Sunday 24 February 2013

A scramble in the woods

Faithlegg Woods are too vertical to plagiarise Bill Bryson and title this post 'A walk in the woods'.  They are also located in one of Ireland's magical corners: just opposite where the Barrow meets Suir and the river(s) turn sharp right and heads South for Waterford Harbour and the sea.  It's long been known for magical properties as the townland which incorporates the headland just East of the village of Cheekpoint is called Russianside - which must be Ros an sídhe: the headland of the fairyfolk.

ANNyway, yesterday a pal of mine from Russianside way organised for Andrew Harrington of the Mammals in a Sustainable Environment project to give a guided walk along the marsh and up through the woods to look for evidence of otters (Lutra lutra), pine-martens (Martes martes), red-squirrels (Sciurus vulgaris), bats (Chiroptera), and the introduced bank vole (Clethrionomys glareolus) which is quietly displacing the native wood-mouse (Apodemus sylvaticus). We saw and inhaled the heady aroma (new-mown hay and/or rotting fish to the aficianado) of some otter spraint (poo to you) on the edge of the marsh and other evidence of mammals from the other end of the digestive tract up in the woods.  Turns out that squirrels and mice access the nutritious bits of hazel nuts and pine and larch cones in distinctive ways - the bits they leave behind are quite diagnostic.

You have to be real quiet to see mammals which in any case are rarely out and about at noon in February, so the MISE folk document them with other, non-invasive means.  We've come a long way in the techniques of identification from my days as a jobbing field biologist live-trapping voles (Microtus pennsylvanicus) in Massachusetts meadows, and taking a capillary-tubeful of blood from the infra-orbital vein.  Actually, in those days I was the 'prentice, handing capillary tubes to the real biologists who were poking about in the tiny eye-sockets.  Now they use appropriate technology solutions (covered runway with wet poster-paint and white paper to capture foot-prints) to census the species; and high-tech molecular biology like PCR to identify individual animals from bits of fur.  The fur is not gathered randomly from the bushes but hoiked off with sticky patches inserted into baited tubes.  Very clever.

Things are looking up for an appreciation of science and the natural world if, from a very small community, you can get 40 people from tots to pensioners out in the woods paying attention, when they could be in Tesco paying for groceries.

Found Soup

About 35 years ago, as a reasonably young scientist and ridiculously young father, I was invited to give a paper at a conference in Sicily. It seemed like a good idea at the time to set off for the event in a tiny sky-blue Citroen Dyane . . . with my partner and our infant son . . . and her brother and his guitar . . . and a tent and a bucket for nappies. The Citroen was a real work-horse, the last production-line car that came with a crank-handle to start it if the battery was flat. It also had a roof made of rubberised canvas that could be rolled back to make the world’s least sexy convertible. This clearly advantageous attribute for travelling through France and Italy in the height of summer was somewhat off-set when it was slashed by vandals two days before we left Dublin. But, nothing daunted, we made a temporary repair by sewing up the slashes and sticking a roll of Fablon self-adhesive plastic on top with the intention of buying a second-hand roof from a breakers yard somewhere in France. We had neither time nor money to get a new replacement. As it happened, we never fixed the roof, as our gimcrack solution worked fine in all but the most torrential downpours and we had a bucket to catch the drips.

 Money was tight so we worked out that the cheapest way to get to Calais was to catch the Larne to Stranraer ferry even though that required a drive of 200 km in the wrong direction. Clearly we were time-rich if cash-poor. We stopped in London to visit the Italian State Tourist Board to pick up some maps and found that they had just started a cunning plan to encourage motorists to visit their country. You could obtain heavily subsidised petrol vouchers if you bought them with a currency other than Lire in a place other than Italy and they would redeem unused vouchers less a 30% handling fee when you returned home. The back of an envelope was quickly mobilised and we bought just enough vouchers to take us the length of Italy and back.

 France was great but Italy was marvellous: it was hot and the air smelt of pine-trees; we swam in the luke-warm sea; bread and olives cost half nothing, the cheese wasn’t red (or indeed white) cheddar and the wine was red (or indeed white) and plentiful. The conference went well and so, mission accomplished, we headed north and for home.

