Thursday 30 April 2015

Dry ice? It's a blast

What could possibly be wrong with carbon dioxide? Our lungs are full of the stuff. I've mentioned the toxicity of carbon dioxide twice before. The first was for the "humane" killing of lab mice, which seemed to this witness to be a pretty desperate brutal way to terminate anything.  Earlier I described the killing of several hundred people by carbon dioxide asphyxia in the surroundings of Lake Nyos in Cameroon in 1986.  In both cases, the carbon dioxide, being heavier than air, displaced all the oxygen upwards. A very similar case almost happened at my place of work about ten years ago. 

A lot of biological reagents are shipped in styrofoam/polystyrene containers containing a shovelful of dry-ice = frozen carbon dioxide.  If scientists were six-year-olds they would be disappointed every delivery day when a large [40x40x40cm] box arrives and after unpacked is found to contain only a tiny tube full of some necessary but frightfully expensive reagent. Dry-ice sublimates (goes directly from solid to gas without becoming liquid] at any temperature above -78oC, so it makes a handy coolant, because doesn't go soggy if delayed in transit and dissipates as vapor into something a lot less obviously poisonous than sarin or cyanide.  Any large biological research institute will have some plan or protocol for recycling the dry-ice which arrives surrounding a delivery - the gal in the lab next door may need to ship a sample out the same day and it would be silly to buy dry-ice for that purpose. The standard practice for dealing with surplus dry-ice is to leave it in the styrofoam shipping container with the lid open or dump it into a sink; a few hours later it has all gone into the circulating air.

You can have some innocent fun with dry-ice.  If you put a knob of the stuff in an old plastic 35mm film canister and put it in your pocket, it will sublimate and build up pressure until the lid blows off with a satisfying >!pop!<.  You can repeat the trick many times by replacing the lid; huge fun at a cocktail party as nobody can tell where the sound is coming from.  You can also do something which is dip-stick dangerous but not obvious-to-all-thinking-people hazardous. This is what happened one evening at work.  Poorly trained researcher, knowing s/he wanted some the following day, put a shipping container full of dry-ice in the walk-in cold room and left for the night. Another researcher, known for favoring an early start, came into the lab before everyone else, walked into the cold-room and was pole-axed by a wall of unbreathable, invisible, ordourless carbon dioxide which had filled the almost air-tight box of the cold-room.  Luckily she fell out and back, luckily the floor area of the lab was large so the CO2 puddle was not thick enough to cover her head, luckily the doors were open, luckily it wasn't in the cellar, luckily someone else came in a good bit early for work, so we didn't lose a colleague. Dry ice in an enclosed space?  Don't do that at work, kids.

The math is: the molecular weight of carbon-dioxide is 12+16+16 = 44, the density of dry-ice is a bit more than water 1.5g/cc.  So a mole (gram molecular weight) of dry-ice occupies about 30cc maybe a tablespoonful. Avogadro's gas law states that a mole of any molecule will, as a gas, fill 22.4 litres of space.  That tablespoon of solid material will make enough gas to fill a couple garden buckets.  This is what builds up the pressure in the film-canister until it gives at the weakest point.  Bigger quantities in tougher containers will make a much louder noise. Blowing up a 2 lt soda-bottle is hazardous enough but imagine if the receptacle was made of two thin glass walls inside a light steel container, like a Thermos vacuum flask.  That would make some serious shrapnel.  This last weekend a chap called minusbat in Islington, N London contrived to have a near-death experience for his family with dry-ice and a vacuum flask.  Nobody died but . . . please . . . don't do that at home, kids.

Wednesday 29 April 2015

Tristan & Isolation

We're a long way (2000km further North) from Bouvet Island, which we alighted on briefly in January. Tristan da Cunha is named for, indeed was named by, Portuguese explorer Tristão da Cunha who came up against them in 1506.  That's more than 500 years ago, at the very dawn of the European voyages of exploration. Everyone knows that Columbus sailed the ocean blue in 1492 to discover the New World.  Fewer appreciate that Vasco da Gama's voyage to India via the Cape of Good Hope came five years later in 1497. da Cunha was on his way to India when he discovered the archipelago of which we treat. It is really among the most remote places in the World and by all accounts there's not a lot for entertainment.  If you want to take a gal to the dance for example, there isn't much choice: there are only 300 Tristanians all at all from tots to pensioners, and nobody wants to have a date with his own sister.  There have only been eight surnames on the island: Glass, Green, Hagan, Lavarello, Patterson, Repetto, Rogers, and Swain who arrived there some time between 1816 and 1908, The Patterson line has 'daughtered out' and Mr Patterson's surname and Y chromosome is no longer to be found.  Likewise, while history identified 7 ancestral females, whose surnames haven't come down to us, a study in 2003 showed that there were only 5 different mitochondrial genomes circulating. So two of those lines have gone too. You have to read the original paper to see how many instances of non-paternity there were South of the Line. Each Y chromosome has a characteristic genetic signature ('haplotype') which should be inherited with the surname.  It looks like a Polish sailor left a boy behind shortly before WWI, for example.  And of course boys and girls kick over the traces elsewhere, it's not unique to Tristan.

Thus although there has been an occasional instance of new gene variants coming into this small remote population, the fact of the matter is that the original in-comers were few in number and had a particular set of gene variants, some of which were deleterious [= not-so-good].  You and I and all people have about 23,000 protein-coding genes and many of these have known mutations that are harmless if you have one copy [masked by the other good gene] but can affect your health and well-being if you inherit one duff copy from The Da and another duff copy from your Mother.  These are called recessive deleterious traits, and some classic back-of-an-envelope calculations in the 1930s suggests that we all carry a handful of them.  Your handful will be different from my handful, but your cousin's selection of bad cards is likely to be similar to yours. Many of these defective genes are rare in the normal population, and all the copies of that gene are present in the carrier-state (aka heterozygous). Cystic fibrosis is 'carried' by about 1:20 of the population; Narcolepsy has a similar frequency; Tay-Sachs is rarer at about 1:300. The chances of having a child born with either disease is remote: both parents have to be carriers and they have to make a 1/4 draw of their chromosomes [explanatory diagram] for the child to inherit two mutant genes 1/20 x 1/20 x 1/4 = 1:1600. 

But the case is decidedly altered if there are only 15 people in the population: 1:300 odds no longer apply. Such groups either have the trait, and at a much higher frequency than the rest of the world or they don't.  This bottle-neck is called Founder Effect by geneticists and it's often quirky.  The first small group of Asiatics who walked across the Bering Straits to people America just happened to be all blood group O, so none of their descendants have A or B antigens on the red blood cells. All Native South Americans are group O.  Later sweeps brought in blood group A which is common among Athabaskans and some other groups in Canada and the US.  Blood group B was effectively absent from the pre-Columbian New World. Tay Sachs is much more common among Ashkenazi Jews. It's like that for Tristanians, one or other of the original 15 carried a genetic predisposition to Asthma and another brought the genes 'for' retinitis pigmentosum a degenerative eye disease.  So these maladies are way more common in the South Atlantic than hereabouts in South County Carlow. On the other hand, there are far fewer southpaws among the Tristanians than you'd expect. This is a problem in all small or endogamous populations.

All this poking and prying into the genetics and antecedents of the human guinea-pigs of Tristan and pushing it out into the public domain must make the poor data-providers feel like they are specimens in a large goldfish bowl.  It certainly has me looking for a pinch of salt when historian Simon Winchester claims that he has been banned from the island for telling an old, and possibly true, love story that could have served as a model for Madame Butterfly.  You may read that neat essay, with advantage, for its description of how a sure-I'm-right ethical position was gradually shaken into an appreciation that The Other is not only different, but may also be better.

