Monday, 30 June 2014

Siberia kaboom

The Tunguska Event, the biggest explosion we know about that had no human casualties, happened on the last day of June in 1908, or on the 17th because Imperial Russia was still using the old style Julian calendar. It's called Tunguska because the hypocentre (think epicentre for an earthquake but under rather than over the focus of activity) was near to Подкаменная Тунгуска, the Tunguska-under-the-Stones river, which runs through and under pebbles so you can walk across it without getting wet feet.  The grey blob in the top left corner of the picture is Lake Cheko Чеко, which some say has a magnetic lump buried in its sediment that is the only part of the extra-terrestrial object that struck the atmosphere at breakfast time and exploded.  Those same people claim that the lake was created by that lump impacting with the remote Siberian earth. The long axis of the 700 x 350m lake certainly points to the hypocentre 8km away, but that's not sufficient evidence on it's own. Other people say this theory in baloney and that the object was a dust and ice meteorite, and that accounts for the fact that there nothing could be found on the ground.  As you know, after the Chelyabinsk event a couple of years ago, hundreds of pieces from grams to half-a-ton were recovered from the holes they made in  the snow.

Whatever it was made of, something exploded several km up in the air and laid out the trees in a butterfly pattern of concentric rings (L) as if they had been scythed. 80 million trees were flattened, window-glass was shattered hundreds of km away and an atmospheric pressure anomaly was recorded in London.  This way-above-ground explosion registered Richter 5.0 on seismometers all over Eurasia. It was 200x-1000x greater in TNT equivalents than the Hiroshima bomb of 1945. Make your own conventional explosives comparison? Apart from a few fur-trappers and hunters, the actual event wasn't witnessed directly, and no dash-cams back then.  It wasn't until after WWI, the Revolution and nearly 20 years that the first qualified scientists arrived in the region to take measurements and record eye-witness accounts.  Actually, the Imperial government may well have sent people East in the immediate aftermath of the event, but any records of such an expedition went West in the turbulent times between 1917 and 1922.

Lack of data hasn't held back speculation about the cause: meteorite, asteroid, annihilating anti-matter, black hole, 'natural' H-bomb, erupting natural gas cloud, the Storm-god Ogdy.  Perhaps the most down to earth speculation makes the calculation that if the object had been 4hrs and 47mins later in arriving at the turning Earth, it would have exploded directly over St Petersburg and then we'd really have some data to analyse.

Sunday, 29 June 2014

being right is not easy

I was tribbing Darrel Francis and his team for caring enough about their field of science (cardiology) to re-analyse a huge bouquet of Other Men's Flowers - and finding many of the blooms a bit whiffy.  On three occasions, I've had cause to look really carefully at someone else's data, and in each case I've found it wanting.  Now, it may well be a case of Ascertainment Bias - I can't remember the many many times when such data stood up to my scrutiny.

For several years in the '00ties, I was in charge of the weekly journal club. Each of us in turn would pick a scientific paper relevant to our field of interest, we'd all undertake to read and critically evaluate that paper and discuss our findings.  Well, it was often pretty sad, because there were frequently only two people in the room (me and the presenter) who had made time to read the paper. Although the boss would read it on the fly and usually come up with some ideas.  You don't learn much by sitting there passively listening to a colleague giving an executive summary with powerpoint.  Eeee, in my day, when I were a young graduate student we had the same sort of event, but my memory of it is a hammer-and-tongs shouty-match to see who could find the next laughable error in a paper published in a top-flight journal.  It was rare indeed that a week went by without the authors trying our patience by doing a t-test on a sample of 2 x 3 replicates, or having a a graph without dimensions on at least one axis, let alone having a citation in the text without a reference in the bibliography.  Sure we were young turks out to prove how clever and applied and dedicated to the task we were.  But I tell ya, we were in the ha'penny place when we went across the river to similar events in Harvard.  The graduate students there ate each other, we only nibbled at total strangers.  This told me that the system of peer-review is flawed; not fundamentally flawed, but you have to worry that if a referee or two or three misses the kind of errors which we found on every trip out then they are possibly missing something bigger which only their experienced eye would be able to detect.  We are complacent about the peer-review publication process in the same way that Churchill was about politics: "Democracy is the worst form of government, except for all those other forms that have been tried from time to time."

When I came back to Ireland in 1990 after a decade seeking my fortune in foreign parts, I got a job in the world of bioinformatics and molecular evolution.  I'd been amateuring at the field for a couple of years in England but now I had to deliver.  My boss was one of a small handful of scientists who were interested in synonymous codon usage. It's quite obscure but works on the fact that several different triplets of DNA code for the same amino acid when they are translated into protein.  You'd expect (null hypothesis) that each of these options would be used uniformly or randomly, but in fact some codons in some proteins in some organisms are used far more, or less, than you'd expect by chance.  My task was to assemble comprehensive datasets of all the genes from a species and run them through a set of computer programs to decipher what pattern was followed by that organism and how did it compare and contrast with other species. It meant assembling large tables of genes vs codons counting the instances of each possibility: Gene ACT1 had 14 UUU codons, 30 UUC codons etc.
We got a bit proprietal about it; trying to put one over on rival labs (mostly in France) and doing the most careful analysis we were able for.  One day, a paper appeared doing our sort of analysis on a species that we hadn't gotten round to knocking off - yet.  Worse, it was from a total outsider, who was a bit of an expert about the species in question but, clearly, knew bugger-all about how to analyse the data.  In other words, he hadn't cited any of our papers - harrrumph!  I was assigned to read the paper properly and I did it as a referee should but usually can't find the time to do. First off the numbers in each column didn't always sum to the column-total and the sum of the rows didn't agree with the sum of the columns. The numbers weren't wildly off but they made us question the quality of the analysis that had been carried out on such numbers.  We decided that we'd have to put the record straight and I spent the next tuthree months dragging data out of the literature and from the DNA databases and re-did the analysis in the correct (i.e. our) way.  As a courtesy to the original authors we sent them a pre-print of the analysis just before we sent our manuscript off to a journal.  A sad response came back from the Principal Investigator saying that the whole escapade had been the result of a summer internship that had finished prematurely; the intern had disappeared back home and he, the PI, had scrabbled the paper together before he got really busy for the upcoming academic year . . . and please could we not be too scathing in our discussion.  We weren't, but used the sort of British understatement that is more devastating than shouting that the fellow is a cad and a bounder.

My next project was to construct a phylogenetic tree of bacteria based on protein sequences. In those days as now, the relationships among bacteria are determined by comparing the sequences of one of the structural RNAs (usually 16s) in the ribosome.  So it was of interest to see if proteins were evolving in the same pattern and/or at the same rate as the 16S nucleic acids.  I assembled a dataset of the protein recA that was most widely sequenced at the time and used as the de facto global standard software suite called Phylip to do the analysis.  Phylip - the phylogeny inference package was the brainchild of Joe Felsenstein, who had created it and made it freely available. I really wrestled with those data, because I'd never done anything like that before and I didn't want to have a red face when the paper was published. I checked everything for internal consistency and, in the process, found a tiny bug in the code of one of Felsenstein's programmes: in a particular, peculiar set of circumstances the code didn't sum the numbers correctly.  It didn't substantively affect the results but I wrote to point the error out and became one of an exclusive club of 385 people who have helped inch that project forward in the right direction.

Saturday, 28 June 2014

stem cells a bill of goods

"You were sold a bill of goods" was one of the colorful phrases that I picked up from my late and much lamented mentor when I went from Olde to New England.  It means that someone is trying to convince you that something is worth more than the paper (the bill of goods, shipping docket) it's written on, when it's not. I've been meandering through the backlog of Nature now that I have some Summer space to indulge in such luxuries.  This can throw up some neat juxtapositions: Nature covers the whole of science and wouldn't dream of boring and bemusing their astrophysics readers with stem cell nonsense week after week. But if the stack of unopened Natures is well shuffled you can read 19th June right after 1st May and the old One-Two makes an impact.

On 19 June 2014, Elena Cattaneo and Gilberto Corbellini were given three pages and colleagues Paolo Bianco and Douglas Sipp were given the following two pages to inveigh against the far-too-early commercialisation of stem cell therapy. The first of these articles reads like a cross between sour grapes and a jihad against a particular company - The Stamina Foundation - which is using stem cells to cure a range of life-threatening conditions. The problem is that the company has proffered no peer-reviewed science to show that their product is efficacious against Parkinson's disease or muscular dystrophy. What Stamina offers instead is anecdotes about particular cases where their injections have made patients better.  Q: "What is the singular of data?" A: "Anecdote".  The panoply of saints in the Catholic church relies on anecdotes of a few (or even one) miraculous cures rather than data showing that prayer or veneration or a lit candle is significantly better at achieving what is desired than just allowing time to pass.  But I'm not here knocking faith, it has currency other than delivering the goods. What Cattaneo et al. object to is that a company is turning a handsome profit in Italy selling desperate and desperately sick people and their relatives hope rather than something that has been shown to work.

