Tuesday 31 December 2013

Thalassa thalassa

For the turn of the year, I'll tell you a story of heroes.  It has echoed down 25 centuries, so that it has become legend, but we can be confident that in its essential details it is true. The Christian gospels were written maybe 150 years after all the principals were dead. Cassius Dio's History of Rome (Historia Romana) was written 150 years after the last of the Julian Emperors had been replaced by a motley succession of generals and chancers.  But the Anabasis (Ἀνάβασις) was written by one who was there.  Indeed Ξενοφῶν Xenophon, the author, was central to the creation of the story, because without his leadership, decisions and determination, everyone on the trip might well have perished.  It's a bit odd because, although the story has come down to us as the Anabasis (The Going Up), it is really the Katabasis (The Going Down, The Return) which brings the heart to the mouth.

In 400 BCE, the Greeks lived in a rattle of independent city states (πόλεις), each about the size of an Irish county, some smaller.  They had colonies all over the Mediterranean, from Marseille (Μασσαλία) to Trebizond (Τραπεζοῦς) at the far end of the Black Sea and, of course, Alexandria (Ἀλεξάνδρεια) the Great. They were civilised in that not everyone was farming for their own family.  The Polis could, on the back of a more complex economy, support kings, poets, potters, silversmiths and soldiers.  The Greek hoplite was a powerful weapon of the ancient world: in 490 BCE, a much smaller Athenian force of these soldiers had destroyed a much larger army of Persians at Marathon.  Cyrus the Younger had ambitions to topple his brother from the Persian Imperial throne and hired an army of 10,000 Greek hoplites to help him.  These mercenaries were recruited in Sardis on the edge of Greek world in what is now Western Turkey and marched East for 1500km towards the Persian capital at Babylon.  The Greeks decisively won their engagement at the battle of Cunaxa but their boss Cyrus was killed.

This organised and disciplined body of men were thus unemployed and a long way from home.  Their general Clearchus (Κλέαρχος) and the senior officers went off to negotiate a new contract with the victors and were murdered when they arrived at the Persian camp.  So it was left to Xenophon (see right) and other mid-ranking officers to take charge: they were elected by the soldiers because that's how democracy worked in those days.  Xenophon proposed to march North to the Black Sea and there pick up a boat to sail home in style.  That plan was accepted by the army, despite the fact that it involved an 800km march across deserts and mountains through territory full of potentially and actually hostile forces.  Their camp had been sacked during the battle, so they were without any food or supplies.  They set off in good order and fought and negotiated their way North.

The climax of the journey (the tale of which knocks Lord of the Rings into a cocked hat and has a happier ending than Napoleon's retreat from Moscow) occurs when Xenophon, at the point of greatest danger in the rear-guard, hears yet another commotion at the other (front) end of the army which has come to a halt in a mountain pass.  He urges his weary horse forward to engage with this fresh challenge but as he gets closer he can hear that each platoon, as it tops the pass, is shouting : Θάλαττα! θάλαττα. (Thalatta, The Sea) That's how Xenophon, an Athenian, rendered it in Attic Greek.  Many of the soldiers would have been crying θάλασσα (Thalassa, as many Greeks pronounced it then and all do now) and probably crying as well.  The Sea was home for the Greeks and they were confident that it/she would look after them.  Five days later they marched, still in good order, into the port of Trebizond.  

I hope that you, looking with me at the now not too distant seas of 2014, feel the same surge of optimism and hope.  Good luck!  καλή τύχη bonne chance удача Succes срећно Toi toi toi! 幸運 boa sorte

Monday 30 December 2013

Mr Kipling

The timelessly hilarious joke was used by Donald McGill in his most successful picture postcard - it sold 6 million copies - but was not original to him: it has a long history.  Rudyard Kipling was born in Bombay on 30 Dec 1865 and was awarded the Nobel prize for literature in 1907.  He was the first and still the youngest English language writer to win the accolade.  There is suspicion that it was a Buggins' Turn award, the previous winners having been French, German, Norwegian, French, Spanish Polish, Italian.  But he's probably the only winner of that first decade who is still read today and certainly the only one who has inspired Walt Disney.

His reputation has not been favourable in all times and places.  He was a galloping Unionist and a personal friend of Sir Edward Carson.  His strange poem Ulster [fulltext] published at the height of (yet another) Home Rule Crisis wasn't calculated to win friends in Dublin or Cork:
We know the hells declared
For such as serve not Rome --
The terror, threats, and dread
In market, hearth, and field --
We know, when all is said,
We perish if we yield.
What answer from the North?
One Law, one Land, one Throne.
If England drive us forth
We shall not fall alone!
And five other stanzas in similar vein.  FE Smith, Lord Birkernhead, biographer of Kipling, staunch Tory and one time Lord Chancellor called Ulster "This crazy outburst marked the lowest point yet reached by Kipling's sagging reputation.".  There is a considered critique of that poem here.

From about 1912, for the next two generations, Kipling was despised as a lick-spittle imperialist, shameful in his By Jingo patriotism and his uncritical belief in the white-man's burden.  Because his critics knew that Empire was really a black man's burden and that people 'at home' lived like princes on the back of exploited coolies.  But as George Orwell points out in his critical essay on Kipling's verse that such knee-jerk assessments by people who had not read extensively or at all in Kipling's work are contemptible in their hypocrisy.  Orwell had first hand experience of working, as a police officer in Burma, at the shitty end of Empire.  His despair at having to act out a despicable role at the very edge of his competence is no more heart-wrenchingly felt than in his essay Shooting an Elephant which starts "In Moulmein, in lower Burma, I was hated by large numbers of people – the only time in my life that I have been important enough for this to happen to me".   Orwell coined the phrase "good bad verse" to describe Kipling's: it's memorable, it sings and it stirs but we feel a bit guilty about our enjoyment. Orwell is not contemptible, he's Left, but not uncritically Left and he's thoughtful.  Critical essay on the critical essay on Kipling here. All of Orwell's work is at orwell.ru, and if you don't get the reference to Donald McGill, there's a whole PC essay on him there.

Kipling has been having a bit of a revival since we shed the benefits and guilt of Empire (and middle-class Irish people were beneficiaries of Empire just as much as mill-workers in Manchester and cotton pickers in Sind were oppressed) in favour of globalisation.  His romances are romatic. An Habitation Enforced is one thread that bound us to find The Farmlet where we now live.  The Brushwood Boy is so evocative and compelling is gives me goose-bumps just thinking about it; even though it has strains of Kipling's most annoying baby-talk. Cue Dorothy Parker's "Tonstant Weader fwowed up". The baby-talk is, of course, most apparent in Just So Stories which I never read to my girls because the stories all made me wince and there was never a near enough bucket.  Nevertheless I rate the sign off to The Cat That Walked by Himself: "Then he goes out to the Wet Wild Woods or up the Wet Wild Trees or on the Wet Wild Roofs, waving his wild tail and walking by his wild lone".    If  you're a (civil) engineer you should enjoy The Bridge Builders.  The Finest Story in the World is great time-travel sci-fi. 

So for me Mr Kipling makes exceedingly fine short stories. He's out of copyright now, having died in 1936 so you can get e-copy of a great selection. Not all of them are great - some are dated, some are jaded, some are obsessive about things I care not a jot about - but the best are among the things I'd take to my desert island.  So yes, I have Kippled.

