Sunday, 30 June 2013

The Certainty of Myth

Today, the last day of June, is the anniversary of the 1860 Oxford Evolution Debate.  Everbode kno the story of
  • how Bishop "Soapy Sam" Wilberforce (Grrrr, hisssss, he's beHIND you) tried to diss Darwin's Origin of Species which had been published the previous year
  • how he made some heavily ironic remarks about the antecedents of Darwin and his supporters
  • how Thomas Henry "Darwin's Bulldog" Huxley (Huzzah huzzah!) rose to his feet muttering "The Lord hath delivered him into my hands" and trounced the worthy-but-wrong Bishop by turning his ironies into a potent rhetorical counter-strike.
except that there was no record kept of the "debate" not least because it wasn't a formal item on the agenda of the 1860 British Association meeting in Oxford.  It was rather part of an animated discussion after a long (and boring) formal paper presented by NYU's Prof. John W. Draper "On the Intellectual Development of Europe, considered with reference to the views of Mr. Darwin and others, that the progression of organisms is determined by law."  So there was no written speech, no stenographer, just a bunch of more or less contradictory notes, letters and long-time-after reminiscences. This gallimaufry of sources have been clagged together to become a watershed in the Intellectual Development of Europe where unthinking Judeo-Christian certainties began to lose ground to scientific rationalism. (Huzzah!).

Not many scientists of my acquaintance have, like me, won a Junior Scripture Prize at school and so they're possibly unable to recognise Huxley's sotto voce quip "The Lord hath delivered him into my hands" as straight from the bible 1 Samuel Ch 23 v 7.  Indeed Huxley, the first agnostic (he coined the term in 1869) and key Darwinist, was very keen to get youngsters to read the bible in school and elsewhere as a guide to their moral compass. On the other hand, the Bishop was a vice-president of the British Association for the Advancement of Science and a Fellow of the Royal Society - the key accolade for British Scientists - for his contributions to the science of ornithology.  We was also, like his father, a vehement anti-slavery abolitionist.  So it is hard for me to see the "debate" in black and white, bible vs science, god vs rationalism terms.  And there is at least one contemporary reference to the fact that after their set-to, all the participants went off to dinner together like the gentlemen they were.  Revisionist, less dramatic and more even-handed analysis of the day may be found here and here.

And I bet that, by the time Huxley died in 1895, several people had consolidated the myth into actual memory to believe that they had been witnesses to the altercation.  The human mind can do that.  At least some of the 10,000 extra people, who claimed to have been in the GPO when Padraig Pearse read the 1916 proclamation outside, sincerely came to believe that they had been there.  The rest were blaggers, gassers and chancers, of course.

I find the going out to dinner after an afternoon of vigorous rhetorical exercise very civilised.  Too many of today's atheist fringe of science seem to feel that those of the opposite set of beliefs are not only wrong, but deluded and/or utterly reprehensible.  I hope that the agnostics of science can continue to hold the middle ground.  There is a war going on, particularly in the USA, for hearts and minds on a scripture vs evolution axis.  If we the scientists are to take up cudgels with they the biblical fundamentalists, rejecting the bible unread as antient middle eastern nonsense is not going to fill our magazines. The King James Version is only 789.7 kilowords long, you could knock it off over the summer if you sat down to it.

Saturday, 29 June 2013

Louis Agassiz, his rep.

Louis Agassiz was born near Fribourg Switzerland in 1807.  He studied at Neuchatel, Munich and Paris under such enormous talents as Cuvier and Humboldt. In his early 20s, he carried out one of the C19th's monumentally detailed studies in describing the anatomy of Brazilian fish, brought back from a collecting expedition up the Amazon by Spix and Martius.  He also extended, codified and made true the studies of Goethe, Charpentier and Schimper on glaciers, morains, glacial erratics and cwms.  He was the first person to assemble the evidence for past Ice Ages.
When he was 40 he was was invited to lecture in America, blazing a trail that was followed by Charles Dickens, Oscar Wilde and Uncle Tom Cobbley.  But Agassiz stayed and became a professor at Harvard and founder of the inestimably wonderful Museum of Comparative Zoology.  A new biography of Agassiz by Christophe Irmscher will give you the nuance of this great, flawed, scientist, whom Irmscher characterises as distinctly undelightful.

In his day he was extremely well regarded, honored by having his name attached to a glacial lake, several  mountains, a crater on Mars, an asteroid, a couple of flies, a beetle, a cichlid fish and the desert tortoise Gopherus agassizii.  And Cambridge, Mass, named an elementary school after their famous adopted son.

He tends to get a bad press nowadays, because he continued to believe in the biblical version of the how the world came to be as we find it.  "The resources of the Deity cannot be so meagre, that, in order to create a human being endowed with reason, he must change a monkey into a man."  He annoyed the usually equable Charles Darwin (to whose ideas Agassiz was implacably opposed) to write “How very singular it is, that so eminently clever a man, with such immense knowledge on many branches of Natural History, should write such wonderful stuff & bosh as he does.”  Stuff and bosh, isn't that so 19th century?  But one of his 'attributed to' quotes "Every scientific truth goes through three states: first, people say it conflicts with the Bible; next, they say it has been discovered before; lastly, they say they always believed it." suggests that he was less doctrinaire than we'd like to cast him.

Particularly nowadays in the USA, your body isn't going to get exhumed and burned in public for espousing a belief in God-the-creator as documented in the Bible.  But another aspect in which Agassiz was a man of his time, seems to put a righteous hair across the ass of people today.  There is no doubt that Agassiz was a 'racist': be believed that "the white race" was superior to "the black race", he went so far as to commission a series of photographs of (naked) African-born slaves from North Carolina, so he had data to point out the differences.  And he lectured on the subject extensively.  There is no doubt that almost all the white people and, I daresay, a good chunk of the blacks who listened to him agreed with his thesis.  He died in 1873, 140 years ago this December. We've shifted our ground since then: we're much more of the thinking that "Those intellectual and moral qualities which are so eminently developed in civilized society, but which equally exist in the natural dispositions of all human races, constituting the higher unity among men, making them all equal before God."  Now who could have said that?  It couldn't have been the dreadful, reviled Louis Agassiz, could it?

Anyway, the Agassiz Elementary School, in Cambridge MA, was renamed in 2002 as the Maria L Baldwin School after a black woman who served as the principal of the school for over 30 years a generation after Agassiz died.  Very worthy.  By airbrushing Agassiz out of history in this way, however, it lessens the chance that people will look into their own souls and ask how racist they are themselves.  And if they come up squeaky clean in their conscience for now (it is so much easier to condemn other people than find fault in ourselves), they might then ask how they might have thought and behaved in the middle of the 19th century.  In 2010, an international petition to rename the Agassizhorn in Switzerland after one of the slaves whose photograph Agassiz commissioned was decisively rejected by the communities of Grindelwald, Guttannen and Fiesch, which surround the controversial peak.

And what's with the picture of Agassiz upended with his head in the concrete?  It looks like a statue of Stalin, Enver Hoxha or Saddam Hussein having being toppled by revolutionaries fervently giving shape to the new order.  Au contraire, Agassiz' statue was toppled from the facade of a building in Stanford University by his pal God, during the 1906 San Francisco earthquake.