The therapy under scrutiny hinges on the idea of stem-cells, either pluripotent or at least multipotent. The process of development from a single fertilised egg cell to 100 trillion cells of 100, or 1000 or 10,000 different types can be viewed as a series of gates which are more or less one way.  That original zygote has the capacity to become any of those 100 trillion. But early on, the embryo differentiates into ectoderm (which goes on to make skin and nervous tissue), endoderm (ultimately lining the gut and lungs) and mesoderm (everything else).  Once a cell is committed to the endoderm option it will not, cannot, ever become a neuron.  Some stem cells (the zygote as an extreme example) can become any cell and they are called pluripotent, other have a more limited (multipotent) set of possible fates.  A haematopoietic stem cell, apart from cornering a helluva lot of vowels, is able to become any sort of blood cell but no matter how much it strains, it's not going to become a neuron either.  Tricking about with new haematopoietic stem cells is what happens when you do a bone marrow transplant after killing all the existing white blood cells, some of which are cancerous, through radiation and/or chemotherapy.  It is the one tried-and-true situation where stem cell therapy has been shown to work . . . more than it screws up the patient with side-effects and new and more immediately fatal diseases.

In the capitalist West we like to believe that the Market is always right, or at least will find its level.  If a wheel-barrow doesn't work or breaks after a week's normal use, then nobody (else) will buy it and the producer will go bust or re-jig the product so it is fit-for-function.  But governments have long recognised that consumers are often as thick as pig dribble and gullible to boot, and need to be protected from the chicanery of entrepreneurs, shop-keepers and insurance-salesmen.  In the arena of medicine this is particularly important because the sick may not be at their swiftest and the downside of a medical intervention may take years to become manifest.  Therefore the Irish Medicines Board, the FDA in the USA and the European equivalent require that all medicines are licensed and that they can only be approved if it can be shown that a) they work and b) they do no harm.  Of course it's a bit more complex and utilitarian than that - interferon alpha therapy is pretty good, for some people,  at damping the symptoms of hepatitis C, and there are side-effects (nausea, headaches) but they are nowhere near as bad as untreated hep C.  To be licensed you first have to show that that your novel drug works in animals, then that it has no bad effects (ooops) on a small sample of healthy people (usually young males), then on a small sample of sick people to check that people are essentially the same as lab rats (often not true), then on a larger sample of patients under regular medical scrutiny and check-up.  All this takes time, and a failure at any stage means you have to start again.  The usually quoted figure is $1 billion to bring an interesting biomedical finding to market. When our noble and selfless BigPharmaCorp is a $billion$ down before the first packet of pills is shipped there is a certain pressure to cut corners consciously or unconsciously. When you look at the data you find that a disturbingly large proportion of biomedical science research is a bill of goods (cannot be repeated and replicated) because of inadequate statistics, inadequate sample size, wishful thinking, or unconscious bias.

Back in the 1st May 2014 edition of Nature there was an editorial and a News in Focus piece reporting the results of a meta-analysis in the British Medical Journal BMJ of all the studies that had investigated stem-cell therapy for heart disease. When you have a heart attack or heart failure, some of the cardiac tissue dies never to be regenerated. A few years ago, some bright spark had the idea that injected mesenchymal stem cells MSCs, derived like their haematopoietic cousins from the bone marrow, would be able to regenerate into heart cells or, failing that, at least stimulate an inflammatory response to encourage the development of new life-giving blood vessels.  The logic seemed sensible or at least possible and, as a lot of fat white men with money get heart attacks, it has been widely investigated. The BMJ study, fronted by Prof Darrel Francis of Imperial College London, looked carefully at 49 separate studies. The studies that passed muster under this intense scrutiny and reanalysis of their materials and methods showed that there was no clinical effect. I've previously channelled Trisha Greenhalgh's rule for reading scientific papers: if the M&M are wonk then you don't need to read the rest of the paper because the results, let alone the conclusions, cannot be relied on.  The Imperial group found that only methodologically flawed papers showed any positive effect.  And the flaws were many and various: tables and figures with conflicting data; inappropriate statistics or statistically impossible results; dead people continuing to report their symptoms; patients coded both as men and women.  Now these-all could be mere typos, or have an allowable explanation, or be trivial given the sample size of the study, but it doesn't inspire confidence in the conclusions if nobody has caught these rather obvious errors before it was too late - getting into print is too late.  It means that 2 or 3 referees and an editor have nodded it through without doing their job; it means that the Principal Investigator hasn't really scrutinised the work of the team; that they haven't sought effective statistical advice; that they can't add; that they can't use ExCel properly.

One of the perps, a famous cardiologist from the famous Mayo clinic offers the fact that his paper was peer-reviewed as an excuse as if science ran a system of double-jeopardy - if you have gone through the peer-review process once then you and your data are home-free.  Another offers "We strongly believe in the science and results we have seen with adult stem cell therapy for coronary artery disease" which may remind you of the Catholic catechism "We firmly believe and confess without reservation that there is only one true God, eternal infinite (immensus) and unchangeable, incomprehensible, almighty and ineffable, the Father and the Son and the Holy Spirit; three persons indeed, but one essence, substance or nature entirely simple."

If someone offers your Dad stem-cell therapy after his heart-attack and you, or your insurer, are going to pay big money for the privilege, Just Say No (thank you).  If your government funds a much larger Phase III clinical trial based on these sort of data, tell them you'll be saying No at the next election.  If you're a shareholder with BigPharmaCorp sell Now because the company is going to be $billion$ in the hole in five years time . . . unless they massage their data too.

Updated Aug 2015 to correct spelinge: s/Catteneo/Cattaneo/

Friday, 27 June 2014

Potemkin to potatoes

Maybe I'll start a new series about "chemists who are famous for something else".  The obvious choices are Margaret Thatcher, British Prime Minister; Александр Порфирьевич Бородин, Alexandr Borodin, romantic composer; Primo Levi, survivor and author; Chaim Weizmann, First President of Israel. Sometimes there is a rather close connexion between chemist and celebrity: Weizmann's research into military munitions was directly instrumental in the foundation of Israel and his billet as Head of State. Primo Levi's best book Periodic Table would not, could not, have been written without his chemical training. But there is no very well articulated argument that Thatcher's chemical training helped her to the pinnacle of the political pole. And Borodin's daytime job as a professor of chemistry didn't, in any way that I've heard about, inform his music: he wrote an opera about Prince Igor and the defense of Ukraine, not Élie Metchnikoff and Buttermilk.

Ukraine? Who mentioned Ukraine?  Isn't that going to set Bob the Cat in Ireland really among the pigeons of Kiev and Lviv/Lvov/Lemberg. Ivan Beshov was the son of a judge who was born just outside Odessa in the Crimea. He was trained as a chemist but that was not exciting enough for a young chap and in 1902 he enlisted as a sailor (see R as an escapee from the von Trapp family) in the Black Sea fleet of the Russian navy. After some trials and tribulations including a court martial for Leftist leanings, young Ivan found himself assigned to the Battleship Potemkin Князь Потёмкин Таврический in 1905 where he worked as a machinist in the engine room. There was a war on in the East; Japan had just (27 May 1905) given the Russians a terrible drubbing at the Battle of Tsushima Цусимское сражение to emerge as a world power. It was a blow to Russian prestige and particularly to morale in the Imperial Russian Navy.

