Thursday, 31 July 2014


And the captivity of this host of the children of Israel, that are among the Canaanites, even unto Zarephath, and the captivity of Jerusalem, that is in Sepharad, shall possess the cities of the South. Obadiah 1:20.

This is the only mention of the place Sepharad / Sefarad / Sfard in the Old Testament.  But like early American settlers named their towns after places in the Bible (Lebanon NH, Dothan AL, Salem everywhere), the Iberian Jews referred to their home-place as Sefarad and they themselves accordingly became Sephardim (  סְפָרַדִּי) which distinguishes them from the Ashkenazi Jews of Northern Europe. They landed up here because Islam was particularly tolerant of any monotheists "the people of the book". That's not to say that Muslims are notably anti-anti-semitic, they can't even extend tolerance to different sects (Sunni, Shi'a) of their own religion and nor can Christians (Cathars, Catholics, Protestants, Quakers). Al Andalus ( الأندلس‎,) was a Garden of Eden and pleasure to live in or see, and after the 70 AD expulsion of Jews from Palestine by the Romans in a Stalinist relocation, many of them finished up in the paradise that the Emirate of Cordoba [in about 1000 AD all the green bits L] was making out of the peninsula. The next 500 years was a long drawn out process which gradually whittled the Empire of the Arabs to a tiny enclave in Granada. This reconquista is marked by the many towns and villages across Spain with the suffix de la Frontera. Jerez de la Frontera is where they make Sherry, for example.

Los Reyes Católicos  Fernando II de Aragón e Isabel I de Castilla united the Christians for the final push South and gave the Muslims a good drubbing at the Battle of Granada in late 1491, which led Emir Muhammad XII, whom we know as Boabdil, to surrender the city and the complex of rich agricultural holdings in the surrounding countryside to Ferdinand and Isabella (everyone in this story gets their name mangled).  The treaty of surrender was pragmatically tolerant and allowed the Jews and Muslims to retain their holdings. Pragmatic because the Muslim peasants were the only people with generations of experience managing the irrigation system. But within 3 months the Catholic Kings got a bee in their bonnet about the Jews and on 31st March 1492 signed an edict of expulsion to take effect four months later on 31st July the same year. Which makes them a tiny bit more compassionate than Idi Amin expelling the Ugandan Asians with 90 days notice in 1972.  It took just over 100 years before the patience of the Catholic hierarchy for converting Muslims finally reached the end of its tether and the remaining followers of The Prophet were also expelled in 1609.  Those of both faiths who chose to remain had to convert and became Nuevo Cristianos or Conversos.  If you think that Anne Frank had a hard time hiding away for 4 years in Amsterdam, reflect on these people having to live a double life for generations. The Inquisition would be happy to take denunciations from the neighbours if they were seen to refuse a pork chop or behave a little strangely at Easter / Passover.  Those Sephardim who weren't knifed for the diamonds they were rumoured to have swallowed, took their faith with them and went to seek their fortunes elsewhere, notably in North Africa and the Ottoman Empire (Thessaloniki, Smyrna, and Sarajevo absorbed many). They also took their language Ladino which is based on medieval Spanish the way Yiddish is based on medieval German.

Now here's coincidence that has bothered me for a long time. 1492 is one of the dates that everybode kno, like 1066.  Because
in fourteen hundred and ninety-two
Columbus sailed the ocean blue
which at the time was a small-small thing compared to the momentous events in Al-Andalus but a giant step for mankind. There is a bit of whisper that old Cristoforo. who was born in Genoa but didn't speak Italian and left a weird will, was Jewish and that he sailed on the first tide after the Alhambra Degree became absolute. Now that's not true!  He waited until 3rd August.

So far, so far away. But the Spanish government, for reasons which are beset with fuzzy-thinking, are in the process of passing a law to give Spanish citizenship to the descendants of those expelled more than 500 years ago.  There is an estimate of 225,000 being the Jewish population of Spain in 1492, and there are 45,000 now.  But the Irish diaspora, running the Chicago police department and supplying an occasional POTUS, outnumbers the current inhabitants of the island by at least 10 to 1 and possibly double that.  So the bureaucrats working under Spanish Minister of Justice Alberto Ruiz-Gallardon will have to work out the logistics of his sentimental gesture (see also Turing, and Guildford for further examples of revisonist nonsense|). Someone has published a list of qualifying surnames in Israel and there has been a lot of interest. Apparently the ability to speak Ladino will also allow you an EU passport. As Judaism is a matrilineal religion (because everyone knows who your mother was but your father could have been the milkman), then I can imagine an enterprising company getting a kit to test the mitochondrial genome (which is inherited from the mother because the sperm delivers no mitochondria to the fertilisation process) for "Sephardism".  Testing the Y chromosome is as irrelevant as looking to the surname for establishing Jewishness.

There was a minor scandal in 1990s Ireland when the Prime Minister Charles Haughey organised an Irish passport for a Maltese businessman who had been generous to his Fianna Fáil party.  If my pal Malpica is correct in his assertion that Spain is much better at corruption than the Irish, then there is going to be an unseemly scrum for Ladino classes in South America.

Wednesday, 30 July 2014


My first job after my PhD was in the Genetics Department in the University of Newcastle upon Tyne. It was the quintessence of a Red Brick University - staffed and studented by ordinary people and integral to the local community.  The campus was on the very edge of the downtown shopping district which meant we could support the economy on our lunch-breaks.  But it cut the other way also, because every Thursday evening in term-time there was a Public Lecture in our biggest theatre.  The lectures could be, and were, about every topic under the sun and I made a point of going to them all - you never knew when it was going to be a blinder. It was all quite formal, with a Chair to introduce the session, and a vote of thanks afterwards.  One night, the speaker discarded the lectern and microphone and came forward to sit on a big mahogany desk at the front of the stage. As he swung his feet and asked for the next slide, he told us the story of his discoveries in East Africa and got starry-eyed and insistent about the importance of dietary fibre in the prevention of colon cancer - complete with pictures of a cross section through a flush-toilet containing "a floater" to indicate how we were to know if we had sufficient fibre in our diet.  It was the funniest, most engaging and most informative talk that year. His name was Denis Burkitt and he came from a family of evangelical christians in Enniskillen.

After WWII service in the RAMC,  his vocation insisted that he stop in Uganda to help the dispossessed.  One day he treated a small black child who had a tumour at the angle of the jaw.  The next day, looking out of the surgery window, he saw another child with a similar growth.  As he'd never seen such a condition in a child back home in the WEA, he was disturbed and intrigued. Not unlike William McBride noticing several limbless infants and eventually fingering thalidomide. As such tumours were untreatable at the time, it might have been more sensible to concentrate on diseases where his training could make a difference.  Burkitt on the contrary went up to head office in Kampala to dig out all the records of childhood cancers in the archives of the medical service of the colony. There were lots, but they weren't everywhere, so Burkitt went along the road to the Surveyors Office and got a map of the colony on which he marked each case with a cross.  A few sleepless nights and gnawing at the data and he twigged that the tumours were much more likely to happen in regions which had year-round hot and wet weather: regions where malaria was endemic. He assumed that he was dealing with a something that was transmitted along with the malarial parasites by the vector mosquitoes that hatched in large numbers where warm puddles were ever-available.  He was wrong, wrong almost right.

