24 March 2013

Winter Triage

Just over twenty years ago, in the midst of the last big recession and against the advice of all our friends-and-relations, we returned to Ireland.  We’d left, with our infant child wrapped up in a handkerchief and tied to a stick, to seek our fortunes in England, Holland, and America.  We hadn’t found a fortune but we had grub-stake enough to think of settling back home.  The infant child had a green passport but was really no more Irish than a Chicago policeman and his accent was clearly from across the water. So we decided that we’d reinforce his sense of cultural identity by wrapping him up in the Leaving Certificate.
The job that was going to fund this ambition was in Dublin but at the tag-end of a glorious summer I signed the lease on an old farm-house out near the airport.  The farmhouse was huge, rambling and embedded in a working farm recently transformed into riding-stables.  Huge and rambling was convenient because, from yard-sales and junk-shops on two continents, we’d accumulated a mountain of possessions: hundreds of books, dozens of plates, three wardrobes – which we stored in the spare bedrooms - and a spider-plant for the bathroom.  The glorious summer turned into winter, and we saw why nobody before us had rented the farmhouse for more than 12 months.  The windows merely slowed down the wind, you could see daylight round the door-frame and the walls were 2 foot thick and wept condensation.  A bale of briquettes loaded into the grate would roar heat up the chimney to be consumed in minutes while leaving only the memory of heat in the room.  Did we sleep with hats?  It would certainly have been sensible.  But we stuck it out for 5 winters partly because we were well ‘ard but mostly because the spring was such a relief.  
In due course, in the depths of the third winter and after a gap of eighteen years, we were blessed with another child.  A few weeks later in the dead cold dark of night the baby woke up to be fed and after a moment we noticed a curious orange glow on the curtain.  It took us a groggy couple of minutes to twig that it was not street-lighting but a fire in the landlord’s hay barn. I startled out of bed, woke the landlord and his family, called the fire-brigade, shucked on some clothes and went out to help. The hay-barn was roaring a plume of bright sparks into the dark sky, much like our living-room grate but much louder, and everyone in the yard was bright orange on one side and throwing a long black shadow the other.  It seemed sensible then, though cracked in retrospect, to go into the adjacent stables and push a couple of the horses out of their boxes with the heel of my boot without pausing to consider that they might kick back.  As the fire spread, the landlord’s grown-up son heroically dashed into the edge of the inferno again and again; flopping backwards into an old trough to cool down before going in for another pair of horses.
At some stage in the night, the fire-brigade announced that if the wind shifted a tad, then the farmhouse itself might be in danger.  So I went back home and we prepared the baby for evacuation: we had more than a handkerchief to wrap her up in but even that only took a few minutes.  With time stretching, the child safe and nothing more to be done for hay or horses, I started to reflect on what to save if the wind did indeed change and come whistling through the letterbox from the still blazing barn.  Top of the list was my recently acquired, brand new and absurdly expensive Macintosh LCIII computer which I accordingly double wrapped in bin bags to be taken outside.  The evidence of my contributions to horse-rescue show that I was clearly not thinking straight that night.  What I should have rescued were the photographs: the computer was only money but the photos were irreplaceable hooks on which to hang memory.  
NotsUNdayMisc XII

Saturday, 23 March 2013

Reasons to be cheerful

What I’ve learned in 11 weeks:
Why radon is dangerous (it’s the polonium, stupid).  The difference between a thermistor and a thermocouple.  That nitrous oxide is created by internal combustion engines because it’s HOT in there and the carburettor is delivering 80% N2. The potassium content of bananas; the alcohol content of poitín; the calcium content of milk, the magnesium content of milk o’magnesia; the moisture content of malt;  the sunset yellow content on Lucozade; the pH of tea. Less is more. Why the ozone hole is bigger over Antarctica than the Arctic (it’s the continental weather, stupid).  How to use a spectrophotometer – and begodde it’s used every day. The hardship and heroism that people go through to get an education. That far more CO2 is fixed by marine algae than all the trees on the planet.  Five different ways to measure the concentration of glucose in water.  How to be productive in 10 minutes between lectures.  How to do molarity calculations. How not to do molarity calculations.  LESS is MORE. How to get the IRQ - interquartile range - in ExCel.  How to do an ANOVA - analysis of variance – in ExCel, and get the correct answer, without having a clue about what you’re doing or what you’re done. That the two tiny peptide hormones oxytocin and vasopressin are produced in the posterior pituitary, are 80% identical and their genes are next door to each other in the genome. How a ditsy approach to syllabus may have good learning outcomes.  That young people are brave in the matter of public speaking.  How to retrieve the number of the missed call from my Cisco phone (thanks TKD!).   That not knowing is the springboard to understanding.