Now here’s a funny thing; the nearer we got to the border the more anxious the people at petrol stations were to talk to us although, for all we understood, they might have been discussing Wittgenstein or the World Cup. We stopped several times so as to maximise the amount of cheap Italian petrol we had on board when we hit France and had to start paying ready money for it. At the end of a long day, it was nearly dark, the border was in sight, and high in that alpine pass was the Last Chance Café and Garage. We hadn’t eaten properly since breakfast having long since spent the last of our Lire but we were still in credit for petrol. When she saw the plates on the car, the lady who operated the pump addressed us in English because she’d once been a Welsh girl from Pontypridd who had married the chip-shop and followed him home to Piedmont. She shed light on the earnest but opaque conversations that we’d induced in her competitors back down the road because she offered to buy, for cash, any spare petrol vouchers we might have, as she could turn a modest profit on them through the State Tourist Board. She also suggested that we might like to walk up to the café and spend some of that cash because, late as it was, she had a tureen of minestrone made hot and thick according to her mother-in-law’s recipe, and if the child didn’t fancy that then she’d sort out something else for him.

 Found money is all very well but found soup trumps it in spades. As you hear, I’m still talking about that soup more than half a lifetime later.
NotSundayMisc 8

Friday 22 February 2013

Romancing the numbers

A favorite book of mine is Edward MacNeil's Mathsemantics (available for under a fiver at Amazon:  It's about how even math-savvy people's math skills go pear-shaped when problems aren't presented on squared paper: they can do 5 + 3 no problem but go south when the task is 5 oranges + 3 apples.  If that makes you go "Wha'?", then  go read the book.  MacNeil is big on getting his employees to guesstimate numbers: leveraging the (perhaps few) facts that are available to come up with something that can turn an honest profit by being more accurate or more reliable than the competition.  A couple of anecdotes suggest that he won't leave that sort of thing in the office but does a bit of Socratic method round the dinner table.  I guess the kids enjoy it if they've grown up with it - but I wouldn't be totally surprised if they run out of the room screaming (and hungry) when he enjoins them to guess the number of rice grains on his plate.  That's a bit of a long preamble to a question that No.2 Daughter asked in the car a few months ago:

"How many people make a proposal of marriage in/on the Eiffel Tower every day?"

Being in the car meant that we couldn't google up the answer and even if you have google AND WolframAlpha at hand, it's not straightforward.  I'll let you give the conundrum a whirl yourself.

Wednesday 20 February 2013

Emergency Exit, BASIC

At last, after 6+ weeks, I've been tasked to teach something within my competence . . . I thought.  Instrumentation and Computing (Inst&Comp) is moving on from the measurement of density and the measurement of light to the &Comp part of the course.  The class is this Friday, so today the course leader gave me a hand-out and said that QuickBasic was loaded on all the computers in the Physics Lab and I should be okay if I just followed the protocol.  I'm not a total nerd, but I've been around since before the Sinclair ZX80 and have, at various times, learned Fortran, PL/1, Basic, Pascal, C, and Perl: some by formal course and some by seat-of-pants.  As it happens all the formal course languages quickly disappeared from view because I didn't need to use them in and immediately after the course.

First BASIC program in the &Comp manual:
CLS                                 (which  CLears the Screen)

which I promptly modified to the more standard:

So far so good (as the man said when passing the 17th floor having fallen from the top of the Sears Tower).  As I say, I've learned BASIC, I've written programs in BASIC, heck, I've written games in BASIC - although you can't write very exciting games in 1K of memory on a ZX80.  So I thought I'd add a wee loop to my gem, and dug deep to recall how that was done in BASIC :

This started printing HELLO WORLD again and  again and  again and  again until the words disappeared off the top of the screen and still kept printing.  Somewhat desperately, I tried to recall how to stop a process in BASIC.
STOP I tried, then EXIT, QUIT, break; <esc>, CTRL-C, CTRL-X, CTRL-Z, q, q!, X, F1, F2, F3 . . . eventually I resorted to the IT Crowd's "have you tried switching it OFF and ON again?" and that stopped its gallop.