Sunday 29 December 2013

Dracunculus blogospherensis

If, from the title, you're expecting grim stuff from the tropics about malaria, loa-loa the eye-worm, or Dracunculus medinensis the Guinea worm, then I'm sorry to disappoint you. One of the wonderful things about studying biology is finding out the weird and wonderful ways in which organisms make a living.  Vampire bats (Desmodus rotundus) licking at bleeding mammalian hocks; koalas (Phascolarctos cinereus) subsisting entirely on Eucalyptus leaves (blehhh!); while in lichens a fungus gives house room and protection to a photosynthetic alga which pays rent in sugars. In many ways the internet is a rather simple ecosystem with primary producers like me lashing out mostly original material, albeit material that has been seeded or fed by other entities on the plains of the blogosphere.  We are insignificant serfs barely visible except to a very limited (Dublin, Bath, Boston, Kiev, Smolensk and Cape Town for me) readership.  Much more successful are the consolidators (I lurk on 3quarksdaily, metafilter, neatorama), who read the original copy, discard the mundane filler, and re-post the Good Stuff from several-to-many sources. They can make a living out of this because they can deliver thousands of readers to advertisers.  There are also hybrids who write original stuff but also read and re-post.  And of course HarryPotter rules apply: some blogs have been around a little longer or are a little bit more interesting/readable and they get a million times more page views. The blogosphere is probably a moribund medium - hot sexy people are using different modes of communication.

If the blogosphere is dead or dying, the carcass is crawling with bloody blogoparasites who batten on to this creative stew and make a living by selling advertising placement with very limited expenditure of effort but huge cost to the groaning infrastructure of the internet - very much like spam. Spam is now so effectively filtered out of our mail-boxes by Gmail and Yahoo that we don't realise (or care) that 70% of all e-mail traffic is comprised of this nonsense. 

I allow, indeed encourage, people to add comments to my posts on The Blob.  So I was delighted a few months ago when someone wrote a flattering comment and invited me to visit his page.  That page was trying to sell Venetian blinds and I was at a loss to explain what we might have in common.  I get so little traffic (haven't gone viral yet . . . must . . . go . . . viral) that I read all the comments people write.  Then a few weeks ago one piece of my deathless prose about Milk O'Magnesia, written many months ago, started to attract a certain amount of interest.  I thought at first it was because somebody had tweeted the post or put a link on their Friendface climbing-frame.  Then I found numerous comments on the post by Anonymous:
Anonymous has left a new comment on your post:
And it generates a higher harvest of the foods involved. In fact, everyone will discover this activity enjoyable and rewarding. The sky really is the limit using the type of fish you can grow (provided you'll find no bans on doing so). Also visit my web-site: aquaponics
Anonymous has left a new comment on your post:
Inspiring story there. What happened after? Take care!
Take a look at my website; corel draw.com free download (http://Vodent.com/?p=2755) 

WTF? What does it mean?  It's clear that English their first language is not. And the second comment is so generic that it will make someone somewhere click through to Vodent.com or the Venetian blind place I mentioned earlier.  Why are these parasitic cretins invading The Blob? They must have a robot which sniffs out blogs which allow anonymous comments and they must be selling their services to the people who have a product to advertise or sell.

Other posts on The Blob have now gotten similarly infected and I have had to a) disallow anonymous posts there and b) change the URL of the post.  That's a bore, it means that Google is going to have to find me afresh and my ambitions to be the Bieber of the Blogosphere are (for the moment) thwarted.

Saturday 28 December 2013


I returned to Ireland in 1990 funded by a retraining fellowship that was designed to re-package biologists from out-moded disciplines as biotechnologists.  Up till then I'd been a population geneticist which in the 1980s was at its nadir of interest and novelty.  My gaffer-to-be and I made a case that bioinformatics was a subset of biotechnology, so I was excused from ever having to flip open an Eppendorf; which act had previously led to one of my NDEs.  That retraining fellowship, intended to last a year and facilitate repatriating The Boy to his natal city, grew into a career that has kept me continuously in employment since then.

In the early 1990s, the operating system of choice for bioinformatics was called VAX/VMS a proprietary software interface with DEC computers. DEC's VAX computers had become the de facto standard by beating the competition in a HarryPotter winner-takes-all race.  The attempts of another company to wrest some of the pie from DEC's grasp in the early 1980s is detailed in Tracy Kidder's brilliant, gripping book The Soul of a New Machine, which you'd be better off reading than this, shorter, historical memoir.  I got to know quite a lot about VAX/VMS in order to load updates of the DNA database when they arrived and make them accessible to users.  But abruptly in about 1993, everyone I knew in the world of bioinformatics switched to UNIX based operating systems and I was back at the bottom of another skill-set tower-block which I was obliged to laboriously climb.  We were still using DEC computers, which were still running VMS, but the company offered UNIX as an alternative O/S.  As ever, I followed the herd because I was never going to be competent enough or confident enough to go it alone.

Meanwhile in another corner of the pre-WWW internet a chap called Linus Torvalds was developing a free version of  UNIX which was called Linux, partly after the author. He was another member of the finlandssvenskar or suomenruotsalaiset, born in Helsinki on 28 Dec 1969, so in 1990 he was a young chap writing up his MSc with a thesis "Linux: a portable operating system".  His parents, student lefties, claimed that they named him after peacenik and Nobellist Linus Pauling.  Linus himself claimed that he was named half for a "Nobel-prize-winning chemist" and half  for a "blanket-carrying cartoon character". Which suggests that he is fundamentally a nice bloke with a sense of humour.

The Linux business model has been that lots of people developed modules and features of the fundamental operating system and these were incorporated and made internally consistent, so that it did everything you'd ever wished for in an O/S.  If it lacked some function you could write it yourself and send it in.  Every line of code was visible if you wanted it to be, so that made further developments much easier.  It is extremely likely that the server which is handling your access to the internet, and another which is hosting this blog are both running some version of Linux.  Because of this radical community-centred project is offered free, Linus Torvalds will never be as rich as Bill Gates. Linux buffs have a tendency to the messianic in their comparisons with MS Windows but lots of companies are making a profit and employing lots of people delivering the basic operating system in a way that is as easy to operate as Windows.  But for old stagers like me there is always the option to run programs and make changes from the keyboard without tricking about with a graphical user interface (GUI) or the mouse.  They say that Torvalds is now only responsible for about 2% of the lines of code that make up the operating system named after him.  He is nevertheless among the most significant individual contributors - that indicates how big is the community which serves the servers.

Friday 27 December 2013

Turing Test

I mentioned Chuck Yeager in passing while giving tribs to Jeana "No Relation" Yeager.  Before he broke the sound barrier he'd been a fighter pilot in WWII.  I think we might now follow the Russians and start calling the catastrophic early 1940s The Great Patriotic War Великая Отечественная войнаas as we move relentlessly to simplify history into black and white.  After being given orders to shoot-up anything that moved, Yeager whispered to a neighbouring pilot "If we are going to do things like this, we sure as hell better make sure we are on the winning side".  Amen to that.  Dreadful things happen during wars and the evil in the tale is never limited to the Other (losing) Side.

Alan Turing was given a retrospective pardon on Christmas Eve.  He broke the law just over 60 years ago and was given a particularly repellent punishment .  Having been convicted of  'gross indecency' (as The Man called normal homosexual behaviour back then), he opted for 'chemical castration' by being pumped full of a synthetic estrogen rather than being banged up in chokey like a normal con. Having lost his libido and gained a pair of breasts, Turing engineered himself a fairy tale death a couple of years later by consuming a poisoned apple.  The specificity of the punishment reminds me of stories I've been told about bizarrely detailed punishments meted out on children in Irish secondary schools in the 1980s.  One colleague of mine spoke of a classmate being compelled to sit in an open Georgian window in such a way that, when the teacher shut down the sash, it made contact with all the little perp's vertebrae as it came down.  How could a normal person set that up, in all its precision?

The Turing Test was one of Turing's several Great Ideas.  If we cannot distinguish the responses of a computer from those of a human being, then the TT claims that artificial intelligence AI can be considered to have occurred or been achieved.