Exactly a month after this disaster, the commissariat sent out some maggoty meat (L as re-created in the film) from shore and, rather than condemning this and sending it back, the ships cooks were ordered to cook it up for the crew's dinner. Any sailor's job a hundred years ago was hard, the pay was appalling, the conditions often brutal and the discipline was ferocious because The Man hadn't been able to think of a better way to make sailors obey orders instantly. The only solace was that the food, if unexciting or even unappetising, was plentiful. But that day on 27th June 1905, the infested gloop was too much and the crew refused to eat it.  A martinet of a First Lieutenant called out and armed the Marines and threatened to shoot anyone who refused the sustenance that His Imperial Majesty Николай Александрович Романов had provided.  Then he did shoot someone and all hell broke loose.  The crew mutinied, killed several of the officers and dumped them over the side and then didn't quite know what to do next so they returned to base at Odessa where a General Strike had been called and was in the process of being repressed. This allowed Sergei Eisenstein Сергей Михайлович Эйзенштейн to imagine the iconic Pram on the Odessa Steps scene in his film of the events. A case could be made that this is the most cited scene in the film-buff's archives.  But you can make you own mind up after you've watched the whole film and ask if it is really any better than Harry Potter and the Goblet of Fire.  After a series of rebuffs in Crimea, the mutineers cruised off to Romania where they scuttled the ship, surrendered to the authorities and obtained political asylum. Meanwhile Machinist Ivan Beshov obtained false papers and legged it to Turkey, sailing round the world before the mast on several different ships until he washed up on the beach in Dublin in 1913.  He found his feet there, changed his name to John Beshoff but not his orthodox religion even after he married a lovely catholic girl from County Tipperary.  They opened a chipper in the centre of Dublin that quickly acquired the reputation of producing the best haddock Melanogrammus aeglefinus and chips Solanum tuberosum in the country.  Their sons and grandsons expanded the business, so that there are now a handful of outlets where you can buy their inimitable battered Dublin Bay Prawns Nephrops norvegicus, as they call scampi in Ireland.  Actually everyone calls it scampi now because it sounds tastier than something that has to fight for breath with the sewage outfall that debouches into the bay.

Иван Бeшов/John Bеshoff had the rare distinction of out-drinking Taoiseach Charles J Haughey and died at the age of 104 in 1987 having achieved the rarer distinction of being the last survivor of the Potemkin Mutiny and indeed of the Russo-Japanese war.

Thursday, 26 June 2014

Cider with Bob

Just before I left for a long walk in Spain ten years ago, I was at a wedding in the church in Slad, near Stroud, Gloucester. In the churchyard is a gravestone with the Inscription Laurie Lee / 1914-1997 / He lies in the valley he loved.  In the visitors book, someone had written a tribute to Laurie Lee (R, on the fiddle), saying that the inscriber had just returned from Almuñécar.  I added my own comment that I was, in two days time, going to be in Vigo at the other end of young Laurie's journey.  These were both insider references to the best Bildungsroman of them all: As I Walked Out One Midsummer Morning. Maybe that's putting it a bit strong: To Kill a Mockingbird, and Narziss und Goldmund also have a claim in my booklist.  But for heart-achingly evocative travel writing AIWOOMM must be near the top of any list.

I was back in Stroud just ten days ago. And begob, in Dau.I's favorite hang-out, Black Books cafe-bookstore, they were handing out postcards pushing The Woolpack Cider Festival Sat 28th June 2014 to celebrate the centenary of Laurie Lee's birth on 26th June 1914.  I was annoyed with myself that this event had crept up on me without my poetdar giving me much notice. According to my Stroudy contacts, they are a bit worn out with the celebratory events in Slad and the other Five Valleys. There's even a Treasure Hunt and I love treasure hunts.

Laurie Lee was a poet who is famous for writing Cider With Rosie his nostalgic memories of growing up in a remote rural England Between The Wars. CWR became the set-book for British teenage examinations and sold a million copies. If you can read the culminating encounter with Rosie under a hay-wain "Then she took off her boots and stuffed them with flowers. She did the same with mine" without remembering the heart-pulse and wonder of your own adolescent fumblings, it must be too too long ago. It's getting a bit hazy for me. That occurs near the end of the book which is wrapped up smartly with the description of  a 1000 year old way of life, based on the horse, being parceled up and thrown away in the decade of Laurie Lee's teenage years. "At a local memorial after Laurie died, it was announced that the real Rosie was present and would now stand up, whereupon four old ladies rose from their seats."

Whether to avoid getting snagged by a local lovely and having to settle down or from a poets relentless restlessness, in 1934 at the age of nineteen, Laurie threw a spare shirt and a fiddle into a haversack, kissed his mother and walked out of the valley to seek his fortune.  He busked his way along the South coast of England before turning North to London. There he falls in with a bohemian crowd;  working in the building trade; living in a garret; scribble scribble scribble; until his wanderlust takes him off again.

Where?  Well he had a single phrase of Spanish "Un vaso de agua, por favor" learned from a girl back home who'd lived in Buenos Aires and that seems a good enough reason to buy a one-way boat ticket to Vigo in the NW corner of Spain.  He spent the next year walking and busking his way zig-zag across the country. At about the same time, his contemporary Patrick Leigh Fermor was walking across Europe in a different direction.  If Slad had rapidly moved into the mid-twentieth century, much of Spain was still stuck in about 1227.  The descriptions of the dusty roads and the broiling sun "The violence of the heat seemed to bruise the whole earth and turn its crust into one huge scar. One's blood dried up and all juices vanished; the sun struck upwards, sideways, and down, while the wheat went buckling across the fields like a solid sheet of copper" cries out for an ice cold beer. Laurie eventually finishes up in Almuñécar just as the whole country starts to throw off the medieval shackles of church, army and landlord. For a few brief weeks in 1936 everything and anything seems possible, somewhat like the Summer of Freedom in the USA in 1964.  But in Andalusia, where Franco's Nationalists rapidly achieve the ascendancy in the Civil War, the shutters come slamming down again to reinstate repression and the previous power structures.  Many of Laurie new friends will be killed in the process but, in a rush that precludes deciding to, the poet is rowed out to a British destroyer sent from Gibraltar to rescue His Majesty's subjects.

Parts of Republican Spain held out for another three years, giving Laurie time to return to Spain the hard way, smuggling himself over the Pyrenees through a blizzard to fight, almost as briefly as George Orwell, on the Left side of that titanic and tragic struggle.  AIWOOMM is a Bildungsroman because you can see the protagonist grow in stature as events unfold. Spain inspired him and woke him up, so it is entirely appropriate that the festival in Slad on Sunday should feature Cider and Flamenco.

Wednesday, 25 June 2014

crimethink doubleplusgood

We live in a world with far too much conformity.  It's too much trouble to think things through or marshall evidence both for and against before adopting a position. We all too often adopt a position that keeps us in the comfort that we surely deserve even if it dispossesses a thousand others of theirs. Ever bought a pair of named-brand trainers without thinking too deeply about what fraction of the purchase price goes to the women who made it out in Indonesia?  When you pay 75c for a litre of milk, do you reflect on the fact that the supermarket makes more by shifting it from the delivery truck to the shelves than the farmer makes by getting up at 0500hrs every morning?  Does it have to be like this?

If we can't take up contrarian positions ourselves, at least we should respect those who do.  They add to the joyful diversity that makes life on this planet interesting.  But more importantly they might, just might, make us reconsider our inner certainties.  There was something stubbornly mulish about Eric Blair/George Orwell (looking young and idealistic L): he'd do things out of cussedness when, with his Old Etonian tie and extensive circle of well-placed pals, he really didn't need to.  I think my favorite of his books is Down and Out in Paris and London. It contains this useful tip "Roughly speaking, the more one pays for food, the more sweat and spittle one is obliged to eat with it." After slaving and surviving at the very bottom of the catering trade in Paris (Valenti and St Eloise is an ironic story from those times) he hears that he can secure a cushy number "looking after a tame imbecile" back home in England. On arrival, he finds that he is misinformed and that his sinecure won't start for a month. Rather than rocking up to any of his friends and kipping on their sofa for a couple of weeks, Orwell chooses rather to go sleep in a series of itinerants' hostels because they cost ninepence or a shilling a night rather than 7 shillings and 6 pence for a cheap hotel. Part of the adventure is consciously looking for copy as a journalist, but part of it is a willingness to experience how the other half lives rather that just writing indignantly about it.
Note for those younger than 55: the £ sterling was divided into 20 shillings each of 12 pence.  In the early 1930s, by statute, an agricultural labourer was earning about 1 shilling an hour; a machinist in a factory slightly more.

I've written already about Orwell's critical evaluation of Kipling, at whom his leftist friends used to sneer.  Orwell was prepared to work at his reading and found that although the jingoism, racism and sentimentality in Kipling is indeed objectionable, there is nevertheless something inspiring in the both the quality of the writing and the ideas expressed. I've been very grateful that Orwell gave me permission to like An Habitation Enforced.

