Monday 31 March 2014

Clear and present danger? Not!

Last Sunday The Beloved and I went to a 60th bday party.  20 people, aged 9.3 to 93, sat down to a long table to a slap-up feed and then listened to some tribs to the birthday girl, then had cake and coffee.  On the way there, we stopped to buuy tea and milk in the village and found it heaving with people and chock full o' cars.  As I sat there live parked, I noticed a young mother struggling to get a push-chair out of the boot of her car and wrestle it into submission.  From the other side of the car trotted the load - a girl-child with two fully functional legs.  The distance from the car to the church whither everyone was bound was about 150m.  We raised three children and never owned or used a pram, buggy, push-chair or stroller.  Our experience was that, by an amazing evolutionary adaptation, by the time each child got too heavy to carry s/he was able to walk, or at least you could prop the wee thing up against a lamp-post and take a breather.  Why would you want to spend £500 on a piece of kit that fills your car-boot, inhibits the normal development of your child's legs and fosters dependency?  Carrying your child is effectively a hug, and youngsters can never have enough hugs.

At lunch I was talking one of the brothers-in-law and he mentioned how he and his sibs wondered and wandered through south Dublin 50 years ago for all the daylight hours and nobody even thought about getting worried let alone calling the police because they hadn't come home for lunch. This may remind regular Blobbies of my childhood boat trips on Lough Derg. The world has not gotten more dangerous, but we have nevertheless gotten more anxious.  There is an article in The Atlantic The Overprotected Child at the moment addressing this issue which mentions one father's estimate that his 10 year old had spent a total of 10 minutes in her entire life unsupervised by an adult.  The same article notes that in 1970 England 80% of 10 year olds walked to school but in 1990 less than 10% did so.  After a couple of play-ground accidents that resulted in multi-million dollar settlements to the parents of an unfortunate chap who fell on his head, towns and councils and local governments safetied everything up so that all the equipment was surrounded by rubber tiles rather than scabby grass or tarmac.  The number of play-ground related accident-and-emergency admissions shifted from 1:1452 (1980) to 1:1156 (2012) and the number of play-ground related deaths across the whole US fell from 23 to 13.  Those are vanishingly small numbers.  To compare, there are 1.9 million road traffic accidents causing injury including 43,000 deaths in the US each year.  There is even evidence to suggest that rubberised safety features, which don't actually have much impact on head-injuries, increase the number of long-bone accidents because the kids are less cautious/sensible.

Of course those deaths are tragic and we would all go to some expense to prevent that tragedy happening to anyone in our community.  But would we spend every available tax dollar providing helmets and chest-protectors for every child in the play-ground and making sure that a life-guard was present at all times with a defibrillator at the ready.  Not if that meant that there was no fire-service in our town, or that the streets were over-run with rats because the trash couldn't be collected, or that there was nothing to prevent strangers driving past the play-ground at 100km/h.  But it's not about the money, it's about whether we are turning our children into people who are incapable of taking responsibility for their own actions.  It will come home to roost, because if the younger generation can't take care of themselves they are definitely not going to have the inner resources to look after us in our old age.

"Better drowned than duffers, if not duffers won't drown"

Sunday 30 March 2014

The Man who Planted Trees

I've planted hundreds of trees, for myself and for friends-and-relations.  Actually, of course, I haven't planted them for me but rather for my grandchildren - and yours.  This has usually been not much fun because, being disorganised slack-bobs we always seem to have 1000 trees to plant right at the end of the season.  But even if we get the timing right, the tree-nursery will inevitably deliver all the trees together and there is a certain amount of sell-by date pressure to get the roots back in the dark-and-wet.  Some of my tree-planting pals put a lot of work into each treelet, cutting sods and turning them root-side up to suppress the immediately surrounding weeds.  Me, I tend just to lash into the task: cutting a slot with a long-handled spade, less complex than a slane, or a loy, but without a T-shaped cross-piece. Cut stuff stomp, cut stuff stomp . . . Sure some of them don't take, but you can get a lot in when you get the rhythm.  I've often thought that one man and a boy could fairly zing through the work because the heavy lifting alternates with fiddling about in a bag of baby trees and the latter task could be allocated to the 'prentice.

But I didn't want to talk to about me today, because it's Jean Giono's birthday.  Huzzah!  Giono is more or less completely unknown outside of France and even there he's a bit passé.  He was almost exactly the same age as Marcel Pagnol who is a little more famous in Anglophonistan because of the films Jean de Florette and Manon des Sources, which were box-office successes with subtitles.  And lovely films as well.  Pagnol made three of Giono's stories into films in the 1930s.  But in the tree-hugger world, Giono is huge star for writing L'homme qui plantait des arbres, a sliver of a book that speaks loud about the power to change the world.

Giono insisted that the story should be freely available to anyone who wants to read it, so you can catch it on several sites. You can read it in half an hour.  Arvind Gupta has put it into a beautifully produced PDF.  You may choose to read it to your children tonight in bed.  It is also here in plain txt with a bit of explanatory back-story.  It's much better to read it to small children but if you want it read for you by Christopher "von Trapp" Plummer with weird Québécois graphics and poor sound quality, it's on vimeo.  The idea of the story is that small-small actions - planting 100 acorns - endlessly repeated, can change the landscape; in particular they can change the hydro-geology of a region and turn an upland desert into something closer to heaven.

Here's another shorter story about how tilting an ecosystem in one small way can have a quite unexpected outcome on water through a cascade of reactions to the initial intervention.

Saturday 29 March 2014

No smoking

There has been a certain amount of chat on the airwaves this last week to acknowledge the tenth anniversary of the Irish smoking ban which came into force 29th March 2004. Smoking was banned because of the epidemiological investigations of Richard Doll. rather than the polemics of James VI/I, The now leader of the opposition Micheál Martin was then the Minister of Health in the Fianna Fail government.  A previous incumbent Brian Cowen had referred to the Health portfolio as Angola because of the prevalence of land-mines. You have to take your hat off to Martin and some of the senior civil servants in his department for carrying through legislation, against considerable political flow, that changed society in quite notable ways. Pints became separated from smokes and you can now go to a pub with a few friends or a visitor from out of town and not come out feeling in need of an immediate hair-wash.  As my gaffer in Boston used to say "Your rights end where my nose begins" and your smoke was definitely not stopping at the end of my nose but travelling through that orifice to my no longer pink lungs. I've put my conflicted cards on the table about the right to cultivate your own small-cell carcinoma of the lung.

Many countries now ban smoking in certain places, but Ireland was the first to impose a ban on smoking indoors in places open to the public.  That included pubs, hotels and restaurants.  The poor smokers were driven outdoors to loiter in the doorways of pubs leaving their pints inside.  People with vested interests (British-American Tobacco, The Vintner's Association, lung-transplant surgeons) stoutly maintained that it would never work, that the ban would be enforceable, that pubs would close and jobs would be lost.  Jobs were/are hemorrhaging from the pub sector of the economy, so it's not clear what additional effect the smoking ban may have had.  But it was clear from the start that there wasn't going to be a riot over the Right to Smoke - it was a first indication that the Irish are compliant: while the Greeks were setting fire to banks a few years later, the Irish were taking austerity on the chin and merely moaning about it.

The current Minister of Health, James Reilly, a doctor, is quite as anti-smoking as his predecessor and if he had his 'druthers, tobacco will go the way of cannabis in Ireland within a handful of years. There will then be a thriving market in illicit tobacco imports and some hoodlums will become very rich.  The government would, contrariwise, lose the €1+ billion a year which it gets from the excise duty on tobacco.  That amount just about pays for An Garda Síochána.

Now here's an interesting thing, you have the right to cultivate your own tobacco Nicotiana tabacum  in Ireland, and it is quite easily done.  The process of converting the leaves to something that you can smoke rather than something that will enrich your compost heap is all about tilting the process in favour of some microbes and discouraging others.  But there is a huge literature on these matters because there was/is huge money to be made from the industry.  Up until 2010, the EU shelled out €250m a year to subsidize tobacco farmers in Spain, Greece and Poland, and there is some political ferment to re-introduce this support.  One of my neighbours used to grow his own and then process it for his own use.  He doesn't smoke anymore, so I think he's stopped doing that.  Then again, nicotine is an effective bio-degradable insecticide, so he may still be using it for that purpose - must ask.