Shabby and psychotic as the punishment of Turing was, there's something not quite right about his exoneration this week.  It's an easy option that makes most of us feel good about ourselves.  One of the issues that made me queasy was the fact that "we" had committed this grossly indecent act on a man who had been so useful to "us" in The Great Patriotic War.  By exonerating him in 2013 we are condemning our own grandparents for being who they were at that time.  It is not conceivable that we are better or more ethical or less cruel than people 60 years ago - evolution just doesn't happen that quickly. Getting up a petition for righting the wrong doled out to Turing is about as difficult as awarding another honorary degree to Jocelyn Bell-Burnell or Barbara McClintock.  The first petition was rebuffed by the then Minister of State for Justice Lord McNally: "However, the law at the time required a prosecution and, as such, long-standing policy has been to accept that such convictions took place and, rather than trying to alter the historical context and to put right what cannot be put right, ensure instead that we never again return to those times".  I think I agree with that position.  It takes rather more courage than the current shower of politicians possess to refuse such a petition because, however worthy its aims, it is conducive of hypocrisy and smugness. Whatever next? A petition to undead innumerate homosexuals who went up the chimney in 1940s concentration camps?

So here's another Turing Test that we can all, with advantage, use more often.  Before you condemn someone in another place, another time, another set of particular and peculiar circumstances, ask yourself how you would have behaved if you had been there, then.  We can't all come out shiny-white if such a spotlight is turned upon us.  After that, we can turn the spotlight on the invisible unconsidered certainties that we hold today but which will look crude and cruel to our grandchildren.  Now that's difficult; that's a challenge worthy of our attention.

Thursday 26 December 2013

Caldo verde

As Thoreau had it "Our life is frittered away by detail. Simplify, simplify, simplify!"  There is something to be said for fritters (anything fried is good after all) so long as they are not filled with Spam. We used to get Spam fritters for school dinner and even then, as a starveling, I knew there was something wrong about the inside of those things.  So let's concentrate on the simplify, simplify.  I thought about this as I tucked into a humble supper after the slap-up feed that marked the end of term at The Institute.  Even having opted for the goat's-cheese quiche at lunch, there was a lot more saturated animal fat than I'm used to at lunchtime. I felt this in spades last night after a traditional Irish Christmas meal mid-afternoon.  When you have three generations of competent cooks there is likely to be more food than can be consumed at one sitting. And when it is all mmmm so good, it's very hard to hold back. So there were a couple of hours between dessert and bedtime when I felt like a hyena (Crocuta crocuta) who has scarfed down so much gazelle (Eudorcas thomsonii) that he just can't move.  But that feeling passed in time for cold ham&pickle sandwiches to help make bearable watching Morecombe & Wise and Stephen Fry on the telly.. The humble supper, alluded to earlier and thinner, was caldo verde: a soup I came to relish during my walk up the coast of  Portugal in 1989.  (Almost) nothing to it:
  • water água
  • potatoes batatas
  • kale couve manteiga
  • onion cebola
  • smoked sausage lingüiça calabresa defumada
  • olive oil azeite
After trogging 20km a day along the beaches and cliffs of the Atlantic coast, often I was only capable of slumping into a seat and croaking "caldo verde pelo amor de deus".  Because everyone has it on the menu, it was always available and always piping hot.  After half a bowl of this, my equanimity (and my manners) would generally return and I was ready to order a glass of wine and a plate of carne de porco assada or bacalhau à brás.  But several times, the caldo verde was so damned good I just ordered up another plate of it, and devil take the glances from the staff at the restaurant. Also note that the sausage can be a tiny fraction of the whole, only a little more than the dash of salt&pepper; just enough to lift the whole dish to heaven.  I'm with Thomas Jefferson on this, a man who ate meat only as a condiment to the vegetables which constitute my principal diet.”

But you don't want to get doctrinaire about diet, particularly not at Christmas. Pass the ham, please.
Our life is frittered away by detail. Simplify, simplify, simplify! - See more at: http://quotationsbook.com/quote/36353/#sthash.eGWjNb0v.dpuf
Our life is frittered away by detail. Simplify, simplify, simplify! - See more at: http://quotationsbook.com/quote/36353/#sthash.eGWjNb0v.dpuf
Our life is frittered away by detail. Simplify, simplify, simplify! - See more at: http://quotationsbook.com/quote/36353/#sthash.eGWjNb0v.dpuf
Our life is frittered away by detail. Simplify, simplify, simplify! - See more at: http://quotationsbook.com/quote/36353/#sthash.eGWjNb0v.dpuf

Wednesday 25 December 2013

Christmas greetings

Christmas lullaby on youtube
I hope you grow up angry
Just like your dear old dad
I hope you grow up brave and strong
Not like me - all weak and sad
You said "Daddy, daddy,
You're stinking of booze"
I kissed him and said, "Kid,
I was born to lose.
But you have a future
And a big one to say
And I hope you'll remember
All the love that I gave
Shane McGowan was born on Christmas Day 1957, and is still with us, possibly because he is now pickled entirely from the dhrink.  He is reliably on the wireless at this time of year singing Fairytale of New York with Kirsty MacColl, who is regrettably no longer with us having been killed in the year 2000.  But I think his Christmas Lullaby, while not easy, is good for the day that's in it.

Happy Christmas.  щасливого Різдва, Счастливого Рождества, Nollaig Shona duit.

Tuesday 24 December 2013

Christmas Decorations

Some people have me pegged as a Bah Humbug Scroogy sort of bloke when it comes to what I call the Festival of St Mammon.  Years ago, if I hadn't been holding down a full-time job, I'd have made some sandwich boards emblazoned with "Put Xmas back in December where it belongs" and trudged up and down Dublin's principal shopping streets every Saturday in November.  Because, even 20 years ago,  hucksters and merchants started selling stuff immediately after Hallowe'en.  All the WEA academic institutions I've worked in have shut down for at least 10 days from about 23rd December, not opening again until after New Year.  That's a week of productivity (2%!) lost every year: insofar as you can apply commercial concepts of productivity to universities.

I reserve a good pot of spleen for the 21st Century concept of a Kris Kringle (aka Secret Santa) which we've bought into from the Americans.   One of my students at the Institute said that this year his family - parents and eight childer - were going to do Secret Santa to save a mort of money and prevent them all going together when the youngest upsets a candle to start a conflagration of wrapping paper. That's an excellent idea for that family and the planet. I reckon there is no point in doing a Kris Kringle with your colleagues at work unless you're going to be cruel.  The process is in any case rarely secret because it is usually organised by the departmental busy-body who then knows who gave what to whom. That's another reason to rein back on the cruelty, which is best savoured when the victim has no idea who is twisting the knife.  In 2001, I drew myself for the first KK I'd ever been thrown into.  The next day I hunted out an Olde Fashioned Sweetie Shoppe and bought 100g of Olde Fashioned Humbugs which I popped into a jam-jar labelled "Bah Humbugs for Unbelievers" and gave to myself at the party.  Recently, I've got out of it by playing the Oufeller card and claiming I'm too old to know what young wans in the 20s would consider amusing and appropriate.

But I do so believe in Christmas!!  Gifts for small children, a generous cheque from Uncle Jim, midnight mass, saturated animal fat, roast potatoes, ham sandwiches and rissoles, too much wine, falling asleep after dinner, more food . . . these are all good indulgences as the days inch out a little longer.  So on Sunday, we (mostly Dau.II) decorated the Christmas Twig and  I also repurposed the Fruits de Mer to bauble-up one of the old leggy apple trees in the orchard.

Ho Ho Ho.  I'm clearly getting into the spirit of things.

