Big Cat, deadly viruses

I'm a bit of a celeb-groupie and have thrown my underwear on the stage at a good few scientific meetings.  Although I'm not sure what the famous scientists make of, or do with, my capacious boxers. Readers aside "What is it with yer man Bob's obsession with underwear, could he not keep it in his trousers?".  I wrote about how James Lovelock may have remembered me at a book signing in Dublin a few years back.  I left Boston 30 years ago this month to take up my first teaching position in a British University.  Six weeks later Stephen J. O'Brien came to visit my Gaffer because they (and indeed we) had a very strong interest in the genetics of cats big and small.  So I missed that meeting.

Last night I was able to catch up because O'Brien was in the Royal Irish Academy talking about his life's work.  Strictly, he was talking about some fragments of his life's work because we didn't have a two day symposium to hear about the whole 750 paper (so far) opus.  But those fragments were woven into a compelling story that started with inbreeding in Cheetahs Acinonyx jubatus and reflecting on how this reduction in genetic diversity laid them open to attack by pathogens.  The case study was a devastating epidemic of Feline Immune-deficiency Virus (FIV) at a wild-life park in Oregon. From there we went on a romp solemn funeral procession through the Black Death, Plague, Smallpox, SARS and HIV, tallying up the thousands and millions of people who have succumbed to infection down the years. O'Brien's group made a crucial contribution to the fight against HIV/AIDS in identifying a mutation in the CCR5 receptor (CD195) which blocks the invasion of T-cells by the virus HIV.  If you have two copies of this gene variant, you will have considerable resistance to attack by this virus.  

You can find out whether you have that resistant status by sending $100 to 23andme in California.  Their genetic analysis will not only tell you whether you have a touch of the tar brush in your ancestry but will lay out your details for numerous medically relevant gene variants including CCR5-delta32.  But before you go off to celebrate your delta32-homozygosity with a spree of unprotected sex in sub-Saharan Africa, you should reflect on what reg'lar CCR5 is doing on the surface of T-cells.  It turns out that, among other things, two copies of the delta32 mutation lays you wide open to infection by West Nile Virus.  Indeed, as WNV has spread globally (thanks to those Bs Boeing, British Airways and Budget Travel), you can't safely go on your sex-spree aNNywhere. Dang!

That was an evening well spent and tribs to my pal Emma Teeling from UCD's Earth Institute for making it happen.  She worked with O'Brien, on SARS and other things, for three years when he has a Big Cat in NIH.  It's just wonderful that international networking can pay such dividends for the education of the Plain People of Ireland.  And this was the first in a series of talks to launch the new meta-Department, mega-School, so that's a lot to look forward to

But enough already about saving millions of lives in sub-Saharan Africa, what about ME?  After the talk I sidled over to the Honored Guest and introduced myself.  I could see that he was, with punctilious politeness, only half-listening to my story of having missed meeting him a generation earlier when suddenly he twigged the connexion between me and my Gaffer in Boston and lit up.  He said some blushingly complementary things about the tuthree papers we'd written on the population genetics of domestic cats back in another place and another time. So that was an evening really well spent.

Lexicographer

"A writer of dictionaries, a harmless drudge that busies himself in tracing the original, and detailing the signification of words."  That was how Dr Samuel Johnson described himself after spending nearly a decade assembling one of the great dictionaries of the world.  He was/is known widely as Dr Johnson but he never earned it in the normal way, although he was eventually given an honorary doctorate by Trinity College Dublin when he was in his mid 50s.  Like everyone of his generation he had two birthdays OS and NS to take account of the change (in the United Kingdom) from the Julian to the Gregorian Calendar on 14 September 1752.  So Johnson was born on 7th Sept 1709 (OS) but the day was/is generally celebrated after 1752 on 18th September.  For example, his birthplace Lichfield is having a knees-up this weekend.

And to show that  Lexicography is alive and well and living in Chicago, check out Erin McKean and her on-line meta-dictionary wordnik, which offers a word-a-day.  But then so does Anu Garg at AWAD.  McKean's Law aka Muphry's Law: "Any correction of the speech or writing of others will contain at least one grammatical, spelling, or typographical error." been there, done that.

No scientist today working on whatever sort of contract, would tolerate the privations that Johnson endured at the centre of a life in letters.  His great indignant rolling polemic against his 'patron' the Earl of Chesterfield "Is not a patron, my lord, one who looks with unconcern on a man struggling for life in the water, and when he has reached ground, encumbers him with help? The notice which you have been pleased to take of my labours, had it been early, had been kind: but it has been delayed till I am indifferent and cannot enjoy it; till I am solitary and cannot impart it; till I am known and do not want it." calls forth a Wildean "I wish I'd said that", and serves to illustrate how his rich pals imagined that he could live on air and invective.