Friday 28 March 2014

Surfing the branch down

Forty days, more of less, is how long its taken to start clearing up the raffle of trees, brush and branches which came down in the Darwinday storm.  I'm not talking about the small stuff, mostly sceach / whitethorn / hawthorn / may / Crataegus monogyna (all the same species - you can see why we use Latin to communicate).  I refer rather to the four enormous, and one merely large, cypress Cupressus sempervirens trees that filled the garden down on the Waterford coast.  When we first went down there, the neighbours were jockeying for position and some free fire-wood but a brief consult with Chris "The Tree" Hayes indicated that letting them onto the site was possibly dangerous.  For one thing, a couple of tons of roots and earth are likely to sit back into their hole when the counter-balancing tree-trunk is severed. For another, there were some very large broken branches and tree-tops hanging high up in the surviving trees waiting to impale a parsing scavenger, So we decided to hold everyone off until the most obvious problems could be stabilised and/or brought to earth.

Accordingly, I lit out of The Institute after my last class on Wednesday last and hared off South to see if I could help Rossa and Chris, the tree-surgeons from Wexford.  They had been working away all day and had reduced the three trees which fell in the farmer's field to neat looking trunks.  Anything smaller than about 7cm in diameter had been fed through an industrial-quality wood-chipper and spat out the far end as mulch.  That's a mountain of mulch.  I was tasked to drag the branches to a heap near the machine, so that Rossa could feed the monster.  As I went, I threw any long-dead branches, which can be burned immediately, over the ditch and back into the garden.  After that, we went back into the garden and started cutting branches to put some manners on the tangle in preparation for the long day's work the following day.  Soon enough it was falling dark and so we stopped.

The next day, I got up early to collect all the ready-to-burn branches into a single heap near the front gate, in case one the neighbours runs out of coal.  After a while, the boys came out and I was back to hauling branches to the chipper, but this time I kept my saw handy to cut any big bare pole-ends off for fuel.  It was hard to imagine using ALL of wood-chip mulch that had been created. While we were hauling and chipping on the ground, Chris was disappearing further and further up the trees cutting out the hangers. There was a bit of discussion about what to do about a huge lump of timber that was caught at two points about 15m up in the trees. It was suggested that, if it was cut close to the heavier end, it might start to travel earthwards.  Failing that, they could attach a rope and pull t'bugger loose.  Or somebody could just surf it down.  I assumed this last solution was in the nature of ironic banter,  but this is what eventually provided the solution.  Having attached himself by a rope to a solid part of the tree higher up, Chris stepped boldly onto the branch under discussion and started to jump and bounce and shake until at last it started its descent, leaving the impelling forester dangling above it.  It was a pretty good example of the difference between potential and kinetic energy and the earth moved when the branch struck the ditch below the tree.  Don't try this at home, kids.

I had to leave at 11am to drive 100km back up the motorway to teach my lunch-time class in human physiology.  But I felt much better for having started the day with some physical and useful work.  It turned out that the root-balls of both the 'garden' trees did settle back more-or-less into their holes after the top-hamper had been removed, but without any small children or idle spectators underneath.

Wood-chip mulch for sale.

Thursday 27 March 2014

funding fondling

A number of years ago, I was working part-time in Trinity College Dublin.  I'd work mostly at/from home but for two days a week I would be On Site in the lab.  Those two days were pretty intense: participating in lab meetings, giving statistical advice, criticising drafts of thesis chapters, polishing grant applications, trying to find 20 minutes for lunch . . . and suddenly I'd be drooling on my own collar as I fell asleep in the bus home. My boss and I would try hard to attend the departmental seminar on Thursday lunchtime - turning up was what you did for the community.  It was also about the only time when you would have the chance to be surprised by something because the speakers were almost always From Foreign; in the sense that even a speaker from UCD or DCU (the other universities in town) was Foreign.  The students who ran the seminar series would supply sandwiches to encourage people to attend and I learned to be very parsimonious about accepting this free food lest I fall asleep in the middle of our visitor's talk.  But I tell ya that I fell asleep aNNyway many times because the talks were so deadly dull and presented in such a stultifying, powerpoint-propped, droning way.  Most of the senior people in the department sacrificed whatever commitment they might have to community to their desire to not waste an hour of their life over something that was not in, or even close to, their field of interest. The great thing about being a generalist is that so much more of the universe is at least potentially interesting.

One day, the boss was unavoidably elsewhere, so she missed the weekly seminar.  When she came back in the afternoon, one of the graduate students and I were crowing about the best, the most inspiring, the niftiest ("Gad Whistler, I wish I'd said that") talk we'd heard that year; perhaps the best that decade.  The presenter was Aled Edwards from the University of Toronto and he talked about a brilliant example of Harry Potter winner-take-all that is costing science dear.  The Toronto hypothesis was that, after spending $1billion on sequencing the human genome, we should have something to show for it - new genes revealed, new associations of disease with mutations in the DNA, new drug targets, new ways to seeing.  But it wasn't like that! Edwards & Co, analysed two generations worth of scientific literature to count up the number of published papers about specific genes of pharma-medico-biological interest. In particular they looked at druggable targets in three classes: kinases, ion-channels and nuclear receptors, before and after the delivery of the human genome sequence into the public domain by Bill Clinton and Tony Blair (thanks boys!).  That's a lot of data to trawl through, as more than 20 million papers have been published since PubMed indexing started in 1950.

What they found, for all three rather different sorts of protein, was that we are still squeezing the last drops of info out of the same proteins that we were studying before the human genome became available.  This despite a lot of objective data to show that there were lots of very interesting disease-associations and potential therapeutic targets in the "dark-matter" of the genomic universe. The scientific community is still doing same-old same-old on the tried-and-true. Some time ago, Nobelist Roger Kornberg claimed that scientists have a tendency to "fondle their problems" or to use an even less appetising metaphor, to pick at the scabs of their previous research rather than coming up for a breath of fresh air and trying a new avenue to investigate.

Here's one we did earlier with my Yr3 bioinformatics class.  It is a tally of the number of papers published about 4 of the 10 Toll-like receptors that we humans have to detect the hostiles in the environment so that we can mount an appropriate immune response:
TLR PubMed papers PubMed reviews
TLR4 10116 633
TLR5 882 44
TLR7 1689 145
TLR9 3070 274
WTF?  We have ten TLRs, they must each have a(n essential) purpose.  Is it conceivable that the job TLR4 does for us is ten times more important than that which TLR5 fulfills?  D'ye think that some attention to TLR5 might save lives?  Do you think you can make bigger waves because the TLR5 pond is so under-populated? Go to!

There are three good (i.e. bad) reasons for this scab-picking.
1) It is easier for editors and referees to accept papers that are firmly in the context of existing research - critiquing earlier work or building on previous studies or doing the same analysis in a different species or different human population or different cell line.
2) Research funding bodies are chronically risk-adverse - they don't do Blue Skies and minority interest ERRa is blue skies compared to over-analysed diminishing-returns Era.
3) Research depends upon kit, and there are chemical probes available for the Harry Potter proteins but it costs person-years and multi-dollars to develop new probes for the emerging proteins.  The regrettable upshot is that these proteins don't emerge because nobody will risk (investing in) investigating their functions and attributes.

I thought that analysis was brilliant. Like the failures in ethics, failures in statistical power and failures of reproducibility, fondling is systemic in science (blobolinks).  In the Nature commentary that sums up this research, Edwards offers some suggestions about how we might break free of these incestuous shackles of familiarity.  My Institution is too poor to afford an electronic subscription to Nature, so I can't read that on-line but you may be able to.  A longer version of the same material is defo in the public domain.  This sort of research is also quite empowering because it shows you that useful and informative research can be done without horsing through thousands of dollars worth of kit and consumables.