GOTO is streng verboten in most 'adult' languages since at least Edsger Dijkstra' famous 1968 letter Go To Statement Considered Harmful and my disastrous short program shows you one reason why.

Sunday 17 February 2013

Haldane, J.B.S.

"Keats and Shelley were the last two poets who were at all up to date with their chemical knowledge”.  This quotable quip from scientist, Marxist and polymath J.B.S. Haldane suggests that scientific knowledge is not only necessary for anyone who considers himself educated but also has become dauntingly extensive and complex. That insight helps to explain why universities are typically separated into two mutually uncomprehending blocs – the Faculties of Arts and Science: literature, history and philosophy are hard enough without getting to grips with anti-matter and global warming.  That in turn helps to explain why there are so few scientists who can construct a sentence about their work that is both strictly true and intelligible to their own mothers.

As well as being a notable contrarian and part-time curmudgeon, Haldane also had an exceptional talent for sharing his passion for science with ordinary people.  Nephew of cabinet minister and Labour Chancellor Richard Haldane, and son of physiologist J.S. Haldane, he was keen to assist his father by tirelessly, indeed recklessly, experimenting on himself to track the effects of carbon-dioxide and other poisonous gases on the human body.  He went to Eton and served in the Black Watch during WWI; later, with predictable political incorrectness, he confessed that he greatly enjoyed slaughtering Germans in the No Man’s Land of Flanders. Although this privileged background undoubtedly gave him a leg-up, he was clearly a well-educated, smart fellow with a well-honed crap-detector.  As a committed Marxist, he used these talents to bring a wide-spread appreciation and understanding of science to the readers of the Daily Worker by writing a regular column until the paper was suppressed during WWII.  Extrapolating from wrens through pigeons he asserted that if angels had working wings, the muscles of the chest would need to be 6 ft thick.  Similar arguments led him to assert that while a mouse would walk away from a fall down a mine-shaft, a man would be broken and a horse would splash.  Many of these essays are gathered into his book Possible Worlds.

He also deserves enormous credit for using elementary maths to show that in most cases eugenicists are “at nothing” if they attempt to “cull the defective” because almost all a population’s genes for the defect are undetectably hidden in the carrier state.  He showed, against ‘everybody knows’ certainties, that a policy for sterilising or otherwise eliminating those manifesting the undesirable trait would take thousands of generations to halve the incidence.  With such arguments in the 1930s and 1940s, he was the third leg (with RA Fisher and Sewall Wright) of the great triumvirate of mathematical geneticists who put manners on their subject and reconciled Mendel’s work on individual genes of large effect  in peas (tall vs short; green vs yellow; wrinkled vs smooth) with Darwin’s insight that natural selection acted on infinitely small variations.

Always happy to push the counter-intuitive, Haldane maintained that it was more important for scientists to wash their hands before they went for a pee than afterwards: if you’re not sure where those hands have been, you don’t want them to be touching anything important down there.

In his declining years he took a stand against the imperialism and privilege which had served him so well and emigrated to India, becoming a citizen of that republic and setting up a research institute with one of his students.  Haldane died, nearly fifty years ago,  from the effects of bowel cancer and used this as an opportunity to act the Renaissance Man by writing a poem which began “I wish I had the voice of Homer / To sing of rectal carcinoma . . .”. (Full text link courtesy of Dan Graur) He was almost the last scientist who found time to read Keats with attention and write poetry which both rhymes and scans.

NotSundayMisc  VII

Saturday 16 February 2013

Polish the silver

We bin t'gedder naa for forty year and it don't seem a day toooo much. When we were students, My Old Dutch was reading French and Arabic at the Other University.  Sometime about 1974 she heard that an Irish-Islamic meeting was going to be held in Dublin the next Saturday and we went along to see what it was all about.  I won't say that we doubled the audience, but it was close.  I remember one young man standing up to speak for the Muslim community of Galway which he believed to be six (6) in number.  Less than the minyan of at least 10 adult (boys > 13 = adult) males that constitutes a Jewish congregation.  We've come a long way since then, and there are now more than 48,000 Muslims in Ireland according to the 2011 census.  One of them slipped out of my Instrumentation class for prayer on Friday afternoon and we were both a bit disconcerted to find that everyone but me had knocked off and gone home when he returned.