Monday 23 December 2013

The Right Stuff

So long bro', I'll see you before Christmas!  That's effectively what Dick Rutan said to his brother Burt as he and his co-pilot Jeana Yeager flew East away from the coast of California on 14th Dec 1986. They were still flying East when they returned 9 days later in time for breakfast on 23rd December.  They had just flown round the world.  In doing this they had pushed the envelope of physics, of design, and of the human spirit.  Yeager is no relation of Chuck Yeager who had a starring role in Tom Wolfe's book about the Gemini astronauts The Right Stuff.  That Yeager never made it into space but he was the first (or second?) person to fly faster than the speed of sound. People, engineers even, thought it was possible, probable even, that the sound barrier could not be crossed without destroying both plane and pilot: that's why it is called a "barrier" rather than something neutral like "transition" or "1300km/h".

Jeana Yeager met the Rutan Brothers in 1981, when she was 29, at an Air Show because they were, all three of them, barking when it came to flying.  Over lunch they designed an aeroplane to break the record for flight time on a single load of fuel.  That stood at about 20,000km: held by the crew of a USAF B52 bomber since 1962.  Burt Rutan was sure that he could design a plane that would double that record to fly round the world which is, by definition, 40,000km in circumference. Yeager was an accomplished draughtsman and could translate a sketch on a napkin - no kiddin', that's where they roughed out the design - into engineerable parts.  Jeana and Dick fell in love with each other as the three of them threw themselves into the project that came to be called Voyager.  It took more than five years to get the design off the napkin and finally into the air for the big trip.  It takes a huge amount of determination and follow-through to get such a project to bear fruit.  In the end they got through $2million of their own and donated funds and mobilised scores of volunteers who put in 22,000 hours actually building the machine.

This pic is a bit pixellated but gives some idea of the unconventional design that Rutan came up; a regular 4-seater Beechcraft Duchess plane is included for scale.  Voyager had a wingspan of 33m which is about the same as a Ryanair Boeing 737 which is able to carry 200 people rather than just 2 crammed together in a cockpit the size of 3-seater sofa without the cushions, let alone a t'ilet. It weighed just over 1000kg empty, about half of which was the two engines, but had more than 3000kg fuel on board.  Where on board?  The plane looks like it's made from pencils but the wings and the nacelles are as hollow as the structural engineering requirements allowed.  Voyager could get airborne but was a pig to drive especially when over-laden; the front 'canard' wing was a kludge to stop the thing stalling. A few weeks earlier a blade from the propeller had whacked off on a test flight and, as they only had one toy to play with, they were unable to load-test the structure but just had to believe the engineering specs.  Compounding the engineering worries, Jeana and Dick's relationship had stressed out and come apart at the seams three months before The Off but neither was going to cede their seat in the greatest adventure of their lives.  The round-the-world flight-plan required 225hrs air-time.  Up till then, the plane had only spent 300hrs aloft and during that time had experienced 7 major emergencies.  The team was betting that no/nul/zip/zero/nada emergencies would occur in the next 200 hrs - see what I mean? Barking!

You have to have a heart of stone if your spirit doesn't lift as Voyager finally perks up her wings (watch!) and takes off after lumbering along the runway for a nail-bitingly long time. Before the perk-up, those fuel laden wingtips had been dragging along the tarmac, not only slowing the take-off but also sanding off the outer layer of kevlar and carbon-fibre. A normal person would have aborted the flight at that stage but so much had been invested in the project that nobody was keen to do so.  Not least, I suspect, because the plane was known to handle badly when heavy and pilot weren't in a hurry to come down again surrounded by 3 tons of aviation spirit.  The Duchess chase plane took off with Burt aboard to have a look at the damage and concluded that it was symmetrical and that it would be best to knock off the winglets (the vertical whoosits on the wingtips) which were hanging by a thread. So Burt advised his brother to accelerate until these parts of design shook themselves loose.  And it was so, and they were OFF out across the broad Pacific, and en route round the globe.

As I say, a few minutes over 9 days later they returned to California with 98.5% of their fuel expended (100km to spare!) and one engine fritzed out because of an airlock in the fuel line.  They had survived, or made long detours to avoid, severe weather patterns (Typhoon Marge pictured) and had been refused entry into Libyan airspace which also required a fuel-depleting detour: 1986 was between the two Gulf of Sidra Incidents  (1981, 1989)  when US Navy jets shot down Libyan warplanes in murky and rather undiplomatic circumstances.

Voyager never flew again but finished up in the Smithsonian National Air and Space Museum, where you can see the abraded wingtips today. "The near catastrophic loss of the winglets on takeoff proved fortunate for us by reducing the wingspan by two feet and allowing the aircraft to fit snugly into the South Lobby."  That's the kind of laconic competence, can-do and make-do that makes American engineering ingenuity the envy of the world.  What Rutan, Yeager and Rutan achieved is so far beyond the walk of ordinary folk that envy is hardly appropriate - I don't know about you but I feel awe and a head-shaking wonder that such hubris and monomania lucked out and won through.  Nevertheless, hats off and a sweeping bow to them.

Sunday 22 December 2013

Christmas twig

I was taking, I suspect, the high moral ground about Christmas songs.  Must be less Tannenbaum judgmental!  The first Christmas we spent together was two weeks after The Boy was born back in the 1970s. We'd rented a tiny garden flat over-looking the East Pier at Dun Laoghaire and had very little left after the rent (£60 pcm, as you ask) was paid.  But things were much simpler then and the spuds, carrots and cheese we lived on didn't cost much.  On the 23rd we hadn't a tree, partly because the only ones left were motheaten-scrawny and mostly because there was no room - it was either a tree or a table to eat the dinner off.  So on the morning of Christmas Eve I sneaked out into the garden and sawed a small branch off a shrubby tree that had struggled out of the cinders and broken bottles to a meagre existence up against the back wall.  I brought this back inside and jimmied it up so that, if you squinted, the twig looked like it was growing through the wall from outside.

We were the first of our circle to try a spot of reproduction and our friends had been generous to the infant: some stuffed toys and a few plastic knick-knacks, as well as some very gratefully received small clothing.  The toys were looted and re-purposed as tree-ornaments and I think we may have cut some other stuff out of cartridge paper.  I know a red plastic key was detached from a teething ring and hung up and some unlikely creature finished up on the highest point to act the fairy.  I won't belabor the point but our humble make-do Christmas had something in common with an earlier event where a manger was re-purposed as a cot.

Red Key still with us
So that became our tradition: wherever we were in the run-up to Christmas I went out and cut a branch off a tree somewhere and strung it up in a corner of the living room.  The tree's roots were sufficiently developed that the lost branch could be replaced with a few month's photosynthesis during the following growing season.  This is not true of the misfortunate, exploited noble fir (Abies procera) which is the usual Christmas Tree, and has a single use life-time. It is a metaphor for all that is wrong about our current economy - buy something; use it once; throw it away; buy another; money is made and bugger the planet. For several years since we moved up the mountain we've left the twig up (it's all good fun until someone loses an eye) after the decorations have been boxed up  . . . and it's been still up the following December. But I'm getting old now and I've passed this baton down a generation.  Accordingly, during a gap between the blustery showers yesterday, Dau.II went out with a pruning saw and, in consultation with her mother, brought back a horizontal hazel (Corylus avellana) branch.  It's still got catkins, so is wholly suitable as a regenerative metaphor for the turn-of-year.  We're waiting for the return of Dau.I today to decorate it.