Wednesday 26 March 2014

Laboratory humour

I've had, indeed am having, great fun teaching my Environmental Chemists but up until now, it has been wholly theoretical.  That's fine with me, because things are most likely to go pear-shaped in my scientific world if I step up to a lab-bench.  But the contract says I am to run six 3 hour practical sessions and I'm now half-way through that ordeal.  My first idea was to analyse the chemical content of 'our' mountainy river as it descends from a peat hag about 370m high down past and beyond our farmlet at maybe 200m.  I suggested hypotheses that a) there might be more nitrate in the water below our neighbour's stock-yard and b) that the pH might increase as the river passed among fields that had been 'sweetened' with crushed lime-stone.  I then invited 'the lads' to think out their own ideas and then we could test them by measuring some physico-chemical parameters like pH, turbidity and, indeed, nitrate in each of several samples.  We managed to eke out 2 sessions doing this on water that I'd spent a Saturday bottling up.

The Darwinday storm took down many trees including at least 7 of our hawthorns Crataegus monogyna which were blown out of our ditches and field-walls over the last 6 weeks. But we didn't lose any ash Fraxinus excelsior.  Sure we lost lots of twigs and a couple of hefty branches from that species but none were uprooted.  That set me to thinking that maybe ash is so firm in its foundations because its roots penetrate the soil wide and deep, whereas the roots of hawthorn are shallow and insubstantial.  Whatever, I thought it should be a) possible and b) interesting to see if neighbouring ash and hawthorn acquired a different mineral makeup because they were tapped into different strata.  OR maybe ash, the species, regardless of location, filtered out and concentrated some key elements to better express their Fraxinushood; and hawthorn likewise its Crataegusness.  So yesterday I got up even earlier than usual to cut off some branches from both species at two different geographical locations.  When I arrived in the lab, I explained my idea and we all set to scraping the soft bark off the cut twigs into four separate piles so that we could 'digest' them into a mineral-rich soup for analysis.  Lesson one: it takes rather a long time to scrape even a couple of grams off a twig with a pen-knife.  Expecting that these modern boys do not habitually carry a pen-knife, I brought in a half-dozen of my own which turned out to have been bought in five different countries. And at least two of the boys was fascinated by these sharp functional objects: having never seen a marlin-spike, let alone used one making a eye splice.

As a further scientific comparison I suggested that we use a) the old-fashioned method of boiling the material up in nitric acid and hydrogen peroxide or b) the microwave digester which can crank up the temperature to 200oC by heating up under pressure.  It was real science (so rare even in college laboratory lessons) because nobody knew what the answer might be.  We quickly learned that a mess of plant, peroxide and acid will boil over as quick as milk on a very hot stove.  So that was a bust and required more twigs to be scraped to start that experiment again.  But that was pretty good because you could see it happening; work out why the cocktails behaved in that messy way; and modify the protocol. The computer-driven microwave digester isn't as flexible and behaves like a black-box through which miracles are wrought, so is a far less valuable learning experience.  I can't give you any results yet because it took us the whole session just prepping the samples, but we're set for a flying start next week.

These students have just finished a 10 week independent research project on all sorts of wild material - worms, sea-weed, rushes, aspirin and sewage sludge.  I was chatting to Seaweed Man about his project as he used a torque wrench to open one of the vials from the microwave digester.  If it needs that sort of kit just to open and close the lid, you know it's really not safe to have me anywhere close.  ANNyway, he said that next time he would tri-digest his sea-weed samples.  "Wow" I said, bamboozled and impressed by yet another technical term from the world of chemistry, "d'ye intend to run it through the machine three times?".  It took him that split second to realise the depths of my ignorance.  "No, I'm going to . try . digest . my . samples next time".  Eeeee, 'ow we larfed!

Tuesday 25 March 2014

Philosophy on the hoof

I was on about End of Life Issues the other day, and threw in an off-hand Dickensian reference to "Barkis is Willing".  This quotation is relayed by David "Go-Between" Copperfield (not the magician!) from the said Barkis to Clara Pegotty as a matter-of-fact unromantic proposal of marriage.  Then I thought of La Manch', and (both) my readers from Ukraine who, whatever their fluency in English, could hardly be expected to have read Copperfield carefully enough to get the reference.  I therefore went off to youtube to see if someone had clipped the words from one of the several films of the novel.

They hadn't; but someone had posted a short video called "Barkis is Willing", which I watched.  As the star of the clip was wearing a Boston Red Sox cap and as he claimed to hail from Cheshire, trained researcher me started googling up +Barkis +Cheshire +philosophy, until I twigged that his reference to "Barkis" was as casual and irrelevant to the topic as mine.  There was indeed no reason to believe that he was called Brian, Billy or Brimblescombe.  In this case a hat was just a hat rather than an identity badge.  The production values of the video are desperate, I think he must be holding his phone at arm's length was he walks through the woods talking about grammar, existence and dogging.  Before a minute has passed, he cites one of Jorge Luis Borges' dense essays "Tlön, Uqbar, Orbis Tertius" from the book Labyrinths. Woo-har, my sort of bloke.  The conceit in T.U.O.T. is to imagine a language where there are no words for things, and how that would affect the way we think.  That's powerful magic because being able to point at an object and say "that is a tree", "there is My Beloved", or  "Usain is bolting", is one of our unconsidered certainties that The Blob makes an occasional point to exposing. You should/must watch the whole flick.  I am amazed that so few (about 500) people have watched it considering how many take an equivalent amount of time viewing auditions on X-factor.

As far as I can tell, the star, director, cameraman, best-boy and key-grip of this and ?2000 other? streams of consciousness is the sole contributor to a channel called conferencereport.  There's a LOT of interesting stuff there: on the nature of time "arse-forward into the unknown"  the relationships among wisdom, knowledge and data, or free-will as well as some seriously weird material on Bush (not the Presidential family), modern dance, and lunch.  Here's one where the picture quality is better than usual because he's propped his phone on a shelf but the sound is dreadful because he's chosen to talk about consciousness and noetics while making (fizz bubble hiss) a stir-fry.  There might be 300 hours of material there; it will be a task to sort out the dross from the gems but the gems are, well, gems.

You may chose (free-will) to be grateful that I spew out stuff in text with occasional pictures, so it's easier to skip over the waffle and see what the take-home message might be.

Monday 24 March 2014

Captain, Sound well oiled

My Old Man was  a sailor, on the pay-roll of the Royal Navy from 1935 until he was retired at the age of 50 in 1967.  I mentioned him in the context of drinking while in charge of a vehicle, which in one of his larger commands was 170m long and capable of barrelling along at 50km/h.  I do not mean to imply that he or any of the crew was 'drunk' while in charge of such a ship, but they certainly had drink taken while at sea. In contrast, the US navy was 'dry': no alcohol was allowed to be consumed on board their ships even when in port. The inertia of large ships at sea is considerable and they cannot be turned, let alone stopped 'on a sixpence' as used to be said of London taxis.  So you need to have some competent person on the bridge at all times in case an emergency requires some seat-of-the-pants decision to be made.  Everyone agrees that alcohol dulls your response times, as does sleep deprivation and the latter was a contributory cause of the first major oil-spill at sea, the Torrey Canyon.  A lot was learned from the Torrey Canyon disaster, not least about the (not) inflammability of crude oil, but also about instrumentation, and its sensible labelling, on the bridge of ships.

22 years and a week elapsed between Torrey Canyon impaling herself on a known hazard West of Cornwall and Exxon Valdez doing the same thing on a known hazard in Prince William Sound in Alaska on 24th March 25 years ago.  But there were a lot of spills in the interim, during which capacity for these mammoth ships had more or less doubled to 200,000 tons poured into a vessel that was three football pitches 300m in length. Although the US Navy is alcohol-free and probably a bit safer for that, the same cannot be said for the US merchant marine.  When the fully-laden Exxon Valdez left Valdez Alaska for a refinery in Southern California, the Captain was well soused and had retired to his bunk to sleep it off.  There was a bit of a misunderstanding in the briefing of the Third Mate who was the officer of the watch that night but a key factor in the disaster was that the ship's RAYCAS collision avoidance radar was switched off. Actually it was banjaxed and had been out of commission for more than a year because the company thought it was too expensive to repair.  For lack of this key piece of modern equipment, the company found itself with a bill of at least $300,million in clean-up costs.  The tale of how the judgment of punitive damages was reduced to something that wouldn't offend of impoverish Exxon shareholders is too shabby and depressing to repeat here: wikipedia time-line bottom-line summary.  The ship itself was salvaged, repaired, renamed, and sailed the seven seas for more than 20 years.  On 2nd August 2012, she was beached on the Gujarat coast to be dismantled for scrap, a process that is not without its environmental and health & safety issues.