Friday, 28 June 2013

Famous Primates

I've written before about Archbishop Ramsey of Canterbury. You’ll excuse me if I don’t write about Archbishop John Charles McQuaid or Cardinal Archbishop Cathal Daly at this time.  I’d rather reflect on some smart cookies who don’t really get enough press – in The Irish Catholic or anywhere else.  There’s not a lot of difference between humans and other primates, indeed we are remarkably similar to mice and aardvarks.  So anthropologists and linguists study our primate relatives in order to understand where we came from and how we got as far as we’ve got.  Linguists?  But humans are the only animals who speak – surely it’s one of the fundamental distinguishing attributes of humanity.  OTOH, you can’t in all fairness define “speech” as sounds from the larynx as this would deny the skill and hence “humanity” to those who are born deaf mute or who have had their larynx shot off in the war.  Forty years ago, reflections such as these induced Allen and Beatrice Gardner to bring Washoe, a young female chimpanzee, into their home and teach her American Sign Language (ASL).  She made remarkable progress not only learning and reliably using a couple of hundred signs but also melding them in novel creative ways to describe new concepts: fridge became OPEN+FOOD+DRINK and duck WATER+BIRD.  Later a female gorilla called Koko showed a similar facility with ASL and other primates have been taught to use specially designed symbolic keyboards to communicate.  It’s not without some controversy: Herbert Terrace worked with the wittily named Nim Chimpsky (Noam Chomsky – geddit?) and found that under laboratory conditions and perhaps with fewer leading questions and positive expectations and, well, self-delusion then Nim was not very good at all as a linguist; managing as few as 25 different signs.  One variable here is that Nim was a bloke, and it may be that male primates are a bit more set in their ways than females – look at McQuaid after all (who was a kind enough chap by all accounts but quite stiff in his theology) – and find it more of a struggle to learn a new way of communicating. 
But before we dismiss the bloke half of the primate world as hopelessly inertia-bound and uncreative, it is as well to remember Mike, a low ranking primate in the troop so intensively and insightfully studied by Jane Goodall since 1960.  One of the criticisms of Goodall’s science is that her very presence altered the local reality and left her studying something a long way from natural chimpanzees in virgin jungle.  She has acknowledged that, by feeding the chimps in order to keep them within observation range, she may have unwittingly increased the levels of aggression within and between troops – when you have a rich resource it’s worth fighting over.  But Mike used the presence of the alien interlopers to good (reproductive) advantage.  In particular, he exploited their trash and recycled his way to alpha-male-hood.  Goodall and her team used kerosene for cooking and lighting and left the empty 5 gallon tins lying around.  Mike incorporated one and occasionally two of these drums into his display rituals and scared the bejayzus out of the other males as he bounded at them through the forest batting these crashnikovs along in front of him.  So creativity and novel behaviour is certainly within the capability of males.  And isn’t that just so typical of boys: make a tremendous noise in “robust play” with a bunch of other boys.
Japanese researchers have made significant contributions to primatology in Africa.  But why go all the way over there when you have your own remarkable native primate just down the road on the Shimokita Peninsula in northwest Honshu?  Like Goodall, the Japanese researchers working on and with the Snow Monkey (Macaca fuscata or Nihon zaru) used to lay down food on the beach to attract the monkeys within sight so that they could carry out their observations.  The macaques relished the sweet potatoes but hated the sand and spent a long time brushing as much off as possible.  It took an immature female called Imo to take a sweet potato down to the sea and wash off the sand.  Not only was this much more efficient, it made the whole thing taste better and she used to dip the tuber in the water between bites.  Interestingly, and in contrast to Mike’s friends-and-relations, other macaques rapidly caught on to this useful habit.  Some more rapidly than others: the first to catch on were other immature females, then immature males, then adult females and even … finally … adult males.   We all know from our experience that intelligence is, not only multiple, but gradated.  Some of us seem to be less smart than others.  Imo is obviously one of the sharper knives in the macaque drawer because she was able to generalise her trick when the researchers replaced sweet potatoes with wheat.  Fed up with picking this delicacy from the sand, grain by piffling grain, Imo scooped up a handful of the mixture and stalked off to the river where she intuited that the grain would float and the sand sink.
The story of Imo tells me that it requires a certain hubris to believe that adults are more intelligent than youngsters.  More experienced sure, but more intelligent?  We could, with advantage, spend a lot more time watching the young and listening to what they have to say.  They are quite possibly asking questions that will be unsettling to our certainties but nevertheless worth listening to and emulating.

Thursday, 27 June 2013

Where do we come from II

One of the long running sagas in human genetics/psychology/anthropology/sociology is the nature vs nurture issue: to what extent we-are-who-we-are is determined by genetics (and more recently epigenetics) or by our upbringing.  The Lord famously answered a pestering Moses with a rather cross "אֶהְיֶה אֲשֶׁר אֶהְיֶה, ʾehyeh ʾašer ʾehyeh" which is usually translated as I am that I am (and please stop obsessing about the details).  But teasing apart the relative contributions can help in medical diagnosis and prognosis.  There is also a lot of unthinking nonsense trotted out by the press in response to press releases after interesting scientific findings.  Headlines like "boffins discover gene for homosexuality" happen
  • partly because too many journalists are Arts Block educated scientific illiterates
  • partly because they are too lazy-arsed to dig one step deeper and write some nuance for a change
  • partly because they are contemptuous of the intellectual capabilities of their readers
  • partly because universities think that having a (Arts Block educated?) press release department is desirable.

Yesterday I wrote about data for establishing the genetic contribution to our makeup.  By a neat coincidence this week the blogosphere is buzzing with a mega-neat set of maps that gives us some data on the nurture/environmental influences on who we are and where we came from. Language and accent don't appear to be genetic at all at all.  A Vietnamese girl adopted sufficiently young into a Carlow family speaks English and Irish like a native. But what elements of the environment dictate how we speak and what we call things??

 Joshua Katz, a graduate student at NCSU (North Carolina State University)  has created some 10 dozen visually appealing and informative maps of English as she is spoke by US citizens.  His data is derived from an online survey created and administered by Bert Vaux and Marius L. Jøhndal of Cambridge University in England.  You can contribute to the survey here.  As the song has it "You say tomato and I say potato, you say egg-plant and I say aubergine and they're all Solanaceae".

The Vaux project asks contributors a series of neutral questions to establish how people pronounce, and what they call, everyday things. Shown left: "What do you call the miniature lobster that one finds in lakes and streams for example (a crustacean of the family Astacidae)?"  The answers stream back: crayfish - crawfish - crawdad - dunno and get mapped by Katz. Don't you just love the use of Latin Astacidae in case the boys from the bayous are confused as to exactly what Vaux means?

I spent four years tooling around in New England and the Canadian Maritimes as a graduate student and as well as eating ice-cream by the quart and salad by the bucket, I ate my fair share of subs ("What do you call the long sandwich that contains cold cuts, lettuce, and so on?") but I also knew that they were known as hoagies, grinders, or heroes. - we were fairly cosmopolitan in the ecology basement.  But some of the answers to the Vaux questionnaire have me baffled: apparently some Americans buy their food in groscheries as if Jimmy Shtewart escaped from It's a Wonderful Life. Hours of fun there! 

Katz is clearly enjoying his 15 days of fame.  He's eclipsed all the other Joshuas when you search for his first name on Google: bigger than Joshua Tree, Joshua Foer, Joshua Slocum?  That's big.  NCSU is riding interference for their media star.  If you want to have Katz speak on your local radio station: Please direct all media requests to at the NCSU Press Office.  And Before you email, please check the FAQ.  NCSU is sinking resources into the project "Special thanks to . . . the entire team over at RStudio for working tirelessly to accommodate the insane traffic demands". 

Lucy Ferris in the Chronicle of Higher Education makes a stab at parsing the effects on her language of living for extended periods in several different parts of the USA at different ages.  Now if that sort of study could be increased from N = 1, it might give interesting insights into when our speech patterns are most labile.  Any fule kno that it is more difficult to learn a foreign language after puberty.  And what aspect of personality dictates that some Irish people adopt an American accent within days of getting off the boat and others are still lilting away decades later? 

Finally, for those who speak English English, you need to buy The Linguistic Atlas of England (1978) a snip at £515.00.  A copy of this great (30.2 x 21.2 x 3.2 cm) book was on open access in the TCD library after it came out and I spent hours looking up the answers to "What do you call a long depression at the side of a field containing running water?" "What do you call the long, tapering, orange-coloured root vegetable with feathery green leaves?"  All sorts of clines, isoglosses, oddities and anomalies appear in the maps.  It almost made me wish I'd been born with the Arts-Block gene.

Wednesday, 26 June 2013

Where do we come from?

The Irish radio station Newstalk has a science magazine programme called Futureproof.  Last Saturday live in the Science Gallery, they did a piece on genetic testing.  The programme's presenter Jonathan McCrea had sent (this is one he did earlier) a saliva sample off to a company in California called 23andMe and they had sent back the results. McCrea was given his results live on the wireless (wired up to a galvanic skin response stress detector) so it was interesting and informative - for McCrea obviously but for the studio audience as well.  McCrea was relieved to discover that his risk of developing Alzheimer's was rather small - because his grandmother had descended into that darkness. He also found that he was 'clear' of known genetic predispositions to cystic fibrosis, breast cancer and some other hazards.  Good for him!