In 1961 he went to London on leave and gave a talk about his work at one of the medical schools.  This lit a fire under a young chap called Michael Epstein who came up to talk to him over a cup of tea afterwards.  Epstein was primed because he'd spent some time working with Rous Sacroma Virus which had been shown to cause cancer in chickens.  Epstein conceived the ambition of being the first to show a cancer-inducing virus in humans and arranged that Burkitt would air-freight samples of tumorous tissue from Kampala to London on a regular basis.  Nothing Epstein or his PhD student Yvonne Barr could do enabled them to isolate any sort of virus from these samples . . . until the day Heathrow was fog-bound and the Kampala flight was diverted to Manchester.  It was two days before the sample arrived at its destination and if looked 'off' - cloudy like it had a bacterial infection - and Epstein almost threw it away.  But a look down the microscope showed that the cloudiness was free-floating cancer cells and that was the first step in being able to see virus particles in the cells when viewed with a powerful electron microscope.  It's a type of herpes virus and now named EBV - Epstein-Barr Virus. Burkitt was wrong to believe that EBV is transmitted by mosquitoes because it turns out that we all (90-95% of adults) have EBV about our persons, but he was right about the malaria connexion. When the child's immune system is under siege from malaria, the EBV can multiply sufficiently to do its damage. It's like MRSA which at least 30% of us have ready to sneeze. That wasn't the end of the story, you can fill in the spaces here, en ook hier.  EBV is the cause of infectious mononucleosis (aka mono or glandular fever) in teenagers - if you haven't had it, you know lots of people who have.  It is also associated with a variety of auto-immune diseases including lupus.

Epstein didn't get a Nobel Prize (although it was a possibility) but he did become Sir Anthony Epstein CBE FRS (giving him parity of esteem with Jocelyn Bell Burnell) and nor did Denis Burkitt who is dead these least 20 years, so out of the running. Yvonne Barr seems, like Beatrix Potter, to have left science shortly after her one great contribution and married a bloke from Melbourne.

This is what makes science so fascinating.  It's never as simple as it seems at first sight.  Nature yields her secrets best to those who are observant, creative, all-the-hours hard-working, communicative, generous . . . and lucky.

Tuesday, 29 July 2014

Hill Top Farm

Hill Top Farm in the English Lakes is the enduring legacy of now world-famous writer and illustrator Helen Beatrix Potter.  She is famous for her ditsy children's books, starting with Peter Rabbit [L].  Luckily her family "had money" because when she hawked her biologically accurate anthropomorphic cutesies round the publishing houses of late Victorian London nobody was interested.  For £11 she published a limited edition which was very well received by family and friends. Publisher Frederick Warne accordingly "took a risk" and have been coining it ever since.  £11 sounds like buttons, but an agricultural laborer in 1900 was bringing home less than £1 a week, so it helped to "have  money".

You could do worse than hunt out the film Miss Potter starring Renée Zellweger and Ewan McGregor (full film in ten etiolated fragments with eSpanish subtitles): it's got a lovely sound-track, no car-chases and an upbeat ending: my sort of film but fluffy. The up-beat ending hinges on the fact that with the proceeds of her books she accumulated a huge land-bank in the English Lakes starting with Hill Top Farm which is now the centre for coach-loads of groupie-tourists.  She was rich, she was astute and she didn't alienate too many of her neighbours. She bought the abutting farm and then other parcels of fells and valleys to something in the region 1700 hectares. She sank further money into developing these, occasionally moribund, holdings into productive farms mostly given over to sheep but supporting a sustainable mixed economy of other livestock, quarries and timber.  When she died in the middle of WWII she made over this incalculably valuable resource to the National Trust and when her husband died 18 month later, the rest of the estate came to the NT as well. The picture shows them the day before they got married. It is likely that, but for this vision and generosity, there would be nothing for the tour-buses to bother with in the English Lake District.  Her reputation for sheep-breeding and -husbandry was legend in the region and she was often asked to judge competitions at agricultural fairs.

It might have been different, she might have been a scientist. Indeed, some people claim that she was a scientist who made significant contributions to the study and identification of fungi, especially in their associations with algae to form lichens. In those unthinkingly sexist times, women were widely believed to lack the intellectual capacity to follow a logical argument, gather reliable data, or form and test hypotheses. Miss Potter was born the same year as Maude Delap over in the West of Ireland who made waves in the world of the development and reproduction of Cnidaria including jellyfish. Because Miss Potter was very well-connected in Victorian London she was able to get alongside competent mycologists and other naturalists with whom she bounced her ideas around. What she learned from these learned men about physiology, development and evolution undoubtedly improved the accuracy of her drawings. That's an interesting comment on the psychology of perception: you can't draw what you can't see and you can't see what you don't understand. One of these insiders read her single scientific paper "On the Germination of the Spores of Agaricineae" to the Linnean Society in 1897. She was not eligible to do this for herself because she lacked a penis. Some comments were made on the paper and, as was normal practice, it was returned to the author for revision.  She withdrew the paper from the publication process and it seems to have disappeared, so nobody is quite sure how much of a contribution to the study of fungal development it was. She continued to draw fungi and lichens with meticulous care and attention to detail but didn't always know what she was recording. Her career in science was thus not meteoric, but it was handiXXapped from the beginning.

The other intriguing thing about the young Miss Potter is that for about 15 years from the age of 14, she kept a secret journal in a code of her own invention.  That's pretty determined: to write 300,000 words (about equal to the contents of The Blob) in an idiosyncratic code so that her parents wouldn't be able to intrude on her mind, the way they assumed the right to intrude on her external life. This diary stops abruptly 4 months before the Linnean Society escapade. I think she found her métier in recording the natural world that she loved and indeed just being in the natural world that she loved. It is unlikely that she would, given the prevailing inertia and prejudice, have had a more fulfilling life climbing mount impossible in Edwardian science.  And I for one am grateful to her for the many happy days I spent on top of the world in the English Lake District.

Monday, 28 July 2014

The Edge: not an abyss but a place to fly

You wouldn't think to look at his appreciative and confident smile (he's just taken a huge ovation at TEDxHollywood in June) that this is a man with problems. In his talk, however, he itemises a list of handicaps any one of which would be devastating for people like me: he's blind, he's paralyzed, he's bald and he's from Nor'n Ireland. But in the same way as Stephen Sutton was not defined by his cancer, Mark Pollock is not defined by his problems. He's not even defined by his solutions, he's just himself: kind, funny, and courageous. He's also outrageously sporty (me = not): winning rowing medals at the Commonwealth Games 2002 ; six marathons over a week in the Gobi desert 2003; running to the South Pole 2004. A bit of an all-rounder like Zatopek? You might think that pitching out of a second floor window and breaking his back in 2010 would put a stop to his gallop, but not so. He's bored in his wheelchair (not to mention the pressure sores) and has spent the last many months in California being a guinea-pig for a pair of robotic legs. Supporting this endeavour has gotten thousands of people across the world off their sofas to Run in the Dark.  It's about getting his mobility back, yes, but it's also about developing a technological solution to paralysis and other forms of leglessless.  I'll recommend another TED talk by neuroscientist Stuart Firestein on the Joys of Ignorance and telling science like it is ("farting around in the dark"), not the way Scientific Method textbooks say it should be. He says something interesting and Pollock-relevant about how techies have taken the last 30 years to reproduce in machines many of the attributes that evolution has taken 2 million years to make functional: face-recognition, auto-focus cameras, how things smell.  But he admits that getting robots that walk without tripping over their own wires has been a very great challenge; but galloping (yee-har) they can do.

And you might wish that, rather than talking at a TEDx event to relatively ordinary citizens (although ticket prices were a humpin' $250) from LA, he was pitching to a TED proper meeting where only the seriously rich can afford the $6K annual membership. Chris Anderson, please note.

What does it take to make a contribution to that sort of science? It takes Mark, so far, 300,000 steps. The same year Mark was running to the South Pole, I was walking along the Camino de Santiago. That trudge of 800,000 steps did me some service although one of his steps was equivalent to 500 of mine, blisters and all. There's also this comparison:  almost every day in Spain I met people on the Camino who had to dig deep into their reserves of courage to carry on with their personal pilgrimage: not only those on crutches and wheelchairs or terminal with cancer but also those surrounded by a black cloud of sadness and despair. Mark's trials (both in the sense of experiment and tribulation) in California are going to make a difference in Kampuchea without him ever going there. But more importantly Mark makes a difference because, like Open University, the RNLI and the Jack&Jill Foundation he shows us the best of what we have within ourselves.