The Alaska fjords were one of the last great marine wildernesses, a sapphire sea teeming with life, a clatter of enchanting islands and a back-drop of dramatic mountains.  Whose idea was it to hazard all this delicately balanced ecosystem  on a gamble for cheap oil so that the plain people of America could drive to the shopping mall every weekend? Everyone who drives a car, is who. The Exxon Valdez made good copy for weeks after the disaster although the ship didn't since and only shed about a quarter of her cargo, although that was more than 40,000 tons of black sludge to clean up.  Part of the problem with the clean-up was an insistence that things be seen to get cleaned up.  So the shore line was treated with high-pressure hot-water hoses which killed the last gasp of surviving life.  Subsequent research has shown that ecosystems are quite robust to such insults and have the microbiological capacity to bio-degrade some of the toxins in the black stuff.
Sometimes it is better to do nothing.

Sunday 23 March 2014

Multiple Organ Failure? Me too!

When you're young you're going to live forever.  That's why young men drive too fast, join the army and play contact sports.  A tuthree days ago, I suggested that whatever you tell them, many young men, no matter how well-informed, are going to choose excitement now even it it involves potential damage later on.

Bio-medical researchers have developed an elaborate charade to deal with the ethics of carrying out risky, potentially beneficial, procedures on sick people.  It's called informed consent and requires that both the pro and con of the intervention are explained to each patient, who then signs a long form to show that they have understood the issues and absolve the doctor and the hospital of any blame if the result is more con than pro.  I call it an elaborate charade because doctors and scientist in general find it really difficult to explain without jargon what they do to ordinary people in order to elaborate all the assumptions involved in the proposed treatment.  If the patient is sick already, and many people in hospital are, the pain and discomfort may inhibit clear and rational thinking, and they're probably too tired to read the whole document carefully.  Not to mention the 20% chance that they are functionally illiterate.

Informed consent is also mobilised when a new therapy has been developed from idea, to petri-dish, to animal model and comes up for its first safety trials in human subjects.  Animal models (lab rats often, or mice) work on the assumption that, as mammals, our genes, biochemistry and physiology are essentially the same as most other mammals.  The Professor of Comparative Immunology at TCD has spend the last ten years or more teasing out the extent to which these assumptions are valid.  A little over eight years ago (13 March 2006), TeGenero Immuno Therapeutics TGIT brought their new mono-clonal antibody (MAb) to CD28 a step nearer to market. CD28 is a protein that props up and interacts with the T-cell receptor on the surface of the immune cells called T-lymphocytes. T-cells are what gets fritzed when HIV uses them to propagate itself, and the symptoms of HIV-AIDS are what results.  MAbs preferentially, directly and specifically bind to their target protein usually changing their function in so binding.  TGIT hoped that their CD28-MAb, code-named TGN1412, would be helpful against leukemia and rheumatoid arthritis. They were, on the basis of lab work with the model primate Macaca fascicularis, optimistic about the efficacy and safety of their new drug.

They sub-contracted an independent drugs-trials company called Parexel to carry out the first human trials, which took place in Northwick Park Hospital in NW London.  Parexel recruited 6 healthy male volunteers and two placebo-control guys to take £2000 and a dose of TGN1412 equivalent to 1/500th of what had been given to the crab-eating macaques.  From 8am, the lads lined up to get their injections at 10 minute intervals, and just after the last dose had been administered, the first chap complained of a headache, and started to blow up.  One after the other, the six men experienced a cytokine storm which led to multiple organ-failure and weeks in hospital.  They have all been discharged but their immune system is now severely compromised and they are almost as much at risk of cancers, infections and auto-immune disorders as people with HIV-AIDS.  The placebo guys only spent a few hours shaking in their boots waiting to collapse into the same state into which they had just seen their new friends degenerate.

But get this: when the news about this debacle reached the public, Parexel and other drug-trials companies were inundated with volunteers - young men who hadn't realised until then that you could get £2 grand in folding money just for putting your life-time health at risk.  Why, they did that every weekend for nothing.

Saturday 22 March 2014

With god on our side

If that makes you think inappropriately of Sturmbannführer and Panzerdivisionen, then you will feel something of my dismay.  When we moved down to the country all those years ago, I went to the local Credit Union and opened an account with £20.  It was a way of committing something to, and becoming part of, the local community.  It was quite inconvenient to get money in or out of the CU because if I was off the farm I was on the way to work not 8km into the local village to buy milk and do a few financial transactions.  Nevertheless we were members of the Credit Union and so got invited to the Annual General Meeting every January.  I went a couple of times because there was a raffle among those who turned up - you got a ticket at the door. The prizes were all donated by local business.  I thought the odds of winning something were excellent - maybe thirty prizes from a bottle of wine or a box of chocolates to a half ton of peat briquettes; to be spread among the 40 people who attended the AGM.  I never won a thing. ("FIX!")  But what stopped me in my tracks and rather quickly stopped me going was the prayers.  At the start of each business meeting the local curate would lead the committee in prayer.  That seemed so wrong - what about the members who were protestant?  atheist? what about people who wanted to check out the financial shenanigans of their neighbours and had no intention of going to mass any time soon?

I was reminded of that yesterday because Phil Hogan the local TD and Minister of the Environment came down to The Institute to open the Dargan Centre.  It's almost exactly 6 months since unser Führer came down to shake a lot of hands and 'name' the building.  As last September, there were to be sandwiches and pastries after the speeches, so I went along for the free food show. The speeches were predictable and allowably self-congratulatory but at least we were spared an buicéad de teanga bocht Gaeilge.  And scutter me pink but wasn't The Institute's (catholic) chaplain invited to utter a few prayers. There was another chap at the lectern who was possibly the protestant token but any prayers seemed to be deeply inappropriate in its assumptions.  We have a vibrant multi-cultural community in the IT - a lot of practicing Muslims for starters.  What is the message they get from this unthinking nonsense?

Our President and The Minister both made reference to local sporting triumphs.  Now what has that got to do with the opening of a new research and innovation centre?  I'll concede that sport has a peripheral place in the life of educational institutions - mens sana in corpore sano, after all - but it shows a want of clarity of thought to tangle up religion and sport (the new religion) with the secular worlds of finance (CU) or technology (IT).

But now that the Dargan Centre was officially open, I could open the registration for the 2014 VIBE meeting which I volunteered to host last November.  And the thought was the deed!  It's set for 9th May 2014: a Friday.  I'm looking forward to listening to some good, maybe some great, science.  If I can tie down some sponsorship, there will be sandwiches and pastries between the speeches . . . and dhrink afterwards.

Friday 21 March 2014

We got the power

Given that title, I could use this platform to give a talk about multiculturalism in which Loreen, a powerful singer with Moroccan parents, living in Sweden, sang a song in English at the opening of Eurovision 2013.  But I won't. Instead I'll make small-small addendum to my piece about the ethics of using lab animals in research and teaching.  I am in the middle of a year long subscription to the general science journal Nature, which I got for an unrefusable €32.  It comes through the door in a plastic wrapper every week and I wish I had time to read them as they come in.  But I don't.  I've only read about 2 books in the last 12 months, down from a pre-Institute norm of >2 each week, so all too often the next Nature arrives before the last one has been unpacked.  During a long weekend, I've been trawling through some of the backlog and came across an editorial from 12/12/13 about how the Animal House at Imperial College London had, despite reams of legislation, carefully written standard operating procedures, and dedicated staff, been found wanting in its duty of care for the animals that it used in its research programmes.