One of the experts on the programme was geneticist and blogger Kevin Mitchell from TCD's Genetics Department. Mitchell addressed another issue that can be teased out from the scads of genetic data that 23andMe is able to wrest from a gob of spit.  The medical prognoses are clearly about McCrea's future.  The pattern of genetic variants also allows The Company to make inferences about where his people are buried. McCrea has a genetic profile shared by many of North European descent including a substantive subset of these variants which point to ancestors from the Hiberno-British Archipelago.  Back further we now know that some modern humans (us) got the ould leg over some Neanderthals before these-our-cousins joined dinosaurs and dodos on the Extinction Express to Oblivion.  So there was an opportunity to jest about the percentage of McCrea's genome that was Neanderthal in origin - a tad above the European average but probably not significantly so. You can make jokes about brow-ridges and Neanderthals and it is deemed to be inoffensive because they're all long dead.  On the global scale of things, the Irish are quite genetically homogenous - not as pure-bred as Icelanders but much more so than, say, US Americans.

If such a programme was broadcast in São Paulo it could get a little more edgy because African ancestry in Brazilians is very poorly correlated with actual skin colour.  Yet darkness is strongly correlated with social class and it is not correct to say that Brazil has no racial prejudice.  So there might not be so much badinage when it is revealed that the 'white' presenter has rather more African ancestry than the 'black' lady who makes the tea off set.  Mark Shriver a genetic anthroplogist from Penn State has shown a lesser but demonstrable amount of black-in-white and white-in-black in US citizens.  Famously in the descendants of Thomas Jefferson and his slave (and wife's half sister!) Sally Hemings, whom he started bonking when she was less than 16.  I've given joy to the growing multiculturalism in Ireland; these genetic tests may help us park racism and take everyone as we find them - all of them, not just the epidermis.

I might mention that the 4th hire of 23andMe was an Irishman called Brian Naughton who got his first degree in Genetics at TCD.  If you sign over $99 to The Company, they'll send you a kit to receive your saliva and within 6-8 weeks they'll get back to you with results.  20% off for second and subsequent samples! If you send a copy of your TCD degree you get it all for half-price (kidding!).  Dau.II is now rooming with another geneticist in Dublin who has shelled out for a test.  Yesterday Dau.II asked if I thought it was a good idea for us all (Bob and Boblettes) to get tested.  She and her sibs have a rather rich brew on the ancestry front (Irish (both left and right footers), Scots, French, Lebanese, Sahel African) and the grand-daughter includes another continent in hers.  I've had a rather fond conceit that my maternal grand-father was London Jewish but my Mum denies this (vehemently), so maybe $99 would help settle the question?

Tuesday, 25 June 2013

All's fair in love and soccer

I was at a pizza cookout at Chris del Bosque's place last night and I forgot to ask him about measuring tons of timber per hectare - sorry, I promised!  But there were rather a lot of blokes around the earthen pizza-oven that Chris and pals built in his yard three years ago, and the talk turned to footie.  In particular a famous 1986 penalty by Zico where Brazilian effortlessly out-psyched the goal-keeper.  It was part of a quarter final penalty shootout against France.  It's on youtube.

In soccer, as in other sports and indeed other aspects of 'real' life, when an arbitrary decision has to be made between two opponents: who kicks off the first half, whether to play the East or West end of the pitch in that half - it is decided by tossing a coin.  At the end of a game if the teams are score-equal, there is a penalty shoot-out with each team taking turns to fire a penalty from the spot 11m from the goal line. If the score is still equal after that ordeal, then the first team to score a goal wins the match.  Who fires first is decided by coin-toss.

But as mathematicians Steven Brams & Zeve Sanderson point out in an article put up in May while the odds may be even at kick-off, they are definitely not even in penalty shoot-outs.  The sudden death after 5 shots each is the obvious advantage.  But being science trained they went off and got some data and found that the team that gets first penalty kick wins 60% of the time - that's a 60/40 = 50% advantage.  That's not an arbitrary decision, so Brams and Sanderson hold that it should not be decided by coin-toss.  It should rather be decided by auction.  Each team bids to go first by saying that they'll take their penalties from a spot further from the goal-line to obtain the 50% advantage.  The odds are then, by definition, perceived to be fair by both sides.  If you think the other side has an unfair advantage you can out-bid them.

I liked that a lot. It shows that even the rock solid certainties about our world and how it ticks can yield interesting insights if you question your assumptions. The + plus magazine where I found the article is a nifty trove for all sorts of recreational math.

Monday, 24 June 2013

Bright yellow

I've become a bit of an aficionado in food engineering.  After my training in food structural engineering in graduate school, I'm developing a slightly aghast interest in food-products.  I have a much more smug interest in food, making a lot of what I eat from scratch myself, but food-products designed by food engineers have a frisson fascination for most of us.  I had a good friend in graduate school who claimed with a certain righteousness that she had never eaten in or out of McDonalds - making her a rarity in the USA, like people who don't own a television.  She mentioned this rather more often than you'd expect from someone for whom the place had no attractions.

Now, while I have eaten in McDonalds (when they cooked their fries in tallow they were just excellent) but I've never eaten a Twinkie the food-like product that foodies love to snicker at. Not so long ago, smoking was allowed, almost encouraged, in pubs.  My boss of the time would only let fall essential work-related information in the pub after work: "I'm going to Illinois on Monday for 3 weeks", he'd say after a couple of TGIF pints.  I'd more or less have to go boozing at the end of the working week.  I'm not saying it was a penance, the craic could be mighty, but I'd come home reeking (sweater, coat, hair) of smoke.  I became quite vehemently anti-smoking: at home for starters.  But when they drove smokers out of pubs and you'd see them flirting and chatting with each other in the drizzle outside the doors of pubs, my indignation sagged and then took up cudgels a bit for the other side.  Jakers, I thought, if you're an adult you should be able to make an informed choice about how and when you're likely to die.  We get told what to do by someone else far too often.
So what is this Twinkie thing?  As you see, it is very yellow.  It is also "Enriched wheat flour, sugar, corn syrup, niacin, water, high fructose corn syrup, vegetable shortening – containing one or more of partially hydrogenated soybean, cottonseed and canola oil, and beef fat, dextrose, whole eggs, modified corn starch, cellulose gum, whey, leavenings (sodium acid pyrophosphate, baking soda, monocalcium phosphate), salt, cornstarch, corn flour, corn syrup, solids, mono and diglycerides, soy lecithin, polysorbate 60, dextrin, calcium caseinate, sodium stearoyl lactylate, wheat gluten, calcium sulphate, natural and artificial flavors, caramel color, yellow No. 5, red  No. 40".  More niacin than water - can't be all bad but 34 different ingredients is 30 more that will make a serviceable wheaty loaf or a pint of malty beer.  You could live for a long time on bread and beer, as William Cobbett stoutly maintained in his delightful Cottage Economy (1822).

His lawyer famously claimed that Dan White murdered Harvey Milk because he was out of his head on Twinkies.  Nevertheless, I never told anyone that they were foolish, let alone reprehensible, to eat Twinkies; perhaps because I didn't know (m)any such people?  Folks who hug trees and deliver their babies at home tend to eat lentils rather than Twinkies.  But I felt a twinge of indignation when I heard that something as popular as Twinkies had become unavailable since sometime last year because of the vagaries of global capitalism.  Something about Hostess going bankrupt because they had over-extended themselves in consuming rival companies.  But also something about eating preferences changing from bright yellow food-products to other equally engineered food-products with better marketing departments:
"Say, Chuck, let's put a star-burst on the packet saying <Healthy, tasty, fat free>"
"Gee whizz, Barf, that's a great idea for our new caramel popcorn".

Whatever the reason, Twinkies have gone from the shops.  Although, the assets having been stripped from Hostess, from July Twinkies will be back on an assembly line owned by Apollo Global Management and Metropoulos & Co.  Adults can therefore again choose to eat them.  Me, I'll line up with foodie Michael Pollan "'Eat food. Not too much. Mostly plants".  That's diversity and that's democracy!

Both, in my opinion, mostly good.

Sunday, 23 June 2013

Ringstone maps

I wrote this last winter about the discovery of more neolithic art-work at the very edge of County Carlow.  I say more because there are lots of these carvings in the Carlow Wicklow region of Europe and Chris Corlett of the Department of the Environment has written the definitive book on the subject. Poor fellow hasn't published it yet because just when he gets it camera-ready somebody alerts him to the existence of another extraordinary chunk of our Arts-Culture-and-the-Gaeltacht that needs to be recorded.  3875m (say 7,370 Egyptian cubits) almost precisely due East of the Knockroe Ringstone is a contender for the finest example of neolithic rock art in Leinster at Rathgeran Lr.