What counts in life is not the mere fact that we have lived. It is what difference we have made to the lives of others that will determine the significance of the life we lead.”  Nelson Mandela

Sunday, 27 July 2014

Legless in Kampuchea

Nearly 3 million people have tuned into TED to watch VS Ramachandran talk about the weirdness of how our brain makes sense of the world. A couple of them are me because I had occasion recently to cite the great neurologist for his thoughts on the intrinsic meaning of the sounds of language.  In the same talk (from about 9:30 minues), he refers to his extraordinary work on phantom limbs.  This is firm belief of amputees that the limb is still there.  They can feel it so clearly that all kinds of aspects of their lives are forced to accommodate something that isn't there.  That's what we do all the time, we try to make sense of the world and come up with rational narratives to explain random events that have happened to us.  It is too much to allow that shit happens - there must be a reason.  If you seed the idea that entirely ficticious events have happened to people - they went on a trip in a hot-air balloon as a child - they will not only come to firmly believe that it happened but invent all sorts of reasons why it happened - Uncle Jim was in town and took the kids for a treat etc.

That would be curious or mildly amusing except that a large proportion of amputees experience their limb as twisted in agony to such an extent that their quality of life falls through the basement into a hell which you and I can barely imagine.  Well, of course, everyone said, that's because you've sawed off the leg and the nerve endings including pain receptors are still raw and still transmitting.  So for years the standard treatment was pain-killing meds.  But Ramachandran and others have shown through a series of damn-clever experiments that the pain is not peripheral but generated in the brain as it tries to make sense of the fact that part of its familiar body is missing.  Motor signals sent to the missing part have no visible effect and the cognitive dissonance is interpreted as pain.  It is similar to the effect when our eyes tells us that the floor on the ferry is horizontal while our semi-circular canals are telling us that it is heaving about in a storm.  The result is queasiness or even what Australians call a technicolor yawn.

Clever experiments are all very well but the neurologists tried a creative therapy based on a low low tech appropriate technology.  They hid the stump behind a mirror in such a way that it looked to the patient like there were two mirror-symmetrical limbs available (situation normal, therefore).  A short course in training - telling the patient to move both limbs in synchrony creates a feeling of oh look my phantom limb is moving under my command. After a while - a matter of weeks - in some people the now under-central-command limb no longer feels painful. I guess the unfortunates who have lost both legs are beyond this therapy.

Ramachandran mentions the Iraq war as a source of missing limbs but you can finish the TED talk and reckon that this is just a quirky anomaly that affects a small part of the case load of this adventurous neurologist in California. California is a long way from Cambodia. But hey, if you want people without legs, then Cambodia is the place to be.  Three decades of war strewed the countryside with twice as many land-mines as people to step on them.  It was one of the places that exercised Princess Di before she died and also helped put in place the Ottawa Treaty which repudiated the manufacture, use or stock-piling of anti-personnel mines. It has been signed off by 150+ countries, so it should now just be a case of cleaning up the residual mines with a minimum of lost limbs and lost lives. There is a shorter list of countries that have a different way of dealing with land-mines - making money from them: why not check to see which side of the fence your own nation stands?  From a science and engineering viewpoint, landmines have been ingeniously improved over the last 60 years. Some clever engineer, for example, designed a feature that makes the explosive charge spring out of the earth to eye-level before filling the air with ball-bearings.

Anyway, that's our shame.  But I can strongly recommend that you take ten minutes out of your life to read the story of  Canadian wanderer Stephen Sumner. He lost his leg in a bicycle-car accident, screamed through several years of phantom pain, then cured himself in the parking lot of the store where he bought a mirror.  With his eyes shining with fervour rather welling up with tears he went off to Cambodia, designed a light-weight unbreakable therapeutic mirror, loaded his bike with samples and went off into the countryside. Whenever he saw someone missing a leg, he'd dumb-show his way through the way to put the pain behind. "I can’t believe no one else is doing this. It’s super-effective. I’d have thought there would be thousands of people riding around with mirrors, but there are not… What is wrong with people?”

Now what was I quoting?  "to know even one life has breathed easier because you have lived this is to have succeeded."  Hats off to Mr Sumner.  Or wave your prosthetic legs in the air: that will do as well.

Saturday, 26 July 2014

Pelvic exam

Whatever the liberals say, men and women are different, and that is nowhere clearer than in the "pelvic region" which is where "pelvic exams" are carried out.  It may seem like an absurd euphemism to refer to a process whereby a woman exposes her private parts to her doctor. But as a rectal exam is often carried out at the same time (while it is available), perhaps "pelvic exam" is the best title to cover an investigation of all the soft-tissue between the hips.  Doctors love inventing kit to make their jobs easier - stethoscopes for starters and they have to buy a speculum [R] to carry out a pelvic exam. As well as kit, doctors have a tendency to baby-talk to their patients - the Consultant Paediatrician we had occasion to visit ten years ago persisted in calling me The Dad. It wouldn't surprise me if some Ob/Gyn chaps say to their patients "I'm just going to put Daffy Duck up your wee-wee".  And did you know that they need a set of specula as well as a couch with stirrups? No, me neither.

It would not surprise you to hear that the tail gets to wag the dog. If the medico has all this gear, then he (it's still mostly he) is determined to use it; so vast numbers of, particularly American, women have for the last generation been subjected to regular, often annual, pelvic exams.  They justify this invasive procedure in the belief that they can detect asymptomatic infection and growths early and expedite their treatment. Well, the American College of Physicians has just issued new guidelines in the Annals of Internal Medicine to say that routine pelvic examinations are unnecessary if not counter-productive in normal asymptomatic healthy women.  In particular, the bi-manual (one in, one out) physical palpation of the uterus and ovaries is useless for early detection of ovarian cancer, although a pap-smear from the cervix may still have utility for detecting uterine tumours.  But a pap-smear is only recommended every 3-5 years rather annually and poking around "down there" leads to referrals to other specialists as benign masses get confirmed in their status as . . . benign masses.  Needless to say, it wasn't difficult to find a gynaecologist who found the new recommendations laughable. “We continue to urge women to visit their health care providers for annual visits, which play a valuable role in patient care” said John C. Jennings, MD, President of the American College of Obstetricians and Gynecologists, and that will be at least $125 each time, thank you. The average annual renumeration for gynecologists in the US is North of $200K.

We've seen similar turn-arounds on prostate palpation - last (and second) time I went for my M.O.T. with my G.P. he said he'd wield his proctological finger if I requested it but as it identified so many more false positives than true positives the current best practice was to rely on a test of prostate-specific antigen that would be carried out on the blood and urine samples that he took off me.  Same for routine mammograms where the detected tumours were just out-balanced by the new tumours induced by the X-rays send through millions of breasts.

Pelvic exam is held to be handy for detecting STIs like Chlamydia by the observation of a "strawberry cervix" despite the fact that only 2% of Chlamydia infections result in the inflammatory expansion of capillaries than give it a reddish glow.  Because they don't have a cervix, men are just asked for a urine sample. It's always structured easier for men.

In Ireland a fantastic amount of the annual budget (€13bn) is sent off to the department of health and every year they over-spend their allocation and rapaciously ask for more. Reducing the number of annual pelvic exams will reduce the number of Ob/Gyn blokes and they could be retrained to operate a comprehensive programme of preventive medicine.  For starters levering 8 year old children off the sofa to run 2 miles to go and buy cigarettes for their mothers.  The children are less likely to get obesity, diabetes and cardio-vascular insufficiency, the treatment of which consumes 70% of the healthcare budget AND their mothers will die earlier and be a shorter time on the pension.