New PPS # issued tp Polish Nationals 2001-2010
In 2001, while pushing the frontiers analysing the freshly delivered human genome, I was sharing an office with a Polish post-doc.  Twice a year (or was it more often?) he had to schlep up to the Garda Immigration Bureau in Harcourt St to renew his, special dispensation, work-permit.  Only 2,259 PPS numbers were released to Polish nationals in that year.  In 2004, just as he was leaving Dublin, Poland joined the EU and numbers of Poles in Ireland climbed steeply.  There are now (again from the 2011 census) 122,000 Poles resident in the country: for the first time topping out the Brits (112,000 UK nationals live in the Republic).  Of course, it's not just the Poles: more the half a million residents in Ireland speak a language other than English or Irish at home and with them they bring pierogi, erwtensoep, spanakopita, morcilla and saag aloo.  I feel better, and fatter, already.

Wednesday 13 February 2013

Local Milk O'Magnesia

Tomorrow morning, bright and early, my first year chemists are going to measure the amount of magnesium in Milk of Magnesia (MoM).  The technician who sets things up came yesterday to tell me that the students will have to double up because they had almost run out of MoM.  Something similar happened earlier in the week when I had to leg it to the canteen to buy the last banana after lunch so that a different class could assay that for Potassium.  The banana was a local cock-up but the MoM shortage appears to be systemic.  Can’t be had in any of the pharmacies in town and it is "Sorry currently out of stock" at Boots.  My pharmacist room-mate confirmed the poor supply and thought it was due to the low profit margin on something that was so “appropriate technology”, when proprietary products like Gaviscon are available for sale.  Apparently it is banned in Australia – perhaps because chronic (constipated) users with renal dysfunction are unable to clear the excess Mg from the system.  Although Magnesium is a minority element in the body (about 25g each per adult), it is crucial for the regulation of calcium and potassium flux.  So muscle cramps are a common enough side-effect of excess MoM consumption.   And the ‘flux’ that relieves the constipation seems to preferentially strip out potassium ions, and this can have severe medical effects. More on line at the NCBI's DietaryReference Intakes for Calcium, Phosphorus, Magnesium, Vitamin D, and Fluoride. If the Irish gumment is going to ban the stuff, however, then let’s have it out in the open and not let my paranoia come to believe that MoM is being banned by stealth to boost the sales of Gaviscon.

A ban here would be a little ironic because MoM was invented in Ireland almost exactly 200 years ago by Sir James Murray who floated a successful business on the insight that notoriously insoluble Mg salts could be dissolved if he bubbled CO2 through the mix.  I share this tit-bit from the wholly wonderful book Ingenious Ireland by Mary Mulvihill.
And if you're really reading this; if you've read this far, you should check out other articles in the side bar.  They're at least as interesting.

Tuesday 12 February 2013

Darwinday 2013 - apprenticeship

Today is Charles Darwin's 204th birthday (which he also shared with Abraham Lincoln - I may have more to say about Daniel Day-Lewis on or about 29 April). Ignore the California datestamp above - it is 12th February at Down House now and has been for 7 hours.

Józef Teodor Konrad Korzeniowski was born of Polish parents in the Ukraine in 1857.  He was orphaned at the age of eleven, started travelling early and found himself aged 17 in Marseille, spending the next few years sailing before the mast on French ships.  In 1878, aged 20, he landed in Lowestoft with hardly a word of English.  He spent the next 3000-odd days in the British merchant marine learning the trade of a seaman and learning the English language.  In 1886, he sat his examination – in English – to obtain his Master Mariner’s Certificate, which recognized his competence to captain any vessel, in any circumstances, anywhere in the world.  He started to write stories based on his ordinary and extraordinary experiences ashore and afloat and became, as Joseph Conrad, one of the most popular authors of his day.  His books have been made into films, like Coppola’s Apocalypse Now, and are still regularly used as set books for school examinations.

