Thursday, 31 October 2013

A bad lashing

Chironex fleckeri  the sea-wasp, a variety of box-jellyfish, is billed as the most poisonous animal in the sea, and that it has taken more human lives than sharks, stone-fish and crocodiles combined. It was brought to my attention this week by the interview with Tom and Dorothy Cross.  Wikipedia offers "The amount of venom in one animal is said to be enough to kill 60 adult people".  Which is not really useful except in the sense of a teacupful of botulinum toxin could kill 1-2 billion people IF it was carefully aliquoted out and distributed on a ng/kg basis to a very long queue of people.  I've looked at such lines of people before at events in the Baltics and Catalonia.  The Botox event would have a queue going 40 times round the world at the equator.  Which is a packing problem similar to the fact that each human cell 30 microns across has 2 m of DNA coiled inside.

The sea-wasp makes its living actively hunting through the seas of Northern (tropical) Australia.  It trails out tentacles loaded with nematocysts, cells which turn themselves inside out when they brush against things that feel and smell right - primarily small fish and shrimps.  This response deposits a tiny poison dart into the prey; as it struggles the tentacles wrap round and deliver more darts. The biomechanics happens really fast "The venom is fired into the skin within 3 milliseconds of being triggered – 10 times faster than the inflation of an airbag in a car crash".  And the biochemistry is zippy as well: within minutes the dead protein is brought into the head of the jellyfish where it is digested . . . in full view because the sea-wasp is pretty much transparent.  

The contents of the nematocyst pay-load is a mix including a pair of largish proteins A7L035 and A7L036. These two are 73% identical and less closely related to other cnidarian toxins but the protein family has no known antecedents or distant cousins.  Like the nematocyst itself, these toxins are unique to cnidarins. Despite their evolutionary distance from other proteins, it looks like there are a few (just possibly seven but I don't really believe my own analysis on that one) transmembrane helixes in their structure. It is therefore possible that their mode of action is to make channels in the cells of their victims and disrupt the delicate homeostatic balance of what's inside and what's out.  However it works, they have a devastating effect on shrimp, fish and humans who get an armful.  They jangle your nociceptors so you feel a intense pain; cardiac arrhythmia follows; then respiratory distress; wild fluctuations in blood-pressure also occur; on a microscopic level you can see some cells burst open; and on a molecular level there is some elevation of potassium. 

But, since records began in 1884, there have only been 64 deaths recorded: most of them children.  Which is about a third of the road deaths in Ireland last year.  So we don't need to worry too much about death but the survivors of a C fleckeri lashing are deeply unhappy - from the pain and from the disfiguring scars of massive local necrosis where the delicate tendrils brushed against you. Like with road traffic accidents we only record and compare the deaths but ignore the far greater number of people who are "merely" injured.

Advice to young Irish people before they emigrate to Australia.
Go to Adelaide or Ballarat rather than Cairns or Darwin. Be a man! Men are hairier than women and children and this can minimise contact with nematocysts which are fast but very short range. Wear clothing - any clothing, tights will give you significant protection.   Research when C fleckeri comes inshore - it's seasonal - and don't go swimming then. Don't whip your arm away quickly - it will ensure more contact.  Don't reach down to your leg when you feel the first stab of excruciating pain - your arms are more useful to you than your legs.  Don't panic.  Don't run about screaming - it will hasten the delivery of the toxins to your heart and lungs. When you get to shore don't pull off the tentacles until you've neutralised the nematocysts with vinegar - pulling will activate the remaining motion-sensitive nematocysts.  Wash off with salt- rather than fresh water.  If it's your child, it's better to pick off the neutralised tentacles with the thick pads of your fingers.  
Just stay in Ireland?

Wednesday, 30 October 2013

Maude Delap a life in the wet

Maude Delap.  Never heard of her.  Maude Jane Delap. She's not in wikipedia so she can't be important. Maude Delap the marine biologist from Valentia Island, Co Kerry.  Nope, sorry

You see what women in science have to cope with?  They are invisible, side-lined, forgotten.  Delap doesn't mind anymore as she's dead since 1953. When she was alive, albeit within a narrow peer group, she was extremely well respected, despite living on an island off an island off an island off continental Europe.  That isolated position was, of course, a far better place to pursue her scientific calling than Berlin or Prague.  She's not in Wikipedia because of the peculiar bias of that omnipresent but not omniscient organ.  Tom Simonite points out that the diminishing number of contributors to Wikipedia are overwhelmingly male and that you need to be a bit geeky to write copy in such a way that Wikipedia will accept it (the articles are written in a kind of hand-cranked code similar to the HTML I used for writing web-sites in 1995). So nobody there has chosen to take their hat off to Delap. As you might expect, she does merit a page in  Mary Mulvihill's great compendium of Irish science Ingenious Ireland (2002) which I've cited before.  More surprisingly, because of its shameful coverage of Irish science, Delap has a respectable entry in The Encyclopedia of Ireland (2003).

Delap was one of ten children of Rev. Alexander Delap, the Church of Ireland Rector of Valentia.  She arrived on the island as an eight year old and was educated by her father and the great outdoors, partly because there was no protestant school on the island.  He was a keen amateur naturalist and his interests fed down to his children, but especially to Maude and Constance, who spent all their spare time in  rock-pools or trolling lines and nets from a row-boat. Living her entire life in (a boat off-shore from) one small community and being engaged and curious, she got to really know her bailiwick.  She reminds me of Barbara McClintock in her pursuit of the small in order to understand the great mystery of life.