Friday, 25 July 2014

Louis Blériot

25th July 1909 was a big day for my Grandmother.  The town of Dover, where she lived from the age of 2 to 108, was hopping from one foot to the other all through that Summer. The previous October, the Daily Mail had offered a prize of £1000 for the first person to fly across the English Channel in a heavier-than-air aeroplane. Several daring young men in their flying machines lined up (or lounged about throwing shapes and smokin' cigars) between Calais and Sangatte getting ready to have a try.  To put the £1000 prize in perspective, the previous year, old age pensions had been introduced in the United Kingdom at 5/- a week or £13 a year.

On 19th July 1909 Hubert Latham took off from his base at Sangatte but had to ditch in the sea when his engine failed 10km from the English coast. He was picked up by a French destroyer. Amazingly, the plane was salvaged from this first sea-landing. The weather closed in after that, but at 0300hrs on 25th July, Louis Blériot was woken up by his colleague and told that the day was auspicious. As soon as the sun rose (it was already light but the Daily Mail rules stated between sunrise and sunset) at 0441 hrs he took off and landed, hard, 36 minutes later on a bit of meadow near Dover Castle. There was nobody there except Charles Fontaine, the correspondent with Le Matin, who batted him with an enormous tricoleur. It was the first time a plane had flown across La Manche. Vive La France! Vive les aéronaute français!  Later that day, along with the whole town, my Granny scooted up to the cliff-top to rubber-neck at the latest arrival, she would have been 16.  From that small adventure, she lived long enough to see Neil Armstrong make his one small step onto the surface of the Moon.  That's a lot of change in a life time. They later put a heavier than granite memorial down at the spot - it's hideous.

Compostella 2004

On the afternoon of 25 July 2004, after taking four days to walk 105km North from the city of Tui just across the Rio Minho/Miño from Portugal, The Boy and The Blob pulled into Santiago de Compostella in NE Spain.  Here we are at the doors of the cathedral:
The chap on the left clearly has a spare tire.  Six walking weeks and 700km later, the golden-tan hat had acquired a dark organic-rich band from boiling 12kg of fat up through the top of my head, and I was in France.  The picture was taken ten years ago. Today, I have no intention of walking 20km.

Thursday, 24 July 2014

Fancy cat

I went down to visit the outlaws yesterday and one of the items on the To Do List was a visit to the Pet Vet with the grossly obese cat which was foisted on them by one of the grandchildren when that child moved house a few years ago. I've been fortunate in my own health, so that I have been to visit my GP 3 times in the last 20 years: one broken wrist, and two middle-aged-bloke check-ups. Thus, while I'm aghast at having to shell out €50+ for five minutes of medical time, it happens so infrequently that it's not too painful.

Last night we shelled out €70 to service the cat!  And I don't mean stud fees. That's the second or third visit this year.  We were persuaded that the cat needed to get her annual immunization against cat-flu and feline infectious enteritis - that was €40. When I say "we", I mean Herself was persuaded because that kind of attention for a cat is more than my thrifty Scottish granny would have been able to countenance; and I can't have the old dear turning in her grave. Immunization wasn't even on the agenda when we left home, either. Me, I think this is a bit of a bill of goods which vets push at their customers in the same way that undertakers gently persuade you that Great Aunt Maud deserves an oak coffin rather than one made out of particle-board. Nobody I know gets their healthy kids a flu jab every year. That aside, the cat was weighed in at 6 kilos and another 1.5kg bag of Royal Canin Reducing feline diet control pellets was purchased for €20.  It is a rare day indeed that I buy food for myself or my family at €13+ /kg.  Even in Ireland you can buy some fancy cheese at that rate and butcher's meat is way cheaper.  But baby's formula milk (another con) is about the same price.  On our farm, additional food for adult animals works out at 25c/kg.

The bulk of this reducing concoction is: "Rice, chicken meal, corn gluten meal, potato protein, corn, natural flavors, herring meal, flax meal, dried beet pulp, powdered cellulose, calcium carbonate, dried brewers yeast, chicken fat . . . and a smidgeon of . . . rosemary [Rosmarinus officinalis] extract ".  I draw attention to the rosemary extract because another Royal Canin product is called CALM and is marketed thus: "has been specially formulated to assist in the management of stress and anxiety in the feline patient." this has "Chicken by product meal, corn, brewers rice, wheat gluten, corn gluten meal, wheat, natural flavors, powdered cellulose, dried plain beet pulp, chicken fat, fish oil . . . and . . . marigold (Tagetes erecta) and (less) rosemary extract".  There are lots of vitamins, minerals, and trace elements but I have to conclude that Marigold extract in minute quantities is claimed to clam neurotic felines.  Is there a difference between dried plain beet pulp and dried beet pulp? And what the heck is brewers rice?  Oh they mean brewer's rice: a harmless cheap filler.

The reducing diet requires the current minders of this feline pillow to feed it not more than 50g a day of the concoction until the beast starts to shed some weight.  I don't see why the old couple can't give the cat 50g of best herring instead or 50g of pork chop for half the price.  It's surely a question of quantity rather than niceties of ingredients if it is a crash-diet.

Wednesday, 23 July 2014

Throwing shapes on the map

Argentina declared its independence from Spain in 1816 and Chile two years later. The default position for establishing a 5600km boundary between these two neo-nations was uti possidetis juris: the scope of the existent Spanish provinces should determine who owned what. It's fairly straight-forward if extremely wiggly for the bulk of this border which is defined by the Andes Cordillera: the peaks and water-sheds of the mountain range delineating the issue. That should be clear except when the water-sheds tell a different story from the peaks. The last glaciation (before Spaniards and possibly before people came to S South America) shifted enough rock that some lakes which used to empty East to the Atlantic (and so be Argentine) now flow West through the Cordillera into the Pacific.
It mattered not a jot at the time because nobody was interested in recreational skiing or mountaineering.  It matters a bit more now because there is a cluster of brine lakes [R] right at the top of the border which are loaded with lithium and lithium is vital for the future of electric cars.  It's quite amicable up there so far because each country (and one for Bolivia too) has its own exploitable salars. The Lakes further South, where there is a dispute, have in general been divided in half with a straight north-south line, without much fuss.
In 1818 Patagonia was a wild and woolly place inhabited by native South Americans and fur-trappers. Darwin passed through the region 20 years later and was shocked at the lack of amenities with which the local people fended off the brutal weather.  In 1881, representatives from the Chilean and Argentine governments sat down to sort out all the disputes so that they could get on with governing and not fussing about any trifling bits of territory which were probably wholly untaxable because nobody lived there, no mineral resources were apparent and nothing profitable would grow. The "Great Powers" - in this case primarily the USA, France and Great Britain - had an interest in the outcome because they wanted to ensure that the Straits of Magellan would be freely available to their merchant shipping.  Weirdly and confusingly the US ambassadors to Santiago and Buenos Aires were called Thomas A Osborn and Thomas O Osborn respectively, and they along with their British counterparts put their oar in the water in an advisory capacity which probably meant the threat of gun-boat diplomacy.
The upshot of this desire not to put the Straits of Magellan under the jurisdiction of a single nation led to the apportionment of half of Tierra del Fuego to Argentina, so that the Eastern end of the Strait at least should be not-Chile. There had been some slack surveying of the area, including by Darwin's HMS Beagle, so that the border as stated in 1881 would have given Chile access to an Atlantic coast at San Sebastian Bay: the bright blue indentation at the N of the Atlantic coast of Tierra del Fuego (map L]. This would never do, so the border was shifted 40" of latitude West, winning Argentina some 600 sq,km of tundra which is less than 4km wide at its narrowest point beside the Bay. Everything South of the Beagle Channel (the narrower wigglier navigable strait between Atlantic and Pacific) was assigned to Chile while Staten Island, 30km East of the point of Tierra del Fuego, became definitely Argentinian.