Friday, 22 March 2013


Reasons to be cheerful.  I've just finished an 11 week teaching term and we're still having loadsa fun.  We've had a couple of days of heavy rain across the country, Enniscorthy flooded at Templeshannon this afternoon and there was a lot of surface water on the roads to and from work, so I was duly grateful I wasn't coming down from Dublino on the bus and getting detoured though Bray and Wicklow because the main road was impassable.  We went north this evening to Tinahely Courthouse to see Jiro Dreams of Sushi and had to take a back-road detour because the Sillellagh-Tinahely road was flooded out. 

But I was so glad I made the effort because it's a wonderful documentary about this workaholic who makes Michelin star sushi in Tokyo, and has been perfecting his craft for 75 years!  He is both Shokunin (craftsman) and Sensei (teacher) to a handful of apprentices who spend a year perfecting the art of squeezing hot-towels before they are allowed to scale the fish.  Curious about the idea of working in and on a small-small project like making a gallimaufry of tuna, wasabi and rice again and again and again until it becomes the quintessence of tuna, wasabi and rice. 

Ah So

Sunday, 17 March 2013

Half Year in Happy Village

I graduated from University in the 1970s with a marginal degree, having booted my final exams.  I’d spend far too much time in the library pursuing my own chimeric interests in science and wilfully paying far too little attention to the actual course in which I was enrolled.  Becoming father to a child in my penultimate year as a student, with all the sleep-deficit that entailed, didn’t help to concentrate the mind either.  So I slunk out of college into a very hand-to-mouth existence living, all three of us, in a bedsit in Leeson Street.

My egregious pursuit of more interesting intellectual fare at college had, however, struck a chord with a visiting professor in my final year.  He had been visiting Ireland from Boston on a Fulbright Fellowship and I completed a final year project with him: about the only scheduled activity in which I was firing on all cylinders that year.  A couple of months after graduation, I found a letter from “my” professor offering me a place in the Boston University PhD program.  All I had to do was muster the first semester’s fees – a matter of several thousand dollars – and he was confident that I’d wing the rest with teaching fellowships.

So the following summer we went looking for the small fortune that would fund the Great Leap Forward in America.  As the Netherlands had a minimum wage of Dfl 10 (about £2.50) an hour - much better than you could hope for in Ireland or Britain – we headed off to the continent to look for work.  A week later, I was all set to take a job making plastic fish-boxes in a factory outside Utrecht (and happy to get it!).  Then I heard from a fellow scientist that Blijdorp Zoo in Rotterdam was looking for a general labourer while they assembled the world’s greatest aquarium exhibition.  Their existing effectives having been tasked to build aquaria and catalogue fish all day and far into the night, someone needed to maintain normal services.  The following Monday, therefore, I became the grunt who was to sweep and clean, lift and scrape while the Great Exhibition Project ponderously accelerated into action.

My work-mates were extraordinarily kind. One of them elected to speak to me at work exclusively in Dutch, despite her being fluent in English, so I would get up to speed with the language.  Indeed, almost all of them had left school as soon as possible because they loved animals but they all spoke two or three foreign languages, knew the Latin names of everything they handled and had extraordinary levels of practical skill.  All my book-learning looked pretty paltry by comparison, but was accepted as a more or less agreeable quirk: like Tim’s hobby as a taxidermist or Peter and Gerhardt’s habit of talking to each other in Morse from having served out their National Service in Signals.

Social inclusion in Holland, while mandated in law with things like the generous minimum wage, is also deeply embedded in the collective conscience.  It soon became common knowledge that I was saving every guilder for my Graduate School fees.  I hadn’t been a week getting my khaki work-clothes wet  before my family was invited to stop camping and share a house a short walk from work.  And, as the work-programme heated up in the Autumn, my work-mates insisted to the management that I should have equal access to any time-and-a-half over-time that was available.