The editorial points out two interesting things.  First is that the core legislation in England dates back more than 100 years to 1911.  In that statute, it is an offense for doctors and scientists to 'infuriate' their laboratory animals.  That requires a much higher standard of welfare than merely ensuring that the animals are adequately fed and watered.  Such a minimum would probably be adequately taken care of by any institution that wanted to protect its investment.  It may be efficient for disease control to house rats in separate cages, but that would surely contravene the 1911 Act - rats are sociable by nature and keeping them in solitary confinement is, if not infuriating, at least deeply depressing and engendering of psychosis if human response to such treatment is anything to go by.

The damning report was commissioned by Imperial College itself on foot of allegations made by BUAV - the British Union for the Abolition of Vivisection who had infiltrated the darker corners of the College in an under-cover operation.  That's heartening, no? Imperial have taken on board a long list of recommendations to change their practice and channels of communication which will benefit the rodents and primates but also ensure that better science is done.  It is also deeply worrying because the failures of care were of the sort that would not have been caught by an official inspection by, say, the RSPCA.  And nobody imagines that Imperial are alone in these things - their errors are probably systemic wherever animals are kept for research.

The second significant point emerges from these recommendations: that statisticians must be brought in before any grant application is written.  They will help with the experimental design, especially in the form of a power analysis.  Power analysis helps you determine, given the expected size of the difference between the two groups, how many cases and and how many controls (hereinafter called 'rats') are required to have a reasonable stab at getting a valid answer.  You don't want to spend €1million housing and feeding hundreds of rats to show that the presence of a Y chromosome in an embryo is a reliable indicator of the development of testes later on.  €1000 would be plenty.  On the other hand, there may be statistically significant associations that only show up if you have many hundreds of observations to compare.  Maybe a good example is the association between passive smoking and lung-cancer.  In any such study there will be plenty of rats exposed to gaspers 24 hours a day who never develop tumours and some which aren't exposed but get cancer anyway.

There . is . no . point in carrying out a study that is under-resourced.  You may get a significant result but it won't be reliable; as Motyl and Nosek found last year and Begley and Ellis exposed on a much larger scale before that.  That's an utter waste of your time and tax-payers dollars.  If you're honest about the expected difference, it may turn out to require such a large sample size that every science dollar in a small country might be required to answer your questions.  Now that may be a sensible way to spend those dollars, but it's never going to happen in any real country because of the Buggins' Turn mentality that ekes out the available cash by spreading it across institutions and disciplines in a way that seems fair but gives None of the successful applicants enough money to get reliable and reproducible results.  I've been saying this for the last decade to anyone who will listen, and although people have been a little uncomfortable at my rant, they have invariably gone on to write grant applications that will a) fund the excellent existing post-doc for another couple of years b) add a brick to the wall of the lab's previous research and c) maintain credibility with the PI's statistically innumerate pay-masters.  Getting such studies published will require statistically innumerate editors and referees, but there are plenty of them.

We not got the power! There I've said it.  You may call me Bob the Thunderer.

Thursday 20 March 2014

CSE contact sport encephalopathy

Here on The Blob, and often in my Sports Science classes at The Institute, I've asserted that sofas were designed to fit my capacious backside. Call me Dr Pangloss. I know I should get up and do more exercise, but I'm much more likely to chop wood, or turn the compost-heap or shovel out a drain than squeeze into shorts and a coloured shirt and run about on the grass with a score of other blokes.  Team sports are a Good Thing because cameraderie and co-operation are part of the human condition which rarely get an excuse for an outing in the dog-eat-dog me-me-me society which is Western Capitalism.  But you don't want to take them too seriously and especially you don't want to take them too competitively.  It really does  "matter not that you won or lost - But HOW you played the Game", which will sound very old fashioned to many of today's millionaire sports-people.  And will sound extremely subversive to those who just make money out of sport rather than participating.  The way games are played in the WEA and more generally in Europe can be compared with their American equivalents in the amount of kit required to participate.  Cricketers and hurlers catch the small, hard, speeding ball with their bare hands, yankee-dogs at baseball seem to need an enormous leather prosthesis.  Rugger-buggers go out onto the field dressed in cotton and lycra, while NFL boys must spend as much time dressing for the match as Henry V did preparing for Agincourt. It will sounded terribly chauvinist but in the European version of these absurd sports you are more likely to be pitting yourself against the best that you can do, while the US embraces a winner-takes-all ethos that I have had many occasions to deprecate.

A tuthree days ago, I had an outing to the pub to watch Ireland triumph in an international sports competition.  I do this rarely but reckon it's better for you to watch sport with other people than alone on your sofa with your six-pack; which in your case and mine almost certainly refers to half-a-dozen tinnies rather than a finely developed set of abs.  In the course of that match, there were a lot of  minor injuries and one case where a star player from the Irish team was concussed and stretchered off the field.  He appeared to be in good health later that evening but you don't want to have that happen to you too often.

If it does happen too often Sexton could finish up like Dave Duerson a star player in the American National Football League who shot himself in the chest three years ago.  In the chest because he wanted his brain preserved for science so that a diagnosis of chronic traumatic encephalopathy (CTE) could be determined.  In due course, his autopsied brain was found to have elevated levels of tau-protein and physical changes in the sulci, which might explain his determination to finish himself off. Ann McKee, a neurologist at my alma mater Boston University,  is accumulating rows (N>250) of brains in bottles to document the trauma.  The ludicrous obsession with statistics that permeates American (and increasingly European) sport is now being put to scientific use because each pickled brain has associated data on the number of, say, sackings (link only suitable for a baying crowd at the Colosseum c. 178AD) that it accumulated while it was still working.

At the end of August last year, the NFL agreed to cough up $763,000,000 to settle a huge backlog of suits against it from former players who now feel they weren't sufficiently appraised of the negative consequences of playing football when they were young-and-foolish.  That sounds like a HUGE amount of money, almost exactly equivalent pro rata to the $200,000 each Erin Brockovich's lawyers secured for herself and her neighbours when another MegaCorp contaminated the ground-water with chromium VI.  The NFL, on the other hand, has a GNP greater than several small countries, so they can afford to pay out such sums to protect their investment from reputational damage.  They also took $1million out of petty-cash to support Ann McKee's research at BU.

I think it's a little disingenuous to blame the NFL for the damage to the brains of their young gladiators.  Do you think that knowing the odds of getting drooly-disabled in thirty years time would stop many young men from having the time of the alpha-male lives now?  I worked for years in Ireland on short-term contracts in science where there was no legal obligation for employers to contribute to my pension; so they didn't. I wasn't young, I wasn't stupid, I wanted to participate in that work at that time and so had to do so under those conditions.  It would be invidious for me to now blame TCD and UCD for abusing me then and insist on full compo when I slip into retirement a few years from now. Or would it ? . . . hmmmmm, must get lawyer.

MAIS revenons nous a notre titre: it is now surfacing that rugby and soccer players are also liable to head-trauma because a few cases of CTE have been documented in former players. Whom to sue?  The Royal Bank of Scotland RBS who sponsor the Six Nations? They by definition have loadsa money. Or the International Rugby Board IRB who surely have a duty of care for those who play on their watch?  In the same way as I can see boxing being banned as not suitable for civilised society, I can see support for a new rule in soccer that puts head-the-ball into the dustbin of history, although young physicist Caroline Puskas suggests that a football has only about 20% of the damaging oomph as a punch to the head.

Wednesday 19 March 2014

End of mouse issues

We're almost at the end of the Manual for Yr1 Biology practicals, two sections of which I've been teaching every week since September.  The last three sessions are mammalian anatomy and the mammal of choice is Rattus norvegicus the brown rat. None of "our" rats were brown of course: they were the product of many generations of genetic selection for calmness, genetic uniformity and coat-colour so were a mix of white and white with black heads.  None of "our" rats were white of course, they were pale yellow from the preservatives in which they had been vacuum-packed at the suppliers.  As I spoke my intro it occurred to me that rats are probably close to average size for mammals especially if you plot the data on a logarithmic scale.  There are 4000-5000 species of mammal and only a few of them are elephants, giraffes and whales; most mammals scurry about the floor of the forest often at night so we have a rather distorted view of the size-range, even with Attenborough talking breathlessly about their antics.