Those old enough to remember the Falklands/Malvinas War in 1982 will not be surprised to hear that the 1881 treaty, which was signed on 23rd July in that year, was not the end of all disputes. "All the islands south of the Beagle Channel" depends on where the channel ends and the open ocean begins.  The map [R] shows Picton, Lennox and Nueva island, which have at various times all been claimed by Argentina as being not Chilean. The yellow arrow identifies Snipe Island, an uninhabited islet which in 1958 came close to precipitating a war between the two nations over who had the right to erect a navigational aid in the form of a lighthouse.  For the last 30 years the Tratado de Paz y Amistad de 1984 entre Chile y Argentina, mediated by the Pope JP II and his representative Cardinal Antonio Samorè, has held the peace in the region. Huzzah!

Tuesday, 22 July 2014


Because it's Edward Hopper's birthday, it's time to tribute-by-parody his best-known painting. You can google up other works inspired by Nighthawks 1, 2, 23. But don't be fooled into thinking that Hopper was only about slightly depressed, gritty-realist urban scenes.  For far horizons to the imagination check out his lighthouses.

Mountain goat, mountain sheep

A weekend in intimate contact with a competent guide took me back 25 years. Towards the end of our stint in Newcastle, The Beloved and I crossed the Pennines for a weekend in the English Lake District. We stayed in a farmhouse B&B, which had been in the same family for several  generations. Then, as even more now, it's impossible to make a living from traditional farming and the B&B was part of the economic diversification that enabled that family to continue to live and work where their people were buried. The man of the house also acted as a guide on the fells and on the Sunday he offered to take us to the top of Scafell Pike, the highest point in England (not the same as the top of Scotland or Wales both of which are higher).  At the end of the day, we were a little taken aback to be asked to stump up £60 (or some such king’s ransom) for the pleasure of our host’s company for a day.  But that was his business and we sh/could have seen it coming.  ANNyway, I learned a lot that day about local history, geology, geography from the sweeping view from the top but I can’t remember a thing about that.  Two things have, however, stuck with me: the first is sticks.  This professional hill-walker in his late 50s used two ski-poles to spread the load as his limbs propelled his frame uphill.  When he was younger, he said, he’d yomped across the hills like a mountain goat but now he felt that his knees could use a little support.  He was an early adopter of these props.  Now, in the Blackstairs ‘mountains’ , the modest rise of which surrounds our home, every third person uses them.  But most of these same pole-carriers are kitted out for months in the Yukon: gaiters, gortex and a compass, maybe a survival bag, water, food for two days. When she was seven, Dau.I, admittedly on a sunny day, walked barefoot to the top of Mt Leinster 620m vertical / 5km horizontal above us.  Which kind of begs the question: How difficult can you make it?  How much clobber do you wish to encumber your day?  Not to mention the fact that, with all this back-up and a mobile phone with GPS, hill-ignorant folk are tempted to take risks that put them beyond their competence and in danger.

The other thing I learned that day is that you don’t need to be a sheep. The Lake District is within 90 minute’s drive of maybe 5 million people which makes for a lot of foot-traffic.  As we approached the top of Scafell, the grass got more worn, and the path more obvious.  We came across a cairn of stones beside the path and in the clear summer air noticed a line of these mini-mountains pointing towards the summit.  We both paused a dutifully paused and added a stone to the cairn.  Our guide stepped forward, picked up another stone and cast it away.  He explained that, while we could do as we pleased, he was against making man’s impact on the lonely hills so obvious and also implying that there was only one way to the top.  His vocation, in this small matter, was to act contrariwise.  It showed me that you can critically evaluate anything that everybody knows and sometimes come down agreeing with Mark Twain: “It ain't what you don't know that gets you into trouble. It's what you know for sure that just ain't so.

Twenty years later, walking the Camino Frances to Santiago, I had many occasions to remember this revelation.  On that pilgrim highway, the flechas amarelas get so intrusive and so managing that people come to a bemused halt at any fork in the road, unable to proceed unless the route was confirmed, eventually a critical mass of pilgrims would agree that left (or indeed right) is the correct way to the City of God.  What you come to realise after 500km is that the correct way to the City of God is The Way itself.

Monday, 21 July 2014

Duffers but not drowned.

Dau.II and I spent two days over the weeklend out on Lough Derg, the lake in the middle of Ireland which is one of several that is both fed and drained by the mighty Shannon.  Readers from Ukraine and Russia may now snicker at the epithet ‘mighty’ when applied to the Shannon which is a paltry 360km long and for the last 200km falls only about 20m.  So it is only mighty in the parochial sense that it is Ireland’s largest and longest river. This Lough Derg should not be confused with the other Lough Derg which is a place for catholic for ritual pilgrimage, penance and fasting.

We were learning to sail. Along with rugby, squash, cricket and shot-putting, sailing is something “I have done” but not for more than 40 years. So I was expecting hoping it would be ‘like riding a bicycle’, something once done never forgotten. Dau.II has never engaged in any of those sports, so was by the old definition a Landsman rather than an Ordinary Seaman, let alone an Able Seaman. We arrived in Dromineer the night before, so I again had the pleasure, at 0700hrs, of seeing the lake in its mirror-glass mode.  As far as the eye could see the lake was utterly flat.  When the working day was ready to start there was a ripple or two but the lake-shore trees were without a flutter, which I think makes it Beaufort windscale Force 1, maybe Force 0.5.

On the first day, with zero wind, our instructor taught us how to start the out-board motor, which we might need anyway to get out of or into harbour or out of a fix like being caught on a lee-shore, dismasted or in a terrible hurry to get to the nearest bar for a pint.  It’s tricky enough, but no worse than a chain-saw and less likely to cut your leg off.  Then we motored out onto the lake and practiced coming up to the quay a few times.  In contrast to driving a car, there is no brake on a boat; but if you approach land at an oblique angle at a sufficiently low speed then you can turn the boat at the last moment so that the boat-side kisses the quay-side and you can step lightly ashore. No jumping allowed.
After that we returned to base for a cup of tea and some instruction on the theory of sailing.  I’d never had that formal instruction – when we were nippers we had learned how to sail in the apprentice mode – going out with someone more experienced and learning by doing.

We also learned a few basic knots. Knots are a good example of compromise.  A knot needs to be secure under the action of natural forces and readily untied when you need to release it. You could moor your  boat by whipping out a hammer and whacking a dozen nails through your mooring rope.  Nothing will shift that including yourself when you want to get out on the water again. Some knots work well only with static ropes while others will tolerate a lot of movement and still be secure. These you need: reef-knot, clove-hitch, round-turn-and-two-half-hitches, bowline.

Still not much wind but we headed out aNNyway to find some; preferably not one of those gusts that precedes a squall of rain.  Suddenly in the middle of the lake and in the middle of a windless doldrum we realised that it was lunch-time and we were all Hank Marvin’.  So we hauled down the sails, fired up the outboard and headed into the harbour at Garrykennedy which is 150m from Larkin’s bar which serves as fine a bowl of chowder as you’ll find East of New England.  That was a pretty good day.

The following was good weather for Duffers.  Sunny spells rather than a broiling hot sun; no rain; wind between Force 1 and 4 variable; the whole day to play with. We headed across the county border which runs down the middle of the lake and went to Co. Clare for lunch. Mountshannon is a strange village that has turned its back on the Lake, so that from the marina there is no visible shop or pub. You’d imagine that there were more people willing to make an honest penny from the owners of these €100,000 motor-boats that tool up and down the Shannon all summer.  There’s got to be more to the potential transactions than charging €7.50 for a toasted sandwich and double that for plate of dinner.   Where’s the water-front café selling ice-creams hand-over-fist and cappuccinos to go.  They have one of those in Dromineer and it appears to be doing a land-office business.