The collective adopt-a-student drive came to a peak when the twice-yearly draining of the water in the crocodile pit fell due.  I was busy elsewhere all day but at knocking-off time in the locker-room I was presented with a bucket half full of coins which had been shovelled out of the crocodile sludge and roughly rinsed.  Someone else gave me a bottle of acetic acid, which we used to clean finger-marks off the aquaria, and said it was just the thing to make old money shine like new.  I was as proud to be presented with that bucket as I was to receive my PhD four years later.
After all I wouldn’t have had the one without the other.

Zondag mengeling elf. NotSundayMisc 11

Saturday, 16 March 2013

St Martin at The Institute

Since starting the Real Science job in January, I've acquired a white lab coat.  It's wonderful - the double-breasted elastic-cuffed sort that has poppers and and wraps round the neck over the shoulder. I think it makes me look The Part - a cross between Richard Chamberlain as Dr Kildare and Gene Wilder as "Dr Fronkensteen".  One of the reasons for togging up in the lab is that it encourages you to shuck on a professional (alert, careful, precise) demeanour.  So it's not really how I look that matters but how I think I look.  Things have come a long way from the coat with buttons that exposed my shirt and tie and failed to protect my nice trousers from the ravages on nitric acid in the 1970s. 

This last Thursday, my tallest student came without his own coat and asked if he could borrow one.  I knew that there were two ratty 'ladies' coats kept for this purpose behind the door of my shared office; but I also knew that either them would look like a bra on Student Lofty.  So I gave him mine (and b'godde he looked terrific - calm, competent, ready for any set task), took a deep breath and put on the other. I don't do mirrors, so I've no idea how I looked but I'm sure, if I had abs, my six-pack would have been obvious and my oxters started to creak.

The following day, I met another lad from the same class in the corridor and lent him my rent-a-coat because he had a class at 9am and I didn't start lab-work until 1pm.  St Martin (of Tours) of the cloak is not the same at the patron of public (in the US sense) schools, who is St Martin de Porres but they both seemed relevant at the end of this week.  Come whatever, I went out to the shed this afternoon and went through the steamer-trunk of clothes unlikely-to-be-worn-again but too-good-to-throw-out until I found last-century's lab coat.  Now I have a spare - and the science can go on.

Irrational approaches

Nobody knows what to call people like me. Bioinformatician?  Bioinformaticist?  Sir? I'm satisfied enough to be a binfus, which has happy overtones of doofus.  To every trade its tool-box and one of the tools I use almost every day to make sense of our evolutionary world is sequence alignment.  Here, for example, are the first 40 amino acids of IL6, an important immune protein, from 3 different species:
 you can see that the rat and mouse sequences are almost identical (yellow and grey) and there is only one case where the human state is identical to one of the rodent species (blue) but not the other.  You can use this sort of analysis to infer that rat and mouse had a more recent common ancestor than either did with primates like Archbishop Ramsey.

So far, so standard.  But what happens if you apply this particular angle-grinder to the troika of famous irrational numbers (FINs)?  That's what I did with the first 200 digits of Phi (1.618etc; the golden section), e (2.718etc; Euler's number; Napier's constant; the base of natural logarithms) and Pi (3.141etc; the ratio between the circumference and diameter of a circle): 

What I'm asking here is if the order of decimal digits of these irrational numbers show a  phylogenetic relationship, similar to rats and mice vs humans.  And it seems that they do!  If you look at the alignment 100 random digits with another 100 random digits, you expect 1/10 of them to be identical.  So the expected value of 200 “pair-wise” aligned random digits is 20 identities.  The more stringent case where the digit is identical in all three numbers is expected in 1/100 of the possible positions and, as expected, we have 2 (grey) examples above.  I find that there are 28 cases where we have identity between Phi and Pi; 19 cases where Phi and e are identical; but only 12 where Pi and e are the same. In each case the expectation is 20 IDs, but there are more than twice as many Phi/Pi identities (green) than there are e/Pi identities (blue).  Yer, yer, the statisticians cry; but it’s a small sample and you’d expect these stochastic fluctuations.  So I did a ChiSq test, with 2 degrees of freedom, and the departure from expectation is more than you’d expect by chance (ChiSq = 6.64, critical ChiSq = 5.99).

So let’s call this Bob’s Conjecture and leave it there for now.  A “trivial” analysis (N=200 * 3) like this is, for a crap programmer like me, more efficient to do by hand.  The next step is to crank up the length of the aligned digital sequence to 1000, then 1 million digits; to see if the conjecture holds for octal and binary representations of these numbers.  Over to you, readers. Goldbach's conjecture has been waiting to be proved, or a counter-example found, since June 1742.