Her immortal fame rests in Edwardsia delapiae a peculiar, rare sea-anenome, autochthonous to Valentia,  which she discovered and which was named after her by Carlgren and Stephenson in 1928. She knew it was rare and interesting because Cnidaria were her special field.  They are interesting because many of them have alternate generations switching between a sedentary polyp and a free-swimming medusa form. For a long time these were considered to be totally different species and one of Delap's key contributions was to catch the microscopic medusae as they were shed at sea from a polyp and bring them into the lab to see what they developed into. She was able to tie the knot between several of these mystery pairs.  To do so required classic creative, dogged science, because these tiny sea-creatures are fussy about their living conditions and, if you look at them sideways, they die.  Directed and informed trial-and-error enabled her to get the conditions right, changing the water regularly (without flushing the objects-of-study down the sink), bubbling air through her aquaria and carefully controlling the temperature were some of the steps that needed her attention and whose parameters she had to determine, record and replicate.

Maude Delap's existence was the inspiration of Tom and Dorothy Cross's Art-Science collaboration about jellyfish.  But rather than drizzly dull Valentia, they chose to make the more melodramatic box-jellyfish Chironex fleckeri the star of their project and spent most of their time in Northern Australia where C.fleckeri zooms about occasionally killing people.  There's another post to come on the nature of the toxin, but that's not relevant to Jellyfish Goddess of the North Atlantic.

She was interested in everything around her: a bit of archaeology, or folklore or local history was grist to her mill and she was a competent botanist.  And lest you think that her interest in zoology was limited to cnidarians, she was the first person to obtain the complete skeleton of True's Beaked Whale Mesoplodon mirus.  When I say 'obtained', it would be more correct to say 'created' because her specimen beached itself on Valentia and she had it hauled up to the garden and buried in the cabbage patch to hasten the de-fleshing and presumably control the smell. These creatures can grow to more than 5m and weigh in at more than a ton.

Her Victorian father, with his extensive brood, could only afford to educate the boys and wouldn't allow Maude or the other girls to leave the family home unless transferred to another man in marriage.  But even after her father died in 1906, Maude refused the offer of a job in the Plymouth Marine Laboratory. Plymouth was a long way away before Ryanair and she spent the next nearly 50 years contributing to science from remote Valentia Island. I suspect she stayed because she was happy where she was and doing what she did.
The Blob's women in science series: Florence Nightingale - Barbara McClintock - Maude Delap - Cliona O'Farrelly - Lynn Margulis - Rosalind Franklin - Jocelyn Bell Burnell

Tuesday, 29 October 2013

Grassing up the cuckolds

"timeo Danaos et dona ferentes" Aeneid. "Beware the Greeks when they bring gifts". Or when they give people ideas. Blonde and blue-eyed children have been in the news again these past days.  A new push on the hunt for Madeleine McCann by the Portuguese police brought a comment from a media-savant that this story would have dried up and blown away years ago if the child had been less photogenic. Another b&b-e girl was discovered under a bed in a Roma encampment by the police in Greece and found to have been 'donated' to the parents by an indigent mother (or not: the story is still trundling).  Our own President was given away to his aunt and uncle by his own troubled birth family, so the practice is not wholly reprehensible - just unregulated. Our increasingly monolithic state feels the need to regulate ever more aspects of our lives.

So something murky may have happened at the far end of the EU but in Ireland it woke up a number of people to the fact that their darkish neighbours had a b&b-e child in their midst and thought it was their citizen's duty to telephone the Gardai.  The Gardai had never been put into that precise position before although they have a key role to play in child protection when snap decisions have to be made often at night.  They took two children (from two unrelated, geographically separated families) into care over the protests and the paperwork of their parents.  DNA tests were carried out and within 48 hours the scientifically (huzzah!) legitimised childer were returned to their parents.  I have to ask "who owns the DNA tests?".  Because those things can be sensitive.  Do you just hand a copy of the results back to the people who have (unwillingly, maybe) given you a buccal-smear or a hair-follicle to analyse?

D'you remember grandfather's portentous comment in Prokofiev's Peter and the Wolf "and if a wolf did come out of the forest, what then?".  I allude to a metaphorical wolf in cuckold's clothing.  What will the HSE and the Forensic Science Laboratory and the Gardai do when the next one of these mother-father-child triads shows unequivocally that the last is not, cannot be genetically, the offspring of the declared father, what then?  And having made the discovery, who knows?  There seems to have been a raree show out in Tallaght last week as media people went out to rubber-neck.  They are not allowed (to protect the innocent child in the family) to broadcast what they find but their press passes allow them to hang out (and know where everyone lives).

Because there's a lot of that about and if the state aspires to regulate extra-marital sex, then a bankrupt state definitely won't have the resources to police it. When I say 'a lot of it about', I mean non-paternity not merely adultery or journalists gawping at the distressed. For the rate of NP, you have the pick from a wide range of estimates: 0.03% to 30%, (four orders of magnitude) depending on what point you wish to make.  These data, all supposedly about the same thing, are difficult to reconcile and/or incorporate into a meta-analysis.  They come from a wide range of sources, some anecdotal, some formal science, some with very large sample sizes and some with small.  The largest estimates of the rate of non-paternity tend to come from legal cases where paternity is actually in dispute and the smaller numbers come from solid respectable bourgeois families and the mid-range estimates come from the dispossessed. I should say that some of these studies predate DNA testing by decades and several of them predate Crick & Watson's elucidation of the structure of DNA - those being based on simple Mendelian inheritance like ABO blood groups and the ability to taste PTC.  The urban legend figure is 10-15% but most people reckon that's too high. I would bet €100 that 3% is within half an order of magnitude (range, say, 1-10%) for random Irish mother-father-child triads.  I'd take a punt that the children of the Oireachtas number about 500, so there are 15 mothers to the Oireachtas who really don't want the state to implement DNA testing at birth, or have widespread testing in the community of legislators.