We can work out more-or-less when the original carved stone was cleft into 4 half-ton blocks. On dit que the upland valley (the Ringstone is about 200m above sea-level) where we live wasn't settled until the last decades of the 1700s. So it wasn't before 1780. A line, representing a field boundary, appears on the first Ordnance Survey map exactly on the line of the dry-stone rubble-filled wall in which the cleft parts of the Ringstone formed the gateway. So the Ringstone was split before 1846. The tesselation of maps below all come from the truly amazing and informative zoomable, clickable, historically layered Ordnance Survey Ireland OSI map of the island.  The red + marks the Ringstone.

Things to note.
1) The housing arrangements changed radically between the first (1825-1846) survey and the second (1870-1910) revision.  From the 1890s to the 1990s, four 1-1.5 ha fields framed the Ringstone gate, but one of those fields was created from two long thinner '1850' fields that had, in turn, been cleared from the hillside <3 generations before.  You'd think they'd make up their minds because each change required moving hundreds of tons of stone with no more help to their hands and backs than a pick, some levers, a stone sled, and an ass-and-cart.

2) The patchwork of fields in '1850' and '1900' along the N edge of the maps that forms the background to the large red dates has disappeared in '1950'.  When the farm was sold in the 1990s, the neighbour who bought the 25 acres above the house spent as much on the hire of a Hymac tracked digger and two dumper-tractors to clear the ditches as he'd spent on the fields themselves at auction.  Six weeks saw it all tidied up and sown as pasture.  A single well directed gallon (5 lt) of petrol can do 600 man-hours of work.  And we fritter the stuff away driving to the corner shop for the newspaper.

3) The SWmost of these four fields, is known through the parish as Crowe's, so I've marked it as such on the 1850 map.  You can see the cabin where Mr and Mrs Crowe and their childer lived.  Several years ago we were digging holes in part of that field to plant a (broad-leaf, sustainable, of course) wood-lot.  Just where the black box appears on the map, the dug earth was busy with broken delph as the Irish call their dishware (It's a corruption of "Delft" in Zuid-Holland famous for its blue-and-white china).

4) A good few years ago I was leaning on the gate in my rustic fashion (straw in mouth so that the jaw didn't look all slack) when a rented people-carrier drove up the lane and de-bussed half a football team of Americans: tall, healthy and good-naturedly affable as only Americans can be. They were descendants of a widowed Mrs Hickey who had sent her oldest children to America in the aftermath of the famine and was brought there afterwards with her youngsters when the older ones grew up and made good.  The present John Hickey has done sufficient research to determine, from C19th census and estate records, that the cluster of buildings in the NW corner of the 1850 map was owned by the Hickey family, indeed it seems probable  that they owned the four fields East of the lane as well.  I sometimes feel that I'm just the care-taker waiting for the Hickeys to return and claim their patrimony like Viggo Mortensen striding into Minas Tirith.  I mention it because, this weekend, New Ross is celebrating the 50th Anniversary of the visit of JFK to the Kennedy Homestead about 50km South of here.  The Kennedys left the Sunny South-East in very similar circumstances and about the same time as the Hickeys.

I wrote in April about the relative population of Chicago and the Scullogh Gap in 1835.

Reasons to be cheerful, part .sg

"A bit of cough and splutter
But no phlegm in the gutter!"
It has been so murky from air pollution in Singapore that it's merited a week-long flag on en.wikipedia's In the news section.  They call it the 2013 Southeast Asian Haze.  The chaps in Singapore call it all the Indonesians' fault. Anyone here use palm-oil?  It's your fault because it is produced by tropical peasants practicing slash-and-burn agriculture for pennies in their rain forest and the ould burning sometimes gets out of control.  I bet there's palm-oil in the lurid confections we buy when we're feeling in need of a treat.  PSI (Pollutants Standards Index) has a 1-500 scale and has been up over 400 ("Hazardous": a category worse than "very unhealthy") in Singapore these last few days.

The girl who invented herself keeps the dog in Singapore and lives there when she's not living out of a suitcase in her AsiaPac peregrinations.  We are all concerned for her: "don't jog outside" we say from afar, "keep the dog inside", "buy one of those white cotton masks that are such a fashion accessory for Japanese cyclists".  But in the words of the immortal Ian Dury, there are reasons to be cheerful even if not necessarily:
"A bit of grin and bear it, a bit of come and share it
you're welcome we can spare it ... yellow socks"
I thought my own additional lyrics at the top of the post enshrined the can-do business as usual spirit that makes you think that Singapore might once have been a British colony and have a persistent racial-memory sort of stiff upper lip.  ANNyway, it looks like the worst is over, with several consecutive readings below 100 "moderate" this morning. Phew, everyone can get back to their offices and make money.

We don't often get those sorts of problems in Ireland - no tornadoes, only the wet end of hurricanes, no volcanoes or earthquakes.  Although my family was personally affected by Eyjafjallajökull when it blew its Icelandic top 3 years ago, and air-travel was suspended.  The daughters Dau.I and Dau.II, then 14 and 16, had chosen to go visit an old friend in Switzerland and had to repatriate themselves 1930s style by train and boat and train and boat.  It wasn't strictly necessary because the girls were well capable of managing on their own (home-educated, not infantalised) but we fired up the network and asked the friend of a neighbour to meet them in Paris to see them across the city to the Eurostar for an allez simple to London.  They got breakfast in London with another old friend.  It was an awfully big adventure and nobody died.  Like the Singapore business, Eyjafjallajökull was all over in a short week.

There are clearly reasons to be cheerful it wasn't like 1783 when, 230 years ago this month, another Icelandic volcano Laki just downhill from the Vatnajökull glacier blew its top and continued to belch crap into the atmosphere for at least eight months.  While Laki was throwing shapes centre-stage another nearby fissure in the crust called Grímvötn was doing its own riffs for about two years at the same time. The quanities are scarcely credible, nearly 14.7 km3of lava was ejected.  That's enough to turn the entire island of Ireland into a car-park covered with 18cm of rock.  The basalt lava stays more or less local, although particulate matter rained down as ash over much of NorthWest Europe: in England 1783 was known as the Sand Summer. For more widespread effect, 120,000,000 tons of sulphur dioxide (which when mixed with water makes sulphurous acid) and 8,000,000 tons of hydrofluoric acid (that is used to etch glass) were send up into the atmosphere.

The Icelanders, in their own under-stated unhysterical way, call the episode Skaftáreldar the Skaftá fires.  But it had serious consequences for them.  Half the livestock in the country died as forage withered in the acid rain.  And what they did eat was contaminated with fluoride as my dandelions were probably contaminated with Caesium after Chernobyl in 1986.  Fluoride is good in small quantities and many governments add it to the water to reduce dental caries but in larger quantities it flushes calcium out of the bones.  It is estimated that a quarter of all Icelanders perished in the rain or from famine over the next year.  The pollution killed thousands slowly across Europe over the next 12 months and probably caused some really extreme weather conditions including a severe 1783/84 winter that did for many more people. One dit que the disruption to the harvest over the next several years annoyed everyone so much that it precipitated the French Revolution in 1789 - but we don't have a control to that experiment.

 Further reading: Erik Klemetti has a nice article in Wired with suitable scientific references.

Saturday, 22 June 2013


One of the harmless processes that helps cement social relationships between domestic and foreign is to "twin" towns. I've no idea how these relationships are set up (Mayor went on holiday there seems most likely) and Navan, Co Meath can't make up its mind, being twinned with both Bobbio and Broccostella in Italy (Chairman of the Chamber of Commerce went on holiday somewhere else?).  But it can work out to widen the cultural relationships as when I encountered Gelsenkirken.
From the other side of Europe we see Україна Ukraine as through binoculars the wrong way round: a long way away and rather exotic  . . . but it's about 7x the size of the island of Ireland when the binoculars are the right way round. As they are likely to join us in the EU before we're all dead and because they are definitely part of geographic Europe, we should pay more attention.
Now I think it's fair to say that the average Irish person knows damn-all about Ukraine (we've been asked by their government not to call it The Ukraine anymore). They might, if prompted, think 'cossacks'. Football fans will have heard of Dynamo Kiev. Historians of the more distant aspects of medieval European history might know about the Viking foundation of Kievian Rus - it was on the way from Scandinavia to Byzantium by river and portage.  Of course we've all heard of Chernobyl because of the heroic efforts of Adi Roche and others nurturing the orphans who were part of the fall-out.  And I had my own alcoholic encounter with Chernobyl's Caesium.
But I daresay fewer still will have paused to reflect on the remarkable similarity in the outline of our two countries.  Perhaps because it only becomes obvious to all when Ireland is tipped forward on its face, as some of its citizens are liable to do after a Saturday night on the batter.  And it turns out that as the Republic of Ireland is divided into 26 counties (I'm going to ignore The North until Ukraine and Belarus become one nation), so Ukraine is divided into 24 Oblasts and the Autonomous Republic of Crimea = 25.  So we can do a pretty good geographical 'twinning' without wrenching the true topological geography too much.  See the map of UkrEire above and the table below.