Saturday 21 December 2013

Living with narcolepsy

I posted a double---header on the science of narcolepsy and cataplexy about a week ago.  But I didn't really absorb what it must be like for those who have it.  The Beloved's big sister e-mailed me last night with a message sufficiently cryptic that I was googling all around me to find out what she was on about.  That's how I finished up watching this short documentary about Dave the Narcoleptic.  He's been living with it for so long that he doesn't think there is any real problem; then in mid sentence he falls asleep standing up and tumbles rag-doll 10m down a wooded embankment.  He dusts himself off and continues - he's just had another of his time-jumps.  That set me off to another micro-documentary about/about Casey the Narcoleptic/Cataplectic. When she falls asleep walking through a canteen, she carries away a table and two chairs; and that made me wonder how often she lays her head into a concrete post (whump) as she falls asleep.  We can to see her laughing herself to sleep to tick off one of the five key symptoms (muscle weakness under conditions of emotional overload). Casey then itemises the things she can't do, including: basketball games, ride a bicycle, drive a car, swim, engage in 'intimate relations'.  I'm just surprised Dave and Casey aren't covered in bruises and stitches.

Century of crosswords

On this day, the Solstice, exactly 100 years ago, Arthur Wynne designed a word-cross puzzle that was published in the New York World. It was the sudoku of its day and the idea was widely propagated until just about every newspaper in at least the English speaking world will include one somewhere in  its pages.  I've made up a few of these in my time, for events or for the hell of it.  The Easter egg hunts with which I tormented my children owe a lot to a lifetime to doing crosswords - my mother taught me the basic conventions of British-English cryptic clues before I reached double digits.
The Arthur Wynne Memorial Word-Cross
01ac. 1781 Planet            01dn. Closed
04ac. Primary virtue         02dn. Unspecified place
09ac. 8/9 water              03dn. Extraterrestrial
10ac. One going forward      05dn. 940 Lenok submarine
12ac. R-O-R' chemical        06dn. Sturm und ?
13ac. Our 4th closest relly  07dn. Joe Kraus 1994 startup
15ac. Our day will come!     08dn. S (aa)
16ac. The only home we have  11dn. Phoenician deity
17ac. Sinaasappel.nl         14dn. ENSG00000100503
22ac. The universe of Cthulu 18dn. 42
24ac. Causes Lesch-Nyhan     19dn. from GAG or GAA
27ac. Khmer temple           20dn. palpable, material
28ac. Radio reflecting layer 21dn. El Asturiano
31ac. Found '94 by Wm Ramsey 23dn. Tashkent IATA
32ac. Remembered             25dn. diff.betw. proton/neutron
33ac. Graphite and diamond   26dn. Sharp medical journal
34ac. American hormone       29dn. Cosy for inuit
35ac. Shipworm               30dn.
Ειρήνη Σαρανταπήχαινα
Answers on New Year's Day (if I remember). Solstice: things are getting brighter from now on.

Friday 20 December 2013

Venting some heat

The Boy, after educating himself, is now a railway engineer - signalling - working in the West of England. He'd have a different job if it wasn't for structural engineers like George Stephenson, who built the Leeds and Manchester railway between 1937 and 1841.  We've met him before at the birth of railways.  At that time Manchester (in red-rose Lancashire) and Leeds (in white-rose Yorkshire) were leading the industrial revolution in Britain as Britain led the world.  The Wars of the Roses are still fought on the footie field in historically correct shirts (red for Lpool and Man U, white for Leeds).  These two great cities are on different sides of the Pennines, a range of hills that runs up the spine of North-central England and that makes communications a little difficult.

Stephenson followed the route of the existing Rochdale canal but at the highest point he chose to drive a Summit Tunnel through 3km of the hill-top - you can't run trains like canal barges up through a stair-case pf locks.  It was in its day, the longest tunnel ever driven, a massive engineering feat: dug by pick and shovel through a geological slice of coal, shale and sandstone which are all comparatively soft.  To keep the tunnel on track a series of shafts were surveyed and sunk vertically from the ground above
You can still see the chimney tops of these shafts today because they were left open to vent the steam from the many passing trains - it was designed as a two-way tunnel, so busy was the route anticipated to be.  Shale and sandstone are easy to dig but also tend to collapse and to prevent this Stephenson lined the inside of the tunnel with 6 courses of bricks laid with "Roman" mortar that would tolerate the weeping damp that was also foreseen.  6 onion-layer courses of bricks over 3km amounts to 23 million bricks laid at a maximum rate of 60,000 a day.  The bricklayers were working by candle light for 9/- to 11/- (that's shillings @ 20 to the £) a day. That's cheap, as were their very lives in those days before Health & Safety - 41 men died, almost exactly one a month on average, in the construction of the tunnel. Which is a little ironic in that Stephenson is quoted as saying "I stake my reputation and my head that the tunnel will never fail so as to injure any human life".  But they did good work those craftsmen, even if some said that the brickwork was rather over-engineered.

The bricks were certainly put through a stress-test (short youtube) on 20th December 1984 when a train loaded with a million liters of petrol derailed in the tunnel and ignited. The train-drivers were able to decouple the first three tanker-cars and drive them out of the tunnel, and the fire-brigade were on the scene from Manchester and West Yorkshire very quickly but they had to deal with something like 500 tons of burning fuel in an awkwardly confined space.  They tried to hose down the fire until they saw the heat of the flames spalling off the outer layer of bricks. As the temperature rose, the safety valves on successive trucks opened and more fuel was discharged.
The firemen then retreated and tried to starve the fire of air by pumping foam down the ventilation shafts. This worked to a certain extent: the hot vaporized petrol whoomphed at 150km/h up other shafts where it ignited on striking the fresh cold air of hilltop.  Flames 50m high ejecting burning detritus and white-hot melting brick must have made the hillside look like Mordor as it set fire to swathes of the vegetation. It was conflagration far greater than Los Alfaques (only 20 tons of propylene) but perhaps less explosive than Sailor Hat and nobody was killed. The bricks melted off the lining of the shafts into heaps on the rail-bed.  BUT, the structural integrity of the tunnel was preserved and eight months later the railway was again open for business. Hats off for engineers.

Thursday 19 December 2013

clap ... clap

I was coming back from work last week when I heard Dr Derek Freedman interviewed on RTE's Drive Time With Mary Wilson.  You can get the thrust of the interview's information on the Indo. Freedman is the Sexually Transmitted Disease/Infection STI bloke in St James's Hospital in Dublin. Apparently he pushed hard for condoms to be available from vending machines in pubs and clubs.  And it is now so.  So thank you Dr Freedman.  Freedman was being interviewed because the STI statistics for 2012 were out and gonorrhoea was up 33%.  Wilson was brought up sharpish by Freedman when she implied in the most oblique way that sex was bad. Freedman grew up in an Ireland where that was true and he wasn't going to have any of that nowadays: he made it clear that sex was fun and generally a Good Thing.  He then went on to deplore the fact that a disease that was treated with expedition and effectiveness by, say, a short course of oral penicillin now requires "injectable gentamicin 240 mg combined with oral azithromycin 2 g showed 100% effectiveness".  I ranted about how the casual use of cheap-and-cheerful antibiotics for "trivial" infections has rendered them obsolete for STIs and other life-threatening infections. Hence the slow hand-clap in the title. But try telling a parent that their infant's ear-infection is trivial. For my Russian and Ukrainian readers, I should explain that The Clap is one of numerous English synonyms for gonorrhoea,; The Pox is usually reserved for syphilis.

Gonorrhoea is caused by Neisseria gonorrhoeae which is closely related to Neisseria meningitidis one cause of bacterial meningitis.  Whatever about treating a case of the clap, there is some urgency in dealing with infection of the lining of the brain.  Years ago, The Beloved's brother went in to see the results after his business partner's wife died of meningitis and strongly advised the husband not to go view the body.  It's the stuff of nightmares.  Another issue is that if you have acquired Neisseria you have quite possibly acquired Chlamidia at the same time which is also a Gram-negative bacterium but susceptible to a different range of antibiotics.  In Ireland Chlamidia is 5x more common than Neisseria and 10x more common than Treponema (syphilis).