For reasons that will become apparent tomorrow (someone else's birthday), I'm going to leave you to read Orwell's essays in your own time to get an education about how good writing can make a difference. Instead I'll talk briefly about Homage to Catalonia, Orwell's account of putting his life on the line for a cause that he cared about.  Instead of reading about the Spanish Civil War in the grossly partisan papers back home, "Hence the truly frightening spectacle of Conservative M.P.s wildly cheering the news that British ships, bringing food to the Spanish Republican government, had been bombed by Italian aeroplanes.", Orwell packed a case and went to Barcelona to fight for the tottering Republic.  He signed up, more or less at random, with POUM Partido Obrero de Unificación Marxista rather than the Popular Front for the Unification of Marxism or the Marxist Workers Front for Unification "splitters".  He was sent to various front lines but was far too tall to fit in the Spanish trenches and within four months he'd been shot in the throat and declared unfit for service.  Before he returned home, he witnessed the internecine meltdown of the Republic as the various left factions fought each other at least as bitterly as they fought Franco. [see also: Shi'a/Sunni; Catholic/Protestant ?] Orwell's own group POUM was comprehensively purged as Trotskyists by other Marxist cadres funded by Stalin. His bitterness at this trashing of an idealistic socialist dream made him a lifelong skeptic about the USSR. In taking this position he was bucking the trend among his leftist cronies back home.  A shocking number of British scientists, anti-Fascists all, were fully rowed-in behind the Stalin regime in the 1930s and 40s looking at horrors of collectivisation through caviar-tinted spectacles, blissfully unaware of the Gulag and even believing that Трохим Денисович Лисенко (Lysenko) might be on to something (the Politburo thinks he's wonderful) in his doctrinaire assertion that plants could be genetically altered by clever changes to their environment.  The round-ups, denunciations and shootings in Barcelona in the early Summer of 1937 led more or less directly to Animal Farm and 1984.  I haven't read 1984 since a good while before 1984 but it still worries at my mind as a terrier shakes a rat. The Newspeak post-title hints that Orwell knew he wouldn't last very long in his own dystopian future.

It was my birthday last week, and Dau.I gave me (for which much thanks) a copy of Orwell's Why I Write in the Penguin Great Ideas Series.  It's Eric Blair's (1903) birthday today. He was born into, the snobbishly precisely graded, "lower-upper-middle-class" won a scholarship to Eton and used his time there to develop his talents as a writer. After his traumatic time as a police-officer protecting the Empire in Burma he worked for the rest of his life by his pen and whatever else turned up. He was always "a bit weak in the wind" and didn't help matters of breathing by smoking a lot of shag-tobacco. He died far too young at the age of 47 from tuberculosis, bronchitis and lungs filled with blood.

Orwell had a strong belief in A Nice Cup of Tea and I'll be making myself a pot of his preferred beverage forthwith. "One sip of this will bathe the drooping spirits in delight beyond the bliss of dreams." Milton. Cheers!

Tuesday, 24 June 2014

Updates on phenolics

If you first heard of triclosan by reading The Blob, you're about as on the ball as me. Which is to say, not very much.  I'm not the only one to react to the possibility of an endocrine downside of this ubiquitous anti-fungal agent.  The State of Minnesota has banned the compound but only with effect from 1st Jan 2017 30 months away.  That's a bit wet, no? If there is a clear and present danger, then surely it should be banned now. If it's not hazardous then stop posturing about it. If you're not sure then do some science to find out! It's a long time since responsible public authorities adopted the Precautionary Principle by which you try to err in parallel to the Hippocratic Oath "primum non nocere" above all do no harm and if there is a hint of harm you stop doing/making whatever it is. I'll open a book on whether triclosan is banned in 2/3rd of the US states before 2/3rd of US States legalise same-sex marriage.

I suggested that triclosan looks a bit like BPA (bisphenol-A) the plasticiser that we add to baby's bottles so that infants can get a good slug of hormone analogues before they learn to speak.  Informed consent Big Pharma style:
"Do you mind if your milk has a little BPA in it?"
"wurble bup bup"
"Can't hear you clearly"
"Bloo bloo"
"You're not objecting? We'll leave it in, so"
I think my position is that we don't want to get hysterical about BPA yet. Nevertheless, in January 2014 the European Food Safety Authority agreed to slash the allowable levels of food intake from a daily 50 micrograms to 5 micrograms per kg body weight.  The EFSA's position is that the public health risk (on our reproductive and nervous systems) is low because there isn't much BPA actually in the environment. Lowering the limits ensures that the level is kept low.  Precautionary Principle again. Good show EFSA!

Secrets for a long life I: Before you start worrying about BPA, you should stop using your car.

Monday, 23 June 2014

Meridian Solstice

Andrew Goodman [L], and Mickey Schwerner [R] were well-to-do Jewish boys from New York, and they absorbed the liberal ethos of their caste.  In a different time they would have gone off with the Peace Corps and taught English to black children in Malawi.  But they came to maturity in the Kennedy years when it seemed possible that the manifest unfairness of their own society could be done away with. In the Summer of 1964 they joined CORE the Congress of Racial Equality and tooled off to Meridian, Mississippi with their eyes all shining to help black people register for the vote. They hooked up with a local boy "J.E." Chaney [C], and were assigned by CORE to set up a "freedom school" at a black Methodist church in Neshoba County. After they left, the parishioners were beaten with rifle-butts and had their church burned to the ground.  Chaney, Schwerner and Goodman returned to Neshoba county to investigate and were quickly arrested by Deputy Sheriff Cecil Price for 'speeding', taken to the County jail, fined $20 and told to leave the county and never come back. They left, but not before the Deputy had grassed them up to his friends in the Ku Klux Klan. At the county border, the boys were stopped again, transferred to the Deputy's car, and driven off into the deep boondocks.  The white boys were given the dignity of being shot at point blank range; Chaney was beaten to bloody pulp first.  His sin being greater because he should have known better . . . and he was black so was a fair target for any redneck hero.

In the Summer of 1955, Emmett Till, a 14 year old black kid from Chicago was visiting his hick relatives in Money, Mississippi. Like the New Yorkers after him, he didn't know The Rules either and out of bravado to show up his cousins as spineless wimps he flirted with a young white women who ran a local store.  The evidence is equivocal about how far he actually went, but it was too far for the woman's husband and his half-brother.  They appeared in Till's bedroom that night, took him off to the barn, duffed him up real good, gouged out one eye and then shot him. They then used barbed wire to wrap a 30kg weight round his neck and dumped the body in the Tallahatchie River.  The perps were exonerated by an all white, all male jury of their peers: presumably people who thought that kind of behaviour was acceptable.  I touched yesterday on the banality of evil, and maybe some of those jurors were outraged, but as our own Edmund Burke said "The only thing necessary for the triumph of evil is for good men to do nothing".  Because he was only fourteen, Emmett Till's torture, mutilation and murder caused a huge stir.  It helped that Roy Bryant and J.W. Milam, having been acquitted, under double jeopardy bragged to Look magazine that they were indeed responsible for the outrage.  William "Nobel 1949" Faulkner, from up the road in Oxford Miss., said " Because if we in America have reached that point in our desperate culture when we must murder children, no matter for what reason or what color, we don’t deserve to survive, and probably won’t."

Meanwhile back to 1964: the trio of CORE activists had simply disappeared.  The community closed ranks and two carloads of Klansmen relaxed into the status quo ante. Up in Washington, it was just not good enough for President Johnston who had inherited the mantel after John F. Kennedy had been assassinated the previous November.  He said he was going to flood central Mississippi with Feds until they discovered a) the bodies and b) who was responsible for their deaths.  It took them 44 days and a tip-off, but eventually the bodies were unearthed from the base of a dam near where the boys were killed.  In the course of their investigations, the FBI found a further nine unaccounted corpses - all black. The strong sense was that nothing much would have happened unless two middle class white men were involved.  A bunch of people, including Deputy Price, were tried for civil rights violations because the State of Mississippi declined to try for a murder rap.  Price was found guilty and sentenced to 6 years in prison - he served 4 and a half. Six other men including the Imperial Wizard of the White Knights were also found guilty. The mastermind of the murder was a Baptist minister called Edgar Killen; he was not convicted because a single juror stoutly refused to convict a Preacher. We've seen numerous examples since that should convince any sane person that preachers are not incapable of doing wrong.

A lot of what we know now about these cases stems from the dogged pursuit of the truth by a journalist called Jerry Mitchell.  He blogs away about the history of civil rights.  Five years ago, he was awarded a prestigious MacArthur 'Genius' grant to pursue his investigations.  By embedding himself in the data, Mitchell has deduced who was the insider who told the FBI where the bodies were buried.  So there was at least one man who wasn't silent.  I think that's my bottom line: evil hasn't petered out over the last 50 years and we need to have someone to look to when there is an option to do the right thing when it is the difficult thing.