The Ramsey Boys

Habemus papem!  The new pope seems to have a welcome core of humility (wooden cross, tendency to take public transport, preference for living in a manageably small apartment etc) which is refreshing.  It reminded me of a story that I have dined out on for decades about a similarly humble Archbishop of Canterbury when I was at school.  That prelate would be seen in his ceremonial kaftan buying his own socks in Marks and Sparks and was the only incumbent to have a chauffeur-driven Ford Fiesta.  I can discover no evidence of this fantasy on the internet – so I’ll have to concede St Martin’s cloak to the catholics (for the while). 

But I did spend some time ferreting through the biography of Michael Ramsey who was ABC at the time.  He became Warhol famous years after death, when a couple of bucketful’s of ceremonial artifacts were discovered in the River Wear in Durham, where Ramsey had lived for a few years in retirement. Seems he had tried to raise money for charity by selling some of the golden trowels and silver chalices that he'd been gifted in his working life but these identifiable artifacts had re-surfaced on the auction circuit to cause offense to the original donors.  That put a stop to further discrete sales but didn't deal with the boxes in the attic.  So he went down to the Prebend's Bridge at the bottom of the street where he lived and dumped all the worldly artifacts in the river.  Maybe he was the sock archbishop after all?  

Michael Ramsey was also known for having an atheist brother, the brilliant mathematician Frank Ramsey.  But not before he'd made substantive contributions to mathematics (logic, decidability, combinatorics), philosophy (he was Wittgenstein's academic supervisor) and economics (he was friend and collaborator of Keynes).  He died at the age of 26 in Jan 1930.

The day after I'd read all this, my pal El Asturiano, sent me a link about interesting numbers including Pi. e, Phi and the Graham Number which is the largest number known: it takes 1000 characters just to describe it.  It turns out that Graham's Number is the upper end of (Frank) Ramsey's Theorem

Big number, small world.

Tuesday, 12 March 2013

Lost & Phoned

Yesterday we had our first pile (a disabling Irish snow pile is about 50mm) of snow this winter which coincided with my first cold in 4 years, so there was excuse enough not to drive 40km into work.  But I reckoned the consequences of having to pick up later the dropped thread of the working week, were not worth a morning in bed. And I think you lose face to call in snow-bound if you choose to live 200m higher than your place of work.  The first 10km down the mountain were slippy enough, so I wasn't about to make any sudden movements of brake or wheel.  Accordingly, as I came abreast of a van coming towards me in a snow flurry, I whacked the nearside front wheel off a rock that had fallen from the ditch.  Two miles on that tire was flat (shredded indeed), so I pulled off the county road onto a little farm-track and changed the wheel.  When I got to work I realised that my phone was absent and assumed I'd left it at home, so sent a webtext to enquire.  No phone but the Beloved said she'd have a look in the bohereen when she left for points South and West after lunch.  Within 2 minutes of stopping she had met two of the three families who use the lane, one of whom reported that the Postie had picked up a phone and wondered if one of the kids had dropped it waiting for the school bus.  A few calls and it has been arranged that their Postie will talk to our Postie, who will repatriate the phone tomorrow. How's that?  Wouldn't happen in The City.  And I won't hear a word of knock against rural post-people - they are for many of us a shining thread in the weft of community.