Malcolm Gladwell’s book Outliers investigates the circumstances that bring out extraordinary talent in different fields. What he finds is that to become an international concert pianist, a million dollar basketball player or a top computer baron, you need to put in 10,000 hours of practice.  You need a certain native talent, of course, and a supportive family helps and some luck as to timing is also important.  But without those 10,000 hours, you’ll only be, at best, very good.  To get to the top, you have to put in the hours.  Because sailing-ships were necessarily a 24/7 business – you can’t let the crew have breakfast, let alone Sunday off, in a typhoon – you can clock up your 10,000 hours in far fewer years, even with some time ashore, than if you  practice the piano rigorously for 2 hours a day.

A couple of years after Conrad was born, Charles Darwin finally published his momentous book The Origin of Species.  This could be billed as the most famous and influential book that nobody has read; certainly most professional biologists, although professed evolutionists every one, haven’t read this bible of their field.  Which is a shame because, quite apart from the scientific arguments and a relentless accumulation of data and case-histories from distant and familiar regions of the natural world, it’s filled with passages as lyrically poetic and evocative as anything that Conrad wrote.  Perhaps the only other fact that is generally known about Darwin is that, in his youth, he’d spent several years at sea sailing round the world in the Beagle and had visited the Galapagos Islands.  That tropical archipelago is a veritable laboratory for the origin of species with each island having its distinctively different finches, tortoises and marine iguanas, and Darwin’s observations on and from the Beagle clearly informed his ideas on evolution by natural selection.

Historians of science have made much of the fact that Darwin took more than two decades between arriving home from his cruise in 1836 and knuckling down and writing his magnum opus which was published in 1859.  Some assert that, knowing his ideas must undermine the then all-prevailing Christian idea of man’s place in the universe, he held off publication to avoid public condemnation.  These same historians are bemused and even critical (hrrmph!) of the fact that Darwin spent at least eight years of the intervening period working intensively on  . . . barnacles.  His exhaustive work on the comparative anatomy and embryology of these well-known, widely distributed but humble creatures which he started in 1846 was published in two chunky volumes in 1851 and 1854.  I suggest that this work, far from being a timing-wasting refusal to get down to his real, if controversial, work, was his necessary total immersion apprenticeship.  Darwin spent his 10,000 hours, neither arpeggiating the piano, nor pacing a storm-heaving deck, nor weaving and jinking on the basketball court; he spent them looking down a microscope making meticulous drawings and measurements of the comparative anatomy of barnacles.  Until he’d served his time, he wasn’t really competent to think deeply enough to order his thoughts and marshal the data for his great work.

Saturday 9 February 2013


Five weeks ago when I could have been quietly fretting about the new job I was due to start aMonda', my mate Chris (tree-surgeon sans peur et sans reproche) announced that it was time to fell out the big standing-dead cypress at my out-law's place on the South coast.  It was a short January day but that old tree rained down in chunks and I schlepped them into heaps until it was too dark to see.  Today being my first opportunity to get down South to tidy up, in the dark of dawn I found my trusty splitting maul and set off for another day's work.  In splitting logs practical physics meets zen master.  Each log is a puzzle that can be solved by a critical insight more often than by brute force.  You are allowed a moment of smugness before you reach for the next log, and in a short time you have to move your anvil because it is being buried by product.  So now we have a quarter-cord of blocks, or maybe more, stacked up a-drying and I feel fine.

Friday 8 February 2013

Mistakes are made

I had the first of three Probation Meetings with my HoD yesterday afternoon: a recently implemented formality put upon the workers at the coal-face by HR.We rapidly established that I was contributing to the process of education and getting appropriate, if rather informal, support from my colleagues and I was given the chance to raise any concerns.  I mentioned finding it odd that, however frenetic the start-of-term mill, I hadn't formally been briefed in health and safety.  I was told what measures were in place already and it was clear that I was not in sole charge of a dozen or more apprentices in the trade of science.  So I was somewhat relieved of my anxieties.