Because justice delayed is justice denied, I'm less thrilled by the eventual conviction of Preacher Killen in 2005, 41 years after he organised the witch-hunt that killed the young men during Freedom Summer.  The case against him was steadily built up by Jerry Mitchell, with help from Allison Nichols, Brittany Sattiel & Sarah Siegel high-school project students. Killen was brought to trial at the age of 80, long after key witnesses were dead and those who survived had had decades to relive and rehearse their contribution to the story. Killen's conviction is the mirror of the apologies for unjust punishments (Guildford Four, Alan Turing) years after the event and offered by people who were in no sense responsible for the original injustice. It's easy to dismiss Killen as a horrible old racist who is finally getting his comeuppance but we can better spend time looking at the ugliness, inadequacy and injustice in our own times and our own hearts.

Sunday, 22 June 2014


21st June has been a good day for injustice. On top of the Old Bailey, the Central Criminal  Court in London, stands this statue of Justice, who is usually represented blindfold but willing to defend (sword), fairly (scales), the administration of justice. The British have agreed to discard the ould blindfold from their symbol because tired old men in full-bottomed wigs feel they have such clarity of vision that they can see the rights and wrongs of a case and instruct the jury accordingly. Do you have jury trials in Ukraine?  They are a mixed blessing, because juries tend to do what feels right to them even when it is not strictly in accordance with the law or the evidence or the judge's summing up.  Two events occurred yesterday that made the news only within their own parish because the injustice happened long, long ago and we've moved on and we think we're more civilised now.

Gerry Conlon died last night aged sixty. He spent 15 years (that's 25%!) on his life in jail. On 5th October 1974, the IRA bombed a couple of pubs in Guildford in Southern England because they were known to be frequented by members of the British military.  Four soldiers and an innocent plasterer were killed.  A few weeks later, the Metropolitan Police, incapable to identifying the perpetrators of these crimes, had themselves a razzia and rounded up four Irish people (the Guildford Four: Gerry Conlon, Paul Hill, Patrick Armstrong, Carole Richardson) living in England. A few days after that they identified another parcel of seven friends-and-relations of Gerry Conlon (the Maguire Seven) and accused them of running the bomb factory that made the gelignite. On the way home last night, I listened to an interview of Daniel Day-Lewis who played Conlon in In the Name of the Father the film of Gerry Conlon's book.  He was asked if it was true if he had slept in prison while filming.  It's a reasonable question because Day-Lewis really gets into his parts: he learned Czech while filming Unbearable Lightness of Being, and carried a long-rifle all the time while shooting The Last of the Mohicans as well as learning how to skin a deer and build a canoe. DD-L's reply was a bit round the houses about how he found it really difficult to get into the mind of a man who, totally innocent, would confess to a murder he didn't commit.  But then he came to the point: no he didn't sleep in prison because every ten minutes for three consecutive night someone banged on the door of his cell with a tin cup and then he was interviewed by two ex-Special Branch policemen for 8 hours.  He then felt he understood, even if all his experiences were play-acting, why Conlon and the others would sign confessions to a string of suggestions put to them by their interrogators. You don't need to waterboard, or pistol-whip people to get them to condemn themselves.  You can achieve what you want by depriving them of sleep and threatening to shoot their family back home in Belfast.

The British Government in their response to the deadly assaults of the IRA suspended Habeus Corpus and allowed The Man, under the Prevention of Terrorism Act, to hold people for seven days without access to a telephone or a lawyer while He convinced himself that the Perp had been identified. Conlon said afterwards that he could, and did, resist the pressure for 48 hours (the previous limit); so clearly the new limit 'worked'.  The Guildford Four promptly retracted their confessions but they nevertheless served as the basis for their conviction a year after the bombings. Interestingly a fifth accused, Brian Anderson, was worn down to a frazzle by his grilling and would have confessed but for the fact that his interrogator was called away for a telephone call and the respite enabled Anderson to brace up enough to resist for the whole seven days. Guildford Five sounds as reasonable as Guildford Four. no?

In parallel, another pair of pub bombings allowed the police to collar the Birmingham Six at the ferryport to Belfast and these men too were given life sentences after they confessed to whatever their interrogators wanted to believe was true.  Two days after those bombings a Marxist splinter group the Manchester Brigade of Red Flag 74 claimed responsibility but the police knew they had their men. In 1977, the Six brought a civil suit against the West Midlands Police for damages; holding that they had been assaulted while in custody.  The suit was struck out on Appeal on the principal of Issue Estoppel.  The fact that British justice chooses to dress up their law with jargon derived from Medieval French as they dress up their judges in the fashion of 1720 indicates how out of touch with modern realities the whole system can be. Lord Diplock estoppled the legitimacy of their claim because it "would otherwise bring the administration of justice into disrepute among right-thinking people".  The implication is that once the law has decided something, you can't question its correctness.  It's probably true that right-thinking people in those days were prepared to believe all sorts of demonising nonsense about all the Irish, so Diplock was weasily correct in his application of Estoppel in that case.  We lived in England in the 1980s and came home regularly to Ireland.  Our neighbours were routinely unable to distinguish between Northern Ireland where The Troubles were in full swing and the Republic where it was all Kerrygold butter and dancing at the cross-roads.  Anyway, they thought the whole island was essentially part of Her Majesty's demesne and would be incredulously annoyed that Sterling wasn't accepted to shops in Limerick.

In the early 1990s,  the Four, the Six and the Seven finally had their convictions quashed and they were set free. One of their lawyers had found evidence in police files that the confessions were drafted, sexed-up in a typescript (all full of copy-editor's amendments and re-writes) and then transcribed back into a handwritten document that looked like it was a verbatim transcript of what the accused was spilling from his bruised kidneys.  They also looked at the evidence of Dr Frank Skuse, the Crown's forensic "expert" and found "Dr Skuse's conclusion was wrong, and demonstrably wrong, judged even by the state of forensic science in 1974."  In other words, any of my final year environmental chemists could have carried out a quantitative test for nitrites more effectively than this salaryman. Skuse later sued a Granada TV programme about his contribution to the deprivation of liberty of his Irish neighbours on the grounds that a chap like him could be wrong without being negligent, as if that somehow made him innocent.

Many people in the UK are still convinced that the de-conviction was all about legal technicalities and that they know that Paddywhack carried out the original crimes. But this knowledge is almost certainly in inverse proportion to the amount of effort the opinionators are prepared to put into reading the evidence.  Regardless, there is a well-nobody-died sense of complacency about the whole sorry story: desperate times require desperate remedies and so on.  And it's just not true, because Gerry's father Guiseppe Conlon died while still banged up in chokey on the day the British Home Secretary signed an order releasing the poor old desperately sick man 'on compassionate grounds'.

Perhaps the most annoying aspect of the whole sorry saga occurred in 2000 when the Prime Minister Tony Blair formally apologised to the Paul Hill's wife for "a matter for the greatest regret when anyone suffers punishment as a result of a miscarriage of justice".  As with exonerating Alan Turing years after his death, there is a gross and grotesque smugness in apologising for what other people did in times past because it implies the we wouldn't have done the same in the same circumstances. While I was over in England, I bought a copy of Are We All Nazis? by Hans Askenasy.  It's an echo of Hannah Arendt's more widely known Eichmann in Jerusalem: A Report on the Banality of Evil. I know that if I'd been a railway-worker in Bohemia in 1943, I'd have continued switching the points or filing the bills of lading as the cattle-wagons rumbled inexorably East. What about you?

I said at the top that 21st June is the anniversary of another failure of Justice, but I'm too depressed now to take my hat off to James Chaney, Andrew Goodman, and Mickey Schwerner who were murdered 50 years ago and buried in a swamp in Mississippi.

Saturday, 21 June 2014


It's a bit says-on-the-tin clearer in Dutch than 'Solstice' which we get from the Latin
sol + sistere = sun-stand-still
but all over the world the sun appears to be at its largest departure from the equator and, in the Northern Hemisphere, it's downhill all the way from now on as it crosses the equator on the Autumn Equinox to bottom out on December 21st. You can measure the time of the sun's pause above the celestial equator to whatever degree of accuracy your instruments and your patience is capable of. Today the high-point occurs at 1051 GMT.  Next year it will be at tea-time 1638hrs.  But the year after that the Solstice won't happen on 21st June because we had to insert an extra day - 29 Feb 2016 - between the Solstices so that the seasons don't drift entirely away from the ticking of the days on the calendar.  On Leap Years, therefore, the solstice happens (late) on 20th June: in 2016 at 2234hrs.  I sort of knew that the solstice wasn't always on the 21st but, until today, I never bothered to find out when and why.