After lunch we beat back across the lake a little faster than we'd gone across because there was a little more wind and we were a little more competent. And despite still being duffers, we did not drown. Just a perfect day, I'm glad I spent it with you.

Sunday, 20 July 2014


From the report from Pravda about dangers in the Moscow Metro Моско́вский метрополите́н: "About 100 people die in the metro as a result of heart attacks. A cardiac arrest may occur because of the sultry air, pressure difference, rumbling trains and intensive flow of passengers. The situation reaches the critical point during summer." Pravda  Правда as everyone knows means Truth, so they must be correct

Bollix!  I hear you cry?  Is this news?  Is this unexpected?  What is the baseline?  It turns out that cardio-vascular disease is the #1 killer in Russia.  About 1 million people die of this (= heart attack) each year.  There are just over 140 million people in the country, which to me is surprisingly small: less than half of the USA and a much smaller proportion compared to the EU.  So every year 1/140 of Russians die from heat attack which is about half of all deaths from all causes.  The death rate is not untypical of Western countries at 13/1000.  What else do we need to know?  The Moscow Metro is vast and really well used: 7 million people use the system every day which is conveniently close to 5% of the whole country - not a lot of people live in Siberia while Moscow is Russia's largest city with 11 million inhabitants.  So you expect 5% of the million fatal heart attacks in  any one year to occur to Metro users.  That's 50,000 but they only appear as one of the people overcome by "sultry air" if they are actually in the Metro system.  I put it to you that the average time spent in this super-efficient mass transport system with only occasional fatal derailments is 30 minutes or 1/50 of the day.

So you expect 1000 people to suffer a fatal heart attack while using the Metro and they've only clocked 100.  Clearly the "pressure differences [and] rumbling trains" prevent heart attacks and the safest place to hang out is underground. And why wouldn't you?  It looks gorgeous. Train-spotters must live forever!
See similar tetchy argument for the death of Linus Pauling.

Saturday, 19 July 2014

Acrylamide in the chips

Pretty much everything that gives us pleasure in eating is due to the Maillard reaction: the browning on chips, roast potatoes, fresh-baked bread crust, steaks, hamburgers, roasted coffee, maple syrup, dried milk, chocolate, malted barley for whiskey and beer.  The rest of the food we eat: porridge, broccolli, boiled spuds is just the stodge and fibre: necessary but not sufficient for a diet that pleases. Maillarding occurs when the amino acid constituents of proteins react at high temperature with 'reducing' sugars like glucose and fructose.  It's not possible to write a chemical equation because, although the inputs are limited the outputs are many and varied: a cocktail of tasty chemicals that are 'mostly harmless'.

One of them is likely to be acrylamide [R] or prop-2-enamide, which was the focus of a report in RTE wireless last night.  I missed the beginning but suppose that some food-safety report must have been published warning us about the dangers of consuming this stuff.  Acrylamide in food has an interesting and quite recent history.  It is used in a variety of industrial-chemical processes and in 2002, some Swedish scientists were called in to assess the toxicity of acrylamide dust in a factory where there was a lot of it about. They cast about for a control population that was unexposed, to establish a base-line and were surprised the find that their controls were also exposed to low doses of the chemical under investigation. The source was tracked down to Swedish crisp-bread but also to the long list of tasty chow mentioned above. At around the same time, it was found that feeding large amounts to lab rats resulted in tumours in every tissue looked at.  But cyclamates and saccharine have also at one time or another been shown to cause cancer in lab rats and accordingly been banned in some countries.  Saccharine used to carry a health warning the US until proper science showed that lab rats were, in this case, a poor model for human metabolism.  Their urine has much higher levels of pH, calcium and protein and these produced crystals that damaged the lining of the bladder to precipitate the onset of cancer.

But acrylamide is not an artificial additive amenable to legislation, it is a natural by-product of baking, roasting and frying and, as a part of the Maillard reaction, may be a desirable addition to cooked food. It turns out that the levels of acrylamide fed to the rats to induce cancer was 900x greater than a reasonable person is likely to get in the diet. A number of epidemiological studies have been carried out to track the impact of a diet high in acrylamide on long-term health.  A few of these studies have shown statistically significant association, while others have not.  This is typical of associations that are so small that they require thousands of cases and thousands of controls to detect any difference. Science has an almost unavoidable publication bias - it's hard to get negative results published while positive results in a field (like diet and human health) that everybody thinks they understand will mobilise your University's publicity department to issue a press release.  This will remove all the equivocation and qualification of your findings and the Daily Mail will reduce the press release to a catchy headline and two paragraphs of excited extrapolation from your results.

The Food Safety Authority of Ireland FSAI will shortly issue a warning advising us to eat soggy chips and discarding the crusts of bread.  If you want to live forever on a diet of cabbage and porridge, you're welcome.

Friday, 18 July 2014

Research: hard work

The universe is infinite and it is the purpose of science to try to discover its truth. Whichever size of infinity you choose, it's still impossible to reveal the-truth-the-whole-truth in one lifetime of science, so each of us scientists carves out a chunk of the playing field and tries to make sense of that patch. Some scientists (some of whom are to be found homaged in The Blob) gallop freely and exuberantly across the plain hunting far and wide to tackle and bring to bay difficult prey; others gallop fast and loose in the wrong direction, bending the truth, fudging their results and misleading the rest of us. The humble foot-soldiers of science, like me, work quietly in a corner putting one tiny experimental brick on top of another to build an edifice that stands up even if it doesn't stand very tall.  It's both hard and easy: easy because with an infinity to avenues to explore you are not constrained; hard because nobody knows what the real answer is.

I put it to you that research in the Arts Block is a bit easier because the whole thing (every word written, every picture painted, every song sung) is finite and it's just a case of hunting out the primary sources and thinking about them.  Easy enough if you choose the plays of Sophocles: there are only 7 extant, the other 116 which he is known to have written having gone up in smoke when Caesar torched the library at Alexandria. Heck, there's more material in The Blob than the entire works of the author of Antigone. Like some Mandelbrot fractal recursion, you can write a whole book on a single phrase like "Standing on the Shoulders of Giants" and presumably a later author can write a whole book on a phrase in that book. Not to mention the fact that the commentaries (Talmud) on the first five books of the bible (Torah) has ballooned out into a dense thicket of points, counterpoints and extrapolations fifty times greater than the word-of-god. Nevertheless, how difficult can it be to get it right?  Too difficult, it seems.

The Beloved, who has been practicing mindfulness for years before it became both chic and debased, has just bought a book Brainstorm: an Inside-out Guide to the Emerging Adolescent Mind by Daniel J. Siegel MD.  The "MD" is from Harvard Medical School and they don't throw those into your car as you drive along Shattuck St. He's now "Clinical Professor Psychiatry, UCLA School of Medicine". Wikipedia says "Siegel is known as a mindfulness expert and for his work developing the field of Interpersonal Neurobiology." Given all the qualifications, you tend believe what he has to say. At the very end of the book he suggests that The Answer to "what a successful adolescence might look like" is a poem by "Bessie Anderson Stanley":  which I'll render as prose because it don't rhyme too good:
"To laugh often and love much; to win the respect of intelligent persons and the affection of children; to earn the approbation of honest critics and endure the betrayal of false friends; to appreciate beauty. To find the best in others; to give one’s self to leave the world a bit better, whether by a healthy child, a garden patch or a redeemed social condition; to have played and laughed with enthusiasm and sung with exaltation to know even one life has breathed easier because you have lived this is to have succeeded.".  That has a sort of Kiplingesque (if you can keep your head when all about you, tee-tum-tee-tum-tee-tum) post-card ring of truth but TB said, "that's wrong, it's written by Ralph Waldo Emerson".  That does not seem to be the case. Actually they are both wrong and, as far as I can deduce from the finite universe which is the part of the interweb which Google thinks I want to see from Ireland, it was probably written by Albert Edward Wiggam in 1951 believing he was quoting Emerson.