Tuesday 28 April 2015

Saying thanks

We don't say Thanks half enough.  It costs so little to acknowledge that someone has done something for you.  In Ireland, the culture of tipping waitrons is nowhere near as highly developed as it is in America, so throwing a handful of change on the table as you leave the café is often seen as enough, if not exactly 'plenty' or 'abundance'.  With two daughters working in the catering trade, it's probably true that the waitron would rather you looked them in the eye when they took your order and brought the buns. Several years ago one Saturday, I went into t'office in TCD and was surprised to meet one of the graduate students from the lab next door shuffling a big stack of papers.  It was Der Tag: the day that her PhD thesis was finally printed and she was collating the copies into five piles for binding at the print-shop.  As you do, I picked up one copy and leafed through to the Acknowledgments, the only bit that anybody but the external examiner reads.  After tribbing her supervisor, her family and her lab mates, she wrote "special thanks are due to Bob "Brain-the-size-of-a-plant" Scientist".  I thought this was so neat and ironic that I laughed out loud, appreciating the deliberate mangling of a tired old phrase with something ambiguous [did she mean the mighty giant redwood Sequoiadendron giganteum or the diminutive genetic work-horse mouse-eared cress Arabidopsis thaliana?]. She was puzzled at my response and, when I explained, got uncharacteristically flustered as she set about reprinting that page 5x with the typo corrected.

In the final year of the biology course in the Institute, all students carry out a final year independent research project. Project students are assigned hours in a particular laboratory each week and peck away at the coal-face under the supervision of a faculty-member. By no means all faculty members opt to dream up and supervise such research projects and remarkably it is optional.  I signed up immediately I was given the opportunity to do so because a) you get some hours off your teaching load and b) it's much more interesting pushing frontiers with some young chap than grinding through a curriculum heavy with ideas and technologies that would not have been out of place in 1915. the project supervisors take turns at acting as the adult physically in the lab. Supervision hours are a bit of a doddle: you can let the students get on with their experiments while you mark lab-copies for another course.  Occasionally one of the students will ask a question on the level of "Where do they keep the pipettes?" but even then you can sit down for an hour and rest the old pins.

Every Monday and Friday morning for the last 30 weeks, I've spent three hours on each day supervising 4th Year Bioinformatic Research Projects. 6x 30 = 180hrs = nearly 1/3 of my teaching load. It's the first year that a whole section of the final year cohort have opted to do a computational biology project, rather than tricking about with eppendorfs, Petri dishes and spectrophotometers in the lab.  This is possibly because that door has never been offered for them to push open; but it's also probably because I caught them at the end of Third Year and gave them 3 hours of war-stories about my triumphs and failures while pushing the frontiers of molecular evolution.  I gave them 3 hours, above and beyond my 600 hour/year teaching quota, because I've only had three good ideas in a lifetime of science and a fourth hour would have been punctuated by very long silences.

In the end, 16 students got to carry out compu-projects in one of the computer suites of the business school. I was only officially supervising half of them, the others were pursuing ideas from one or other of my colleagues. But I was the adult in the room so they became the B team: B for Bob, B for Bioinformatics. This has not been a doddle: for each three hour session I've been gabbing on with someone from the start to the finish of the allocated time. One part of the B-team used to arrive at 10am, leave their kit and pop out for a coffee-and-chat break.  For the rest, some were religious in being there for every class while others seemed to have a lot of other engagements; there was no correlation between this variable and how far their part of the frontier was pushed. It was all the most tremendous fun, juggling all these different investigations in my head.  The kids soon learned that it was hopeless to start a sentence with "Remember what you said last week . . ." On the one hand, I found myself trying to rein back the enthusiasts as they went off the rails of the possible. On the other side of the room five minutes later I'd be pushing pushing pushing a student up what I thought was a gentle intellectual incline and he acted like I was asking him to scale Mt Impossible without iCrampons. And every project was unique: different organisms, different tools, different deliverables. It was mostly about getting each one to to fulfill their potential and a little bit more - not unlike home education with Dau.I and Dau.II all over again.

The deadline for submission of their project report and their literature review [3 copies] bound together as a single document was 1pm on Friday 17th April, which gave the supervisors a week in term time to read and mark the things. Because it was a physical copy, the students had to find me or find their supervisor rather than whack off an e-mail.  I dropped into the class at 10am and again about 12.50 in case anyone had turned up to class or didn't know where my office was.  Nobody there, but as I walked back across the concourse I was stopped by the coffee-and-chat ladies, still acting in concert.  They presented me with a little glossy-paper gift-bag containing a) a mug [R] b) a packet of tea-bags and c) some rich-tea biscuits d) a note "For all the tea-breaks you missed because of us . . . have a drink on us" e) a card signed by everyone in the B-team. They hopped from one foot to the other until I'd opened everything up.  It was >!gulp!< right on the button. They had read me so well - I would have been appalled if they'd spent a lot of money on something that was of no use.  They were really paying me back, touché, in my own kind after all my ironic comments about privileging tea-breaks over work.  Has that ever happened to me before? I reckon not. So thanks!  On the back of the binfo-mug in smaller letters it says "Thanks for everything Bob, love the B Team"  I do I do!

Monday 27 April 2015

Dagging for Ireland

About 15 years ago our black&white (mostly white) cat disappeared one day and a strange but overly familiar black cat came to the door looking for food.  It turned out that our Snuggles had fallen into a vat of sump-oil on a neighboring farm and was in need of professional help. The vet declined to come out but said that Fairy Liquid was yer only man in such cases and we should give the cat a bath.  Apparently, this is what was found to be most effective for cleaning up sea-birds that were victim to an oil-spill. The remedy worked a treat and the cat lived on with us for another long number of years.

Yesterday The Beloved announced that those sheep which are outside the maternity ward (last year's lambs, empties and one pensioner), needed a) chiropody and b) dagging.  Chiropody is basically toe-nail clipping and you need a handy pair of really sharp secateurs to trim the nail back, especially if it is grown over the pad and/or is getting split ends.  The alternative is to take the flock for a gallop up and down a metalled road for a while in lieu of letting the sheep leap about from rock to rock. A life in a soft grassy paddock is not sufficient to keep the feet happy.  The other issue (problem) is having an issue (discharge, matter) from the cleft between the toes where a cut can easily go septic if your lifestyle entails walking through a lot of sheep-shit.

Dagging is what requires the Fairy Liquid especially if the sheep has been scouring recently when the soft dung can mostly be washed off with lots of soap and water. It's like washing your hair - you've got to get your fingers right in there and work in the soap and then give it all a good rinse with a hose.  It was lovely and sunny in the forenoon yesterday and I was just about to start in on this task when I took inspiration from Thor Heyerdahl and the Kon Tiki crew and discarded my socks, boots and dungarees. If I was going to get covered in wet sheep-shit, I thought it would be best to minimise the laundry list. I'm not as buff as Thor, Bengt or Knut were in 1947, but in my khaki shorts and a pair of Crocs I could have passed muster on the good ship Ewe Tiki. While TB held the front end, I got down and dirty at the other with a pair of old kitchen scissors to cut off the solid lumps and soap and hose for the wet stuff,  . Strangely enough the pregnant ewes seem much cleaner than the useless mouths. I was washing my hands for the rest of the day and have had two all-over showers but still smell of sheep.

Two vaguely related jokes:
1. Young feller from The North comes back from college in The South raving about The Dubliners.  Uncle who has seen them on the TV "That Ronnie Drew and Luke Kelly, they look like a pair of sheep's arses."
2. The great thing about using beer shampoo is that the hair is already half cut.

Richard Montgomery

Richard Montgomery was born in Swords, Co. Dublin in December 1738. He attended Trinity College Dublin in due course and after a couple of years of 'study' joined the British army to serve with distinction in the North American theatre of the Seven Years War (1756-1763). When the shot that was heard round the world was fired on 19th April 1775 in Lexington MA, Montgomery threw his lot in with the patriots; bringing his considerable military experience with him.  The following year he led the revolutionaries in their, ultimately abortive, invasion of Quebec and was blown to buggery by a whiff of grapeshot in the assault of Quebec City; he was only 37.  His life was full of chivalry, bravery and romance and his name has been given to 13 US counties, a handful of cities and a number of ships. 