Benzene is flat

Benzene was discovered by Michael Faraday; one of his many achievements in physico-chemical science. He'd been born into a family of the respectable poor and finished a rudimentary formal education at the age of 14 to be apprenticed to a bookbinder.  He spent at least as much time reading the books as binding them and so won himself a patchy education. His story is for another time. As is the much related example of the creative spark of insight whereby August Kekulé realised that benzene must be circular in structure after he dozed off and dreamed of whirling snakes seizing their own tails. We treat here rather of Kathleen Lonsdale who proved that Kekulé's ring structure was planar/flat rather than crinkled or undulating.

Kathleen Yardley was born in 1903, just up the road from The Institute where I work, in Newbridge Co Kildare.  She was the youngest daughter of ten children of a retired soldier who was the local postmaster. It was pretty rough: Kathleen never grew tall and four of her brothers died as children. His wife eventually got fed up with his boozing and shifted herself and the children to Woodford in Essex when Kathleen was 5 years old. She won a scholarship at the end of elementary school and so was able to continue her education rather than going off to work like her older siblings. Like Jocelyn Bell Burnell after her, she wasn't able to do science at her all girl's secondary school but her mother got her into the local boy's school instead.  She was smart and won another scholarship to enroll in Bedford College of the University of London very young at the age of 16.  She worked hard but turned her stature into an asset by coxing the college rowing eight and also sang in the choir. She knocked off her BSc degree at 19 getting the highest marks in physics in 1922, indeed it was the highest mark that U. London had recorded for ten years.

This extraordinary achievement got the attention of local professor William "Nobel1915" Bragg and he gave her a job as a research assistant. Billy Bragg has a great song (HD vevo celeb version) about gender role reversal; clearly his namesake wasn't afraid of the concept 100 years ago.  Then again maybe it was a case of Caitlin Moran's idea that, if you want the most creative people, you can't exclude half the candidates because they don't have a penis.
Yardley got better support from her boss than Jocelyn Bell Burnell but support of the best possible sort for a truly creative and hard-working person. She said of Bragg 'He inspired me with his own love of pure science and with his enthusiastic spirit of enquiry and at the same time left me entirely free to follow my own line of research'.  After a few years, Kathleen Yardley married another supportive man: an engineer called Thomas Lonsdale. They agreed to follow his career rather than hers and so shipped up-country to Leeds for his work. He stoutly maintained that he didn't get married to secure the services of a housekeeper and she sat at the kitchen table doing fearsome mathematical calculations (most of us couldn't do a Fourier transform with a computer let alone with only a pencil, paper and log-tables) while he washed the dishes baked all the family's bread (like me!)and tricked about with homemade physics  and engineering apparatus. It's probably not a coincidence that the Lonsdales were Quakers. While in Leeds, she got a corner of lab in the Chemistry Department and did the ground-breaking work on the structure of benzene and published a single author paper in Proc.Roy.Soc A in 1929, when she was 26.

After a while the Lonsdales moved back to London and had two more children.  Bragg must have perked up when he heard that his star worker was back in town because he secured a chunk of money from Robert Mond, chair of the Brunner-Mond chemical company, and allocated that to sorting out some home help for the young couple so that Kathleen could get back to the bench. She stayed with Bragg at the Royal Institution for the next fifteen years and made enormous contributions, practical and theoretical, to X-ray crystallography. This secured her her DSc degree and in 1945 she was one of the first two women to be elected to the Royal Society.  In 1949 she was given the chair of crystallography at University College London becoming that institutions first tenured female professor. At the end of her career she became the first woman to chair the British Association for the Advancement of Science. Another accolade of more concrete nature was to have a form of meteoric diamond named after her. She was flattered "It makes me feel both proud and rather humble that it shall be called lonsdaleite. Certainly the name seems appropriate since the mineral only occurs in very small quantities (perhaps rare would be too flattering) and is generally rather mixed up!".

She was invited to speak at the Dublin Institute for Advanced Studies in 1943 attending a Summer School with Eamon deValera, Erwin Schrodinger, Max Born and others. She wasn't always doing science, because she spent a month doing time.  In 1943, she followed her Quaker principles by refusing to register for Civil Defense work in WWII and refusing to pay a fine in lieu.  So she had the edifying experience of scrubbing floors in Holloway. This woke her up to the grim reality of what happens in prisons and she followed Elizabeth Fry into work of prison visiting and prison reform  . . . and the politics of peace . . . as well as the day job! . . . and bringing up three children!

It's not surprising that she was an inspiration to women in science but she worked at that too: 'Never refuse an opportunity to speak in schools'.  Dorothy "Nobel" Hodgkin was unhelpfully told that she was mad to get married and try for children after her long exposure to x-rays, but drew solace from the fact that her colleague Kathleen had had higher exposure and three normal children. KL was relentlessly positive about the child-job juggle "My own research life has been greatly enriched by having been broken into by periods of enforced change. I was not idle while I had my three children; far from it. But it gave me the opportunity of standing back, as it were, and looking at my work. And I came back with new ideas." but she was under no illusions that it was hard graft: "For a woman, and especially a married woman with children, to become a first class scientist she must first of all choose, or have chosen, the right husband. He must recognize her problems and be willing to share them. If he is really domesticated, so much the better. Then she must be a good organiser and be pretty ruthless in keeping to her schedule, no matter if the heavens fall. She must be able to do with very little sleep, because her working week will be at least twice as long as the average trades unionist's. She must go against all her early training and not care if she is regarded as a little peculiar. She must be willing to accept additional responsibility, even if she feels that she has more than enough. But above all, she must learn to concentrate in any available moment and not require ideal conditions in which to do so."

She died, only 68, of cancer, maybe the x-rays got to her after all.  Bonnets Off!

Friday, 20 June 2014

Building the Box

As I mentioned, I was over in England gate-crashing a birthday party to which I hadn't formally been invited but which it was quite proper for me to attend.  In the way of having a birthday, I accumulated a ton of good wishes, a dozen cards and a few gifts. Dau.I, who knows me all too well, gave me a glossy A4 How-To book by Dale Power "Do-It-Yourself Coffins for Pets and People". The subtitle is A Schiffer book for woodworkers who want to be buried in the work, which is waggishly appropriate. I've long had the intention of making my own coffin but baulk at the idea of single purpose tools.  Queequeg the harpooneer in Moby Dick famously used his coffin as a bunk while at sea.  As a reader, I've been thinking about how I could make a bookcase about 180cm tall and as wide as a man's shoulders where the shelves could be turned at right-angles to make the elements of the lid of a coffin.  No idea what would happen to the books after they were dumped from their home - but that won't be my probby, will it?  The illustration is one of dozens which show-and-tell you how to complete the task of making a robust wooden box of a particular characteristic shape.  Although the book also points out that this is largely conventional rather than essential for function and that a right-angled box is easier for beginners and perfectly fit-for-purpose.  The pic shows the stage of lining the box with cotton-batting before stapling over the satin (or tweed woven from your own sheep) lining, so that corpse at least looks comfortable.

At the bday party, I was chatting with the local undertaker who is a bit of  a card.  For his 60th a few years ago, he received his guests from his own coffin, so there's another alternative usage idea to ponder.  I was regaling the company with a story of a pal of mine who buried her husband, possibly legally, in the orchard of their home.  She had two pieces of advice:
a) if you're using a shroud rather than a coffin, you need to assemble the ensemble on a plank because corpses tend to be bendy in the middle but with the plank two people can do all the required hefting.
b) you need a lot of cotton wool to stuff the orifices
"Not always but often" added the undertaker.  On the (il)legality of DIY burials in Ireland, my friend's advice to people who want to follow her example is to do it but do it discretely so that The Man doesn't feel obliged to respond. "It's far more trouble, physically and bureaucratically, to exhume a body than to inhume it".

It won't be my probby to deliver the eulogy at the departure ceremony either.  Nevertheless, I picked up an interesting post in Esquire on the matter, which seems to say sensible things about why you might want to do such a thing; or, if asked to do so, how you can make a better fist of it.  Check out the comments as well.  I've written in March about other end-of-life issues, in particular Advanced Healthcare Directives to help your rellies make the key life-support decisions when the time comes.