Table 1. Oblasts of Ukraine meet Counties of Ireland
Cherkasy Offaly OY Cherihiv Dublin D
Chernivsti Sligo SO Crimea (AR) Kerry(Kingdom) KY
Donetsk Waterford WD Ivano-Frankivsk Leitrim LM
Kharkiv Wicklow WW Kherson Limerick LK
Khmelnytskyi Roscommon RN Kiev Westmeath WH
Kirovohrad Tipperary T Luhansk Wexford WX
Lviv Cavan CN Mykolaiv Clare CE
Odessa Galway G Poltava Laois LS
Rivne Loutyh LH Sumy Kildare KE
Ternopil Longford LD Vinnytsia Mayo MO
Volyn Monaghan MN Zakapattia Donegal DL
Zaporizhia Cork C Zhytomyr Meath MH
Dnipro- Kilkenny KK - petrovsk Carlow CW
I've had to take some liberties.
  1. Dnipropetrovsk Дніпропетровськ is clearly a) too long (15 letters) and b) too big - it is Ukraine's 2nd biggest Oblast c) divided by the river Dnieper, d) jings! even its flag is divided in two. So I have divvied it up between the counties of the Carlow-Kilkenny (15 letters) parliamentary constituency.
  2. Chernihiv has for far too long been overshadowed by having the capital Kiev next door, so I've twinned Чернігів with our Capital Dublin to give them a bit of a lift.
  3. I've no idea how Ukrainians view the Autonomous Republic of Crimea. More than half the population down there are ethnic Russians.  It's also a bit murky because the Russian (Российская Федерация) Black Sea fleet is stationed in Sevastopol as it has been since Nicholas I was the Tsar. There has been a fair bit of throwing shapes/negotiating by both sides.  But in respect for its special status, I've twinned the Oblast with the "Kingdom" of Kerry.  Maybe my Ukrainian and Russian readers can clarify.
I won't be shifted on the sub-division of Dnipropetrovsk, however, anyone from East of the Dnieper is welcome to visit us in County Carlow.

Other mappy links on The Blob: BorrisOSTramore - MtLeinster:25000 - Crowe's

Friday, 21 June 2013

I was a food engineer

After giving a rather back-handed compliment to people who make highly-coloured multi-ingredient confections, it is ironic that I should now out myself as a quondam food engineer.

I was never so poor as when I put myself through graduate school in Boston.  I earned a pot of money in Rotterdam, at least partly by scrabbling through crocodile shit for small change. But almost all that loot went to pay for my first semester's fees. Many people see their years in college as the happiest of their lives.  I think I count myself both lucky and happy for those years, when we were still young, when we were fired up with finding out, when our lives were stripped to essentials: food, shelter and friendship.  No car, no house, one pair of shoes, a stock of khaki shirts that I'd worn for work in the zoo in Rotterdam. Every few weeks there would be a special on ice cream at the Star Market across the Mass 'Pike from work.  The handful of us in the basement lab would throw coins into a hat until it came to $1.69 and someone would go to buy a half gallon of ice-cream, the walker getting to choose the flavor.  If that sounds a lot, I hasten to say that we're talking about US (4 lt) gallons not greedy Imperial (5 lt) gallons.  There was only ever a couple of spoons, but you can eat ice-cream almost as quickly with a fork or a foot-rule, although the guy with the spatula was a bit slower.

Even graduate students can't live on ice-cream alone and you'd starve entirely if you had to wait for the free coffee and donuts that the department laid out on Friday mornings, so I was delighted to find that the student's union cafeteria had an all you can eat salad bar.  They charged $1.29 for whatever you could fit in a 15cm diameter bowl.  You just had to get the teetering heap of food to the checkout to qualify.  It didn't matter if it all spilled out across the tray before you got to sit down. There were tomatoes and corn and lettuce and chick-peas and grated carrot and scallions and croutons and coleslaw and dill-pickles and other stuff too exotic to name by fresh-off-the-boat me.  They say that rats, if given a sufficient variety of food, will choose a close approximation to a perfectly balanced diet.  I dunno about that, but I ate a lot of raw vegetable matter when I could make the time to trek to the Union at the other end of campus.  Then my friend Larry told me about making the bowl bigger.  The key was to use iceberg lettuce leaves cantilevered out to increase the diameter of the bowl by as much as 50%. - effectively doubling the load.  Obviously these leaves would flip a lot of food out of the bowl and onto the floor if they weren't properly counter-weighted.  Larry recommended chick-peas but after some experimentation (science where it mattered) I found that the big tomato quarters cemented with chick-peas and coleslaw worked better.  So I became a food-engineer early on in my career and might not have survived without this training - thanks Larry.  I'm not ashamed: a Structural Engineer, Food is not the same as a Chemical Engineer, Food. As completely different as the People's Engineers of Judea is different from the Judean People's Engineers.
Earlier today I gave a rather full-frontal compliment to starving graduate students, because I've bean there. I'm glad they still exist because for a while just after the turn of the century it seemed as if the species was rare to the point of extinction. I was then working in one of Dublin's great teaching hospitals as a post-doc at the frontiers of biomedical science with a couple of dozen graduate students from several different research groups.  We'd all have lunch round a big table in one of the lobbies.  I'd eat my humble sandwich - two slices of home-made bread, with a slice of cheese - and lettuce if there was any in the bottom of the fridge.  Round me the talk was about where to buy the best sandwich: the hospital canteen or the garage across the road which threw in a soda and a bag of crisps for €3.50 or the private hospital canteen where the sambos were made to spec before your very eyes.  I couldn't shake the reflection that they were spending as much on a sandwich as I'd earned in half a week in my first job riddling potatoes in a freezing barn.

On the ground floor was a large and a small lecture theatre and at least once a week there would be a talk or a presentation and the drug companies would send a rep to lay out their wares.  We were never short of pens or post-its, and if the talk was at lunchtime, one of the multinats was sure to provide a big tray of sandwiches for the hungry doctors.  For the first few weeks I'd trip up the stairs after the talk and breathlessly tell the graduate students that ... there ... was ... free ... food ... down ... stairs.  They'd look at me as if I had two heads - we have sandwiches here thanks.  Tiger cubs!

End of Part One

Yesterday was the last day of the academic year at The Institute.  The Admin Staff are going to work through the summer and so are the technicians but the lectures are Off.  So yesterday was a time to catch breath and catch up with some of my colleagues.  A time also to respond students who have flunked one of my papers - some angry, some annoyed with themselves, nobody particularly happy about the situation.    In the evening a dozen of us went out to a bar for a few bevvies as has been traditional over the last several years.  It's the first time I've had to have anything like a conversation with some of the people there. 

When half the folks had left and only the hard-chaws were left my HoD asked how it had been and I tried to say that one of the interesting aspects had been seeing and dealing with a number of different teaching styles.  Because they were different, they hadn't all been my style but it was useful to see that other styles worked too.  There were manual and and wing-it people.  I had a wide experience of classes since January and so a wide experience of co-workers. Some have a written manual for the whole year, with protocols for each predicted experiment, which is handed out to the students, so everyone is on the same page.  In other cases, I was given a few notes scribbled on a sheet torn from a reporter's note-book with the instructions "You might do this on Thursday, I've ordered the materials from the technician". 

With l'esprit d'escalier I was able to reflect on how these styles had impinged upon me personally.  Some of my colleagues were kind and some were respectful and a few were both.  The kind wanted to know if I was okay with my assignments and if I had any questions, they had a tendency to hold the students' hands as well. The respectful seemed to say that I was an adult and an effective and they weren't going to micro-manage me.  There were tasks to carry out, learning outcomes (LOs) to achieve, and it wasn't for them to tell me how these two should marry.  I'm a silverback, I've been on the planet a while, so I can cope with both styles.  But I suspect that first-timers might prefer the former.