If you don't ask, you can't tell what the result of any 3-way test is; but having carried out the test you have to answer, and probably pay, for your actions. Here's a recent editorial in Nature about the issues of childhood genome testing sparked by such cunning plans as the GSNSD Genomic Sequencing and Newborn Screening Disorders project.

Monday, 28 October 2013

Interviewing the Ordinary

D'ye remember my hymn to fulfilling potential and celebrating the ordinary back in May?  I view with increasing loathing the winner-takes-all ethos which permeates too many aspects of our society.  Gold medals, Nobel prizes, the Top Ten, Justin Bieber (bless!), the gross disparity in take-home between the board-room and the shop-floor, VHI money being spent on 1 transplant rather than 100 pelvic floor repairs.  I could go on.  Begob, I just have!  An encouraging word or a positive comment in a lab-book for our median students may make a huge difference to them - they have spent a life-time being ignored by  teachers who devote disproportionate time to their ad astras and disasters.

On Sunday I was listening on the wireless to Aoibhinn Ní Shúilleabháin double-interviewing Tom and Dorothy Cross (again).  I say 'again' because I remember a very similar interview maybe 7 or 8 years ago.  It's great because they are brother and sister but he is Science (molecular evolution of fish) and she is Art (installations, identity, sexuality).  In about 2001, they collaborated on a project about jellyfish which was one of the brief moments when the yawning gap between the Arts and Sciences was bridged. I guess that's why I remember it - I normally have two-week event-horizon - it was so rare and extraordinary. The yawning gap is a particularly apposite phrase because the second law of thermodynamics will put half of all university graduates to sleep and post-modern lit.crit. will dozzzzzze off the other half.

But Aoibhinn's programme is also not so great: we've seen&heard those sibs already, so it's not very adventurous to wheel them out again, is it?

My neighbour, who is more or less the same age as I am, lost his father at the age of 16 and found himself with a widowed mother and two or three younger sibs to look after. The following Monday he went out into the market place as a tractor-for-hire: ploughing, cutting and hauling silage, spreading dung - whatever would earn an honest penny for his family - as well as managing the family's own modest holding.  While I was picking up my very expensive education, he was picking up bacon and spuds on the way home from a hard day's work.  When we blew-in to the valley I often used to meet him in the lane or chew the fat leaning on a gate: we'd talk about farming and science, politics and the weather. I often thought that he'd have benefitted from the education I got, because he was interested and interesting, engaged and insightful. A few years later, my more famous brother Jack, was visiting the farrrrm and met the neighbour and talked round the houses for a while.  He thought there was a great game show to be made with four Irish farmers pitted against four Norfolk firemen and four West Country cider-bottlers. A bit like "Eggheads" on the BBC now.  We waste our human capital because there is insufficient flexibility in the system, the brightest of the dispossessed have no school or crap schooling while the well-to-do buy resources for their dim-bulb offspring.

So the next time RTE wants a pair of interesting friends-or-relations to interview, don't pick the Crosses, nor yet me and The Brother, that would be same-old same-old. Find a taxi-driver they can always talk and they've been around and they might have a different take on things.  Or my farming neighbour - any of my farming neighbours - they've usually got something interesting to say.

I'll finish up back on the wireless to quote Aoibhinn "Looking back, they reflect on Fountainstown, the scene of so many childhood memories, and how the rocks remain unchanged since their childhood."
"the rocks remain" is a rather clever Arts/Science reference being a quote from an operetta by AP Herbert:
"Nothing is wasted, nothing is in vain: The seas roll over but the rocks remain."
and also from a poem by Stevie Smith:
"Oh why do they leave me, the beautiful people, and only the rocks remain, To cry Love me, as I cry Love me, and Love me again"
But it is also the title of a book by naturalist Gavin Maxwell.  The rocks at Fountainstown may be the same now as when Tom and Dorothy were kids and turning blue coming out from the sea, but the water is definitely different. Fountainstown was one of only four beaches in Ireland that failed the EU quality control regulations in 2012, the others being Ballyheigue, Rush and Clifden.

Sunday, 27 October 2013

Finding ELVIS

Elvis Presley "The King" was a phenomenon. He sang and girls cried; his hips moved girls in another way; he served his country in the army, moonlighting 10 Top Forty hits while in uniform; he made films that were part of the canon of Sunday movies in dull drizzly 1960s Ireland. He brought a little light and a lot of sexiness into the world and you can't fault him for that.  So when he died in August 1977 after several years of decreasing health and increasing medicinal and other drugs, some people just could not believe it.  So for the last 36 years people have been seeing him, in Tennessee and even more outlandish places.  On dit que his DNA doesn't match etc etc