Thursday, 19 June 2014

Honey I'm home

Did you miss me?  I've been away in the country next door for 3 days and two nights visiting 3 generations of women with whom I have half my genes in common (me Ma, me Sis, and Dau.I).  I heard at short notice that my twin sister was having a knees-up in the Cafe where Dau.I works to celebrate her 60th birthday.  Those of you who are quick-on-the-uptake will realise that any birthdays are shared by the two of us (and 19 million other well-above-average people). Those of you who are little sleepy will promptly ask us if we are identical. We are (XY, XX) not. As it happens, I had nothing specific happening at work on Mo Tu We this week and so I checked RyanAir and AerLingus to see was it possible to fly to BRS or BHX and still have change from €400.  It was, just, but it meant getting up at 0230hrs to bus to DUB airport and then hiring a car at the far end and tooling about the country in a huge cloud of carbon footprint. I was then on the point of saying meh! and stopping home to mow the grass.

But then I remembered Rail/Sail which is a cunning plan to get foot-passengers to use the ferries across the Irish Sea by bundling a ticket with an onward rail journey. One way on the ferry for a car-less person is €37 but a Rail/Sail ticket for the addtional 220km to CNO (or any other similarly distant station) is only €41.  Such a bargain is to be seized before you reflect too deeply on the idea of spending seven 19th century hours waltzing across the country in leisurely zigs and lazy zags.  In order to travel on a circular tour Fishguard-Dorset-Gloucester-Fishguard, I had to board 9 different trains run by three separate companies. I don't know how they divvied up the 2x€4 among their rapacious corporate selves. British Rail now has pretensions to parity of esteem with air-travel and it is often more expensive to ride the rails.  Each station accordingly has a three letter code just like the well known IATA codes for airports.  Here are all the platforms I trod on this week with their more exotic IATA twins. I'll have to be careful ordering tickets on line in future , lest I catch the 1240hrs to Dnipropetrovsk.
Station Code Airport
Chetnole CNO Chino, CA, USA
Bath BTH Hang Nadim, Batam, ID
Stroud STD Santo Domingo VE
Cardiff Central CDF Fiames, Cortina d'Ampezzo, IT
Swindon SWI Swindon, UK
Newport, Gwent NWP Naval Station, Argentia, Newfd, CA
No IATA, no confusion with stations BPW Bristol Parkway and FGH Fishguard Harbour. It was grand altogether: I spent 16 hours locked in the rail network but that's not more than 2x the time spent getting to, through and from an airport. The view out of  the window is terrestrial and so more interesting than the clouds that are the most exciting thing you see from 10,000m up.  I've never, for one example, seen a bottle-nosed dolphin Tursiops truncatus while waiting in airport security, shoeless and beltless like a POW.

The reason I was able to keep up my implicit post-a-day contract with you, Dear Reader, was that The Beloved had offered to press the Publish button for the two posts that I had ear-marked for the days when I was travelling off-grid. I'm back in the saddle now. That's a metaphor: I have no intention of riding the rural byways of England on a horse like William Cobbett, but b'golly I was tempted on a few occasions to fling myself out of the train at the next teeny station to walk up intriguing lanes in the early Summer English countryside.

Wednesday, 18 June 2014

Stopping topping self

It's those left behind who suffer.  When I was a teenager living in rural south-east England we had a wide circle of friends. To meet them in the summer required a car and possibly a tennis-racket. I passed my driving test first time when I was 17.5 and my sainted mother allowed me to drive her venerable Vauxhall Viva about the county when she didn't need it herself.  On the way home from the 'main' road there was a straight, if undulating, stretch of lane about 800-900m long. I was interested in seeing if I could crank the old bus up to 70mph (110km/h) before the next curve in the road required a rapid deceleration.  This could only be achieved with normal tyres and a 1100cc engine if I came out of the last corner, more or less on two wheels, at a minimum of 50mph (80km/h).  I moved on to other challenges, like girls before I became a single vehicle driver-only statistic. One family in that circle of friends came through those years one short because the middle girl over-dosed herself and didn't survive. They spent the next several years, each in their own torment of agony & guilt, reliving what they could have done differently on that critical night. My driving habits were so reckless as to be suicidal but at that age you are going to live forever and don't have enough experience to feed the imagination of what might happen.

This all came back to me because I was reading an essay in Nature 22May14 called Mental health: A road map for suicide research and prevention by André Aleman & Damiaan Denys two Dutch academic psychiatrists.  They are banging the drum for us to bring suicide into the front line of our focus rather than keeping it locked in the aching hearts of survivors.  Suicide is both shameful and unexciting, so fails to attract the interest and attention of the medico-social research community. If you present at A&E with a garden fork through your foot or having a heart attack, then the effectives can do something; if it involves fancy machines and high tech tests so much the better.  Here's an interesting piece about an ER doctor who gets hit by a car and subjected to all sorts of diagnostics without anyone stopping long enough to bend over her and look carefully at the bits she was reporting hurt.

The CDC in USA claims that the cost to the economy of a suicide is just over $1million.  This figure from Aleman and Denys's article agrees with that assessment although 2/3rds of it are "intangible costs" and only 1/0000th goes towards the funerals.
Their main point about this graph is that £10million spent on utterly unsexy general-practitioner education, followed by psychological and pharmacological therapy has the potential to save 50x as much money in societal costs. These figures are based on 600 avertable deaths. Maybe "intangible costs" are the monetised value of the grief and guilt and remorse that result from a successful suicide. Whatever about the details, let us do this thing! GP training and an info-leaflet campaign can be carried out by people who don't command a medical consultant's salary.  But if the figures pan out they will reduce the numbers of psychiatric consultants required.  Everyone wins except the consultants, so it's unlikely to happen any time soon.

The other graph in the article is a map of the different rates of suicide across Europe.  It looks like the variation is substantive.  Aleman and Denys also report that in Nederland the rate of suicide increased by 30% between 2008 (N=1353) and 2012 (N=1753). They suggest that the excess is due to the financial meltdown but don't critically evaluate whether such a hypothesis stands up to close scrutiny. The effect of the 2008 collapse was demonstrably less in NL than in the PIGS economies of Portugal, Ireland, Greece and Spain.  One who like to see comparable figures for those countries for starters. Neverthless, you'd want your public health people to perk up and find out what's happening.
This also makes you think. Is it credible that there is a real difference in the suicide rate between Croatia >18/100,000 and Bosnia-Herzogovina next door >7/100,000 ?  Or is it that suicide is more shameful, and so less recorded on death certs, to the (muslim) Bosniaks than it is to the (catholic) Croats? I know that it's common for the local GP in Ireland to sign off a death certificate with "shotgun accident" or "accidental drowning".  It's only when the unfortunate hangs himself in the barn or leaves a note and an empty bottle of pills, that charity and compassion cannot soften the blow.

My pal Kevin Byrne is bloggin' now at and he has an interesting piece about the realpolitik utilitarianism of drinking, driving and isolation in rural Ireland

Tuesday, 17 June 2014


I've been on the planet for 21915 days, which I represent above non verbis, sed rebus. The ...15 days is because there have been 15 leap years since I was born.  That count requires a counter-compensation of a compensation because the planets don't talk to each other in integers and our year and our day are not directly reconcilable.  Accordingly years ending in 00 are not leap years despite being divisible by 4 unless the century count is divisible by 4: so 2000 is a leap year and I've had breakfast, but not necessarily cake, 15 times on 29th February. Apart from Francois Jacob, who died last year, I share the bday with Igor Stravinsky, M.C.Escher, and Charles "10" Eames who are all also dead and about 19 million people (many of them Chinese) who are alive - happy us.
Reasons to be cheerful

Monday, 16 June 2014


Szombathely is a town in Western Hungary which has in previous times been called Savaria (or more formally Colonia Claudia Savariensum) Steinamanger, Sombathelj, Sambotel, Sombotel, סאמבאטהעלי.  I doubt if many people are speaking Latin or Yiddish there any more but perhaps the middle four toponyms are current today.  Perhaps any Slovenes in the region could answer?  Although all the names begin with S, they have quite different etymology: Szombathely means Saturday-place in Magyar a reference to the day they held a market; Stein-am-anger, contrariwise means Stone on the green/commonage in German, the Yiddish is a transliteration of the Magyar.  And to put a Czecho-Slovakian cat among the pigeons, it's also called Kamenec, Kamenica.  And we think we're polyglot cosmopolitan when we have two names for Dublin/Baile Átha Cliath.