As a Man of Kent [not to be confused with those spineless Kentish Men), the ship I'm most interested in is the SS Richard Montgomery, a liberty ship [see Blob I, II] laid down in Jacksonville, Florida 15th March 1943 and completed 20 weeks later on 29th July. The following Summer she was loaded with munitions and set sail for Europe with 3,500 tons of bombs, fuzes and other explosives ultimately bound for Cherbourg to supply the invasion of France following D-Day 1944.  In August, she was given orders for the Thames Estuary to be marshalled into the next convoy for France.  The RN officer in charge of the Estuary, based at Southend-on-sea in Essex and concerned at the nature of her cargo, ordered her to wait on the Kentish side of the deep-water channel just off the Isle of Sheppey. A storm blew up, the Richard Montgomery [plethora of links] dragged her anchor, ran aground on a sandbank and broke her back on a subsequent low tide.  Some effort was made to salvage her valuable cargo but only half the holds had been cleared when the now two parts of the hull shifted ground again and it was deemed too expensive and time consuming [there was a war on!] to try for any more. It has been suggested locally that the salvage rights to the carcase were disputed by the dockers of Rochester vs Maidstone and this log-jam helped fuel the decision of abandon ship.

Apart from a, now much diminished, interest in my native county, I have a certain Boy Chemist interest in the explosive potential of TNT; nitroglycerine; meteorites; Chernobyl; Kyshtym; polypropylene; gunpowder; methane; volcanoes; ammonium nitrate; crude oil; and even carbon dioxide. There are 1500 tons of phosphorus and other bombs lying underneath the still visible masts of the SS Richard Montgomery. If it went up it would cause a modest tsunami up and down the Thames, briefly overwhelming the flood defenses on both side of the estuary, it would break all the windows within a 3km radius and severely damage any ships in the immediate vicinity. So far, so bad. One of the older youtube minidocumentaries [Wrecks; Shipwrecks; Time-bomb] on the past and future of SS R.M. has some pundit saying there is no immediate cause for alarm, the cargo is safe until . . . 2015.  But the elephant in the rumour is that the Richard Montgomery was carrying 'insurance against the possibility' that the Germans might use chemical weapons.  On 2nd December 1943, a German air-raid on Bari in Southern Italy blew up the SS John Harvey, another liberty ship, whose cargo of munitions included 100 tons of mustard-gas bombs.  That toxic cloud killed at least 1,000 service-men and an equal number of civilians before it dissipated.

Things have changed considerably over the last 70+ years.  1) Some bright spark in the Planning Department approved the construction, within the potential blast zone, of a huge Liquid Natural Gas LNG storage depot for the National Grid: 0.7 million tons of gas would go up with a whoomph 150x bigger than the blast that flattened Hiroshima. 2) It has not escaped the notice of several novelists since 9/11 that dropping something heavy in the vicinity could trigger the potential energy currently stored underwater.
At the moment, no government minister, no government department is going to own the problem because the clean up costs are estimated to be in excess of £17 million. That's a lot of sugar, but what price the mustard-gassing of 2,000 Men and Maids of Kent? . . . or 8 million Londoners in the LNG scenario?

Sunday 26 April 2015

Mighty Thor

The Blackstairs Film Society is the high-point of our social and cultural life in the remote section of rural Ireland which we inhabit.  On the last Saturday of every Winter month September through April, we get to see a film with subtitles!  They can be earnest like The Seven Brave Tractor Drivers of the Caucasus or classics like Babette's Feast but they are rarely the fluffy rom-coms that I prefer.  Since I had to hide behind the sofa as a nipper for most episodes of Doctor Who, I have a very low threshold for suspense or frighty-bits.

Last night at the Film Soc was the newish biopic from Norway called Kon-Tiki. Trailer. I zipped through the book shortly after I learned to read at age 8 and thought it was a ripping yarn. We had far fewer books back then, but nevertheless it would be hard to avoid it after being translated into 70 languages and selling 50 million copies. So I was surprised to find that there were adults in the room who had never read the book and only had a hazy idea of what it was about.  It is, after all, nearly 70 years since Thor Heyerdahl and his pals sailed across the ocean blue and lots of other adventures have happened since. It took the Norwegians just over 100 days to drift 8000km on a balsa-wood raft [R] from Peru to Polynesia and, to be frank, not a lot happened on most of those days. You can't fill 100 minutes of Aspiring-to-an-Oscar with 6 half-clothed well-bearded hunks eating tomato soup and picking flying fish off the deck, so the demands for drama concentrated on the few dramatic encounters - even with these, nobody died, although their pet parrot fell of the boat and was scarfed up by a shark.  Hollywood required this event to be conflated with another in which one of the men fell overboard from the relentlessly drifting, can't-turn-back raft.  Having one of his quick-reacting colleagues seize a line, plunge in and swim away from the ship back towards his disappearing ship-mate was dramatic enough without having to invent some stage-sharks in a feeding frenzy.  Then there was a big storm; they were outpaced by some fin-whales Balaenoptera physalus; they saw some unworldly phosphorescent creatures; they were excited at seeing a gull because that indicated the presence of land beyond the horizon  . . . and suddenly we are all crash landing on a reef at Raroia.  To string that out to an hour and a half you have to have a lot of lead-in with Heyerdahl growing up adventurous, spending some years in a tropical paradise, and some years being laughed at by people whom he asked for financial support.

One of the imperatives for Heyerdahl was to keep the adventure in the public eye and the only way to do that was a vacuum-tube short-wave radio.  Even as they were getting wet in the Pacific, Shockley, Brattain and Bardeen were inventing the transistor at Bell Labs in NYC and transistor radios didn't become widely available until 1955.  They needed an aerial to transmit and receive signal and the Kon-Tiki was low-slung with stubby mast, so they flew a balloon aloft to raise the aerial sufficiently high.  In the film, the balloon is lost because of the antic of the parrot (who was nominated for a Best Supporting Avian award).  I'll have to go back to read the book to see if this too was a simplification of events for dramatic effect . . . then again maybe I won't bother - I'm not 10 any more and I've still got the whole of Harry Potter to get through.

Anatomy? So yesterday.

Years and years ago, maybe in 1972, I read an article in New Scientist that critically evaluated the then current medical school curriculum.  Why in hell, the author asked, do students still spend the whole of first year carefully dismembering cadavers and quizzing each other to name every knob and dip and muscle attachment on the bones of their personal half-skeleton? In those days you'd buy a half-skeleton because the full one was more expensive and medical students would rather spend the extra £100 on beer.  The author said "still spend the year", because he'd been through the same mill a generation previous and the curriculum was unchanged. IRC his argument was that all sorts of other necessary skills and knowledge were absent entirely from the curriculum because they didn't seem important to Professors of Anatomy in 1872: things like ethics and how to talk to the relatives of your mistakes. CAT scans, MRI and DNA sequences were still a long way in the future but they would have been on the 'missing in anatomy'  list.  Clearly you can't keep adding to the syllabus because the students would be on their pensions before they qualified - something had to go and it was suggested that anatomy was for the chop.  Any doctors who really needed anatomy, orthopedic surgeons for example, could pick it up later or take an advanced course.

I doubt that an article in New Scientist was sufficiently heeded to have changed the face of medical school but it seems to have been prescient.  10 days ago, I was having pre-dinner drinkies in the Senior Common Room of Trinity College Dublin before going into the Dining Hall for Commons and later to attend a symposium on the State of the University.  Blimey, it was hard work.  I'm not stupid and had a very expensive education, but it was difficult to keep up my end of the dialogue which roamed from 20th century Genetics to 12th century Genoa and out to γ-Centauri without missing a beat.  Luckily, I'm old enough and stupid enough to not mind being wrong or asking foolish questions. One of the chaps was a visiting anatomist from The Other University TOU UCD.  At one point he asked, with a rhetorical flourish, how many Professors of Anatomy did I suppose still occupied a Chair in the UK?  The question only made sense if the number was low, so I plunged at "Three", to be told that the answer was One.