This won't be the first, nor yet the last, time when I write about DNA and the genetic code. I've spent the last 25 years scrutinising DNA and protein sequences for money, so it's going to be part of The Blob, or I'm not going to be true to myself. In my homage to Nirenberg and Matthaei, I showed the whole table by which the information contained in the 4 DNA/RNA bases, arranged as (4x4x4) 64 codons, are translated into the 20 amino acids that go to make up all proteins.  The code is redundant because 64 >> 20, so several codon triplets code for each amino acid.  But interestingly redundant because a single change (mutation) in the DNA is quite likely to produce an amino acid that is either identical or quite similar to the original pre-change amino acid. Rather than risk boring you, (You can get the whole thing in a separate tab here) I only show the top 1/4 of the standard table:
UUU Phe F UAU Ser S UCU Tyr Y UGU Cys C
UUC Phe F UCC Ser S UAC Tyr Y UGC Cys C
UUA Leu L UCA Ser S UAA Stop UGA Stop
UUG Leu L UCG Ser S UAG Stop UGG Trp W
Each of the 20 amino acids has particular chemical properties, and a name which predates the discovery of the genetic code by many decades.  The first a.a. was isolated from asparagus juice by Vaquelin and Robiquet in 1806 and called asparagine.  There doesn't appear to be a direct connexion between the smallest amino acid Glycine and the soya bean Glycine max, except that they both have a tendency to sweetness (Greek γλυκός). As proteins are polymers and typically about 300 a.a. long, we need abbreviations to write and identify them. Sometimes it's easier to use the more directly memorable three-letter form: Leu for leucine, Ile for iso-leucine, Ala for alanine, Phe for phenyl-alanine but for long sequences clearly a one-letter code is more compact and convenient: L, I, A, F for the partial list above. Here's the full alphabet:
A Ala C Cys D Asp E Glu F Phe G Gly H His I Ile K Lys L Leu
M Met N Asn P Pro Q Gln R Arg S Ser T Thr V Val W Trp Y Tyr
Ooops not a full alphabet: there are only 20 amino acids and our English alphabet has 26 letters.  So you can't write everything you want in DNA code translated into protein using the convention above.  Missing letters include B, J, X and Z and, most inconveniently, 40% of the vowels - O and U.  As the DNA and protein sequence databases get exponentially larger, you can find all sorts of things in there. Most importantly you can find ELVIS (a partial protein sequence (...-Glu-Leu-Val-Ile-Ser- ...) but not, yet, ELVISPRESLEY.  But we'll never find JESUS in there.

You can check what-you-fancy out yourself: http://prosite.expasy.org/scanprosite/ select
Option 2 Submit MOTIFS to scan them against a PROTEIN sequence database.
enter [YURNAMEHERE] in the box below and click [Start the Scan] at the bottom.  Don't be a sheep and search for ELVIS, there are at least 200 'hits' for that sequence, we now know about that.  (and remember BOJUXZ won't go).  I have a peculiar ambivalence about the prolactin receptor from Tilapia nilotica because the fish has eaten both my daughters. But then again so has hunchback a zinc-finger developmental control protein from Drosophila virilis.

I wrote a while back about Craig Venter playing about with newly created DNA sequence, to create hidden messages as well as a totally artificial life-form.  That was pretty geeky. The Venter Code ignored the 'universal' genetic code entirely although it did use triplets of DNA bases.  According to Thomas P Hopp, Dr. Peyton McKean, a CIA spook, modified the real genetic code to incorporate the missing letters. Apparently the Agency is using this concept to send genetically modified microbes with hidden messages to other places where they can clone and sequence the DNA inside.  Pretty secret, huh? uber-geeky and not really very convenient. Although, as Peyton McKean features in a new book "The Neah Virus: a Peyton McKean Mystery" by Thomas P Hopp, who also wrote "Dinosaur Wars: counterattack" it might all be hokum/fiction.  Buy the book and find out!?

So far so facetious, but isn't this blog called Science Matters?  Where's the SCIENCE?  Well, it's here in a the head louse:
>E0VVQ8_PEDHC OS=Pediculus humanus
MLLLSCILFLFEDVLGSIGDNSFFYINCVQYCDYKFCHSGKQKVHHRALK
NFEYSLWSCIENCEYECQWKTVESFQKRNWPIPQFRGKWPFIRLFGFQEP
ASVFFSVLNFITVLKLILLFRKKVSNSAPYYYIWNLFGLIQLNSWFWSTV
YHTRDVDFTEKMDYISAFILIIYSFYAMGLRYISPSINKKTLLWSIFCGL
FGLNHVSYLWLYNFDYGWSNRSRVVSMEFSSFSITILCLENFYVCSSSRS
NYFTRAYGFSSHFMVVRCARPLARYINYLQYIFFSFCHR

Saturday, 26 October 2013

Vexillology a la Nord

'Television? The word is half Greek and half Latin. No good will come of it." I didn't start the day intending to celebrate the birth of CP Scott (26 Oct 1842), early 20th century editor and owner of the Manchester Guardian.  But his quote about TV turned up in a wholly different context in the the jumble that is my 'mind'.  Scott was wrong about television (some good has come of it), as he was probably wrong about  the militants of 1916 (eager martyrs) and Votes-for-women (cause-undermining fanatics).  But then, as a Liberal MP and owner of the quintessential Liberal newspaper, he preferred to tweak things right in a long-game rather than forge things anew in a revolution. He's not to be confused with CP Snow, chemist and author, who most clearly articulated the rift between Science and The Arts Block which I bang on about so much.