A few of the kids asked how their rat had met its untimely end, and I had to confess that I didn't know but I did say that asphyxiation with carbon-dioxide is horrible to watch.  As someone interested in end of life issues, I also told them that I had done for a lot of mice in my time by stunning and cervical dislocation - that's quick but only works if copious internal bleeding at the front end is irrelevant to your investigations.  At the time I was in the business of extracting, weighing and analysing biochemically their little adrenals.  Mice are small enough, their kidneys are smaller still - maybe the size of a mung-bean - and their ad-renals are about 2mm across and embedded in fat.  Nevertheless after many weeks of practice I could get through a lot of mice in a  couple of hours.  After a year I had a small-small result - not the one I was anticipating, but statistically significant - and wrote it up for the Mouse Newsletter. 

That set me off on a train of memory to a laboratory class I supervised while I was a graduate student in Boston.  It was, in essence, the same as we were doing in The Institute this week: mammalian (mouse Mus musculus there, then) anatomy for student nurses.  But the Course Director thought it might be handy to quadruple up the lesson to include injections, anaesthesia, and stages of death.  As a deeply institutionalised person I was just going to obey orders and follow my instructions.  I was, however, co-teaching this course with a pal of mine who had a moral compass and a far better crap-detector than me, and she put a stop to the Directors gallop.  It was clearly unethical to have student nurses offing small animals with phenobarbitone over-dose, quite apart from the likelihood of them stabbing themselves with the syringe.  In the end we agreed to do the experiment so long as the instructors (me and my pal P) did the injections.

The day arrived, I faced a class of twenty eager young nurses with a bottle of medicine, a syringe and a cage full of mice.  I had to work sharpish because everyone was raring to go and the class was only two hours long.  As I picked up the third or fourth rodent, it climbed up its own tail and sank its teeth into my finger. With a small cry of surprise , I shook my hand with a vigorous flicking motion that sent the mouse flying ptCHOINNNG  over two lab-benches into the midst of the students.  With as much dignity and speed as I could muster (without running in the laboratory) I followed after and fetched it off the floor from among the legs of the students. No shrieking here, they're nurses: well hardened to the shocking.  No reprieve, no second chance for that mouse I'm afraid.

We did the alimentary canal last week.  This week, it will be the urino-genital system.  Thats will be the time to talk about the adrenal glands.

Tuesday 18 March 2014

Slick practice

Pastrengo Rugiati? Never heard of him! Why is he in The Blob? Well, he's a famous sea captain.  More accurately, he is an infamous sea captain. I've written about another just recently who sank The Herald of Free Enterprise and killed nearly 200 people.  Captain Rugiati was put in charge of one of the first supertankers which were a cunning plan to transport very large amounts of oil from source to market or, in the (see left) Torrey Canyon's case, from crude-oil source in Kuwait to the refinery in Milford Haven in West Wales.  We cruise past the oil-refinery every time we take the car-ferry from Rosslare to Pembroke Dock.  It is a beautiful landfall coming from the open sea into the complex of sheltered bays that forms the Haven between a pair of rocky headlands and round some corners.  The ferry dock is right next to the old Royal Navy Dockyard, which was still in business up until 2008.  But the Torrey Canyon never made it to Milford . . .

She was the biggest tanker available at the time.  Too big to fit through the Suez Canal, she had gone all round Africa.  When she passed through the Canaries on 14th March 1967, after 25 days at sea, her owners told Captain Rugiati to deliver his cargo to Milford and get a move on because the tide was going to be sufficiently high on the at 2300hrs on 18th March.  Failure to meet this moon-deadline would necessitate a costly wait for another 5-6 days until conditions were again suitable. Capitalism's economies of scale are thus humbled by the natural world.

The next part of the story is one of normal accidents like Zeebrugge, Kegworth and Windscale. It is extraordinary that a ship just under 300m in length should have an autopilot, as if it could be left to its own devices while the crew went below decks for dinner or a film in the canteen.  Of course I am not suggesting that anything like that happened.  No, they left the ship's cook in charge on the bridge for the night while the Captain slept.  When the skipper woke at first light he found himself on the East side of the Scilly Isles although he was expecting to be on the West.  The autopilot could maintain speed and course but, in those pre-GPS days, it was not sophisticated enough to take account of a powerful current.  Other parts of the instrumentation were also poorly designed, so it was not obvious when the autopilot was ON, which would make the helm unresponsive to human intervention.   Like a Greek tragedy with its own inexorable momentum, as the crew tried to work out why the ship was not responding, the ship continued forward at full (30km/h) speed until the Officer of the Watch realised that they were in the middle of The Seven Stones Reef.  Calls of "Port your helm" and "Full speed astern" were far too late to achieve anything useful - there is an enormous amount of inertia in 100,000 tons of oil travelling at 30km/h and you can't stop it by applying the brakes.  kaRUNKKK!  The Torrey Canyon grounded on Pollard's Rock ripping the bottom out of the hull, and spilling thousands of tons of Kuwaiti Crude into sea.  The crew abandonned ship the following morning but, during an attempt to re-float the ship at the next high-tide an explosion killed one crew-member and injured four others.  The salvage companies gave up.

The British Government hadn't a clue about what to do and, as Pollard's Rock was then in International Waters, they didn't really have any jurisdiction. Nevertheless, first they tried a totally inappropriate detergent, conveniently produced by BP, the company that had chartered the ship.  Then they tried to set the whole thing alight with notNapalm ("wot, napalm? no guv'nor we don't 'ave any of that"), bombs, missiles and drums of aviation fuel.  It's a boy-thing and young pilots get so few chances to make big bangs in peacetime.  The русские (1967 was almost exactly the middle of the Cold War) looked on with some complacency to see the British planes miss this large sitting-duck unarmed target 25% of the time. I remember watching it nightly on the evening news for several days. A few years later an article with this illustration appeared in the educational kids weekly "Look and Learn".  L&L was by far the cheapest, but possibly the most effective, part of my very expensive education.  There's nothing like it available now with the possible exception of Aquila.

Torrey Canyon was the first monumental environmental disaster, so you can only really blame the decision-makers for what they did at the time if you have 20/20 hindsight.  Everyone learned something from the disaster and their response to it; every slick (and there have been at least ten biggies since) we learned a little more.

We may look back on it now as rather small potatoes as we chop down the last tree on Borneo.

Monday 17 March 2014

Parading in Patrick's Paradise

Lá Fhéile Pádraig
Six months ago, I gave a wholly inadequate summary of my days as a Sambista.  I thought it would give a better of view of my true self to blow up this picture of me as a bird of paradise shaking a chocalho more or less in time with a crew of other people in red and white.  I think the feathers rather suit me, no?  This photograph was taken 10 years ago today during the Dublin St Patrick's Day parade.  In 2004, we were still a community band with a youth wing from The Flats, and a commitment to running workshops in schools to improve youngsters' sense of rhythm and sense of self.  We made all the costumes ourselves by turning up every Saturday during January and February to fool about with scissors and craft-knives; cardboard and fencing-wire; feathers, fake-fur and sequins.  I learned that dress-makers won't let you use their scissors on paper - it blunts the tools of their trade. I made a lot of yoke-thingies that spring.

Within a year, the community facade crumbled from within as an internecine spat saw half of our effectives splinter off to form the People's Front of Samba.  In 2006, after our Glorious triumph in 2004, we were back in the Dublin StPs parade.  It was different: the Celtic Tiger was throwing money about like it was rice at a wedding, nobody had either time or interest in making our own costumes. The Dublin St. Patrick's Day Parade gave our group a a steamer-trunk full of money if we agreed to be anchor-tenants on the day.  So the gaffer went off to Brazil and commissioned a sweat-shop in one of the favela's of Recife to make 100 soccer-themed costumes.  It was probably cheaper that way than just buying the raw materials in Ireland.  But that's not the point!  I felt we'd sold out or been bought out. On the other hand, we had forged strong links with the Brazilian-Irish community and a bunch of them agreed to march with us: the boys kicking footballs about as only South Americans can and the girls stripping down to 3 sequins a piece to shake their booty.