He then went on to explain that Anatomy is making a come-back.  It is now the sexiest area in medicine because of computers and nano-technology.  This assertion fell on fertile ground because one of our students presented an amazing paper at Journal Club a few weeks ago: why every MRI research group should have a low-budget 3D printer.  The student pushed that paper because it was right on topic for his own project. MRI machines are set up for humans but what if you want to do some imaging on the head of a mouse to develop a therapy before starting in on human brain surgery. You'll need something to hold the mouse's head still and a 3-D printer can print a snug fitting head-cradle about 15mm across from the analysis of a set of photographs of the mouse's head. You can make another for the next mouse or if you change to rats - the technology is scalable.  The details are impressive: you can load your printer with MRI-transparent plastics for example. And the economic argument is compelling: an MRI machine costs somewhere north of €250,000;  modern 3D printer can be had for less than €1,250 [0.5%] and the consumable materials can be bought for less that €25 a pop. The peripherals and consumables are dirt cheap so it is easier to make optimum economic use of your fancy big instrument. This is why TV commercials often have such high production values; the company is paying half a mill for a 10 second broadcast slot so their ad had better look really slick.

You don't need a skeleton anymore because the human body has been entirely digitised in a scalable fashion: you can zoom into the inner ear and print out the incus, malleus and stapes and see how they articulate.  If dealing with three bones that are each about 4mm long is too fiddly, you can print out a 10x sized model and work with that for, say, teaching purposes.  They have working models of human muscles, that don't have soft-parts made of proteins but are functionally equivalent, the same size and made of little rods, pistons and cam-shafts. You can print a generic human heart!  But then starts the catechism:
Q. Who is going to inform the boffins about all the anatomical variants in which the human heart is fashioned? [* footnote]
A. Someone who has a life-time's experience in looking at them.
Q. Where might you find such an expert?
A. In the Yellow Pages.
Q. Would you be looking for a Professor of Anatomy?
A. Sorry, the last one in England just passed on and his vacated chair has not been filled because the old chap never developed any marketable intellectual property.

[25% of adults have a persistent leak between the right and left atria of the heart because their foramen ovale failed to snap shut at birth].

Saturday 25 April 2015

Yes, Minister

We live here in Ireland in a parliamentary democracy. It is salutary to reflect on what makes the difference in getting elected to represent the people. After a long session consuming alcohol and yakking the previous night in Dublin, I caught a bus down South to go back to work.  It was a busy day, with a number of tasks to tick off:
  • Marking two Excel exams from my final classes on Wednesday
  • Attending a PhD viva and congratulating the candidate
  • Delivering three research project reports to colleagues in Teagasc on the other side of town
  • Meeting of the Research Board
  • A few re-hydrating cups of tea
  • Wait on James Reilly, TD. Minister of Children and former Health Minister
I was a little discommoded, I won't say annoyed, at the last item because it appeared on my To Do List with only 26 hours notice.  It didn't appear only on my list, of course, dozens of people were requested-and-required to be in key places on campus as the Minister sailed through pressing the flesh. No elected representative wants to see a creche, a milking-parlour or a factory unless there are voters inside.  So just before lunchtime, I dropped my mark-book, shrugged into my white-coat [needs a wash, looks authentic] and loped off to the Dargan Centre which was formally opened by local TD Phil Hogan thirteen months ago.  You can't expect the Minister to trudge up two flights of stairs to visit our environmental research coal-face, but we have an elevator: very modern with two glass sides. Its arrival on the top floor was a a little like swinging the net up onto the deck of a trawler because it was brimful of suits.  "How many suits does it take to propel a Minister?"  I asked my HoD.  I had barely loosed this quip before I was shaking the fist of the Great Man while being introduced (as Jim Scientist;  sigh!) by our Director of Chiromancy.  About 2/3 of the suits were officers of the Institute: the Quidditch Coach, the Dean of Basilisks, the Elder of Zion etc., but the others were the usual suspects from the Party corps de ballet. The only sitting Fine Gael TD for the Carlow-Kilkenny constituency was there, of course: a good photo with a minister [any minister will do] is worth on average 23.7 votes in next year's election. The other FG CW-KK TD Phil Hogan has, since he had his tour of the building in March 2014, become an EU Commissioner in Brussels [basic pay = €247,992] and vacated his seat in the Dail.

About 3 minutes after I was introduced to the Minister, I was shaking his hand again like the was no tomorrow [Groundhog Day reference] and being asked to talk about Lithium in the Blackstairs: possibly the most exciting and potentially damaging thing to happen in the constituency this century.  But you could tell he wasn't really interested, his radar was scanning over my shoulder for another hand to shake. I asked one of our suits who was the well turned out baldy guy on the visitor's team, and it was David Fitzgerald, county councillor, who is hoping to continue to Keep Kilkenny Beautiful [and Right] while upping his gross pay from CC=€16,724 to TD=€87,258, which is a little more than I'm pulling down.  It looked like the Minister had instructed the Candidate "Stick close to my shoulder, boy, and let me do the talking." as he worked the room - it was an anthropological wonder to see everyone presenting themselves to the alpha-male: we're just primates. The style of Reilly's boss Enda Kenny is miraculous to see - that's why he's Taoiseach.

Friday 24 April 2015

Almost ewery day a birthday

It's lambing time again.  Last year it was a long drawn out process and we finished up with 3 bottle-fed ewe-lambs and 11 males . . . or so we thought: a final check as the boys went off to the factory revealed another ewe-lamb and 10:4 is not a significant departure from the expected 7:7 ratio. So we can't complain, but resolve to do better. Because we lamb so late it is a particularly bad idea to get the youngsters pregnant in their first adolescent season. I know farmers who go for it, and deal with the extra work and a higher proportion of difficult deliveries and confused new mothers.  But we don't have the stomach or the competence for that sort of hardship, so we carefully kept the four 2014 lambs in a separate paddock when we took delivery of the ram for his three weeks of hard work. To look after them we left our oldest, least-toothed ewe 'Patch' in the same field. She has been firmly retired from the maternity circuit after leading us such an unhappy dance last Spring.

After the Ultrasound man cast his verdict in February, we had three 'empties' - adult ewes predicted to be carrying no lambs. These we drove in with the teenagers and concentrated our attention on the maternity field.  Tsk, wasn't the first sign of ovine fecundity this year the delivery of a still-born lamb to one of last year's lambs?! Over the next few days, two more of her sisters produced unexpected offspring. Three tupped empties + three untupped preg. How does that work?  You can see why the ancients stoutly maintained that babies were delivered by storks because clearly our regime is a little hazy about who is doing what to whom. After the lamb-mams, two doubles (with a 2 written on the right flank) gave birth but the first one delivered in the field in the middle of the night and we lost one of the lambs to the fox. Score = 2 dead; 5 alive.

Of course, we were most worried about the ewe reportedly bearing triplets but she has shed her load (3M) just as darkness was falling and we've brought them all up to the poly-tunnel with the other mothers,  Today was the last day of classes for the academic year: I'm ready for the 0200hrs feed if it should come to that. Score = 8 live lambs.

A sense of self

Last night I went to a family gathering in TCD and I don't think anyone there was more closely related to me, in a genes-in-common way, than, say, Michael D. Higgins, our noble President. But it was still my family.  Just like at a family wedding or funeral, I met people who were part of my cousinage but whom I'd never actually met. And I also caught up with people who had disappeared off my radar for more than a decade as we met again - a little heavier, a little greyer, with more children or a new partner. The head of the family was hosting a party to celebrate the award she won last year for being the Best Mentor in All Ireland. And we, who had been made better people by her solicitous care and pushing to fulfill our potential, were there to say thanks. The official ceremony in Athlone last year was pinned on the lapel of a meeting of Science Foundation Ireland: where those who run this prestigious research support quango get to have some face-time those who have benefitted from the largesse. It was like a TED conference except that everyone's tab was being picked up by we-the-taxpayer.  At TED, the audience cough up $5,000 a head for the privilege of meeting [other] charismatic creative people.  As a humble and not notably successful foot-soldier of science, I would never have gotten past the door on my own scientific research record.  I got my free dinner in November because I wrote a piece in The Blob which became part of the package that got Our Gaffer noticed.