Vexillology is the study of flags.  Like telly, it is derived from Latin (Vexillus) and Greek (logia) roots.  It's rather weird how much attention we give to these distinctive pieces of cloth.  The US Congress needed 1000 words in 1942 to elaborate the punctilio required for the stars-and-stripes, how and when to hang it, as well as "The flag should never be used for any advertising purpose, nor embroidered on cushions or handkerchiefs, printed on paper napkins or boxes, nor used as any portion of a costume."  Etiquette has slumped since the Vietnam War in the USA and elsewhere, with the flag on coffee cups, underpants, paper napkins and flip-flops.  A sense of identity is greatly facilitated by the 2 or 3 colours adopted by the GAA committee in each of Ireland's counties more than 100 years ago.  Black&Amber for Kilkenny, Red&White for Cork, Red&Black for County Down (and internationally for the Spanish Anarchists, and parochially for the Mt Leinster Rangers).  It is my contention that having three colours rather than two in the flag for Carlow is why they have been so crap at both branches of GAA since the foundation of the state.

This spring Dau.II embarked in a concerted push to win some home-education for herself before she left home to continue her education in the University of Life.  This consisted largely in sacking out on the sofa downloading so much video that she smashed through our wireless broadband allocation one month and we faced a bill for €90 at 2c a MB.  That's a lot of Masterchef.  She alternated this passive basking with the greater challenge of sporcle quizzes.  She absorbed a lot of information in this way and she's smart enough to be able to use the data, somewhere, sometime.  So this quiz is for you, petal:


Who swears allegiance to each of these flags?  Some of them are genuine (acknowledged by the UN or the People's Front for Vexillologists), some are a bit more aspirational and one is a complete fantasy in a project to imagine Nordic flags for any and all countries.

More links to Flag-waving on The Blob.

Forty Years On

I would like to review the play Forty Years On, Alan Bennett's brilliant, edgy, dated satire about the English
Quote:
Franklin: Have you ever thought, Headmaster, that your standards might perhaps be a little out of date? Headmaster: Of course they're out of date. Standards always are out of date. That is what makes them standards.
UnQuote
But I have another 40 years to celebrate today.  Cue Peter Sellars singing My Old Dutch My Old Dutch and me, we did indeed spend a chunk of time in Holland.  I met The Beloved 40 years ago on the evening of 26th October 1973.  It was different times.  In April, I was reflecting briefly on the three-centuries life of my (1892-2011) grandmother, and the changes that had been wrought in her lifetime by the growth of air-travel which was, of course, science fiction when she was born and became reality in her teens.  We met in TCD, as you do when you're both students in Dublin, had a fragment of conversation and went our separate ways towards bed.  When we left the campus through different gates, we found that we couldn't go back even if we wanted to, because the whole college was on lock-down by Security and the Gardai after Minister of Justice Paddy Cooney was jostled and heckled by "students and Internationalists" before he could make his prepared speech about the prison system.  The minister had to leave through the back-door via the kitchens.  So that's a change: you don't find students rioting about perceived injustice much nowadays and I don't think there are many Maoists left in the country.

We did get to meet again, largely through the good offices of a woman who was in my science class and in the same hostel dorm as The Beloved.  Cue LP Hartley's Go Between.  Because there were no cell-phones in the those days.  Dammit, there were remarkably few telephones.  You had to apply for one to be installed by P&T (Posts and Telegraphs), it could take weeks or even months, doctors could insist that they be prioritised and doubtless you could expedite your own process if you knew in which hands to place the brown envelope.  So we had to make assignations in advance, or by letter (with a stamp!) or a note carried by our Go Between. A meeting has both a time and a place, so we had to be careful to specify which corner of St Stephen's Green we were to meet. I remember one early date when I visited each one several times to be sure to be sure because TB was running late.  We had to meet in such public places because she was living in a hostel run by LSU nuns where Y chromosomes could come in the front door but not leave the vestibule immediately behind it.  I, on the other hand, had a room (to myself) in digs in Sandymount whose landlady viewed women as corrupt and corrupting.  But meet we did and we walked out.  And walked, and walked: along the canal, out to the Pigeon House and round and up and through what was left of Georgian Dublin, so that we got to know the city intimately as we got to know each other.

Friday, 25 October 2013

Materials and Methods

A couple of days ago, I endorsed Trisha Greenhalgh's advice that you can safely ignore any scientific paper which has a flawed Materials & Methods section.  So M&M is important: it's a record of what you used and how you used it with sufficient detail for someone else to replicate your work and see if they get the same results.  The Economist just recently had an intelligent lay-person's view of the worrying findings by Begley and Ellis, John Ioannidis and others of a widespread failure to replicate sexy, high-impact papers.  The failure in replication is probably because the original findings were cutting edge, novel, of substantive biomedical importance and . . . wrong.  There's a whole supplement in Nature on the matter from April this year which appears to be open access.  And a chunky article in The Atlantic about Ioannidis.  So nobody can claim that they know nothing about these issues and that SS Science is steaming ahead without an iceberg in sight.

In The Institute, we're training the next generation of scientists and one of the ways we are doing this is insisting that each student keeps a lab-book for each course and writes up each experiment or investigation in the particular and peculiar style in which scientists keep their records.  Teachers of science will each have a particular bee in the bonnet about some aspect of these reports.  Me, I get all hot and bothered about people writing down spuriously accurate numbers which have been lifted wholesale from their calculators.  Some deprecate the first person and want everything written up in the passive voice.  Others want students to write micrometer as μm, not as um which is far easier to find on the keyboard and, in context, is unmistakable.  There are excellent reasons for insisting about each of these elements of style.  If you inculcate correct, professional looking reports early in the career, it will pay off later, so we should probably be a bit dogmatic for absolute beginners even if we let the older students have some slack.  