In the morning I had a word with the Chief Technician and made an appointment for getting up to speed on accidents, laboratory, recovery from.  Then I went into my 9am 3rd Year biochemistry class where we were tasked to measure protein content in malted barley using the venerable Kjeldahl technique. As this was developed in 1883 by Johan Kjeldahl while working for the Carlsberg brewery, measuring protein in Irish malt 130 years later was almost commemorative. The process involves boiling up the sample in concentrated sulphuric acid until it releases all the nitrogen as ammonia.  So we're motoring along grinding and measuring when I notice that one of my students has managed to immerse her fore-arm in a puddle of conc. H2SO4 and is quietly hosing it down in one of the sinks. It wasn't pretty: with (acid) burns if you can feel it, it's usually too late to avoid damage. Thanks to my briefing a few minutes earlier, I knew who to call and what should happen next. And it was so.  You can legislate and regulate for avoiding that accident in future, but science labs tend to be awash with unknown unknowns, so I'll be especially solicitous of my 1st Year (absolute beginners) Chemists when I meet them next Thursday.

Thursday 7 February 2013


Dang, but I hate MS-Excel.  I've spent an hour trying to work out how to get years as a label on the X-axis.  It's not because I'm stupid: it's quite straight-forward using R or GD.  ANNyway, I thought I'd practice - I'm teaching this stuff after all - by displaying another interesting data-set chosen by one of my 1st Yr ICT students. It shows some quite weird collective behaviour.  In the mid-90s, the Irish Government decided that the old clunkers which were rattling around on the roads were a hazard to health and safety.  They implemented a scrappage scheme whereby, if you had a car more than 10 years old, you could send it off-road for recycling and claim £1000 off the cost of a new car. At the time it seemed an entirely appropriate way of using fiscal policy to drive desirable behaviour among voters. It also seemed a good deal to us and we traded in our 13 y.o. Vauxhall Astra for a new blue Skoda hatchback, which cost £8,000 and small change.  It's not clear from the data, however, that the scheme really had any effect on new car registrations which had started to climb from about 1993 and didn't lunge upwards in 1995/6.  The graph shows clearly the cliff as 2008 moved into 2009, the recession started to bite and new car sales fell to a third of what they'd been previously.  It seems to show an effect from the second €1,500 scrappage scheme started in Dec 2009: boosting car sales in 2010 by 50%.  Far from being another fine example of social manipulation to improve road safety and the burden on Emergency Rooms, this second scheme felt more like a boondoggle to preferentially support car-dealerships in contrast to other businesses, who could all have done with a bit of govt support at that time.  

Notice something odd about the data?  What is driving the anomalous peak in the year 2000?  Were we collectively so relieved to have survived Y2K that we all went on a spend-spree?  Were 00 registered cars madly more desirable than the years either side?  And here's a sobering fact.  Those 225,000 new cars cost their owners (assuming 20K a vehicle, which must be the right order of magnitude) €4.5billion at a time when the annual tax take was about €60billion. That's how to develop a growth economy - buy a really expensive piece of kit, then scrap it after ten years and buy another.

Monday 4 February 2013

More equality on the pitch

My first year ICT class delivered product on Friday - a 5 minute talk and a 2 page report - on something that interested each of them enough to make the effort.  I was delighted with the quality of the presentations and learned a lot. They were on such disparate topics, that I spent a chunk of the w/e following the intriguing leads they indicated.  One lad put together a compendium of records about the Rugby Six Nations Contest, which is conveniently finite in extent – 2000 was the first year Italy upgraded it from Five Nations.  So I was checking up on that, when I came across a summary of the points scored at each match, for each of the last 13 years  . . . and a total for each year.  These data seem to indicate that the average score in a rugger match is plunging.  One of the other mini-projects was about world population growth (inexorably upwards) so I thought I’d do a mashup of these two trends.  I couldn’t easily find an annual estimate of world population, but did find ( a surrogate in the annual increase in the population of Ireland, which is conveniently similar in size to the audience/congregation at a rugby match in Lansdowne Road.

The idea that one effect might cause the other is a joke.  Nobody I know – and I’ve asked the only person I know who has played rugger in the last decade -  has a convincing explanation for why the competition in rugger should be getting tighter.  Indeed if that’s what the numbers indicate.  So I invite comments, especially from people who know a hooker from a handsaw.