But back to Freedman, who seemed positively avuncular in his good-will towards those who have made a wrong call up against a wall outside a disco but firm in his belief that the consequences had to be faced up to.  He has been positively cited in a discussion about where to go for help/advice/treatment when you suspect you may have acquired a dose.  That discussion is interesting because of the dilemmas that folk face - your own GP may be obliged to shop you to insurance companies; everyone knows why you're going to visit a STI clinic; GPs don't really know enough; nurses at STI clinics are really supportive etc etc. Freedman's advice is both before and after. First off he acknowledges that drink can fling sense out the window for 'before', but urges us to be especially careful with people we don't know well.

"What constitutes safe sex? Knowing your partner, at least their first name and phone number. Starting any relationship with a condom and keep it on until you know them really well. "Going bare is something special for somebody special." Give breakfast. At least then you can talk and get to know the person you have just been with. Like any sport a return match is proper etiquette and it gives you both an opportunity to meet again without the overlay of alcohol, and to see if it is worthwhile going on with." From below the break in the Indo Article.

For 'after' the advice for worried punter and for health care practitioner his advice is quite stern and uncompromising:
  • keep yourself in your trousers until you get a clean bill of health
  • wait a week for things to incubate
  • get all your orifices checked out (this is no time to be shy - you weren't last Saturday)
  • get a blood test as well
  • get an appropriate course of treatment
  • get rechecked after 12 weeks
The characteristic discharge isn't always present especially if the infection is lodged in the throat or what doctors refer to as the back passage.  For us horse-riding protestants, the back passage is the corridor between the kitchen and the wine cellar where we used to down the old jodhpurs and roger the maids.  For some more down with the hood advice in more direct language ('back passage' is here 'bum') look to SpunOut the not-for-profit website created by young people for young people. And for the attention limited Tweeting generation, just get the T-shirt: "Gonorrhoea: hard to spell, easy to catch"

Wednesday 18 December 2013

Masters of Imm

Although The Institute wound up its teaching term last Friday, there was still teaching to be done.  So I spent Monday and Tuesday up in The Smoke doing four sessions on molecular evolution for the almost new MSc in Immunology.  I've done similar courses before when I was supplying bioinformatic infrastructure to the plain people of Ireland back in the last century. It was on my feet for 5 hours on two consecutive days but at least I know now NOT to kneel on the floor when getting down to the level of a student working away at a computer. If you do this in your youth, you'll finish up with chippy's knee and barely able to walk long before the end of your working life.  I had primed the students (N=19) to come with a gene of interest to work on.  So the first day they discovered where and on which chromosome their gene was located but also where the equivalent gene in mouse could be found. They found out the size and some of the functional attributes of the protein that came from 'their' gene.  But before all that I gave them a pre-quiz: asking them questions to which they would more likely know the answer after they had completed my course than before. Q4: put these five biological entities in order of size
  • glucose
  • T-cell
  • mitochondrion
  • T-cell receptor
  • hypothalamus
I was relieved that almost everyone got almost everything correctly ordered.  This is different from many students at The Institute who don't seem to care/grasp that a molecule (glucose, T-cell receptor) is smaller than a sub-cellular organelle (mitochondrion) which is smaller than a cell (T-cell for example) which is smaller than an organ (hypothalamus, adrenal gland, kidney). On the second day, I asked them to estimate the relative sizes (chekkittout!) of each of the 5 objects.  Sure now, a T-cell receptor is part of and so smaller than a T-cell; but how much smaller?  A little of the "that's easy" confidence drained away because nobody could confidently tell me about how big a cell is tsk! let alone tell me how big its TCR receptor is.  Probably only half of them could instanter recall the formula for calculating the surface area of a sphere from its diameter.  The ratio between the diameters of the T-cell and its receptor is 1:5000 or this . to a large beach-ball.

The other task I gave them on day I was to name the 20 amino acids that are produced by the "Universal" genetic code: this was an obvious task because there were 19+1=20 of us in the room. The quality of this student cohort is indicated by one of them briskly pulling me up on the "20 amino acids" because she knew that in some species in some circumstances the UGA 'stop' codon is induced to produce the 21st amino acid selenocysteine.  I opened a box of chocolates, threw down a couple of markers and said they could have a sweet IF they could write the three-letter code for any of the known protein amino-acids. The quality of this student cohort is indicated by one of them asking me about taurine which is (almost) an amino acid which led to a brief discussion about other amino acids (ornithine) that have key roles in biology but not in building proteins.  It was very brief because there was an unseemly scrum of students round the white board fighting for access to markers and chocolates.  The tide didn't go down until all the dupes had been removed and the last amino acid had been identified. The quality of this student cohort is indicated by the fact that they stuck at it until they had solved the problem to their own satisfaction - the chocolates were entirely incidental.

The next day, I gave them a bit of a harangue because it's one thing the know the name of 20 somethings but that's only useful if you know their attributes - which are big, which small, which basic, which hydrophobic.  If they remember nothing else from from the day, I hope that they will have internalised Willie Taylor's Venn diagram: it is key to making sense of protein sequence data. 

These people, from all over the world but currently in Dublin, are hot.  If you senior guys in Kiev "Привіт колеги" are looking to hire bright, engaged, competent young scientists you'd better be putting a competitive package together: there are only 19 currently available.  If you young guys "Привіт прохолодні молоді люди" in Kiev are looking for a great taught Master's Program, I look forward to meeting you next year.

Tuesday 17 December 2013


Film-buffs and horsoholics may believe there is only one Trigger: the "Four-legged Friend" of Roy Rogers, but triggers feature prominently in the world of immunology and cancer.  Humans, and mammals in general, are so robustly healthy most of the time because of redundancy built into the immune system - if one ploy fails to block a pathogen, then another is waiting in the wings. But sometimes the immune system is too clever by 'arf and over-reacts.  Then you develop an autoimmune disease as the mechanisms used to attack 'foreign' cells suddenly turn on cells that have up to now been recognised as 'self'.  Clearly this doesn't happen every day or we'd ALL have lupus (SLE), rheumatoid arthritis, type I diabetes, or Sjögren's syndrome.  Whereas lupus is only really common in alternate episodes in boxed-sets of House.  One way of explaining the incidence of these troubling conditions is that you have a genetic predisposition like DQ0602 which I mentioned yesterday, and you're okay for years and then some environmental challenge jumps the immune system off the rails. You get a flush of the runs after ingesting Campylobacter jejuni from a dodgy chicken pie and your immune system mops it all up over 3-4 days. Guillain–Barré syndrome occurs because a few days later your immune system, all hyped up and spoiling for a fight, occasionally recognises or imagines a structural similarity between something on the outside Campylobacter and something on the outside of peripheral nerves. The nerve damage may take years to recover if it ever does.  It's Lombard Street to a china orange that something similar is involved in multiple sclerosis (MS), but we haven't identified the trigger there (the smart money is on a virus).

Yer takes yer chances in the rough old world of infection and immunity; sometimes you get a bad break.  But now you can choose to stack the odds in your favour in this desperate lottery by getting immunised. About 1 million people played this card in Ireland (22.5% of the population of the Republic) to avoid getting the H1N1 'flu that was certain-sure going to go pandemic in the winter of 2009-2010. They were injected with a vaccine called Pandemrix. You can see from the graphic that the urgency of the programme abruptly went off the boil for the last week of 2009, where protection from a life threatening illness took second place to having a Christmas knees-up (most of us) or lie-down (the poor overworked health-care professionals).  Some of those million immunized people may have therefore not gotten 'flu, not spent days in bed or in hospital, not died.  So that's clearly a good thing.