So I told my two 3rd year classes that I didn't see any point in them transcribing the M&M for each experiment from the nicely typed and neatly typeset manual into a crabby scrawl of ball-point pen in their lab-books.  For the first couple of weeks, several in each class couldn't shake the habit and, accordingly took 20 minutes longer on the writing-up than their peers who wrote "Materials and Methods - see page 28-29 of the Manual".  On the third week, I blew up because one of my students had found a gross typo in the M&M (a row of figures which didn't add up correctly in a table describing the volumes required to make up a particular concoction).  Is there, I asked, any value in transcribing this stuff with all these errors and internal inconsistencies without any sort of processing by the higher mental centresAre you, I added, human being or automata?  This is the second or third year that the manual has been printed and used by a couple of hundred students and a good handful of lecturers and all of them have dutifully followed the protocol and written it up without any of them noticing that one of their test-tubes has short measure. Typos are forgivable - I keep finding them in The Blob - but I try to make sure that tables are internally consistent, that the row and column totals sum correctly.  Life is much easier now with spreadsheets to keep track of these things.

Thursday, 24 October 2013

In the teeth of the evidence

Teaching final year Environmental Chemistry at The Institute is the best of fun and I keep unearthing facts that are relevant to the course and really interesting as well.  I hope the students are finding the whole thing as riveting as I am.  I have no intention of teaching the whole thing as an exercise in I talk and flick through powerpoint slides and you listen and maybe take notes.  That's the worst possible learning protocol and I have to prep a lot of powerpoint slides.  Far better to have the students find stuff out for themselves - it's much more likely to to stick in their heads then.  There are some things I get conflicted about - I'm a scientist, but I'm also a tree-hugger, own a pair of Birkenstock sandals and didn't send my kids to school.  One of the issues where I'm less certain than I'd like to be is fluoridation of the water-supply to prevent dental caries.  So I thought it would be good to crowd-source a solution to my F dilemma by hosting a debate on the matter.

As a first step, I surveyed my class as to their unprepared knee-jerk position on fluoridation, getting them to tick one box from
"Fluoridation of water is  . .": wonderful [ ] good [ ] dunno [ ] bad [ ] divil's spawn [ ]
Based on that, I divided the class into two cohorts pro-F and anti-F and told them they had a week to prepare their positions.  Last Thursday I bumped into one of my colleagues who said that she'd been asked for her opinion on the issue and reported that her questioner was quite passionately engaged in the project.

Earlier in the week we had the debate, which I lubricated with a box of chocolates - the irony of which was lost on me until the kids started to show grim pictures of carietic teeth.  Their material was well-researched and presented with good humor and cogent arguments.  Afterwards I resurveyed everyone as to their position.  The first finding was that the exercise had polarized opinion to the max, nobody was now anything less than certain about fluoride whereas before there had been several waverers.  I had to award the accolade to the anti-F people because they had shifted 3 opinions towards their position whereas the pro-F chaps had only dragged one person towards theirs.  I was particularly taken with two pieces of evidence that supported the anti-fluoridation position. One was that dental caries has fallen precipitously over the last 40 years both in countries that add fluoride to the water and those that don't. The other was that in Ireland we spend about €4 million a year adding fluoride to the water but that after leakage, industrial and agricultural consumption, car-washing, toilet flushing and bathing, only 0.1% of the processed drinking water is actually drunk. That seems grossly inefficient. So until I critically evaluate the quality of their sources and the statistical significance of their analysis, I confess to leaning towards anti-fluoridation.

Wednesday, 23 October 2013

In the lime-light

For the last several years a student from The Institute has been given a prize by Clogrennane Lime which operates just down the road at the edge of the Castlecomer Plateau near the evocatively named Bilboa.  Of course it's not just any student who gets the cert&cheque but whoever does the best analytical project in 3rd year and stays on to finish up in 4th year.  Today the award was presented by Joe Connolly, Quality Control Manager from the company and graduate of The Institute.  He carries a lot of other portfolios as well, Clogrennane being a small, dynamic and growing company.  One reason for a modest award ceremony is to bring all our chemistry stream students (and others, too) together to celebrate the success of one of their number.  But another is to use that occasion to show-by-example that even an 'unfocused' student can make good with the right support.

Joe left school and dropped out of NUIM after failing an element of his first year assessment.  He then spent 2 years in a meat-factory before realising that, good as he was at cutting sheep-carcases, he could cut a better dash back in college.  His return to education was diluted by drink and good times and he failed 2nd year and had to repeat it.  But he was given the opportunity to do something real by landing, with the help of staff at The Insititute, a work-placement at Clogrennane.  Working in the summer and winter vacations, and clearly being an asset at the plant, a self-described waster metamorphosed himself into a first class honours graduate with a job and a shining future.  Brilliant!  That's a story which is repeated time-and-again in the IT sector.  People are given a second chance: if they failed to shine in the artificial world of school-education, if they tried some career and found it was a bad choice.  Often these people are a good pair of hands: the people on whom the future of Ireland as a technological nation (FITNA) depends.