Very interesting. In the midst of the canapes last night, one of my old work-mates turned to me and said "It wasn't me who told you to go back where you came from?  I hope it wasn't!".  It would be dishonest to say no, so I said "Yes".  She was about as embarrassed as I was, which is to say not very much because we both have a sense of self that is on the positive side of the scale.  But then, like the denizens of Lake Woebegone, pretty much everyone is on the positive side of that spectrum: we all re-write history and our recollection of events to put ourselves in a more positive light.  I'm glad I wrote the original anecdote in quite neutral terms and didn't conjure her up as a malignant racist hag with one tooth and a pointed hat. It was quite redemptive to see her acknowledge the darker side of her nature: hoping that it wasn't true about herself but being honest enough to recognise that it might have been. It's really hard to change our true selves but the first step is to look in the mirror with clear eyes and some sense of critical appraisal.

I had a running battle all night at the reception, in the pub afterwards, continuing as we spilled out into the chilly street after midnight a little the worse for the dhrink.  Battle isn't the right word, but 'discussion' doesn't capture the sense of ding-dong no holds barred exposure of the dark teatime of our souls.  At issue was what we should do having recognised that there were better scientists in the World than we were.  Was there any point in puttering along in the peleton of La Tour de Science?  The metaphor of science being a race with only one winner is, frankly, repellent.  And yes, we all acknowledge that there are lots of subsidiary prizes: the maillot à pois rouge is given to The King of the Mountain in the Tour de France; you get promotion if you publish enough papers. The reason why cyclists whistle round the corner in a group is that they can all go faster if they share the burden of pushing the air aside.  Geese Branta canadensis in flight do it, and we're surely smarter than geese, you silly goose.  We should be more collegiate and supportive and less competitive in science. We'll all go forward faster if we share our data and give our time to those younger or less fortunate than we are. We scientists have a certain talent, a lot of training and a mountain of accumulated knowledge, so we must continue put bricks in the wall of science for as long as our society will support us. It is a privilege but also a duty. Science is a way of knowing that has delivered much of what makes life good to live - indeed it has given life itself to billions of people who didn't get smallpox, malaria, polio or tuberculosis in this and the last century.

There are two points.
1) The stellar scientists, Nobel Prize winners; landers of the million euro SFI fish; the creators of papers in Nature and Science are all standing on the shoulders of giants. But they are also standing on heads and hands of quite ordinary people who are filling in the chinks left by the last Great Leap Forward.  Unless we do that, there is no necessary-and-sufficient foundation for the next major foray into the unknown. My Institute's core business is to supply an essential part of this infra-structure; people who are a good pair of hands: who can run the instruments which generate the data - reliably, safely, and reproducibly; 40 hours a week, 48 weeks a year. Each of the Big Guns needs a team of people doing their job processing the samples, dreaming up new ways to do their work more efficiently, and being prepared to give that extra push if a deadline looms.
2) We have no idea where the next great breakthrough is going to come from. If we keep on pushing at the frontiers of something we care [bit of passion is allowable here] about and do the job with attention, and with accuracy, and with honesty but not with blinkers, we might, just might, be the one to discover the Secret of Life the Universe and Everything and today's stars will be eclipsed by our small but incandescent flame.

Thursday 23 April 2015

Dark Brew

I was on about Irish soda bread the other day and "Dark Brew" might, in that context, bring Guinness to mind but I'm going further afield than Dublin today.  The far side of the world indeed, to talk about Soy Sauce. In my youth soy sauce was utterly foreign.  I went to a Chinese restaurant about half a dozen times before I was 18, but we never had soy sauce at home where the only available added flavorings were salt, pepper and mustard; and maybe an ancient tub of curry powder.  Only recently, I've taken to adding soy sauce to a wide variety of food to give things a bit of colour and flavour. What flavour?  Umami! which, in my soy-free youth, hadn't been discovered as the fifth taste after salt sweet sour and bitter. The flavour umami depends a lot on the presence of glutamate, the salt of glutamic acid [D, glu] one of the 20 amino acid building blocks of proteins.  You will have met it, maybe in excess, as mono-sodium glutamate MSG in the Chinese restaurants we all go to more often nowadays.  Soy sauce is loaded with glutamate because it is, like bread and beer, a fermentation product. Unlike the yeasty staples of the Western world, soy sauce depends on a different species of fungus called Aspergillus oryzae or possibly A. sojae.

The ingredients of beer and bread, even without Reinheitsgebot purity regulations are really simple but in the East, the Aspergillus molds are given a more complex cocktail to work on, consisting of cooked soya beans Glycine max, [roasted] wheat Triticum aestivum (occasional barley Hordeum vulgare) and some sort of brine.   Often the fermenting brew is more complex too, including some lactic acid bacteria LABs, some regular yeast and, in some parts of the world including Korea, some Bacillus subtilis.  The brine must be there to inhibit the growth of other microbes, because LABs are often quite salt-tolerant. All these species will have a complex variety of genes and their enzymatic products which have been selected over hundreds of years to give a product that is a) safe to consume and b) tasty.  As a new-comer to soy-sauce eating, I just go to the Asia Market and buy 750ml of Pearl River Bridge Light Soy Sauce which is manufactured in Southern China and shipped over the whole world, it is tasty but also cheap.

Cheap suggests that it is made in a chemical process rather than by slow fermentation. If you want something that is rich in glutamate for the umami kick, you can get there really quickly by adding a protease [or even 1M caustic soda NaOH] to a mash of soya beans which will break down the proteins into their component amino acids, some of which will be glutamate.  We carry out a similar chemical attack in Ireland to make soda bread (as I am doing even at this moment to warm the kitchen) rather than a slower fermentative process with yeast that will have time to develop some subtlety of flavour.  In all manufacturing process, but perhaps particularly in the food industry, time is money, and less time is more profit. The several new start-ups in Ireland making various high-alcohol beverages need to be heavily capitalised because their first batch of product is required to sit on a shelf (supposedly developing wonderful flavour) for several years before it can be sold as "Irish Whiskey".

A feel-good story is circulating in the East and now on the blogosphere about a soy sauce company that was destroyed in the Fukushima tsunami and has now after four years started selling the same old product which they are rebranding as Yagisawa 'Miracle' Soy sauce. The current CEO, Michihiro Kono [L with a bottle of the miracle], is the ninth generation of this family firm that has been producing soy sauce for more than 200 years.  One of the things that people learned the hard way in Hurricane Sandy and in the 2011 tsunami is the importance of maintaining back-ups.  Kono-san's whole factory, including his precious and meticulously maintained microbiological stock strains, was filled to the brim with a salty, oily sludge from which nothing could be recovered. But he had left some vials of these stocks with a local university medical school, where they were pursuing some woo-wah theory about the anti-carcinogenic properties of the soy sauce or its ingredients.  The laboratory was similarly inundated and its contents swept away but one of their workers providentially found the carton of Yagisawa material safe-and-well some distance away.

Like Irish Whiskey, Yagisawa is a quality product that must sit tight for 2 years before being sold, and it has only started selling in the last few months, but sales are recovering well with a different direct-to-consumer marketing strategy it looks like new markets will open up. They are supplying one toney Parisian restaurant. It is particularly feel-good because the company kept all its surviving staff (one died in the waves) on the payroll when they had nothing to sell and contributed in all sorts of ways to the local community in the wake of the disaster.  Maybe you'd like to support it, too?  A crowd-funding site raised $1.5million to getting the company back on its feet. More deets. Same deets. More.

Wednesday 22 April 2015

Three good things about Wexford

We live very remote near the middle of Ireland, so there isn't much excitement.  Last night I came home from Work, had a quick feed and drove off in the opposite direction to the ancient (Veisafjǫrðr was founded in 800CE by the Vikings) town of Wexford.  I had >!two!< science events to attend. 