Sunday 3 February 2013


I didn’t meet my grand-daughter until she was fully ten weeks old.  Her parents live in a different country and it took a while for them to decide what colour passport would go best with her bootees.  But eventually this Mohammad  came to our mountain and we gazed with a certain silent astonishment at each other.  But there’s no point in making strange with strangers, you just have to wade in and introduce yourself, bring them into the warmth and make them feel comfortable.  That’s good manners and that’s foundation of all amicable relationships.

Grand-mothers of my acquaintance, both actual and anticipatory, seem to be wholly engaged with both the idea and the reality of their station but us Seanathreacha play harder to get.  Plain incredulity and bemusement about the situation plays a part in this but it’s also driven by the cultural norms whereby Irish men, even new men, don’t really do child rearing.  Of course they change nappies now, pour cereal for the breakfast, and stay at home all evening while Herself goes out to her reading circle.  But they never really step fully into the responsibilities of managing self, household and dependent children sustainably and all at once.  They make the excuse that, as men, they are not equipped for multi-tasking.  Looking after a couple of children for a few hours is apparently so all-consuming, that matching the odd socks, washing the dishes, clearing the bedroom floor of lego and feeding the dog have to be put on hold.

But being  a grandfather makes allowance for this pathetic blokey inadequacy.  You’re no longer expected carry out the heavy-lifting of child-rearing: you get all golden moments and leave the awkward, sordid and difficult to the child’s parents.  That’s what I’m hoping for anyway.  And we of the previous generation have a duty to provide an alternative view of what’s normal, permissible or desirable.  It’s roughly true that recession and boom flop back and forth in time with the generations.  So my parents, growing up in the hungry 30s, inculcated in me a recognition of the value of thrift and education.  The young parents of today (Hrumph!) never knew that sort of deprivation so can’t grasp why virtue should accrue to a clean plate and think nothing of spending as much on lunch as I got for my first weekly pay-packet.

But here’s the extraordinary thing: when The Child was a couple of months old, my boy took the family’s latest addition to visit his own great-grandmother.  This redoubtable old lady powered through the 100 year ribbon a couple of weeks before the meeting: blind for the last ten years and a little drifty at times – especially after a small Friday glass of Bailey’s – but still clearly with us.  A hundred years ago, the world was a much simpler and less technological place, where much of what we now take for granted was only admissible in science fiction. Folks a hundred years from now will look back on our nifty technology as crude and makeshift.  But in all things that matter - courage, being funny, intolerance, kindness, and deceit – we will be recognisably the same. So youngsters need way-marks on their journey and with five generations simultaneously on the planet there’s lots of possible role models and alternative viewpoints as my grand-daughter sets out on her pilgrimage of grace.

 Each generation believes they are creating something anew but each is reacting to the mistakes of their parents.  This see-saw effect tends to put alternate generations on the same side of the play-ground.  So there’s hope that we’ll be good friends: I’ll push her pram for the next few years and she’ll push my bath-chair later on, and whoever is pushing we’ll be roaring with laughter at the same jokes.