The Social Liaison Officer (SLO), whose childer are a little bit older than some and so has the head-space to organise such matters, had ordered up some chipolata sausages, chicken nuggets and samboes to be delivered from the local hotel after the first couple of rounds.  We had one graduate student in our midst who acted in a gratifyingly hank-marvin manner (not to be confused with the legend) and hoovered up this robust fare, so there was little waste - there's a waste/waist pun there which I'll leave my British readers to elaborate in the comments.   Fado fado in Boston, I was a graduate student, too, so I was still able to bring home my breakfast and lunch wrapped up in some tinfoil and a paper napkin.   And when I left at nearly 11pm with the imprint of the bar-stool etched on the seat of my pants, I thought it was a good way to finish my 165 days of hard graft, when I haven't had much time to actually sit down.

Thursday, 20 June 2013

A Perfect Basket

This lovely piece of basketry was made by Iizuka Shōkansai one of the Ningen Kokuhō (Living National Treasures National Geographic Documentary that may be "blocked in your country") of Japan. LNTs are skilled practitioners of a craft who hold the flame of a particular tradition so that it doesn't futter out from disuse. I wrote yesterday about apprenticeship and respect.There is a necessary trade-off between training the ignorant and treating them like imbeciles.  There should be a clear distinction between ignorance (you haven't been on the planet long enough to know stuff) and stupidity, but they are too often conflated.  It's a bit like the does he take sugar disrespect for people who can't articulate because some key motor neurons were shot off in the war or traumatized at birth.  When you leave the entire training of students to following a rigid protocol to reproduce a well known finding about how the world ticks, you let them develop their muscle memory and practice their technique. That's good.  But you diss their creativity and the sub-txt is that they will never be as good as Newton, Kepler or Darwin. That's bad.  And the training in technique is usually badly integrated because it is fatally tied up with getting through the syllabus.  When Step 7 doesn't work, we rush on to the next experiment rather than making everyone do Step 7 again and if necessary again, until they (or at least many of them) get it right.  That's science. Rushing through the syllabus is not.  I think we're frightened of putting young would-be scientists to repeating things because the attention span has shrunk to a news bulletin and we worry that we'll turn them off science entirely if it seems too hard.

Now get this: Iizuka Shōkansai spent the first decade of his life as a basket-maker learning the correct technique for cutting the bamboo!  When you get to graduate school and start taking ownership of your own experiments - "if this doesn't work I am sunk" is significantly different from "if this doesn't work we'll see if we can have better luck with something else".  You have to think about what you do and probably write it down in meticulous detail, so that when the experiment doesn't work, you can tweak the protocol and try again.  It's usually the buffers, lads, so throw them out and make 'em up from fresh.

In Ireland we have a parallel set-up to Ningen Kokuhō called Aosdána. There are nearly 4 times as many members of Aosdána as there are Ningen Kokuhō in Japan which has a population 25x greater than our island.  And you may bet your sweet bippy that none of them spent 10 years cutting-the-bamboo, mixing-the-paint, sieving-the-clay-for-stones or making-the-tea and being sent-for-the-glass-hammer (ho ho, robust humour).  In 2003 Gill and Macmillan published The Encyclopedia of Ireland. It is 1200 pages long, A4ish in size and 7cm thick.  You can get it 2nd hand for £15ish on Amazon which is a good deal because the postage for this 5kg tome is the same as for a slim volume of poetry.  When it came out, we sat around  a copy at coffee in the premier science department of Ireland looking for living Irish scientists.  There were about 4.  The Professor summed up our chitty indignation at being on the wrong side of the Arts/Science divide: "If you're an art teacher in a VEC in Kerry you get your paragraph, but you need a Nobel prize to rate as a scientist".

For the boy-scientists among us, Jacob Bronowski's great investigation of the history of human culture devotes ten minutes to making a sword, following the Ningen Kokuhō Getsu in the process of taking the sword through.  It's not a lot different from making croissants (fold-roll-fold-roll) which I haven't had time to blog about but I will, Oscar, I will.

Wednesday, 19 June 2013

Taking the bell through

When I was in high-school I had a two-year affair de la tete with my mentor and biology teacher Mr Wilkinson.  Many and varied were the stories he told us, lots of them off-topic and several off-colour ("Q: How tight is a duck's arse? A: Water-tight" eee how we larfed) but many of them have stuck with me and some stuck by me in the 40 years since I said goodbye-and-thanks.  One tale concerned a bell foundry.  Each laborer there had his own task.  One would weigh the copper and tin and  a pinch of magic into the crucible, one would tend the fire, two more would pour the molten bronze into a mold made by a third, another would tune the bell by chipping flakes off the inside with a cold-chisel, and the two apprentices would polish the final product until the Master Founder was well-and-truly satisfied.  Each man was, or was becoming, an expert in his craft, and each knew that he was dependent on those who came before and after him in the production process.  This sense of incorporation was made concrete by each man periodically taking the bell through.  To do this he had to perform all the tasks in order and stand over the final product.  If nothing else, this made clear that each task had integral value and that even the polishing required patience, application and attention to detail.

I've just come from a meeting with some of my colleagues to thrash out when and by whom the elements of molecular biology were going to be taught next year, so that when the students emerge from the four-year course they can claim a well-rounded and broad-enough mastery of the subject.  That's aspirational, but let's hope that we can get closer to the ideal having started communicating amongst ourselves.  One benefit has been to find out who is master-minding the 3rd Yr course Molecular Biology & Immunology which I'm going to be contributing to next year.  This MM has put together a set of practical experiments that is informed by him having just finished his PhD in molecular biology.  Each week the students will carry out a task (or two) in a protocol that will discover something that nobody else knew when we started.  It's a high risk strategy because of the dependencies (if the process founders at Step 7, there's not much to be done about Step 8) but the potential rewards for learning and self-esteem are mighty.  So much learning even in university follows the Wenceslas School of teaching:

In the master's steps we trod
Where the science lay dinted
Heat was in the very sod
Which the {Hooke|Joule|Krebs|Luria} had printed.

that it's great to be doing real science with The Yoof.

It reminded me of my own undergraduate career in the last century, which was rather less inspirational, for much of the content, than my experience with "Old Wilkie" (who was/is probably only ten years older than me).  Even when you're taught your Intro Physics by a Nobel prize winner (ETS Walton - Ireland's own/only science Nobellist - in his last year before he retired), it's still a drag to be tricking about with springs  to replicate Hooke's law Ut tensio, sic vis almost exactly 300 years after the autodidact had sorted it out for all time.

But in my second year, one of the lecturers came back full of beans from a sabbatical stint in Davis, California.  He wanted to identify and isolate a particular class of "petite" mutants in yeast, so that they could be mapped w.r.t. similar already known mutants.  They were called petite because their mitochondria-challenged colonies grew small.  The rate of spontaneous mutation in baker's yeast Saccharomyces cerevisiae is about 1 mutation in every billion DNA bases per cell division.  You might guess that mutations in 1000 of the bases in the genome would sufficiently challenge the mitochondria to make the cells grow petite.  That's a guess based on: a gene being on average 1000 bases long; several sensitive genes being involved in normal growth; and several of the mutations being sufficiently benign as to be undetectable on a petri dish.  So every 1,000,000 cell divisions you might hope to see one tiny slow growing colony.  What better, thought the Machiavellian Dr California, than to have 5 dozen students spread suitably diluted yeast  cells on hundreds of petri dishes for a few weeks and look for dinky colonies, like the one red-arrowed here.  This was boring, repetitive, painstaking work that went on forever . . . and I was stoked! It was the high-point of my week after week - would I find a petite colony? would any of us find a petite colony? would a petite colony be found in our lifetimes?  I was being respected as a co-worker, I was doing real science, I was pushing the frontiers.  If next year we can get a couple of students to feel something of that passionate engagement, it will have been worth it.

Tuesday, 18 June 2013

Last orders

We don't have a television - not for 30 years - we don't miss it but we do miss out on whole prairies of popular culture.  We are a bit behind the pack but two nights ago we got The Relief of Belsen out of the library for edutainment.  It's a Channel-4 made-for-TV movie about the British RAMC medical unit who were first on the scene at the concentration camp.  They were presented with 45,000 inmates and 45,000,000 typhus-bearing lice which they needed to contain and cure - in that order.  After sorting out and separating the foul and clean water, they sorted out a delousing station, triaged the the sick and brought them out of the camp in batches and into a make-shift hospital.  That was one thread. 