First off at 1845hrs was the launch in Wexford Library by the Wexford Naturalists' Field Club WNFC of their publication on the distribution of damselflies & dragonflies "The Odonata of County Wexford".  Notice how they correctly place the apostrophe [Naturalists'] in their name, they must care about the details.  This book is short on pages N =44, but rich in illustrations of the 23 species of Odonata that have been recorded in Co Wexford.  Each species has a distribution map showing where it is found in each of the 10km squares that comprise the county,  This is very much a people's science project, not funded with an enormous grant from Science Foundation Ireland, but driven by the enthusiasm of a handful of the members of the WNFC.  I was talking to the authors Nicholas Egan and Chris Wilson afterwards while getting my copy of the book signed.  It is particularly useful because it is a snap-shot of what we know now about the distribution of these beautiful insects.  So it serves as a bench mark against which to compare future sightings - or more depressingly likely, future non-sightings as some of the endangered species on the list become rarer to find and finally blip off the radar entirely.  The book will help me make a better call on identifying what I'm seeing when I next go walking the Barrow not entirely oblivious of the wild-life around me.  One of the most heartening things in the book is a full page, in small print, listing all the contributors of data from 1893 [first scientific record of Odonata in the county] until late 2014.  If you see a damselfly in a particular location at a particular time then write it down; it may be the only record of that species in that 10km square, or in the county, or in the country.  But you could also just reflect on how pretty they are and what evocative names they have been given by people paying attention: Ear Cutter, Hawker and Devil's Darning Needle.  But please, please, use the Latin name so that your colleagues in Hungary or Uzbekistan know what you are talking about.  The WNFC supplied a grand selection of home-made cakes and cookies to sweeten the event; thanks for that too.

After all that, I stepped out into the chilling evening to calm down and walk across town to the third meeting of the Wexford Science Cafe which convenes on the third Tuesday of every month in "Johnny's" aka The Sky and the Ground, South Main Street.  In February, four sciencekateers got together over a few drinks to see what could be done about the dominance of the Arts in the edutainment of the plain people of Wexford. The Wexford Opera Festival dominates the consciousness of the town to a quite Harry Potter degree - which needs an antidote or at least an alternative. We agreed then that we would take turns to present something [paper, movie, interesting rock, walrus baculum] once a month that would start things off so that we could talk about science.  In March, because it was uppermost in my mind [what with the Royal Society's 350 years and all] and whatever's there gets blurfed out in short order [The Blob], I led things off with a mad-eyed rant about Spandrels.  Incidentally here's the transcript of a recent interview with Dick Lewontin  about Spandrels and much more by David Sloan Wilson - not for the faint-hearted: it's not 'fluffy'. Last night The Gaffer announced that she would talk about immunology of the honey-bee Apis mellifera. This is really really important because of CCD colony collapse disorder which is devastating commercial bee hives across the US and elsewhere. Commercial bee-hives?  Could we not manage without industrial production cheap honey?  Maybe, but could we also manage without almonds, kiwifruit, melons, oilseed rape and a long list of other species that depend on bees for pollination? Well, it was a romp, from Jenner [and Jesty] and vaccination, through polio and HIV, to whole genome sequencing and immune gene discovery by computer.  We could have talked all night but eventually forced ourselves out into the now frankly freezing street and home.  All great fun, must do it again soon . . . and we will: 8pm Tuesday 19th May 2015, The Sky and the Ground, South Main Street, Wexford. All welcome!

They say that good things come in threes, and they did.  As I walked down the street towards the pub, I met Chris Hayes, tree-surgeon, broadcaster and and philosopher incommming from the other direction.  He professed to be Hank Marvin. I put on my best starving graduate student face [once you've been there, it never really leaves you . . . or it can be put on effectively] and he dragged me next door to the Premier chipper and bought us both a Wexford rissole. I've finally eaten a Wexford rissole!  Like sausages, you really don't want to enquire too closely about how these things are made but you haven't really lived until you've tried this fistful of food-groups [carbohydrate, fat, protein and much much more].

Tuesday 21 April 2015

Wot's a university, then?

And, more to the point, what is a university now?  Last Thursday night, after a slap up feed worthy of Bunter the Owl of the Greyfriar's Remove, I crossed the Front Square to a Panel Discussion in Trinity College Dublin "Are Irish universities committed to enlightenment ideals? Recent and forthcoming developments in Irish higher education policy and legislation". The panel consisted of a handful of minor celebrities in the politics of higher education and each was given 10 minutes to make a point or two on the subject.
At issue is the fact that third level institutions, both Universities and Institutes, are striving to reconcile the enlightenment ideals under which they flourished with the modern pressures to measure and monetize ‘outputs’ and 'deliverables'. Over the last twenty years each college has acquired a bureaucracy of intellectual property [IP] staff whose job it is to milk any ideas the staff and students may have and convert them into money. This is to help pay for the infra-structure, including the IP drones and the waitrons who serve Commons, which allows The Effectives space to think. If the desire is to develop a larger number of useful ideas, the solution in our current world is to impose a lot of bureaucratic requirements to measure the ideas as they develop and penalise people who don't have enough ideas often enough.

I know Two Counter-productive Damnable cases where very smart young scientists had their cards marked because they hadn't published anything for a couple of years. They had been clever enough, confident enough and ambitious enough to plunge into a new and exciting field, which venture, because new and exciting, took some time to develop. They disdained to dribble out some least publishable units LPUs as a needless distraction from the difficult task of conning their ship towards a New World. But the bean counters noticed and delivered a morale sapping memo, notwithstanding far-above average contributions to the intangibles of College life - quality teaching, solicitous mentoring, thankless committee-work. Both of these cases were women and both of them shortly thereafter became Fellows of their institution because happily their small team of adventurers into the unknown returned laden with scientific treasure . . . in spite of rather than because of The Memo!

I'm with Thomas "To have a great idea, have a lot of them" Edison and believe that if you trust creative people to do what really engages them, even playing a long game, then the ideas will come . . . some of which may make a return for we-the-taxpayer.

The panel touched on some interesting themes:

1)     The invidious position of short term contract staff (ahem! self included) who are a long way from academic freedom because they need to toe the party line to ensure shoes and toast for their kids.  It is difficult for them to question managerial diktats, which may not be evidence-based.

2)     In my lifetime several assumptions have been widely accepted that were insufficiently questioned at the time: the housing bubble, the stupidity of women, sinfulness of miscegenation. Universities are among the best place to train (a subsection of) the people in skepticism & critical thinking so that they can apply evidence-based advocacy to expose nonsense that “everyone knows to be true.

3)     The absurdity of obsessively measuring the measurable because it is impossible to measure the intangible.  This applies unproductive pressure on all academics – if you only get kudos for publishing in English and off the island of Ireland then you will bow to pressure to do that even if the opposite might be holistically better.  If your research outputs can be measured (H-score, impact factor, citations etc) and valued, then you’ll spend more time on gaming that system and less time helping students to a quality education – dammit: you can hive the teaching off on a graduate student or a 20-something contractee while you go stellar.

4)     As central government funding has plummeted so its insistence on interference has increased.  In AerLingus you expect a 5% stakeholder to button their lip and defer to a 40% shareholder; but somehow governments think that they push their ideological weight about and force forward the latest faddy organisational details about without paying for the privilege.

5)     Universities (and ITs, probably) are loud in their insistence that they can manage their own affairs, especially if government isn’t ponying up the cash [see 4) above] and the academics are especially sceptical when bankers and bank regulators and their cousins, who have soiled their own nest to the tune of €60billion of bale-out, aspire to run Third Level Education.

6)     There is a certain irony, after all this adamant independence, that Universities (and ITs)  are incapable of self-regulating in the area gender balance and are always asking government to legislate on the matter.

7)     Because the auditorium was full of intellectuals, a chap could be found to make the point that there were unacknowledged tones of patriarchy in the Enlightenment and quoted a string of post-modern critiques of neo-Hegelian dialectics. Encyclopédists Denis Diderot and Jean d'Alembert were both men and Tom Paine wrote The Rights of Man.  Maybe we don't want to adhere to those ideals???

8)     The high point of the night was when Tom Boland from the HEA started his analysis with “. . . address the issues of entitlement and the university”  oops red face start again “. . . address the issues of enlightenment and the university”.