But in the relevant period 32 people started showing symptoms of narcolepsy.  You really wouldn't expect so many cases of this rather rare condition to blip up the HSE statistics in such a short time.  So Darina O'Flanagan and her colleagues at the Health Protection Surveillance Centre (HPSC - our equivalent of the CDC in Atlanta) carried out a retrospective study to see who had recently come into narcolepsy and whether they had been 'flu jabbed (N=30) or not had the jab (N=2).   In young people aged 5-19 the risk of narcolepsy was, from these figures, calculated at 5.7 per 100,000 person-years for vaccinated vs 0.4 per 100,000 person-years for unvaccinated: 14x more likely to get this condition if you have the jab.  But still extremely unlikely to get the condition.  81 cases of narcolepsy were revealed when notes were compared with Sweden and 79 cases when Finnish data was considered: the odds up North were similar to those in Ireland.

The vaccine Pandemrix was invented by GlaxoSmithKline GSK and patented in 2006, it consisted of an antigen from an H1N1 strain of influenza virus, an 'adjuvant' called AS03 and some preservatives. Adjuvants are often added to vaccines to goad the immune system into a response: inorganic alum (aluminium sulphate) has been used for decades for this purpose.  It looks like the immune system of the vanishingly small fraction of youngsters, who had the jab AND THEN developed narcolepsy, goes on the rampage and attacks the part of the brain that produces orexin.  Presumably they are DQ0602 positive  for starters.

These unfortunate narcoleptics were in the news last week because an apparatchik (аппара́тчик) from the megalithic Health Service Executive HSE (of which HSPC is part) issued a diktat to say that these affected narcoleptics couldn't have their legal costs (of their suit against the state) covered by the state . . . and he was promptly over-ruled by the head of the HSE: probably because The Boss recognised a public-relations disaster when it jumped up and bit him. 

Who to blame? There are plenty of lawyers who will, for a cut, offer to sue the State, the HSE, the Department of Health, and GlaxoSmithKlline and Uncle Tom Cobbley to vindicate the rights of these people and indemnify them for the results of their mis-call in the matter of whether to have the jab or take their chances with the 'flu. Do I hear you cry "moral hazard" you uncaring brute? The cases are so rare that they would be impossible to pick up in any reasonably sized epidemiological study carried out by GSK before they released the vaccine to the public.  And here's another thing: there is evidence from China to suggest that, regardless of vaccines and GSK, by contracting a dose of H1N1 flu you are more likely to get narcolepsy.  Whom do you sue then?  Set your lawyers Dewey, Cheatem & Howe on Clotho, Lachesis and Atropos?

Monday 16 December 2013

Asleep on the job

Most of us have fallen asleep in a lecture - the lights go down, the power-points start to flicker past, the voice-over drones and . . .  zzzzzz.  I found it was fatal to eat half of a free sandwich offered to encourage attendance at lunchtime Departmental Seminars - only a quarter and I had a chance of staying awake beyond slide 5/80.   But falling asleep at inopportune moments is only one of the symptoms of nacrolepsy. Distressing as nacrolepsy  is for narcoleptics and their families, its diversity of symptoms opens a fascinating window in how our bodies work in normal circumstances and how every player in the sub-sub-microscopic genetic and biochemical landscape has to multi-task.  We only have 23,000 protein-coding genes to play with after all: about 10% more than Caenorhabditis elegans and that worm is only 1mm or 1000 cells in size.

Perhaps the least expected co-symptom of nacrolepsy is
  • cataplexy - a sudden muscle weakness often under conditions of emotional stress: anger and fear, but also laughter - cataplectics really do tend to go Ha Ha Bonk
Other symptoms are sleep-related:
  • nightmare-quality hypnagogic (falling asleep) and hypnopompic (coming awake) hallucinations.  
  • sleep paralysis - inability to move and/or speak when falling asleep (how scary is that?)
  • a real quick drop into REM (dreaming) sleep.
Then again perhaps cataplexy falls into the same bin because one of the 'symptoms' of normal sleep is loss of muscle-tone.  And the hypnagogic hallucinations could be seen as part of the instant REM sleep - we usually have 60-90 minutes of relaxation before the dream-scape starts in our head. Clearly something or somethings are regulating a lot of quite disparate effects to control normal sleep. And I think we should all be grateful that we forget most of the dreams we have. Seemingly, it's because nighttime sleep is so bitty that the body needs to catch up during the day.

And at an epidemiological rate of 1:2000 it's not uncommon!  That's a little more common than, say, cystic fibrosis (1:2500) and about the same prevalence as Parkinson's and MS; all of which get a much bigger press than narcolepsy.  But a lot of this lies hidden as sufferers and their families cope - I know quite well three people with MS and three other people with Parkinson's but I don't know anyone with narcolepsy despite the fact that there are at least 2000 in Ireland.

Narcolepsy has a clear genetic component, or it wouldn't have an OMIM number, that's for the gene NRCLP1. But it's more complex than that because there are other OMIM entries for NRCLP2, NRCLP3, NRCLP4, NRCLP5, NRCLP6 and NRCLP7.  Seven different genes at different places in the human genome have all been shown to be associated with the condition.  So you can see why scientists get petulant when the press reports that Dr Mephistopheles has found The gene for homosexuality, schizophrenia, gout or any other traits with complex causation (or etiology αἰτιολογία as we like to call it to bamboozle outsiders).

At a molecular level, nacroleptics almost always have greatly reduced levels of a neuropeptide HCTR/hypocretin/orexin (all synonyms) in the brain and the cerebro-spinal fluid.  Orexin is made by the gene NRCLP1, so that's a direct connexion - banjaxed NRCLP1 means no orexin which is known to be the main mediator of sleep and arousal, but orexin also has roles in feeding behaviour, fluid balance, and hormonal regulation.  So far, so not so simple: to switch on the gene that makes orexin must involve a cascade of other genes (probably NRCLP2-7) and if you banjax any of those then you're going to have lower levels of orexin.  This all makes it complex and difficult to a) work out what causes narcolepsy b) how to cure, avoid or treat it.  One factor that seems to predispose is what variants you carry among the HLA Major HistoCompatibility (MHC) genes.  Notably pretty much ALL European narcoleptics have variant DRB5*0101-DRB1*1501-DQA1*0102-DQB1*0602 (known to its friends as DQ0602) but so do 15% of the normal population so this immune variant is necessary but not sufficient. Specific HLA variants are known to be associated with predisposition to a number of different diseases and it turns out that the same DQ0602 that does for you with narcolepsy also protects you from diabetes. There is a suggestion that narcolepsy - which often kicks in during adolescence - starts because an autoimmune reaction specifically attacks the orexin producing neurons in the brain.  That's like rheumatoid arthritis where the capsule of the joints is attacked by the body's own immune system.  But it's more like Guillain–Barré syndrome where the immune system attacks the nerves. That is triggered by exposure to Campylobacter jejuni and common cause of chicken-driven food poisoning.

If this is ringing bells, you might like to contact the narcolepsy support group at
http://www.sleepy-heads.org/; me I'm just glad I don't doze off in the normal oufeller way too often.

Follow on to this.