The other thread was sorting out a suitable diet for people who had been existing (living would be an exaggeration) for months and months on about 800 daily calories of cabbage soup and black bread.  Bully beef - of which the soldiery had a lavish supply - came straight up again, and dried milk was not much better.  Next they flew in some plane-loads of tinned 'Bengal Famine Mix' which had worked a treat in a cholera epidemic in India in the 1930s.  But the starving Häftlingen refused the mix of beans and sugar . . . until some bright spark thought to add a liberal dose of paprika to the curd.  This gave it a whiff of a ghost of the idea of once familiar goulash and it was gobbled down by the Russian, Magyar, Czech and German survivors and it stayed down.

But no life-line was ever made of two threads and the death-rate in Belsen was still making grown men in the RAMC weep with frustration.  Then the carers realised that killing the lice and doctoring the food wasn't enough to turn the corner from an existence into something worth living.  They also needed to recognise their patients: to ask for a name and home town and not write it down (all the records had been destroyed by the SS), to hold a hand, to provide some lip-stick. 

- o - 0 - o -

The Beloved's grandmother has been in this planet for 102ish years - nobody knows exactly which year she was born in the Sahel some year before the First World War.  Up to the age of 99ish she was cared for by her daughter, who had herself been drawing the pension for at least a dozen years, although the older lady was blind and increasingly frail.  Midwinter three years ago, this fragile situation snapped and the Granny was admitted to a Home.  Periodically nursing homes in Ireland get a very bad press because of some exploit by an investigative journalist masquerading as an orderly and making a revealing video.  But this place in West Waterford is pretty good.  I won't push the eulogy because I don't go visit often enough to have data on the matter.  Apart from anything else, I don't have a 'control' nursing home  to visit for comparative purposes.  

But I have witnessed two oft repeated and interconnected anecdotes which give me confidence that this old lady is in good hands.  Every Friday afternoon, clinketty clink, a drinks-trolley is pushed into the common room and the residents have a tipple on the house.  The lads (outnumbered about 4 to 1) tend to sit round a table in one corner and sip a glass of stout or a whiskey, the ladies have their cliques as well and tend to sherry or baileys.  That's very civilised.  It recognises the residents as people and helps lubricate their social life in the traditional Irish way.  One of the nurses' aides, who works in the Home for a tad above the minimum wage, is married to a pork butcher. Every Friday, she brings in half a pig's face or some crúbin (on her own nickel) and the lads pick over the delicatessen as they sip their dhrink.  I've put my name down for a place if and when I get too crocked up and broken down to be looked after by my family and it's not just about the pig's face.

Monday, 17 June 2013

Taj Mahal

Here's a nice picture of the Taj Mahal - it looks like a water-colour  . . .  because it is: this is a crop of the standard postcard to show just the reflection (reversed).  Why today? Because it's the anniversary of Arjumand Banu's tragic death in 1631.  She has come down to us as Mumtaz Mahal the chosen one of the palace and she was married to the great Mughal Emperor Shah Jahan.  She was also the mother of the ruthless and austere Emperor Aurangzeb who deposed his father, executed three of his brothers and reigned for nearly 50 years.  All antient historie now.
Modern history section begins here. The other Taj Mahal used to be on the corner of Lincoln Place and Clare Street just opposite the back gate to Trinity College Dublin.  Everything is on the interweb including a short history of Indian Restaurants in Dublin, whence I lifted the photo and this great vignette: "Larry Gogan’s ‘Just a minute’ quiz on RTE Radio 2. When asked ‘Where’s the Taj Mahal?’, a contestant famously replied ‘opposite the Dental Hospital’ ".  There's also lots of good stuff on early growth of the Indian community in Dublin and I've written about the exponential increase in Ireland's muslim community.

At about the same time that The Beloved was studying French and Arabic at The Other University, we went out for dinner at the (Dublin) Taj Mahal with a mutual friend who'd been born in Middlesborough but grown up in Ballinasloe - twas a long way from Indian restaurants she was r'ared.  This was long and long before chicken tikka marsala became the most popular meal in Britain, and the Taj put helpful notes in brackets (mild, medium, hot, very hot) after the dishes on the menu so as not to surprise the clientelle too much. 
It was bit like the three bears in the fairy story. The Beloved plunked for Vindaloo (very hot) because her mother sprinkles chili on her cornflakes; I'm so boring (as child I always ordered plaice&chips at any restaurant) that I ordered something 'medium' and our pal cautiously picked a 'mild'.  It wasn't a bit like the three bears in the actuality.  We all struggled, none of the dishes was 'too cold' or 'just right', they were all, as we perceived them, flaming hot. How does that work?  Is it nature or nurture?  Can you train yourself up to tolerate chilis that create physical blisters in the naive?
Penguin photo credit.

A star is born every minute

Yesterday I wrote about being happy because it was Barbara McClintock's birthday, partly because she was one of the truly great original creative thinkers of the 20th century, but also because her capacity for happiness was so inspiring.  17th of June was Francois Jacob's birthday for 93 years until his death last month gave me reason to celebrate his long life.  I was born at 0050hrs in 17th June in England, so I have a choice of birthdays: either today because it's on my birth-cert or, because I jeer at the absurdity and hubris of jigging about with the clock each Spring and Autumn, yesterday because that was the date in GMT.  This option was borne in upon me when I was a teenager and used to calculate and construct birth-charts for myself and my friends - poring over tables and then getting out a compass, protractor, foot-rule and a fine black Rotring pen.  The first instruction was to subtract an hour if you were born in the BST season and then if necessary look up the tables for planetary positions of the previous day.

I calculated a birth-chart soon after The Boy was born in 1975 because I had the tables and the mental toolkit well-polished.  When Dau.I and Dau.II were born in the mid-1990s, however, the 1900-1975 tables I had didn't cover those years, so I let the whole thing slide.  One of the earlier tools that became available on the WWW interweb were robots that would take a submitted time and place of birth and calculate a chart showing where the planets were on the ecliptic at that time. So I was well late, but I did eventually get charts made up fo0r the girls as well.  I think such a chart makes a very acceptable, even framable, gift.   And because my readers (hi both of you) are insatiably curious, I'll show you mine here:
You must compare yours to see what is the normal/allowable variation.  There is plenty of choice for robot: just Bing up "birth chart calculator".  A couple of things fall out from the chart 1) the sun is at the bottom which means that I was born close to midnight (yup!) 2) the moon is almost exactly opposite the sun which means it was close to a full moon that night (yup!) 3) all the planets are crammed over on one side of the sky - dunno what that means 4) Mars is very close to the moon - dunno what that means either.  I like to make sense of the world, so I turn to experts in interpreting what birth-charts mean. Let's look at just a small part of one such site:
Uranus is in 21 Degrees Cancer.
For you, and for your peers as well, the demand to be free from entangling emotional bonds is of paramount importance. You have a unique and unfettered view of family life and will be attracted to experimenting with freeform styles of relationship commitments. This may lead to a rootless, unsettled lifestyle.
Neptune is in 23 Degrees Libra.
You, and your entire generation, idealize all of the various experimental approaches to relationships -- including "living together", the formation of communes and collectives and the whole concept of "open" marriages. There is a stress on weakened commitments on an emotional and contractual level, but there are heightened expectations of the level of commitment and mutual support on the spiritual and metaphysical level.
For you, peer review of a life experimenting with genez of various living forms and collecting data to test.
It's uncanny how accurate these can be.

And it's easy to be ironic, snitty or rudely dismissive about such matters.  There are data however: PMID 12741653; 23152637; 21777120; 19179880

Sunday, 16 June 2013

Barbara McClintock

Today, 16th June, we have plenty to celebrate.  It's Bloomsday (the day on which James Joyce set Ulysses) for the literary and it's Father's Day (yet another day on which you are required to support Hallmark Cards) and for trekkies it's Captain Picard Day.  Then there are the birthdays:
  •     George Gaylord Simpson - palaeontologist
  •     John Tukey - statistician
  •     Georg Wittig - synthetic chemist (Nobel Prize 1979)
  •     Alexander Friedmann - of the expanding universe
  •     Barbara McClintock
Take your pick, mates, but I choose McClintock (and it's my blog so I get first dibs).  She spent the last 70 of her 90 years immersed in science.  A large part of it immersed in corn fields crossing Zea mays plants just like I spent part of the summer of 1976.  Here's a picture to show her extraordinary stature, hanging out with the boys:

You might think that 'stature' is a cheap joke at the fact she's the smallest chap there apart from the dog.  But you'd be wrong as the caption says "Barbara McClintock as a graduate student at Cornell, 1929. (L-R standing) Charles Burnham, Marcus Rhoades, Rollins Emerson, and Barbara McClintock. George Beadle is kneeling by the dog."  The boys with whom McClintock is relaxed and relaxing are GIANTS of mid 20th century plant breeding and genetics.  Beadle bagged his own Nobel in 1958. I love this picture, she is so happy in her own skin, happy to be doing the grunt work, her 10,000 hrs.  The funny sporrans that Rhoades and Emerson sport are bundles of paper bags - as essential for corn-breeders as a hammer is for a geologist.  You pop a bag over the tassels at the top of the plant to catch the pollen and/or over the female flower to prevent stray pollen screwing up your cross.