In 2004, we travelled, in our ramshackle home-made costumes, from S to N in brilliant sunny weather. Two years later it was really cold. We assembled up North of Parnell Square, it wasn't raining but there was a whipping wind and Brazileiras promptly turned blue when they took off their coats for The Off.  My hands were so cold I thought I'd drop my stick - I had been promoted to one-stick-and-a-hand on a little side drum they call repinique.  But once we started moving everything warmed up and by the time we were rattling down North Frederick Street the percussion was pretty tight and the dancers were unbelievably loose.  I daresay there were some heart-attacks among the suits and soutanes on the official stands near the GPO. I don't know - I was too busy not fluffing the beat, not whacking my own fingers and not stepping on the heels of the woman in front.  Here I am in the middle supported by two pillars of our community:
Photos by the canny and clear-eyed Sean Dwyer Contacts Blog
It's not the same sitting on the sofa watching it on the television.

Sunday 16 March 2014


We're not expecting lambs until the beginning of April.  We are pretty green as farrrmers but we can count 5 months from the appearance of our ram-on-loan. In true country style our neighbour came and told me that we had an addition to the flock before I knew anything about it.  A ram-lamb it is true but we're hoping for a favorable (F>>M) sex-ratio when everything is counted in.  The only explanation for the early arrival is that the ewe must have been one of three that we bought in to get numbers up for the official census in December.  The friend who sold them to us did suggest that one of them might be preg.  Anyway, there's a lot to be said for a safe delivery in which I wasn't even tempted to intervene.  Photo courtesy of O'Manch the honorary Irishman

Okay then, Rugger it!

I'm not quite the least sporty person I know, but I really don't pay much attention to such antics.  I used to share a house with two long-haired botanists and their long-haired cat.  On Wednesday nights I'd get home after an evening shaking out rhythms on a repinique with the samba school of which I was then part.  The lads were then deep into the sofa watching Match of the Wednesday, and I used to sit it out with them making snarky comments about the referee and outrageous English puns on the players names.  All good fun and mostly harmless.  My attitude to sporting fixtures is the same as Dr Johnson's view of the Giant's Causeway "Worth seeing? yes; but not worth going to see".  You wouldn't catch me spending ready money to see a match of aNNy sport, but I'm not going to sweep my cloak about me and Leave The Room if one appears on the television.

Yesterday evening, it was Ireland's final match in the 2014 RBS Six Nations Rugby tournament.  If they could beat France, they would be best overall for the year (huzzah!).  It was also Brian O'Driscoll's last match in a Green Jersey. La Manch' is staying with us to learn English and he's keen to get as much as possible out of his time in Ireland - drinking Guinness, eating bacon&cabbage, saying "Jayzus" a lot, and downloading hours of Irish music.  He announced that he was going down to the pub to watch the Match.  I wasn't sure if the nearest pub - deep in GAA-land - would be showing the match, so I said I'd drive us in to the metropolis of Borris (pop. N=800; pub N=8) and we'd watch it together.  The Beloved had gone and bought him a bright Irish Rugby T-shirt so it would be clear that for the next hour and a half he would be O'Manch.  Accordingly, 10 to 5 found us on stools at the bar in O'Shea's drinking beer.  It was quite civilised, a generous dozen people waiting for the match to start and stools for everyone who wanted one: rugby is a rather a minority sport in Ireland.  Up to the age of about 13, I used to play Rugby myself, but the rules have changed since then and we were about equally confused about why penalties were imposed when the referee blew the whistle.  
The other thing that has changed is HD TV with slow-motion replay, so you can see what happens to someone's head when it is brushed out of the way by a walking mountain like Bastareaud. In real-time you see a successful, not to say courageous, tackle. You can see it here at 18:39. In slow-mo you can see what whip-lash is all about. Sexton was concussed, orthopedic-collared, and stretchered off the field.  He seems to be alright now, and the fact that he scored two tries in this crucial International match probably makes him think his whacking was worth it.  The final score was down to a two-point difference, if France had scored at all in the last few minutes it would have meant a turn over.  Perhaps as important, it would have meant that England would have won the six nations, the prospect of which causes quite normal well-educated Irish people to have kittens.
A victory for Ireland against France in Paris - a great event for the St Patrick's Day weekend.

Saturday 15 March 2014

Effortless Grace

In the WEA, we hand out PhDs if you sit at the feet of your mentor for 3 years, or a little more, carry out some original research and write it up as a thesis.  When I did my PhD in the USA, we were required to attend two years of formal courses with other experts in relevant fields, then sit a Comprehensive Exam before officially starting our research work.  Of course, this is not how it happened in reality.  None of my grad school pals sat on the thumbs of their curiosity while studenting for two years and then metamorphosed into a research butterfly.  I was quite complacent when I arrived in Boston: with a marginal degree from the Best Department in the Best University in Ireland, I thought I knew it all.  Or at least knew enough.  Those two years were an eye-opener and I learned a lot about things that were just not acknowledged in the narrow and over-specialised bachelor's degree course back home.  And my Comps were Comprehensive Exams, my thesis committee of five set me a day-long examination paper on whatever they thought was important - history, ecology, genetics, evolution, mathematics, anthropology.  It was gruelling, challenging and a little inspiring.  At about tea-time, I threw down my pen, shook out the claw that my hand had become, and vowed that it was the last examination I'd ever take; and so far I've stuck to that promise.

I was thinking about this when I was reading about Grace Chisholm Young's viva after submitting her 1895 PhD thesis ("Algebraisch-gruppentheoretische Untersuchungen zur sphärischen Trigonometrie" as you ask) at Göttingen "which consisted of probing questions, in German, by several professors on conic sections, geometry, differential equations, physics, astronomy, and . . .  the area of her dissertation."  It was the first PhD thesis ever awarded to a woman in Germany.  You may ask why a woman with such a British sounding name was doing a PhD in Germany.  It was because the UK was still decades from according women in academia parity of esteem.  I was writing recently about Clara Immerwahr, who obtained her PhD a few years later in Breslau.  Immerwahr was a chemist who married another chemist and I think she became deeply unhappy in her choice: she finally shot herself out of her misery.

Contrariwise, the life of Grace Chisholm has the ring of happiness.  Her older brother was given the full monty as regards education - boarding school, then a scholarship to Christ Church Oxford (which didn't admit women until 1978!) finishing with a First in Literae Humaniores.  He went on to be editor of Encyclopædia Britannica, so he was clearly no slouch intellectually.  Grace and her sister didn't go to school but were educated at home and groomed for "good works and a good marriage".  Problem was that she was a formidable mind with a particular and outstanding grasp of mathematics.  She went to the women-only Girton College, Cambridge where she fell in with another really sharp mathematician called Isabel Maddison.  At one point, for a jape, they took the exams for Final Honours School in mathematics at the University of Oxford and out-gunned all the blokes. After Cambridge, as I say, she romped off to Göttingen for her PhD.  Shortly thereafter she returned to England to look after her aging parents and married William Henry Young who had tutored her in mathematics when she was going through Girton. They were remarkably prolific academically, knocking off more than 200 mathematical  papers and several books.  Their biographers have been exercised as to who contributed how much to this steamer-trunk full of maths and the consensus seems to be that, while she deserves some credit for several of his single author papers, the reciprocal probably isn't true.  But partitioning the credit is not really the point: they were a good team and must have struck creative sparks off each other as flint and steel. They were prolific in other ways as well, having 6 children together in short order before WWI.  Not content with excelling in mathematics, Grace also took all the courses for a medical degree and learned six languages as her family tooled round Europe in the 1920s and 30s.  She taught each of her children a musical instrument in between making formal contributions to geometry and set theory.  And she wrote a well-regarded book on sexual reproduction for children called "Bimbo and the Frogs".