There are several versions of this quote and I use one of the tools in the molecular evolution toolbox, which I've used before, to compare two such:

CLUSTAL W (1.83) multiple sequence alignment
         ***************    **********************************:.  .**
         ************************************:  *********************
         ************              **********************************
Emerson  ------------------------------------------------TOKNOWEVENON
Emerson  ED
Wiggam   ED
Dang, it could happen to anyone in the days before word-processing.  You're copying something in a hurry from a printed page to make a deadline and you substitute persons / people and approbation / appreciation and the sky doesn't fall. But having been educated in TCD the home of the Book of Kells, I am aware of cases where medieval scribes made copy errors that mangled the sense of the manuscript because ther latyn was nott uppe to scratch. Here's another mol.evol tool used with effectiveness for Arts Block research.

This is probably what Ms Stanley wrote in 1905 (Wikipedia agrees):
He has achieved success who has lived well laughed often and loved much
who has enjoyed the trust of pure women, 
the respect of intelligent men and the love of little children 
who has filled his niche and accomplished his task 
who has left the world better than he found it 
whether by an improved poppy a perfect poem or a rescued soul
who has never lacked appreciation of Earth's beauty or failed to express it 
who has always looked for the best in others and given them the best he had 
whose life was an inspiration whose memory a benediction.
Sort of the same sentiment as the Emerson/Wiggam but not much better rhyming. It's easier to cite Emerson, of whom everyone has heard, than Stanley, who wrote this one thing for a newspaper competition in 1904 (or was it 1905?).  It shows that you're working at your sources if you cite minority-view Stanley but it shows that you're not working hard enough if you clip the wrong verse.

Matter a damn? Not! Except that you are now advised to take everything else that Siegel writes about mindfulness, interpersonal neurobiology or adolescence with a damned good shake of salt.  It's like if you turn in a thesis full of spelinge errurs and impenetrable grammar or ask for a character reference from someone (like me this Summer) whose name you can't be bothered to spell correctly.  These things don't invalidate what you say but they sure do make it harder to accept your statements on the nod.

Thursday, 17 July 2014


Pinch of salt time.  The math-pop writer John Allen Paulos has a great book called "A Mathematician reads the Newspapers" in which he cites examples of headlines that have brought him up all standing: "Duh, that's can't be true".  It is the sequel to Innumeracy: Mathematical Illiteracy and its Consequences which is, IMO, fresher and better but both books are informative and readable.  They help tune into nonsense.

I have two loyal readers in Russia (and two in Ukraine, so you might think that people at the further edge of Europe might stop squabbling about Lenin, Oil and The West and see how much common ground they have in reading The Blob). My interest in events in Russia is accordingly higher than my interest in events in, say, Venezuela where lots of oil is produced by nobody reads El Blob - so forget them.  If you hunt hard you will have heard about a recent derailment in the Moscow Metro which killed a couple of dozen people and is currently under investigation. One tragedy stands on the shoulders of another and many reports refer to the Aviamotornaya (Авиамото́рная) escalator disaster in 1982. In that case, new operating machinery for all escalators was being installed across the metro system including at that station.  You really need something to help mass transport in such places because the platform in 150m below ground and that's a long way to walk. There was sufficient redundancy designed into the system, but the engineer who installed the back-up emergency brake hadn't read the instruction booklet, so it was wired incorrectly. Everything was fine until one of the steps derailed and stripped off the gears of the drive mechanism putting the loop into neutral (= freefall).  The brake didn't kick in automatically and the the hand-brake was also disabled, so 100 passengers were whooshed to the bottom and dumped in a heap.  Eight people near the bottom were killed.  As it was in Soviet times, when everything mechanical must work fine because all the engineers have a red star on their lapels, the event never made the newspapers so the rumor mill clicked into action instead. Dead people on escalators must mean that they were sucked into the mechanism and turned into hamburger - and it was so . . . not!

Not believing Wikipedia, I thought to check other sites for better details and assumed English Pravda would be authoritative but this headline Moscow Metro Kills Over 1,500 Every Year is where my Paulos-trained crap-detector kicked in.  Can't be true, and it's not.  It should read Moscow Metro Injures Over 1,500 Every Year which is less exciting but less fatal. Lost in translation?

Wednesday, 16 July 2014

Cost benefit beer.

Calculation time!  It's a while since I waved my arms at some order of magnitude numbers.  Recently I was remembering the multiply-fatal Lac Mégantic derailment and left a question hanging about how dangerous is beer. In a famous incident in October 1814, 500 tons of beer Niagraed out of a vat in London and drowned 7 poor people in the local cellars.

The per capita annual beer consumption in Ireland is close to 100 lt. We're way behind the Czechs and about on par with ethnic Germans, Poles and Balts. The total quantity consumed is about 475 million litres, for a population (Republic only) of 4.6 million. Which shows how goofy some of these out-trotted statistics are: for per capita beer consumption we're talking per every head in the country including those that have just emerged from the womb.  ANNyway, every day 1.3 million litres of beer goes down Irish throats.

There were in 2011, a record low number N = 162 of road fatalities. Which is the result of an extraordinary collective effort to reduce this toll of unnecessary death - as recently as 2005 there were 396 deaths on Irish roads. In any year about a quarter of the dead are pedestrians and maybe 3% cyclists. I'd guess that half of them have drink taken so there is a drink-related death on the Irish roads one day in every five.  I've suggested before that, as the Irish government has a commendable policy of reducing road deaths and as RTE, the state broadcaster has a less commendable policy of reporting every road fatality on the national news, it would be a useful standard operating procedure SOP to report the blood alcohol level of every dead car driver.  But I'm not particularly interested in beer-induced road deaths, I trying to get an estimate of beer-induced any deaths.  Irish Water Safety are getting a lot of airtime this weather and they say 1/3 of 150 annual deaths by drowning involve The Drink. Because of their ear for ghoulish quirkiness, the RTE news-editors told us a couple of weeks ago about a young woman, a wedding guest, seriously injured because she had fallen from a hotel's first floor balcony head-first onto the roof of  car parked below. Would you agree that the odds are Lombard Street to a china orange that alcohol was involved? I'd hazard a guess that every two days there is an alcohol related accidental death in Ireland: half of them (0.5 x ~162/365) from cars, 1/6th from drowning, the rest from other situations where machinery and alcohol don't mix: PTOs on farms, chain-saws, lawn-mowers, gas-ovens, ladders and I'd guess a lot of plain young man silliness like the neknomination craze that swept one of our students to death earlier this year. Let's note that 50% of the alcohol consumption is beer, down from 70% 20 years ago - we are. like continental sophisticates, delicately sipping a lot more wine nowadays.

Thus every day in Ireland somebody gets killed because somebody has drunk too much beer (those somebodies are often the same person). Over the same period, 2.6 million litres of good ale, refreshing lager and nutritious stout have been drunk, giving hundreds of thousands of people a chance to cool down a hot curry, restore fluids after some strenuous Summer work outdoors, lubricate an awkward conversation or, indeed, achieve a temporary oblivion from their private hell.