McClintock's journey was harder than most, she has the distinction of being patronized by more of the greatest geneticists who ever lived than any other person. Most of the women in science could be safely ignored as they typed up the manuscripts and made the tea for The Men.  McClintock left her mentors and colleagues of 1929 and pursued her own nose for what was interesting in genetics using a minority organism rather than the lab mouse or Drosophila.  Remember that 1929 was 24 years before Crick and Watson 'discovered' DNA, so molecular biology hadn't been invented.  One of her early huge contributions was to show that a particular knobbly anomaly on one of the chromosomes of corn exactly tracked the expression of a particular characteristic in the adult plant. This required years of careful crosses (generation time in Drosophila is a couple of weeks, in corn it is a full year), meticulous record keeping, and a double life with her own sheaves of paper bags in the hot corn-field sun alternating with hours in a laboratory staining specimens and squinting down a microscope. By this hard graft she established a base-line of how inheritance worked in her organism and published a map showing where all the genes then known were located on their respective chromosomes.  She was developing her peculiar, particular, unique feeling for the organism in the evocative phrase used by Evelyn Fox Keller for her biography of McClintock.

Then she noticed cases where the inheritance was not straightforward.  She became intrigued by 'variegation' where some of the kernels on a cob or some of the cells in a kernel would have a different colour to that of their reg'lar sibs from the same parent.  Oh ho, she thought, new mutant, that's interesting.  But the colour of these weird kernels was not stable.  It would be there in one generation and then disappear and then pop up again.  Remember that each cross she carried out to try to nail down what was going on took a whole year.  I have this idea, I'll try this experiment, I'll put another candle on the birthday cake, and I'll check the results.  Dang! that's a bust  . . . but I have this other idea . . . und so weiter as Gregor Mendel might have written during his own decades-long hunt for reason and mechanism in the living world.

McClintock's feeling for the organism developed to a most extraordinary degree until she could think herself really small and become a particle inside the cell that was jumping about from chromosome to chromosome.  If I jump thus, I disrupt this gene and the cell I live in will grow up one colour, but then if I side-step and jump so the colour changes again.  She knew how it worked, knew it didn't only affect colour, knew it was of staggering importance to genetics and so she went out on the circuit to explain and publish her findings.  And it was like she was talking in a dream, she'd look out into the audience and see only bafflement on the faces of the men (it was almost entirely men of course).  And they would patronise her afterwards - suggesting that she couldn't do the math or that her methodology was faulty - and snicker at the bar that evening about how odd she was.  So she stopped going to meetings and carried on crossing corn year after lonely year, until in 1967 at the age of 65, she officially retired.

Then it all lurched the other way. After about 20 years in the wilderness her work on genetic control and regulation was replicated in other organisms initially by the late great Francois Jacob  and Jacques Monod.  To call it rehabilitation would be to grossly understate the reaction.  Everyone was falling over each other to heap honours and hard cash upon her.  In 1979 she was given honorary degrees from Harvard and Rockefeller Universities.  In 1981 she was awarded the very first MacArthur Fellowship, as well as a Lasker Fellowship, the Wolf Prize and the Morgan Medal.  The Horwitz Fellowship followed  in 1982 and in 1983 the Nobel Prize for Physiology and Medicine - not bad for a woman who'd worked on maize all her life.  And in 2005, 103 years after her birth she made it onto a US stamp.

She has become the poster-girl of role-models for young women in science.  The easily told story of "the struggle, the triumph" that sanitizes and codifies McClintock's life and contribution has become inspirational children's books about her life. The 10th Anniversary edition of her biography comes with quizzes and worksheets so that it can be used as the basis a Women's Studies module.  But this is to diminish her, she was much more than a woman, she was a shape-changer: both infinitely small and larger that the century that was coterminous with her life.  And she was happy:
"I was just so interested in what I was doing I could hardly wait to get up in the morning and get at it. One of my friends, a geneticist, said I was a child, because only children can’t wait to get up in the morning to get at what they want to do."
The Blob's women in science series: Florence Nightingale - Barbara McClintock - Maude Delap - Cliona O'Farrelly - Lynn Margulis - Rosalind Franklin - Jocelyn Bell Burnell

Saturday, 15 June 2013

It's Exam Time

I wrote about the executive power of examiners before yesterday's examiners meeting and was quite happy about the decisions we made in contrast to the story I told of another committee. The objectivity of the numbers was tempered by compassion and it was clear the The Institute's regulations had been informed by many other examiners meetings which must have experienced some pretty bizarre circumstances in the past - so here the codification by The Administration makes life at the coal-face easier. 

The results are tabulated in PDF files and rather than print out a couple of dozen copies on trees, the PDFs are projected onto a screen so that all the examiners are on the same page.
PDFs (portable document formats) are designed to be read as (paper) documents so the 12pt % numbers in the boxes are barely visible at the back of the room.  As this is the only time that the sheets are scrutinised, could they not be written so that the numbers themselves (the data!) but not the surrounding bureaucratic guff were printed larger, so they filled their box?  Now here's another thing, the tabulated results for each student are printed on The Yellow Sheets.  Each column is headed by a course code "HS1278" or "CO5066" in the tiny 12pt print The Administration prefers, so the committee chair reads out the course name for each column.  You then know that your results are in Column 2 and you can ensure that the marks you gave have been faithfully transmitted to the official sheets.  And when there is a query about compensation or compassion, you can quickly resolve the issue because you know where the relevant data are and so does everyone in the room. Thus everything can be processed efficiently. Several different groups of students (repeat candidates, honours candidates, diploma candidates etc) may be sitting the same group of subjects, so their results appear on different sheets.  That's fine.  But the order of the course code changes for each candidate category.  The committee chair reads out the column names ... you then know that your results have lurched right to column 7 and can contribute to the meeting.  Over the day, 20 people listen to these readings-of-columns maybe 3 or 4 dozen times.  So the reluctance of The Administration to change their time-honoured practice doesn't scale up.  20 people * 50 yellow sheets * 10 seconds adds up to 3.5 person hours of extra time for the reading alone to which must be added the extra time required as old buffers like me forget that the column has been changed again and start questioning the official results.  Old buffers like me, not me myself personally.  An hour of Admin time two weeks ago would streamline the process downstream for this year and every subsequent year.

And while we're in exam season, I'll point you at an interesting set of data downloaded from an examination website in India by a student at Cornell last week.  Debarghya Das, who had sat the exam last year and who was a geek-colonel, was challenged by his mates back home in Kolkata (we used to call it Calcutta) to get them a preview of their marks before the results were announced.  Mr Das was not hopeful, but rose to the challenge and had a look at the site, to find a glaring security flaw in the coding of the site (javascript embedded in the html in plain sight) and a flaw in the way schools (numbered 001-999) and candidates (numbered within schools 001-999) were encoded.  So instead of getting the scores for a handful of his mates, he wrote few hundred lines of code and scraped the results of 200,000 students into an ExCel spreadsheet.  Ooooo data.  You can see some commentary on the exploit and on the practice of examiners across the world at metafilter.
You can follow the story which shows all sorts of weird anomalies in the data indicating either a) a flaw in the way marks are processed in India or b) a flaw in the way ExCel processes very large datafiles - see the metafilter link for suggestions. 

But I'll abstract one figure to show you where it's likely to be human finagle. The figure left shows the distribution of ~125,000 marks for the Science paper.  It seems that some marks are impossible to obtain. Notably, no candidate has scored 32, 33 of 34% on this exam.  The pass-mark is 35%.  So the examiners don't want to waste any time at their meeting on borderline cases.
As Bob's Law for Examiners Meetings - 2% of the candidates take up 50% of the time - probably applies in India as it does in Ireland, this is clearly a better way of streamlining the process than piffling about changing the PDF font-size.