Johnson was famous for other things, like his opinion of The Giant's Causeway "Worth seeing? yes; but not worth going to see; or his eulogy to our own Oliver Goldsmith "No man was more foolish when he had not a pen in his hand, or more wise when he had" a sentiment echoed in verse by David Garrick 

"Here lies Nolly Goldsmith, for shortness called Noll,
Who wrote like an angel, but talked like poor Poll" 

and his bewildered contempt for Scotland through which he was dragged by his friend and biographer James Boswell: ". . .the noblest prospect which a Scotchman ever sees, is the high road that leads him to England. But it is dictionary that we credit and excerpt today.

COUGH A convulsion of the lungs, vellicated by some sharp serosity.

DEPUCELATE: To bereave of virginity. 

NETWORK Any thing reticulated or decussated, at equal distances, with interstices between the intersections.

OATS A grain which in England is generally given to horses, but in Scotland supports the people.

PATRON One who countenances, supports or protects. Commonly a wretch who supports with insolence, and is repaid in flattery.

PENSION An allowance made to any one without an equivalent. In England it is generally understood to mean pay given to a state hireling for treason to his country.

And for dessert, less you think that Johnson's is the only dictionary with a sense of humour:
ECLAIR A cake, long in shape but short in duration (Chambers 20th Century).

Viva la Arts Block!

Another Herzog heard from

Apart from coming between Hungary and Jamaica  in an alphabetic list of countries, Ireland and Israel have certain historical parallels.  Both are recent additions to the list; both were/are partitioned; both were mid-wifed into existence by bombs and kidnappings and neither left that sort of thing behind after they got their seat at the UN.  Ireland, a generation older, seems to be emerging from that cycle of reciprocal atrocity.

As you know, I'm rather a fan of Werner Herzog the film director.  I'm also rather a fan of another Herzog, no relation, one-time President of Israel, who makes a nice connexion between the two countries. Chaim Herzog was born in Belfast and grew up in Dublin, going to Wesley College, despite the fact that he was Jewish rather than Methodist.  It would have been hard to conceal this fact as his Da was the Chief Rabbi of the Irish Free State, as well as being a fully engaged Gaelgoir republican.

Young Chaim left home at 17 and emigrated to Palestine where he joined Haganah one of the militant organisations that was campaigning for a Jewish homeland. They'd be called terrorists now, and possibly were back then. I had a good friend when I was a teenager whose father had been kidnapped in 1947 by the Irgun, another paramilitary organisation like Herzog's group Haganah.  He was released within a short while, having spent his time in captivity discussing the merits of Bach and Mozart with his captors.  But don't imagine that the transition from Palestine to Israel was a gentlemanly affair.  Just read the Bunche Report or Google up Folke Bernadotte.

But this is getting ahead of myself.  Herzog joined the British army at the beginning of  WWII and served in Tanks all over Europe, helping to liberate some concentration camps as that conflict came to an end.  With that experience and training, he was an Effective in the war that broke out in 1948 immediately after the foundation of Israel, and eventually became a general in the IDF.  But after a decade of fighting he trained as a lawyer in Britain and qualified as a barrister, and then practiced the law for several years.  After that he went into politics and was the Israeli ambassador to the UN where his anti-anti-zionism speech is accounted by some as one of ten speeches that have changed the world.  In due course he was elected to the Presidency by a narrow margin in 1983, but returned for second term 5 years later.  It's what you might call an adventurous life for a young chap who played rugger in Dublin as a teenager to finish up, not Captain of School but President of a country.

Chaim Herzog was born on 17th September 1918.

Turn-over

We had a lovely day yesterday.  We drove 180km West to Cork to celebrate the 18th birthday of Dau.II who left home at the beginning of the summer to seek her fortune in the wide world.  She is mad about the cooking right now and has a flair for it particularly the cake department.  A few years ago we cut down a small ash tree (Fraxinus excelsior) and took the trunk off to one of the last working water-driven saw mills to be planked.  I intended to make a kitchen table from the 30mm thick planks but shortly after that we bought the last (slightly shop-soiled) table from the Shaker Store in the Quaker village of Ballitore Co Kildare as they went out of business.  So the planks languished for several years without an obvious purpose.  Then sometime last year Dau.II said she would cut them up and make them into chopping boards as gifts for her friends-and-relations. That didn't happen but today, after a couple of hours work planing and sanding, I presented her with a chopping board cut from a tree whose roots are still locked in the soil of the place where she grew up (she couldn't walk when we bought the farrrrm).  I think that's rather mystical: like Odysseus carrying a oar ἀθηρηλοιγός into the far north in his old age.  Whenever and wherever she cuts an onion and dices some carrots she'll be home.