Joe Connolly also told us a story about how he had a crucial insight into the problem of increasing the solubility of one of their products while taking a break from several days of intensive experimentation and discussion.  Thinking, trying, testing, bust ... thinking, trying, testing, bust.  Tea-break, Ah-HA. I can't tell you the details lest that intellectual property gets back to the competition.  It was as good a description of true creativity in science as anything told about Poincaré or Hamilton or Barbara McClintock.  No Nobel or immortal fame for young Joe, but a clear item on the bottom line for the company; more people employed (including Joe) for longer; better product produced more efficiently; happier customers and a better world.  In a life-time of science, I've had a handful of good, original ideas, and none of them have had such an immediate pay-off for society.

Ranking University - absolute bloody nonsense.

I had to be really careful typing the title.  "Nanking University - absolute bloody nonsense." would have gotten me a visit from the Chinese Thought Police or at least the erasure of The Blob from Google-China.  I was listening on the wireless a tuthree weeks ago after one of the several-available World Rankings of Universities was published.  My alma mater TCD came top in Ireland (huzzah huzzah) and the good journalists at Newstalk asked Prof Vinny Cahill, the Dean of Research at Trinity for his opinion.  It shocked me how unwilling Cahill was to critically evaluate the value of such an accolade, preferring to bask in the arbitrary attribution of points that had put his/my University at the top of the list.  The essence of science is to be critically aware of any short-comings in your data and analysis - especially if they agree with your hypothesis.  There is a great book called How to Read a Paper by Trisha Greenhalgh.  Her advice is to start reading any paper at the Materials & Methods section.  Any serious failing there saves you from having to read the rest: no matter how persuasive the title or how significant the results.  GiGo (garbage in - garbage out) is an unforgiving god and is ignored at your peril.

On 13th October, The Sunday Times published its annual rankings of British and Irish Universities. The management of The Institute (the place where I work) promptly printed dozens of posters announcing its designation as Institute of Technology of the Year 2014 (huzzah huzzah).  That's okay, the management are not necessarily trained in Science and even if they are, their skills lie elsewhere.  Margaret Thatcher, for example, was trained as a chemist but preferred to run a country - more of a challenge.  Management can quite legitimately preen themselves a bit and retweet any positive publicity - it's their job.  There was, I am glad to say, more healthy skepticism and even bemusement amongst my scientific colleagues: how-in-heck did we get the top accolade if, by the ST's own criteria, four other ITs were better?

The criteria used by the Sunday Times were six in number, but they chose to weight Leaving Certificate points 2.5x more than the other parameters (why?  It is not explained):
  1. Median Leaving Cert Points obtained by incoming honours degree students (wt 250)
  2. Research funding (not research impact) got in 2012 / FTE staff (wt 100)
  3. % of students employed nine months after graduating (wt 100)
  4. % of high quality (1st/2.1) degrees awarded (wt 100)
  5. Student/Staff ratio (wt 100)
  6. % of students who had completed their degrees within 5 years of starting (wt 100)
Total 750 points.  Here again, TCD came top in Ireland: it may even have been the same survey which Prof Cahill was so chuffed about at the beginning of the month.  The best University in the UK is, as you ask, U Birmingham (huzzah huzzah), runner up U Leicester (one huzzah).  In the same box in the ST supplement as these gongs were announced is a list of Top by Subject from Aeronautics (Cambridge) to Tourism (Surrey) - Zoology seems to get bundled up in Biological Science so a full A-Z is not possible.  In none of these did Birmingham or Leicester feature, so I presume their top ranking is either arbitrary or subject to a well-placed envelope full of folding money

The ST acknowledges that TCD's 4% lead is being eroded as the hungry pack champ at the heels of the alpha University. Here you can see that UCD is 'better' at research than TCD:
Uni LC Res Emp 1st St/St Comp Total
TCD 125 84 93 73 60 81 606
UCD 198 93 94 62 60 78 583
Ratio 1.09 0.90 0.99 1.18 Same 1.04 1.04
If I was Prof Cahill's opposite number in UCD, I'd ask why is Leaving Cert input so over-weighted; surely, in a technological nation looking towards the future research should be given the 2.5x boost.  If you do that, then UCD edges out TCD 605 to 603 (huzzah?).  Needless to say the journalists at Newstalk and everywhere else, trained in the Arts Block, weren't interested in interviewing the Runner-Up no matter how close the gap.  Statistical insignificance is too complex a concept to deal with if the whole segment is allocated 180 seconds between the latest road deaths and the scores at the US Open.

*skeptic alert: the following analyses compare the average values of X and the average value of Y and ignore the range and error-of-estimate associated with that single tweetable metric.  Within TCD, for one example, when I was a watch-keeping non-comm on the bridge of SS Genetics, we were extremely parsimonious with handing out Firsts and used to snicker at Zoology (whose students we regarded as affable rugger-playing bohunks looking at things-bigger-than-a-breadbox through binoculars) who awarded a generous handful of these precious certificates each year.


The other criteria are in some sense uncorrelated with each other.  But if the quality of the degree means anything in these straightened times, it is that it gets you a (better) job.  Those two parameters should show some sort of relationship.  And they do . . . not.  Only with the eye of faith and by illegitimately eliminating the extraordinarily good employment record achieved by IT-The-Blanch (in the bottom right corner) is there an upward slope here.  The Correlation Coefficient (r) - a measure of association between two variables (1 = perfect positive correlation, 0 = two completely unrelated variables) = 0.11 which is, as we say, not significant.  So the proportion of 'good' degrees awarded is an institution-internal metric only hazily associated with the objective quality of the students winning them.  Let's accordingly eliminate that criterion as subjective and irrelevant.  As TCD showers out 1st Class Honours degrees like confetti, under this rule TCD (and UCD) are knocked out by UCC which had champion research results. By tricking about with the data in this way you can make any one of the top 4 or 5 Universities become Best University.