Good stuff, glad I went.  I'm glad we have such a thing as a university where this sort of informed debate is normal, where certainties are questioned and where young people can start to polish their crap-detectors.

Monday 20 April 2015

Food for Thought

"Oculi omnium in te sperant, Domine. Tu das iis escam eorum in tempore opportuno. Aperis tu manum tuam, et imples omne animal benedictione tua. Miserere nostri te quaesumus Domine, tuisque donis quae de tua benignitate sumus percepturi, benedicito per Christum Dominum nostrum"

Last Thursday night I was invited [not me personally, it was open to all] to attend a Panel Discussion in Trinity College Dublin "Are Irish universities committed to enlightenment ideals? Recent and forthcoming developments in Irish higher education policy and legislation".  With such luminaries as Tom Boland the CEO of the HEA (Higher Education Authority), Senator Sean Barrett, Steve "blogger" Hedley, Mary "author" Gallagher, and Maria "maker" Slowey to speak, I was not required to open my gob . . . except at 'Commons' the meal consumed by the Fellows and Scholars [and the Provost if he wants] every evening in the oak-panelled formal dining hall [R: the Fellows get a table cloth] of the college.
I have accordingly top-and-tailed this piece with the formal Latin grace that is intoned from a lectern before and after the meal. The grace is spoken by the Scholar-of-the-day and this is now more likely to be an astrophysicist than an expert on Cicero. Listening to some youngster's poorly articulated mangling of the language of scholarship was a penance to the Professor of Greek and the other old dudes who had actually learned Latin at some stage.  In recent years the grace has been taken in hand by Trinity office-holder called the Public Orator, so that the ritual words have now taken on a distinctly Italian, moderately sexy, cadence, which is surely an improvement.

The food is another matter.  It doesn't seem to have changed in the 40, 30, 20, 10 years since I was last at the Commons trough - I go about twice a decade. You get three courses - soup, meat-and-two-veg, pudding - and today's chefs probably spend more time on sourcing ingredients but are still required to slap down 200 covers and have everyone out within the hour.  I gather that the menu was:
Soup: Sweet potato & fresh coriander
Main Course: Chicken coq au vin
Potatoes: Creamed potatoes; Vegetables:Peas
Dessert: Rhubarb pie with fresh cream
But the soup might have been asparagus, or potato, or split pea.  It was tasty but not distinctive. The menu was just like what I used to avoid at lunchtime in the Staff Dining Room in the first job I had in a British university.  I used to watch in amazement as my colleagues trenchered through a gluten-with-everything meal every weekday lunchtime and wondered how they managed to stay awake during the afternoon . . . maybe they didn't.  I certainly nodded off for part of the first presentation at the symposium on Thursday - only for a couple of minutes but my circulation could not cope with 'alert' and 'digest' simultaneously.

If that sounds like carping ingratitude, it's not: because the food is peripheral to the process.  The institution is what it says on the label - Commons: the Provost, Fellows and Scholars come together every day - the meal is midday on the weekends or 18.15 M-F.  This trinity is what runs Trinity! The legal name of the College is “the Provost, Fellows, Foundation Scholars and the other members of Board, of the College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin”.  The scholars are the brightest of the bright and shoulder the gown if they can get a First Class Honours mark in a special exam in their field taken during their second year in college.  This entitles them to rent-free rooms in college and all their meals for a period of five years, so it can start them off on a post-graduate career in the olde Alma Mater. It's bloody hard work to make the grade unless you are a walking genius. The meal includes, on demand, a half-pint tankard of Guinness.  Likewise the Fellows are regular teaching Faculty who have excelled in scholarship in their field of research.  Excelled in scholarship is much more than sitting at your desk thinking great thoughts - you will have published, each year for several years, two or three or six peer-reviewed scientific papers in prestigious journals.  Or you might have written the definitive biography of Wittgenstein, or a history of the Plantations of King's County, or discovered a new planet.  All these endeavours will have required mental effort that would melt your brain or mine.  Fellows also get free food but as they are no longer starveling students, and as the norm is to have a family to go home to, not many of them turn up to meet each other at the top table.

The point of the meal in common is that you can meet all the people in the college community who have made a commitment to a life in their heads. The Professor of French can find common ground with the latest hot hot-dog nanotechnologist and it is to be hoped that fruitful collaborations are born in the discussions over the soup. It's the same among the Scholars who get to meet a lot of other sharp young people and solve the problems of the world and compare notes about their teachers. You may declare that this is an elitist anachronism, and you would be right, but you would be wrong to call it a Bad Thing

‘Tibi laus, tibi honor, tibi gloria, O beata et gloriosa Trinitas.  Sit nomen Domini benedictum et nunc et in perpetuum.  Laudamus te, benignissime Pater, pro serenissimis, regina Elizabetha hujus Collegii conditrice,  Jacobo ejusdem munificentissimo auctore,  Carolo conservatore, caeterisque benefactoribus nostris, rogantes te, ut his tuis donis recte et ad tuam gloriam utentes in hoc saeculo, te una cum fidelibus in futuro feliciter perfruamur, per Christum Dominum nostrum.’

Sunday 19 April 2015

Wot's the Blob then?

Turns out that it is really ordinary stuff:
This graphic composite is from three word-clouds created by Wordle.  It is partly that wordle was in my mind because I helped design an invitation to a friend's Vollbringungverherrlichung. I'm sure my German readers will be cringing at that mangling of their ancient tongue - Tribfest is what I mean: you can always say something shorter in English than any European language. What wordle does is take text, any text; count the words; exclude the ?100 most common words [the of to and a in is it you that etc.] in the language; and blurf out the rest sized according to their frequency. The other reason for today's post is that I just lashed up my 900th post, and I though to mark the occasion.  The three graphics summarise the content of [from the top] posts 601-900; 301-600 and 1-300.  If I cared enough, I'd process the data to look for trends but I like that nothing really stands out - year, people and like [my biggies] are 117, 94 and 64 in the list of common English words.So Wordle probably uses a more subtle algorithm than excluding the commonest words.  Stop words is a concept that helps search engines and the like behave efficiently: you might want to exclude the and who but allow fans to find The Who.

I have, it seems, just been murbling on about normal life in my head and skimming stuff off the top of that ferment every morning. You can keep to yourself any thought about the unlikely juxtaposition of 'normal' and 'my head' in the same sentence.

Saturday 18 April 2015

Earthsea? Magic!

It has been a pleasant conceit of The Blob to slag off the cult of Harry Potter, mostly on the grounds that it cannot be that good.  No matter how much you have enjoyed the books; no matter what dreams you have had about quidditch triumphs or pulling a rabbit out of an owl's hat - Potter doesn't deserve its winner-takes-all success. Somebody needs to whisper in your ear that there are other books out there that should be read before you set off on your second Harry Potter.  The great god BBC has recorded two of Ursula le Guin's best books and The Wizard of Earthsea will be available to hear in just under two weeks time on Monday 27th April 2015.  Neil Gaiman has described it as simply the best book about Wizard School.

Meanwhile you can hear Le Guin's [L hand] gender-bender novel The Left Hand of Darkness now.  You can, if you prefer, go off and read the books because they are still in print despite being published decades ago. LeGuin is now 85 and looks it; and is content to look like an old woman, comfortable in her own genuine, crinkly, skin as she explains in a wonderful interview recorded to launch the recordings.  These stories might be fantasy or science fiction but they are also stories for adults which inform us about today's issues perhaps more than they informed people about the times when they were published.  'Darkness' addressed the issue of gender and sexuality and ponders the consequences of there being a spectrum rather everyone fitting into one box or the other.  This is much more widely accepted now and therefore many people are happier in their own unstraight-forward skin.  Consultant endocrinologist Donal O'Shea was on the wireless a week ago suggesting that 1:10,000 or 1:20,000 people might feel that they just aren't whom their external genitalia determined them to be at birth.  That's a tiny minority, far less than the number of people who are blind or Down's syndrome or have cystic fibrosis but it's still half a million people across the planet who need accommodation for their sense of gender.