NotSundayMisc V

Saturday 2 February 2013

Close encounter

In the last post, I paid homage to a colleague of mine who was a Good Pair of HandsSome people have a knack, an intuitive grasp of the physical world – even if that world is invisibly small.  The rest of us have to work really hard to improve their practice.  Some gradually develop their skills but there are others who remain a liability to themselves and those around them.  I did get better, but it took me six months of slog and even at the end of that time, it was still Hard Work.  In those days, you had to label the DNA with radio-active phosphorous, cut each double-helix into precise lengths with enzymes and run the DNA fragments out along an electric gradient.  The larger fragments travelled more slowly and you could visualise the distance each bit had gone by clapping the whole caboodle up against a sheet of X-ray film (the autorad) and leaving it in a light-proof box for ten days.  For reasons which were then and are now murky, the box had to be developed in a -20oC freezer.  The radio-active phosphorous would not only fog up the X-ray film – hopefully in nice crisp ethanol-free bands indicating the size of each piece of DNA – but also could be absorbed by the careless body where it was liable to cause cancer and an early death. As radioactive sources went P-32 was fizzy! We were therefore required to work with a sheet of plexi-glass between us and any radio-active material.
Towards the end of the summer, the pressure was on and I needed to get things squared away by the weekend, so while everyone else was at lunch I was busy in the lab pushing back the frontiers alone. I was a dab hand now at modified Step 7, so I lifted that day’s rack of eppendorfs out of the waterbath and started flipping open the lids for Step 8. On the second tube, a drop of radio-active condensation flew out of the lid into the corner of my eye.  Simultaneously, from the corner of the other eye, I saw the plexiglass shield, which should have been protecting me from such a misadventure, standing ineffectually 2 feet to my right. 
I don’t think I shrieked, but I did clap one hand to my face and stumble over to the sink where I rinsed out my eye under the tap for a llllooonnnngg time.  From the sink, I went to the Geiger-counter and heaved a sigh of relief when, as I thrust the detector up to my orbit, that didn’t shriek either. 
As a scientist, ideas come to you at the weirdest moments.  Several weeks later, I was walking home through the summer evening and I realised with shoulder-sagging certainty that the reason the Geiger-counter hadn’t registered was because, in my incompetent panic, I hadn’t switched it on!
Twenty-five years on I’m still expecting an ocular orbital tumour to appear.

Friday 1 February 2013

A Good Pair of Hands

Once upon a time, and a very good time it was, a new minted population geneticist got his first job in an English university.  After three rather intensive years developing the courses I was teaching and wrapping up a couple of projects hanging over from graduate school in Boston, I was starting to run out of steam. To be honest, I wasn’t working on much at all, when the woman who ran the molecular biology lab across the hall decided to recruit me.  I was tasked to measure genetic variation in clover (Trifolium repens) using RFLP.  So I started: plant clover seeds - grow grow grow – harvest a handful of leaves – shatter in liquid nitrogen and grind really small  . . . and you’re ready to start extracting the DNA.  That was restful, especially watching the plants grow, well within my capabilities and the crack and bubble from pouring liquid nitrogen into the mortar was mildly exciting.

The subsequent DNA extraction was, however, firmly in Eppendorfland and I was decisively out of my comfort zone.  But I would lose face if I gave up at the first hurdle and returned to my office to look thoughtfully at the ceiling, so I persevered.  The process from harvest to results took several days: several days to wait until it was clear that I’d booted another experiment.  First the DNA had to be extracted from the grey-green dust that remained after the liquid nitrogen had boiled off.  Then it had to be Fragmented by Restriction enzymes into Lengths to reveal diagnostic Polymorphisms. “RFLP” might be a little clearer after that last sentence. It just required that a written protocol be followed carefully – why a (literate) 5 year old could do that!  And so, with my tongue stuck out the corner of my mouth, I persisted in following the protocol all the way to another disappointment. 

The depth of my driftness was shown up when the brilliant Cypriot post-doc who was working back-to-back with me, turned round one day (was she a tad exasperated?) and asked, with elaborate patience, “Well Bob, and what are you doing now?” 

That was easy: and I replied, with deferential politeness, “Well, Elli, I’m on Step 7 of the protocol ‘Open Eppendorf and evert over a paper towel for ten minutes’ ”.

“Yes, yes,” she replied, “but what are you doing?”Followed by a quick-fire rhetorical supplemental “How was your last result? Was it a smear?”

“Yes, (how did she know?)” I replied, “I just can’t seem to get the DNA bands to run out nice and crisp.”

“That’s because your Eppendorfs are still filled with ethanol, which Step 7 is meant to get rid of  . . . I find”, she continued, “that the evert-over-paper-towel business never works, so I just pop the open tubes in a 60o water bath – it’s quicker and more effective”.  With that, she turned back to her own station and carried on pushing the frontiers.

That’s what they call A Good Pair of Hands.  Some people just know what is happening in their experimental material, and because they know, they are not afraid the alter The Protocol if that seems likely to get better, quicker or more reliable results.   

The clueless are slavish.