Me, I don't think we should follow out-gone Health Minister James Reilly in banning cigarettes.  I guess the tobacco lobby have won that battle now that Reilly has been reshuffled to a different government position.  Kevin Byrne has opened the debate about imaginative proposals to balance the the cost of beer-driven death vs the clear-and-present benefit of beer in rural Ireland. Neither of us have really considered the general life-shortening aspects (cirrhosis, heart-disease, cancer, dementia) of excessive alcohol consumption: I'll clearly have to come back here wearing a different hat. There is something repellent when government mounts the white horse of moral crusade and legislates to prevent something of which it disapproves. Romeo and Juliet laws spring to mind. In framing legislation you research relevant data and extrapolate imagined scenarios and write the law in best legalese. The Irish Council for Bioethics thought long and debated hard about end-of-life issues but there will be a particular and peculiar set of circumstances that aren't covered by their wording for advanced healthcare directives.  A helluva a lot of road-miles are driven with alcohol on board for each fatality but no sane person believes that we can eliminate road deaths entirely even if we make drink-driving a capital offense.

Tuesday, 15 July 2014


I was bigging up Lynn Margulis last year because I knew her well and her course BI504 Evolution had a huge impact as I sat through it with shining eyes in graduate school. In her course, Margulis marginalised humans, indeed mammals, indeed vertebrates as a slightly boring and rather uniform wart on the edge of life's diversity.  She championed a five kingdom division of the living world: Animals, Plants, Fungi, Bacteria and Protochtista.  In 1980, when I took the course, she was happy with the first four bins but acknowledged that Protochtista was a bit of a grab-bag consisting mostly of unicellular organisms that had a nucleus (so were not bacteria) but didn't comfortably fit in the other three kingdoms: including human parasites like amoeba, trypanosomes, giardia but also various algae and things you find in pond-water. But she was wrong, and the timing shows that it takes some time for even a smart, iconoclastic scientist at the peak of her game to absorb new ideas.

Because at the end of 1977, Carl Woese and his post-doc George Fox, had shook all the toys out on the floor and started putting them into different boxes.  They were able to do this by exploiting a new technique for classifying microscopic organisms that didn't depend on growing them on Petri dishes.  It turns out that many, even most, small-small t'ings cannot be grown on a Petri dish no matter how you trick about with the ingredients in the agar. One of the reasons why everyone knows about Escherichia coli, although few can spell it correctly, is that it can be cultivated in vitro (on a glass Petri dish). E.coli, far from being the gut bacterium, in fact contributes less than 1% to your intestinal flora. Before Woese and Fox, microbiologists did nifty things looking at the size, colour and shape of colonies growing on agar in dishes, measuring the metabolic chemicals that went in and out of those colonies and looking at the size and shape of the microbes under a microscope.  I've spent a very enjoyable year in The Institute doing this C19th science with our Yr3 Food and Fermentation Microbiology students.

It took pretty much everyone a long time to take on board this radical shake-up of how we viewed the living world, but like Barbara McClintock, Woese, knowing he was right,  just kept plugging away gathering more data. Woese had been working for the previous decade and a half on nucleic acids DNA and RNA, trying to suss out the genetic code and, when that was sorted by himself and many others, churning out sequence information particularly of structural RNAs in the ribosome.  The ribosome is the biochemical machine, shaped like a teeny cottage loaf, which translates RNA into protein codon by codon.  It consists of maybe 60 different proteins held together with three strings of RNA.  In 1977, Woese and Fox published a classic paradigm-shifting paper in PNAS which suggested that although two bacteria might look identical (oval blob) down a microscope they were as different as two things can be and still come from from the same planet. In particular they recognised that "things without a nucleus" (i.e. different from us) should definitely not be lumped into the same bin. Executive summary and context by Jon Eisen.

This picture is a recent assessment of the state of our knowledge.  4/5ths of Margulis' kingdoms make up the pale green branch pointing upwards and plants / animals / fungi which are effectively the visible portion of the living world are three twigs on a limb of a branch of the whole tree. So you can see why she might have talked up a storm on W&F 1977, but as far as I remember, she did not. [I've gone back and checked my notes from the course and she did mention that the 16S rRNA from methanogens was very different - but that meant that methanogenesis was 'early'; rather than that bacteria of her fifth kingdom were polyphyletic]. The animal 'kingdom' is so well embedded in our language and understanding of life's divisions that the three major groups identified by Woese and Fox are referred to as Domains. It was intitially thought that the recently identified Archaea were ancient hold-outs from a primitive earth living in extremes of temperature, or in weird chemical stews in geologically active ponds.  It being so difficult to cultivate a given microbe in the lab, it's taken a while to realise that Archaea are found pretty much everywhere and that several species are extremely abundant and impact significantly on cycling of carbon (whoop whoop global warming alert) and nitrogen on the planet. Also note the implication that Archaea are more similar to things-with-nucleus Eukaryotes than they are to the rest of bacteria - although this view is under intense scrutiny now.

The other important consequence of the technique of RNA sequencing is that you can pull up a net full of sea-water or an aliquot from the intestinal flora or a shovelful of contaminated soil and get a good Petri-free idea of the number and types of the invisible organisms that inhabit those environments.  This bears on diagnostics, environmental chemistry and numerous other fields. Woese died a couple of years ago, but today is his birthday 15 July 1928.  Hats off!

Monday, 14 July 2014

Drafting the Professor

Youtube has many tributes to Sugru from a surprising variety of geeks and techies. And I've shown how this stuff has consolidated my inherent thrift. Here's an Arts Block story tribbing the iontach-ábhar.
Once there was a young block-head from the forest called Sceach Bunoscionn whose legs got crushed by a falling tree.  But with the help of a crutch and a walking stick he was able to hirple about without a bother, although he did get teased for the way he walked. He was as clever as wooden-top can be and when he grew up he went to technical college. There he did exceptionally well, taking courses from Forestry 101, through Arboriculture, Introductory Tree-surgery, Tree pathology, pests and parasites (TPPP), Propagation & Grafting, Vernalisation for Seeds, and on to Apiary and Pollination.  He wrote his thesis on Deforestation in Indonesia which won him accolades, not only in his own college but in the University in the capital. After several years of successful field work in Sumatra and Sulawesi, he returned to take up the Chair of Tropical Forestry at the University.  Nobody could pronounce his Irish name so he changed it to Thorn Hirple

The Professor acquired a reputation for wild eccentricity, and not only in his hair. Theatre was integral to most lectures and juggling hatchets to at least one. One day while visiting a neighbour's farm, some fiesty lambs came at him in a bunch - thinking he had milk - knocked him over and broke his arm. This allowed him to shock the students by coming to class with his fractured limb on his head. But the Provost declared that this was bringing the University into disrepute and Professor Hirple should shape up or ship out (the Provost had done time in the US Military). Hirple was mortified and went off and got legless in the tradition of Ben Battle:
And used to war's alarms;
But a cannon-ball took off his legs,
So he laid down his arms!
When he woke up from his three-day blinder in Strasbourg, he had no memory of how he'd crossed several national frontiers and found that he'd changed his name to Hagedorn Humpeln and signed up for a five-year contract with La Légion étrangère. The Legion's surgeons were able to fix his broken arm with a spot of black Sugru under the oxter. He survived basic training, grew to enjoy La Boudin [blood-pudding], marching v e r y  s l o w l y and proudly wearing his white képi. His academic qualifications were not much use, except in the Legion's table quizzes, but Sceach was not a one-trick pony and in the military his many other skills and abilities came to the fore. In the last year of his contract he was promoted to Sergeant, with white Sugru chevrons for being conspicuously plus dur que les autres mecs durs de la légion.  The Future Needs Fixing but with its extra white bracing Sgt Humpeln's left arm definitely doesn't.

Mon dieu, c'est Le Quatorze Juillet, it faut que nous chantons La Marseillaise.  If you prefer a more pillowy tribute to La Belle France, go back a year on The Blob.