After lunch at The Strasbourg Goose - slap-up feed; too much meat; can't eat cake - rather than Micheal Pollan's more civilised "'Eat food. Not too much. Mostly plants" we went North to St Anne's, Shandon to ring out Happy Birthday on their octave of bells.  These are the Shandon Bells famous in song and story and the church is rather fine.  This summer they have hosted a Community Arts project involving as many as 1500 people from the locality.  They made some hundreds of flags all shapes and colours and strung them from the bell-tower of St Anne's in a dozen of the most beautiful catenaries (which as any fule kno is a hyperbolic cosine function).  Catenary comes from the Latin word for chain catena, same root as the cadena humana that stretched across Catalonia last week.  As it was blowing a gale yesterday these colorful catenaries were often curving horizontally rather than than sagging heavily like chains tend to do and they were making that wholly evocative whukkering sound that flags make in Kurosawa films.  But like a kitchen board carved out of a tree from home, these strings of flags seemed richly symbolic: created by the community, anchoring the celestial to earth, circling time itself, tying mother church in knots . . .

Birth and death

Today is celebrated as the birth of passenger railways with the opening of the Liverpool and Manchester Railway on 15th September 1830.  Except that it's not: The Stockton & Darlington Railway had been running for the previous 5 years.  But it is true that the opening of the L&M in the presence of the Prime Minister (the Duke of Wellington) and the Home Secretary (Sir Robert Peel) and many more of the Great and the Good, did make it an event worth reporting.  That publicity certainly helped the flotation and the L&M was financially successful from the get-go.  The publicity also went ballistic because of a concurrent tragedy.

George Stephenson had designed the railway with 4 parallel rails equidistant from each other and 4 ft 8.5in (1,435 mm) apart.  I'll have to dig down another level to work out why that distance was chosen and not, say, 5ft even or 1.5m.  But the 4 track design was chosen partly for redundancy: trains could run on the middle pair if the outer rails were broken or being repaired.  But with the lateral overhang of each carriage above the wheels, there was only 20cm spare between trains. William Huskisson, the local MP and a rising star in Tory politics got caught between two trains while talking to the Duke and died after he was run over.  He thus became the first casualty of the Railway Age, except that he wasn't: that honour goes to a blind American beggar-woman knocked down by a locomotive on the S&DR in 1827.  But as Wikipedia has it, Huskisson was "the first railway fatality to be widely reported".

While we are on transport firsts everbode kno that Rosa Parks was the first black woman arrested for refusing to give up her bus-seat for a white man. Except that she wasn't: that honour goes to Claudette Colvin a 15 year old young-wan who had been arrested for the same 'crime' earlier in 1955.  But between arrest and trial, she fell (ooops pregnant-while-unmarried) and was dropped like a red-hot brick as a fulcrum for leveraging civil rights by the respectable NAACP black community.  It was much better politics to mobilise support for a poor middle aged seamstress. Colvin's boy was born in 1956 sufficiently light-skinned that, without anyone looking at the facts of the matter, she had the sin of miscegenation added to unmarried sex and sitting down in the wrong part of a bus. At the time it was hard to decide which of these offenses was most serious.  Read all about it in the Grauniad. And thanks to QI talk for the pointer.

Blue colourblind

Because these images are clipped from http://allrgb.com/ their originals all have exactly the same amount of information in the Claude Shannon information theory sense.  The conceit at allRGB being that you are tasked to create a 4096x4096 pixel image that includes all 256x256x256 = 16777216 possible RGB colours from #000000 to #FFFFFF.  The fact that you can describe the effective information in the left hand picture with far fewer words than the fractal tree in the middle or the Mandelbrot detail on the right gives a clue about how we keep pictures small on The Blob. I care about these things after the years when every byte that came onto my computer at home had to squeeze up a thin 15km-long copper wire.  I use the wonderful IrfanView to reduce the size of pictures by half or to 10% and the byte-count collapses to the benefit of my copper-wireaders in Bangalore, Ballygobackwards and Bohemia.  Somewhere on the checker-board is cerise, magenta, sky-blue and kelly-green and every colour you've ever seen on a screen, but effectively it's "8x8 512pixel squares alternating light and dark grey" which  description is 52 x 128 bits or about 0.2kb.