So, they ask, what's the deal with Saturday-market? Well, I reply, it's not just that it is the birthplace of St Martin de Tours, he of the generous cloak. It's also a place which celebrates Bloomsday.

Bloomsday commemorates the day James Joyce met the-love-of-his-life Nora Barnacle and asked her out for a date which happened on 16th June 1904 on South Leinster Street in Dublin. I doubt if that's why they planted a car-bomb there just under 70 years later. Years later when Joyce was writing his masterpiece Ulysses in Trieste, he decided that his life-in-the-day-in-the-life novel Ulysses would be set in Dublin on the day he met his beloved.  He used a copy the 1904 edition of Thom's Street Directory and his walking memory to research the locations because he was in exile from his native land. His fictional protagonist Leopold Bloom was a second generation Dublin Jew whose father Virág Rudolf came from foreign.  As a fictional creation, Joyce could have picked any town in Central Europe as the father's birthplace: Antwerpen/Anvers; Wrocław/Breslau; Львів/Львов/Lemberg.  But he chose Szombathely and the city fathers, acknowledging the honour, have a bit of a knees-up every 16th of June.  So do lots of other people in Dublin and elsewhere.  There was an enormous street party in Dublin on the centennial in 2004 with lashing for free sausages and rashers which were served picnic-style on Celtic Tiger skins. Me, I keep my devotional energies for Darwinday on 12th February 2013, 2014.

Now, I have read Ulysses: all 265,000 words of it.  It's about as long cover-to-cover as The Blob and if you find me obscure and convoluted at times, you should try Ulysses!  Actually, unless you're doing it in college with a group of students and a competent teacher and a bunch of commentaries, I wouldn't recommend Ulysses unless you've over 40.  A lot more of it passed over my head when I ploughed through it as an 18 year old, than when I dipped in again at twice that age. But I can't be bothered to read it again and again. I'd rather be flitting about making sense of my real world than trying to get a grip on one man making sense of his fictional world.

I'm posting this early so you have time, like Leopold Bloom, to fix some mutton kidneys with a fine tang of faintly scented urine for breakfast, burned for verisimilitude if you are a purist, and not fill up on toast.

Sunday, 15 June 2014

Mary Somerville, the first scientist

Mary Fairfax was born in 1780, the daughter of a British admiral Sir William Fairfax. In keeping with her times and class, her brothers were educated for university while she was expected to learn how to sew and look pretty enough to secure a husband. Unfortunately for everyone's peace of mind she developed a passion for mathematics and physical science while still a child.  Her father returned from yet another stint at sea to find that his elder daughter was 'a savage' and sent her across the Firth of Forth to a boarding school for ladies at Musselburgh.  She spent her tenth year there learning the rudiments of French and English grammar and little else. When she was allowed to leave she felt "like a wild animal escaped out of a cage", and that was the end of her formal education.  A few years later, her art teacher introduced her to Euclid, so that she could master perspective, but she found the mathematics a much more interesting challenge than getting her painting correct.  She scrabbled an education eavesdropping on her brother's lessons with m'tutor and was often quicker at the answers than he was.

She married a naval officer, Samuel Grieg, in 1804 who shortly afterwards died leaving her with a substantial inheritance and two sons. This gave her an independence uncommon in those days when a woman might be transferred from father to husband at marriage along with some furniture and couple of horses. In 1812 she married William Somerville an army doctor with an interest in science and he was much more positive in his support of her researches than the men of her previous lives.  The couple travelled and met many of the great men of science of the day, including Jean-Baptiste Biot and Pierre-Simon LaPlace.  Laplace was a giant of science in his day, called the French Newton, le meilleur mathématicien de son temps en France and other flattering terms.  All you chaps who have jumped on the Bayesian statistics band-wagon should realise that it was Laplace who really thrashed out this branch of probability.  After an earnest to-fro about the physics of space between Mary Somerville and Laplace he is supposed to have said "There have been only three women who have understood me. These are yourself, Mrs Somerville, Caroline Herschel and a Mrs Greig of whom I know nothing."  Ho ho: make that two women, M.Laplace.

Mary Somerville went on to translate Laplace's Mécanique céleste into English, but more importantly her The Mechanism of the Heavens elaborated and illustrated Laplace's great work so that it was readily understandable by people who didn't have a brain the size of a planet: it was read with advantage by people who were fluent in French. This provided an enormous service to the progress of science: making things easier to understand is not the same as dumbing it down.  Or as she said "I translated Laplace's work from algebra into common language". She had found her métier - the exposition of science.  She went on to write three more immensely readable books "On the Connection of the Physical Sciences" (1834); "Physical Geography" (1848); "Molecular and Microscopic Science" (1869) which all made money for their publishers.

In his review of  On the Connection of the Physical Sciences in 1834, William Whewell coined the word scientist because clearly "men of science" was no longer able to ring-fence all the workers at the coal-face of science.  I think she was a woman you had to know to appreciate. The record shows that she didn't make any big discoveries herself but she made an enormous impression upon her contemporaries.  Shortly after her death, a committee of Oxford dons named a new non-denominational college for women after her.  Somerville College is now co-educational but has a startling list of alumni including Britain's only female Nobel scientist  Dorothy Hodgkin.

The Blob's Women in Science listing.

Saturday, 14 June 2014

The last refuge of the scoundrel

A month ago my street cred at The Institute was given a boost because I had organised a conference which brought all kinds of VIPs from the major Universities of the country to our humble education factory in the Midlands.  The conference was awash in the cross-discipline of bioinformatics and molecular evolution in which I spent twenty-five years swimming, and it was great to be able to host all my pals and Bring The Word to our own students.  One of the key analytical tools of the field is the idea of multiple sequence alignment MSA which enables you inter plura alia to track details of the evolution of protein sequences. This tool has been seen by our colleagues in the Arts Block as having value in comparing text as it accumulates typos with each transcription. Before printing, which is long-and-long before computers, copies of texts, sacred and profane, were made by a hand holding a quill pen and errors used to propagate. MSA has been used to identify the original copy of Chaucer's Canterbury Tales from among the dozens of manuscripts which have survived. That's scholarship. I've also used the technique in a weirdy way to compare the order of digits in the transcendental numbers e, Phi and Pi.  I still don't know what my analysis means and encourage my highly intelligent Ukrainian and Russian readers to stop bickering about Crimea and help me out on that one. спасибі! or even спасибо!

Now I'll park the numbers and get back to aligning and comparing plain text to see how it evolves in recent historical time.  I didn't know much about the Pledge of Allegiance which American school-children do at the beginning of every school week, except that The Boy pledged it with everyone else when he was in primary school in Boston 30 years ago.  I didn't twig, for example, that it is a comparatively recent addition to the political landscape of the USA. It was invented by a Baptist minister turned socialist called Francis Bellamy in 1892 as part of the celebrations of the 400th anniversary of the arrival of Christopher Columbus in the New World. Bellamy agonized about the exact wording; filleting part from Liberté Egalité Fraternité because he knew that equality was a long way in the future for a) women and b) blacks in his country. "Indivisible" acknowledged that the nation was still smarting from a bloody Civil War which had ended less than 30 years previously.
His original version was simple, sincere and accompanied by a salute which required each child to raise his/her right hand towards the flag. Ahem! That was changed during WWII yielding the high-ground of expansive salute to mein Führer and his brown-shirts; but replacing it with a hand to the chest which, to me, has equally embarrassing overtones of breast-beating.  Over the next 60 years, The Pledge got longer and more obvious and idiot-proof until, on this day 60 years ago. President Dwight Eisenhower added a final nail by inserting "under God" after "one nation". So Jefferson's Republic finally and explicitly became a theocracy, and 14th June is designated Flag Day to recognise the adoption of a flag by the founding fathers on that day in 1777.

Here's an MSA generated by ClustalW and tweaked by me afterwards to show where and when change accreted to the Pledge between 1892 and the present day,
1892  IPLEDGEALLEGIANCETO-MYFLAG--------------------------AND--THE
1893  IPLEDGEALLEGIANCETO-MYFLAG--------------------------ANDTOTHE
      ******************* : : .                           ***  ***

      *********************************        ******************

Catechism: Do I mind if people believe in god? Do I think that religion is a private matter? Do I see parallels between theocratic states such as Iran and the USA?  Is that something to be concerned about? Am I a little uneasy about saluting flags, singing national anthems and wearing uniforms?  Do I remember Dr Johnson's definition of Patriotism?