Sunday, 10 March 2013

In The Now

I was going on yesterday about how BMI normal and ideal have changed places since the neolithic.  In The Information, James Gleick mentions, almost in passing, a change in attitude between Athens in its Golden Age and the present day.  It's about being at an event rather than recording that event.  We are fire-hosed with information now, so much that it's hard to pan out the gold from the wash. Gleick notes that the Library of Congress, whose original aspiration was to obtain a copy of every book ever published, is now extending its brief to recording every tweet - lest some hidden gems are discarded with the dross.  Partly this is because we can and part of it is an admirable respect for the Future - who knows what might be useful or interesting to those who come after us?  But we could surely have some editorial policy if only to reduce the redundancy: do we need to keep a 1000 retweets of Stephen Fry's tweets?
But what do I know?  In the mid 1990s, when I was trying to maintain a local copy of the DNA database (which was small enough then to make local copies a sensible aspiration), I was indignant that the database was being filled out with ESTs.  These are short, kinda-crappy-quality partial sequences which I felt then were just making it harder to find definitive full-length, high-quality, well-annotated gene sequences.  Less than 5 years later, a student of mine used these very ESTs to compile a complete inventory of the innate immune system of the chicken; years before 'proper' sequences became available with the complete chicken genome.
I have a techie friend who because he can records every action of his children as they grow up.  It's so obsessive that the kids have never seen the right side of his face.  He's so intent on the future that he's missing the present.
Gleick contrasts the tweet archive with an image of an Athenian crowd spilling out from the theatre 2500 years ago after watching the latest play by Sophocles. Because there were no camcorders then, the audience had been paying attention and because they were paying attention they were every one of them enturmoiled by the transcendent and eternal truth about the human condition that they had just witnessed and participated in.  In contrast to every shaggin' tweet, only seven of Sophocles' 90+ plays have come down to us - they can still move us to tears, I'm desolated that more haven't survived the mills of time and loss, but just maybe less is more. 

These boots aren't made for walking

Emil Zatopek
...was born 90 years ago in Koprivnice up near the Polish border in Czechoslovakia; he was a soldier and he ran.  When he was off duty he ran off into the woods in his army boots: through snow if he had to and with a flashlight if it was dark, until he was miles out of sight and hearing and dropping tired . . . and then he ran back again.  When you look at footage of his contorted face and the desperate striving of his limbs, (Commentator Red Smith wrote that Zatopek "ran like a man with a noose around his neck...the most frightful horror spectacle since Frankenstein...on the verge of strangulation; his hatchet face was crimson; his tongue lolled out.”) it is impossible to believe that he ran for joy.  He ran because that’s what he did. 

There are times when sport is so compelling that even the most dismissive anti-athlete can be brought to the edge of his couch with a dry mouth and tears starting as they witness a triumph of the human spirit.  Of course, there are other moments of such fluid grace and decisive action on the field that you can relax knowing that no mere mortal could achieve the feat.  But when an athlete draws deep on their reserves of grit and courage to finish the race, you can be inspired to believe that you could, in suitable circumstances, tap into some deeply buried inner resources of your own.  And when your team scores the winning goal, or in Ireland’s case secures another triumphal draw, the sense of elation transcends all sense and sensibility.

As the world emerged shattered from the Second World War, Zatopek represented his country at the 1948 London Olympics, came second in the 5,000 meters and won Gold for the 10,000. He could communicate in six languages and laughed a lot, so he made good copy for the international press.  In the Olympics barracks (the athletes were housed back then in Nissen huts on two wartime aerodromes), his kindness and multilingual skills made him popular with his fellow athletes, and he advised younger runners (clearly with a sense of do what I say, don’t do what I do!) that touching thumb gently to forefinger while running forces the arms to relax and so conserves energy.

Four years later, the Communist regime in Czechoslovakia assembled a team for the 1952 Helsinki games with Zatopek as their star runner.  When his middle distance colleague Stanislav Jungwirth was dropped from the team because his father was a political dissident, Zatopek folded his arms and refused to represent his country unless Jungwirth went too.  The rump of the Czechoslovak team arrived in Helsinki to be met by a huge crowd at the airport chanting Zatopek’s name, so the government back home had to cave in and send Jungwirth and Zatopek on the next plane to Finland.

Having knocked off Gold medals in both the 5,000 and 10,000 meters early in the schedule, Zatopek shrugged and entered his name for the Marathon: a distance he’d never run in competition before.  But he had a cunning plan: at the start of the race he edged close to English World marathon champion Jim Peters to see how to run long distance.  It was a hot day and Peters set off at a blistering pace to burn off the opposition.  Six miles out, Zatopek, still battened onto Peters’ shoulder, with a beginner’s confusion asked if the pace wasn’t rather fast for such a long race.  Peters attempted a little gentle British irony and replied that, on the contrary, it was too slow.  Zatopek nodded his thanks, took the advice literally and powered off into the distance.  He arrived back at the stadium with no-one else in  sight and the crowd ROARED, then started chanting his name “Zatopek Zatopek Zatopek” all through the final circuit until he breasted the tape to win his third Gold of the games.  The Jamaican relay team seized him and carried him shoulder-high round the stadium to universal acclaim. For all the razz and all the matazz in London last summer, there was nothing to match that glowing hour.

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