Sunday 15 December 2013

Not so esperanto

Today puzzle time, for the birthday that's in it.  See how much of the following tribute you can figure out before lashing the whole thing into Google translate.  I've changed colour for some proper-name clusters. If you have a little Latin, you'll find it easier than cracking the Enigma Code.
 Ludwig Lazarus Zamenhof naskiĝis Лейзер Заменгов Leyzer Zamengov en la urbeto de Bjalistoko , en kio estas nun norda orienta Pollando. La urbeto ŝanĝis manojn kelkajn fojojn kaj pleniĝis de diversaj homoj tipa por Centra Eŭropo ĉe la tempo. Li naskiĝis en la jaro de Darvino Origino de Specioj estis eldonita je 15 decembro 1859. Lia uloj estis litova judoj kaj Leyzer parolis Rusa , Jida kaj Pola kiel infano : tre eble ĉiuj samtempe , se la familio de la Amato estas io por iri de. Ili kreskis ĉe alia vojkruciĝo en la Sahelo en Okcidenta Afriko kaj Mashup ilia diskuto kun Hausa , Franca , Araba kaj la Angla. Leyzer poste lernis la Germana, Franca , Latina , Greka , Hebrea , Hispana, Angla, Litova kaj Itala . Liaj samurbanoj en Bjalistoko estis ĉiam ĉe alies gorĝon anstataŭ festi la riĉecon de multkulturaj ebleco. Zamenhof naive kalkulata , ke homoj estis malagrabla ĉar ili ne povis paroli la saman lingvon. Dum 5 minutoj en la kompanio de ia hazarda duono de la loĝantaro estus rakontis al li , ke homoj estas malagrabla ĉar ili estas bastardoj . Tamen , li elspezis ĉiun rezervaj momento de sia laboro kiel sukcesa okulo - doktoro konstrui sia nova Internacia Lingvo , kiu aperis por esti nomata Esperanto - kio signifas plenan de espero en tiu lingvo. Li kaj lia edzino Klara havis tri filojn de Adam , Sofia kaj Lidia . Zamenhof mortis en 1917 , sed liaj filoj estis forkoformajn en la holokaŭsto kaj pereis tie kune kun la tuta kulturo kiu estis nutrata de Zamenhof kaj lia internaciisma sonĝoj. Esperanto estas ankoraŭ ĉirkaŭ , apenaŭ vivas kaj komplete malsukcesis atingi siajn esperplena celoj. Duoble tiom da homoj (560,000) parolas Kimra por komenci. Pardonu Leyzer , bela provo, sed neniu cigaron.

Saturday 14 December 2013

One Cycle

The sing-song yesterday was less excruciating than it might have been.  The scientists all (not all of them mind, but a good couple of dozen) got up and sang together - old and young, students and faculty, admin and technicians.  Regular readers (привет постоянные читатели) will know how important I believe this to be. Then we ceded the mike to the Engineers, the Central Admin, Grade VI and Above, the semi-professional contralto, Father Trendy, and an immensely tall chap with a fine tenor voice.  A lot of folk had donated cakes and cookies, catering supplied warm tea and we all staked up €5 for a poor local wean in hospital.  My HoD was sitting beside me and remarked how much he enjoyed this tradition - one of the few times in the year when the whole family of The Institute got together.  He was only a little deflated when I pointed out that the cleaners were all sitting at that table, the secretaries there, the physicists over there, the biology graduate students next to the buffet (proper place for post-grads) and the Engineers all together as well.  But it is ever thus the world over. There is nevertheless a sense of family about the place - you may not like everyone but you still know them and feel a common sense of loyalty.

After a quick trip back to the office to mark more lab-books we were called back to the canteen for the Retiree's Dinner.  This is free-in and catered by catering. There was turkey&ham or goat's cheese quiche followed by cheesecake or Xmas pud, which I manfully tamped down on top of the scones, short-bread and Dundee cake of the morning.  I asked where were all these Retirees on whose back I had just fed. I had hardly closed my gob on this question when the President stepped up to the mike. She commented on the fact that we are Institute of 2014. I've been quite negative about this piece of unscientific silliness. The Pres claimed that, when the data was being gathered, students from The Institute were asked what was the least good thing about their place of education.  Our lads apparently said "leaving the place when we're done".  If that's even partly true, that indicates that we're doing something right.

Mais revenons a nos retraités.  Anyone who has served their time and retired in the previous year was given an eulogy by their Line-Boss, and a gift from the President as well as a slap-up feed.  It's a Good Thing to say out loud what people may have written on the going-away card earlier in the year.  The recognition and appreciation counts for a lot - offsets the sense of being financially undervalued.  I could well believe the old chaps when they affirmed that it had been the best years of their lives.  It's been my best year this decade: I've now completed one academic cycle.  It's hard to credit what a difference 11 months and 600 contact hours with students of such a wide range of ages and abilities (not to mention 200,000 words on The Blob!) has made to me.  I hope I've made a small-small difference to some of the students . . . и вам уважаемые читатели.

Friday 13 December 2013

All over bar the singing

Today - the end of term.  Busy day yesterday - marking the exam I set the day before, invigilating another exam, a journal club in the middle of the day, and a good few cups of tea.  I still have a couple of hours marking ahead of me today but I signed up to sing a couple of Christmas carols "Xmas novelty songs" with the other scientists, so I'll be roaring out the chorus mid-morning.  Chorus of what? I hear you say?  "Grandma go run over by a reindeer".  This is a loathsome confection: secular, cynical and condoning avarice.  I don't know where our HoD sourced it but none of the rest of the "choir" had heard it or even heard of it.  If you have a bucket handy you can see-and-hear it now.

But trained researcher me can now reveal the back-story.  The song was written by Randy Brooks for his pal Elmo Shropshire - a C&W singer - and released for the Christmas market in 1979. Elmo has a degree in veterinary medicine and goes on stage as Dr Elmo. He looks uncannily like the seepy compere at the end of Little Miss Sunshine. He recorded the song with his then wife as Elmo & Patsy and invested $40,000 of his own money in studio production.  Over the next few holiday seasons (no youtube back then), the ditty went viral and Elmo recouped his investment many times over.  $million$ are mentioned.  He and other creative people are wrangling with Sony over the carcass of the song that should have died - there are royalties from ringtones and downloads.  This serves as a metaphor of all that's wrong with Christmas.

Christmas is fine, it's good even, if you cherry-pick from what's available rather than feeling obliged to take the whole sorry 21st Century farrago on board..  A little saturated animal fat, especially if it is well roasted into potatoes, never harmed anyone; small gifts to small children are probably a Good Thing; a couple of glasses of wine is said to be great for the circulation.  I also think the whole event should hug The Solstice rather than start to extend its grasping hands right after Hallowe'en..  There I've spoken.  Now I have to go sing.

Thursday 12 December 2013


Christmas time is here, by golly,
Disapproval would be folly,
Deck the halls with hunks of holly,
Fill the cup and don't say "when." 
Well it's NOT here yet, it's nearly two weeks away, but nevertheless I'm sure you're getting antsy about what to buy for that tiresome and rowdy nephew who, last year, knocked your favorite coffee-cup off the table and broke it. I could suggest a folksy remedy for disguising ritalin as smarties and Tom Lehrer has his own solution:
Relations, sparing no expense'll
Send some useless old utensil,
Or a matching pen and pencil.
"just the thing I need! how nice!"
Here's an idea that will go with young Bucko's attention span limitations but keep him quiet in a corner until the brother ("phew!") takes his family back home.  It's a book, it's chock-full of data, it makes you think, indeed some pages make you stop in your tracks and it costs £5 delivered. I lashed out and bought 5 copies - one for each of the families I know which have extremely well-behaved, savvy and symmetrical teenage and sub-teenage boys.  But it will work for girls also.

Today I got an e-mail from that nice chap in Amazon who sold the package to me: "did '1,339 QI Facts To Make Your Jaw Drop' meet your expectations?".  Well yessir! it surely did.  You could get sniffy and call it knowledge for the tweeting generation but it still lives up to the QI mission statement to be quite interesting. Sampler here at TYWKIWDBI.

How does that work though?  It's 350 pages long, bound with a sort of hard-cover, it's been researched and written by the QI team, published by Faber, typeset by Palidrome, printed by CPI in Croydon, trucked to Amazon in Fife, unpacked, warehoused, discovered by an amazonadrone, packed up and posted, air-freighted to Ireland, unbundled in Port Laois, trucked to our Post Office and driven up our buckety land by Paddy the Post. Jings! If I wanted to post the thing back to England it would cost €5 for the stamp! Part of it is economies of scale.  And Amazon doesn't just sell books.

Bingle Jells!