The Mandelbrot link above points to his 24/7 talk at the 2006 Ignoble Awards.  That's 24 seconds to talk comprehensively about something than matters, followed by a 7 second executive summary.  Poor old Benoit blew it on the talk (any rambling or parenthesis and the time-up whistle comes before you've finished the first sentence) but summarised his huge contribution to the understanding of our world as "Beautiful, damned hard, increasingly useful, that's fractals".  Like with Globish, such constraints force us to think about what we really mean to say.  Eric Lander, a good showman, has clearly thought about and practiced his nanolecture on the Genome and thought about his summary "Genome, bought the book, hard to read".  And although her talk on Biology is too wordy and technical I like Dany Adams' summary "If it can get infected, it's biology".

And while we are on colour, what are we to make of the La Bandera Astoriana which Wikipedia says is an alpha and omega suspended from a golden (Pantone PMS 109 yellow) Cruz de la Victoria on a blue (Pantone PMS 829) ground?  Because . . . there is no such colour as PMS 829!  I've asked El Asturiano about this anomaly but he took a lurch sideways to tell me about The sacred cave of Covadonga and King Favila who was killed by a bear. The Bear is celebrated by Asturian Republicans, which is rather like the Catalans celebrating the Fall of Barcelona in 1714.   More discussion on the Asturian flag's blue tone.

And thanks to The Blue (Metafilter) for starting me down that rabbit hole.

The Ring of Nonsense

The Blob has been trying (very trying indeed) to promote some critical awareness of numbers: that a billion is a thousand millions not two of them, that sort of thing.  If you can train yourself up for this, then you can reliably guesstimate even quite large, or indeed small, numbers.  A tuthree weeks ago I had occasion to look askance at the statement that 2 million people from the Baltic SSRs held hands to help achieve their own freedom.  Even though great change requires great effort, that number seemed a little too big but not insulting-the-intelligence too big.

The Catalans are on the streets. I've pointed the finger of scorn at a group of Irish pundits for aping the antics of their cross-channel puppet-masters.  What is a clever idea the first time it's dreamed up, can seem tired and derivative when somebody else does more or less the same thing elsewhere.  I was giving tribs to the Balts last month for mobilising a million peoplein 1989 to hold hands for freedom by forming The Baltic Way.  So my admiration is but muted when I report that 1 or 2 million Catalans were out two days ago to form a human chain across the region in SW Europe where that language is spoken.  Via Catalana followed the route of the old Roman road Via Augusta and everyone seems to have had a lot of fun.  I do like the fact that Diada on 11th September commemorates a 1714 defeat for the Catalans in the War of Spanish Succession, it shows a sense of irony and humility.  And I like the geekiness of having official hand-link time set for 17:14hrs.  I wasn't aware that ICANN had approved a top level internet domain .cat in 2005 so that Catalans don't have to acknowledge their de facto existence in .es or .fr - the language is spoken N of the Pyrenees. 

In 2004 and 2006 I was a teeny cog in the St Patrick's Day parade in Dublin.  In 2004 before our little internecine meltdown, our Samba school was really together.  So much so that we won a nice piece of Waterford glass for being best in show (or best band in Cork/Derry/Louth/Tyrone colours, or band with the nakedest Brazilian dancers, I forget).  Here's a picture (you can see my face lower-centre in the sea of red - the trousers and shoes were white) of me being real serious playing the chocahlo.  I had to be real serious otherwise I'd fluff the beat and never get back in time with everyone else - it was hard work for me but I persevered in a way I never did with swimming.  So I know exactly how long the Dublin StPs parade route is - 2.5km.

At about the same time, an innumerate spokesperson from Bord Failte or Dublin Corporation claimed (big us up why don't you?) that half a million people had watched the Dublin parade. And not on the telly - on the street in the Irish weather. Could that be true?  We know that there were 4.5 million people in the country, 6 million on the island, and more than 1 million of them lived within an asses roar (or a DART journey) of O'Connell Street.  Furthermore, the hotels were heaving with tourists. If the Balts could muster 2 million for freedom, is half-a-mill not possible for a party?

Some bright spark at the time (I've tried to track-back to name this canny chiel, but can't turn him/her up) looked at the statement critically.  Not as what might be possible from the population available, but rather what was physically possible on the street.  Those million Balts in 1989 were stretched over 600km and three countries, whereas Bord Failte's putative gawkers were spread over just 2.5km and three Dublin postal districts.  The parade route has two (E-W or L-R) sides to give a viewing front of 5000m, the bright-spark reasoned, so every meter would have 100 people craning past each other's umbrellas to catch a glimpse of me shaking my elbows loose.  I was on the inside looking out and it just wasn't like that - it wasn't a fifth of that.  10 seconds thought and the back of an envelope exposes the claim as nonsense.