"Effortless Grace" is not quite right as a title.  She worked damned hard and put in tremendous hours with her children, her mathematics, and her many other commitments.  But I get the feeling that, all along the way she was supported and encouraged.  By her parents initially and then by such key people as W.H. Young who taught and much later married her; Arthur Cayley who sent her to Felix Klein in Göttingen. Klein who took her on and supervised her PhD thesis, and was famous for the Klein Bottle (shown right full of beer) a sort of n-dimensional Möbius strip. Even the enormous Georg Cantor had this to say of one of her books "Es ist eine Freude für mich, um zu sehen, was mit Fleiß, Geschick und Erfolg, den Sie gearbeitet haben, und ich wünsche Ihnen in Ihrer weiteren Forschungen in diesem Bereich auch die besten Ergebnisse, die mit einer solchen Tiefe und Schärfe des Geistes auf beiden Teilen Sie Ihre Sie können nicht umhin zu erreichen. (It is a pleasure for me to see with what diligence, skill and success you have worked and I wish you, in your further researches in this field as well, the finest results, which, with such depth and acuteness of mind on both your parts, you cannot fail to attain).

When the phony war of 1939-1940 hotted up with the invasion of France, Grace decided to repatriate two of her grand-children from Switzerland to England.  She was almost too late, having to bundle the two kids and herself onto the last plane from Paris to London.  She never saw her husband again, because both of them died before the war ended.  From reading some of her letters, she must have been good fun, you'd like to have had lunch with her, and it's her birthday (1868) today!

Bonnets OFF (women in science series).

Friday 14 March 2014

Let's not go swimming?

Irish can be a beautiful language.  This summer Tourism Ireland will not be exhorting French, German and American tourists "in iúl dúinn dul ag snámh i séarach" because that is not inviting our visitors to have a pint of stout and commune with Cuchullain and WB Yeats.  It means rather "Let us go swimming in a sewer" which is likely to be the reality of their experience.  The EPA has today issued a damning report on the quality of waste-water treatment in Ireland.  

In eight, admittedly small, places (Inchigeelagh, Kilmacsimon, Burtonport, Kerrykeel, Roundstone, Omeath, Arthurstown, Ballyhack) it is unfair to damn the quality of water-treatment because ... there ... is ... no ... such ... treatment. The toilets from all these seaside resorts are flushed straight out to sea.  So don't swallow if you go under while surfing or swimming off-shore and give your kids some rubber gloves along with a bucket-and-spade.  The following larger urban places are still not compliant with the 1991 (!) EU directive on secondary (i.e. effective) sewage treatment: Killybegs; Clifden; Youghal; Cobh; Passage West/Monkstown; Ringaskiddy/Crosshaven/Carrigaline; Arklow. While the much longer list of villages with grossly inadequate methods for dealing with their toilet waste reads like a Bord Failte brochure: Ballyvaughan, Clarecastle, Kilkee, Kilrush, Liscannor, Ballycotton, Castletownbere, Castletownshend, Ringaskiddy Village, Timoleague, Whitegate/Aghada, Bundoran, Falcarragh, Kilcar,  Moville,  Ramelton,  St Johnston,  Rush,  Ahascragh, Carraroe, Kinvara, Spiddal, Belmullet, Killala, Ardmore, Dunmore East, Duncannon, Kilmore Quay.

The report shows that we are getting better.  94% of urban waste-water now gets secondary treatment which is three times more than a decade ago.  But "secondary treatment" is often a set of mystical passes masquerading as secondary treatment because only 69% of the secondary treatment plants actually achieved compliance with the EU standards.  Part of this is because the capacity of the plants is not sufficient for the number of houses they serve, which is probably a consequence of moral hazard during the building boom: you could build and sell and profit from lots more houses if you were not obliged to put in the necessary infrastructure. Cleaning up the outfalls will take money, tax-payers money, my money to fix. That's really galling because, on the farm, we deal with our own toilet waste ourselves so are really careful what goes down the U-bend.  The EPA is also uncompromising in its condemnation of management of these plants. According to David Flynn the EPA's Environmental Enforcer "The causes of one in three sewage plant incidents reported to the EPA can be attributed to inadequate management practices by operators."  In other words, the operators are not fit for purpose: that will require elementary education such as they could obtain in my Environment Chemistry course at The Institute.  I could tell them that ferrous sulphate is cheaper than aluminium sulphate as a flocculant but not so good, so it's more cost-effective to spend a little more on your consumables.  A properly qualified Environmental Chemist could teach them a lot more.

The current government is even at this moment rushing through a grandiose and costly plan, not to fix the useless and inadequate plant across the country which is now delivering Cryptosporidium to the drinking water and turds to the beaches, but rather to create a national umbrella body called Irish Water which will replace the water treatment responsibilities of the existing County and Urban District Councils.  Irish Water hasn't opened its doors, let alone the flood-gates, but has already spent €50 million on consultants.  And we can rest assured (or scream with frustration) that not one of the current operatives (one can scarcely call them 'effectives'), which Irish Water are now obliged to take on, will get sacked.  There is a certain irony in the fact that even as the Irish Government is in a tearing hurry to consolidate water into a single MegaCorp, they are dismantling the Health Service Executive back to its regional components after a decade of new structures, additional levels of bureaucracy, and fat, fat salaries for senior managers. There's hope in that EPA is clearly not going to roll-over to let Irish Water scratch its belly.

Thursday 13 March 2014

Hello again Kitty

It ain't what you don't know that gets you into trouble.
It's what you know for sure that just ain't so.
” Mark Twain
I quote this Twain-ism a lot because it exposes our foolish complacency and reluctance to change our minds.  I am not now going to talk about cute pink things marketed at pre-adolescent girls (ハローキティ Harō Kiti will be dealt with later) but about a savage attack on a grown woman fifty years ago today.  Kitty Genovese's death in 1964 was packaged into a neat story that made us feel ashamed to be human.  In that tale, which I've mentioned in passing twice before, Genovese was brutally stabbed to death in the middle of an apartment complex in NYC in the middle of the night.  Although her screams woke up some dozens of people, they all turned over and went back to sleep.  This was all codified in the psychological literature as The Bystander Effect and numerous experimental psychology investigations have shown that the phenomenon is widespread.  If we believe that someone else will pick up that drunk homeless person, then we don't bother.

Kitty Genovese: The Murder, the Bystanders, the Crime That Changed America by Kevin Cook has looked carefully at this received wisdom and shows that a lot of what we 'know' about Kitty, her murder and her neighbours' reaction to the events is just not true. The book has just been reviewed by the Christian Science Monitor. Cook's book is not to be confused with "Fifty Years After Kitty Genovese, Inside the Case That Rocked Our Faith in Each Other." by Albert Seedman & Peter Hellman or a handful of similar books published on the half-century bandwagon.  It's like what we all know about Rosa Parks starting the the civil rights movement in 1955.  That may be true but she she wasn't the first black woman to refuse to give up her bus-seat to a white man.  That honour goes to a much younger fitter woman called Claudette Colvin. But when CC fell pregnant (shock) possibly by a white man (horror) between her crime and her trial she was dropped by the desperate to be respectable NAACP.  Similarly Cook makes the point that Kitty Genovese was a lesbian and, if this was known at the time, her case would have made mere ripples rather than waves. See how easy it is to reduce a complex human soul to a one-dimensional label like "immoral", to make it easier for us to snap a judgment without either jury or evidence. "She was a daughter and a sister and a lover and a colleague, She wasn't just a victim".  James Solomon.

The scale of the Bystander Effect was much less than was reported.  As the murder started happening at 0315hrs, rather than at tea-time it was hard to find any witnesses, let alone 38 of them cooking, watching television and ignoring.  The 38 witnesses, which have come down through history were actually 38 entries in the relevant pages of the polite blotter, but came to vivid life through a misunderstanding at the briefing of a New York Times journalist.  But 'tis an ill wind that blows no good.  Perhaps these errors of fact and errors of emphasis served a good purpose, including setting up a 911 in NYC which spread across the country as an easy to remember, short, universally applicable number to call for immediate help . . . if, for example, you hear your neighbour getting brutally attacked in the middle of the night.