Another persistent theme in Le Guin's works is the magic power of knowing something's true name and how we must be circumspect in sharing this information with others.  This a common theme in many cultures and would have been absorbed by the child Ursula as she was raised by Alfred and Theodora Kroeber, ground-breaking academic anthropologists from Berkeley California.  From the beginning Ursula was introduced to The Other: whether that was Ishi the last of the Yahi people or the foreign academics who came to visit with the Kroebers. The effect on the young writer was for her to embrace difference as the complement to herself rather than seeking to become more like girls of her age and class in a comfortable bath of sameness.  I first read the Wizard of Earthsea about ten years ago and wondered how I had missed it when I was a teenager and how much of a difference it would have made to my sense of self when that was still plastic.  It's never too late, though.  If you read it now you'll benefit from it, if you have a child to read it with, so much the better.

Friday 17 April 2015

Ten Stars for Starter

For the last thirty years I've been making the bread at home. That's pretty much all the bread: occasionally someone will lash out and buy a french-stick from the supermarket which is about as close to a French baguette as my croissants are to the real thing made in a patisserie in Lyon or Bordeaux.  The other day, I was shopping in T€$co late in the evening and bought a tiger-loaf that was at its sell-by date and going for 38c. Over Easter someone popped it in the oven to liven it up and it cooled down in a puddle of pap - it was repellent! Won't do that again.  Recently I've been making sourdough: maintaining a sustainable culture in a plastic tub in the fridge and bringing it out every tuthree days.  I split the slobber into two parts - put one part into a mixing bowl for "today's loaf today" and adding a scant handful of wheat flour and some water to the remainder.  Over the months I've been running this protocol, my 'starter' has changed from what I was given by a friend last year.  It consists of at least two species, indeed two kingdoms, which prop each other up in a mutualistic relationship that neither would be able to support on its own.  One is some sort of yeast, a uni-celled fungus, which is closely related to Saccharomyces cerevisiae that bakers and brewers use to make the products that give us so much simple pleasure.  The other is a Lactic Acid Bacteria LAB probably Lactobacillus casei but possibly L. sanfranciscensis. It's certainly possible that several species of LAB are part of the community in my tub.

I have to remember to leave the starter brew out on the counter for a while after feeding it, so that it has some time at its optimal growing temperature - which is not a fridgy 4oC - but not so long that it will get out-competed by the rogue microbial flora that hangs out in our kitchen.  It is called sourdough because it is slightly tangy from the incomplete fermentation of the glucose that is supplied by the flour. LABs produce acetic and lactic acids in varying amounts depending on which species is working, the temperature, and whether or not there is oxygen present.  It tends not to rise as dramatically as regular white bread, but I'm working through several bags of Matthews Cotswold Crunch Flour which was on special in Aldi a few weeks ago so it's been good for my teeth and I daresay my bowels. Occasionally I'll cheat and add a teaspoon of dried yeast to the mix for extra loft. There is something quietly satisfying about making your own bread - the working time is very little - maybe 15-20 minutes - although the elapsed time is nearer that in hours.  I like the idea of using the residual heat in an airing cupboard or beside the wood-burning stove to such good purpose as causing the dough to rise.

Fermentation processes usually make a more interesting product than their chemical equivalents. The Irish have a long tradition of making bread by substituting baking soda / sodium bicarbonate and acid instead of yeast to make the bubbles that give bread its lift.  I do this as well, especially when instant gratification is called for, but other stuff happens when you have a biological fermentation - more complex breakdown of proteins and sugars. Bicarbonate may also damage thiamine / vitamin B1, so there is a certain irony in Irish people making wholemeal soda-bread for its nutritional benefits and then destroying one of the key beneficial ingredients in the cooking. You should be a bit leery of using a lot of baking soda if you have blood-pressure issues because it is one quarter sodium by weight.

In a world increasingly samey, home-made bread has this virtue - every loaf is different but every loaf is good.

Thursday 16 April 2015

Flying to France

I was born in Dover because my mother was born in Dover and she went home briefly to deliver  babies before resuming her peripatetic life as a sailor's wife.  Her mother witnessed the triumph of Louis Blériot's arrival near the white cliffs of Dover from France in 1909.  Having been shown that it could be done, a bunch of people attempted the same feat but it wasn't until 16th April 1912 that a woman achieved it.  On that day Harriet Quimby, daring American aviator, took off from Dover and landed on a beach near Calais a few minutes later.  That was pretty cool - berluddy freezing actually because the Blériot XI was just struts and string:
She dressed up in a distinctive purple satin flying suit to combat the wind-chill whenever she went aloft. One reporter gushed about a “Dresden China aviatrix”. It must have been a bit like flying a motorbike. Quimby was born in 1875 and had a career as a journalist, so was well-placed to take part on the birth of motorised transport.  Initially she was an automobile geek and drove at least once at 100 mph (160km/h!) in a car.  I get an anxiety attack just thinking about the feat, given the flimsy construction of the car and crappy roads of the day.  She wrote regularly in her column about cars and their maintenance and so was a huge force for empowering [actually and metaphorically] women: vaaRRROOOM.  But when she saw her first airplane while covering a aeronautical meet, she was totally smitten.  In August 1911, she became the first American woman to get a pilot's licence (#37!) from the Fédération Aéronautique Internationale.  In April the following year she flew the channel and would have achieved immortal fame if it hadn't been the exact opposite of a slow news day, what with RMS Titanic visiting Davy Jones's Locker the day before.

By July she was dead!  After returning from Europe, she went the rounds at aeronautical events, often as the star attraction but on 1st July 1912, while taking a turn with a passenger on the second day of  the Harvard-Boston Aviation Meet, her plane inexplicably pitched forward and flung both people out of the cockpit.  With no hand on the throttle the plane came back to earth and landed in a salvagable condition.  Not so the aviators who plummeted 500m and hit the water of Boston Harbor with a fatal slap.  It is an enduring mystery: with little data the story has been inevitably filled up with unsupported speculation.  What is known is that Quimby was an early advocate of pre-flight check-lists and seat-belts - she loved speed but had no death-wish - but she died anyway.

Wednesday 15 April 2015

Scores of survivors

Today's the day 103 years ago that RMS Titanic plummeted nearly 4,000m down to the bottom of the ocean. I haven't seen the filum at least partly because I think yer man should change his name to Leonardo diCastanea because he is so wooden but acknowledge that the song is an effective <yorp> earworm <glark>.  About a year ago, I shared an analysis of the rates of survival amongst different classes of passengers in the sinking of the RMS Empress of Ireland, women and children didn't come out of that disaster well . . . or, indeed, alive.  The contemporary headline above claims a much more chivalrous outcome and the final tally from the British Board of Trade via Wikipedia seems to bear the headline out:
Group Class N Live Dead %live %dead
Children First Class 6 5 1 83% 17%
Second Class 24 24 0 100% 0%
Third Class 79 27 52 34% 66%
Women First Class 144 140 4 97% 3%
Second Class 93 80 13 86% 14%
Third Class 165 76 89 46% 54%
Crew 23 20 3 87% 13%
Men First Class 175 57 118 33% 67%
Second Class 168 14 154 8% 92%
Third Class 462 75 387 16% 84%
Crew 885 192 693 22% 78%
Total 2224 710 1514 32% 68%
On the Empress of Ireland you were far better off if you were a) adult and b) bloke, but it's more or less the opposite on the Titanic. Of course your chances were much less if you were in steerage than if you were loaded into the lifeboat in silk pyjamas.  And that's a crucial difference between the Titanic and the Empress, the former went down within 15 minutes of the collision while the Titanic stayed afloat and more or less vertical for ten times as long.

The Titanic herself is not surviving so well, she is currently being consumed by Deferribacter autotrophicus, Shewanella profunda (don't you love the names?) and other iron-reducing bacteria that can make a living in profoundly adverse conditions - it's dark and cold down there.  But iron is a limiting resource in many oceanic environments and metabolising the hull will cause an increase in biomass in the deeps.