Now here's a metric that might serve to identify the colleges that do more than sit on their hands for four years while their students party. There is a wide discrepancy between average incoming Leaving Cert score but a pretty good correlation (r = 0.64) between that and % 'good' degrees awarded.  (Taking the latter with a pinch of salt as discussed in the previous paragraph). So you'd be looking for those institutions that fall above the trend line in the graph on the left.  These include Waterford and Carlow ITs and Dublin City University. These institutions appear to take kids from school at one level and spit them out four years later a little higher up the hill.

Mais revenons nous a nos data. On p.5 of the 13/Oct/13 Sunday Times Colour Supplement that reports all these findings, you can see the data from which my table and graphs are abstracted.  They claim that for DCU (ranking 4th) 186+68+94+69+64+83=583  but it doesn't.  It sums to 582.  What differ you may cry? It's only 2 parts in 1000 off.  It differs, sunshine, because if the Sunday Times can't add up a row of numbers correctly, there are likely to be other more substantive errors elsewhere in their report.  So I can (Greenhalgh rules okay) dismiss the whole thing as lazy, irresponsible, arbitrary and tendentious nonsense.

I want TCD to win and my own employer did win, but it's still nonsense. 

Tuesday, 22 October 2013

Ketchup and cornflour

Thixotropy, shear-thinning, refers to the process when a gel or sludge liquifies when shaken or stirred.  You know it best in tomato ketchup where a stout thump on the base of the bottle will slide some of the contents onto your chips. Many printers inks are thixotropic so that they can be squirted out of a nozzle as a liquid but not roll about the page after they arrive. You rely on it more essentially as a property of the synovial fluid in your joints - when the joint flexes it lubricates, when movement ceases it supports.  In the natural world, this is similar to quicksand which looks solid enough when at rest but liquifies when sheared by your foot. Thixotropy in the clay layer was probably an element in the acceleration of the mountain-side into the lake at Vajont.  Christchurch, NZ mostly situated on a flat coastal plain astride the Avon River sustained significant damage from liquefaction of subsoil under buildings during the 2011 earthquake.  For the same reason Boston, large tracts of which are built on landfill in Back Bay and similar areas, has one of the highest ratings in the USA for earthquake disaster potential.  Earthquakes are very rare on the seismically stable East coast, but if one should occur it Boston will be like a house of cards in a gale.

The opposite of thixotropic is a dilatant fluid that becomes thicker when sheared, shoved, scooped or stirred.  The best example of this (lots of fun in the kitchen) is a mix of cornstarch and water that you can scoop quickly up in your hand and then have run through your fingers - preferably back into the bowl. Or you can scale up - but you have to be quick!  If you didn't, like me, fail Ordinary Level Physics check out "non-Newtonian fluids - you'll be able to understand it.

On 21st October 1966, the primary school in the village of Aberfan situated in a valley in the heart of the South Wales coalfield near Merthyr Tydfil was engulfed in wave of sludge and rock that came down the mountainside through the fog with a roar sounding like a jet-plane crashing.  116 children and 28 adults were crushed to death or suffocated under tons of loose spoil from the local coal-mines which had been casually dumped on the uplands by the National Coal Board.  Out of ignorance and negligence at least some of these spoil heaps were dumped on natural springs and in any case there is a lot of rain in the Welsh valleys.  What seems to have happened is that one face of a slag-heap slumped a few meters after days of heavy rain and that shearing shock caused the rest of the saturated artificial mountain to liquefy like ketchup.  The total volume shifted was about 150,000 cu.m but 40,000 cu.m of that finished in and on the village school - it was buried 10m deep in places.

In the aftermath, Lord Robens, chairman of the National Coal Board, behaved in a way that was not so much shabby as callous and duplicitous, as well as rapacious in the very worse tradition of 19th century robber-barons.  It brought home to thoughtful people that, for all the high-minded aspirations of the left, there really was little difference between capitalism and state socialism in their actions on the ground and in tribunals. Robens started off as a leftist MP for a mining constituency in Northumberland and a minister in the 1945 Labour government.  He used his appointment to the NCB by the Conservative government of Harold Macmillan to transform himself into director of this and chairman of that as if he'd been born to it.  I don't think it's insane to suggest that Robens sowed the seeds of disillusion that sprouted in the election of Margaret Thatcher's Conservative government 12 and a half years later.

Monday, 21 October 2013

Tapping the Admiral

Aa tuthree months ago I was writing about the institutionalised haze of alcohol that befuddled the British and other navies for a couple of hundred years. Then a tuthree days ago, I was bloggin' about the poor, so desperate for booze that they were happy to drink beer in which their neighbours had just been drowned. Given that back-story, on Trafalgar Day (that's today for all ye lubberly readers who weren't brought up in a sailor suit like Bob von Trapp) it's inevitable that 'one' would think about Tapping the Admiral.

On the 21st October 1805, after Horatio Nelson was shot through the spine while standing on his quarter-deck at the Battle of Trafalgar. He was carried down to the orlop deck and died at tea-time three hours later.  The common sailors were buried over the side, but the Admiral was immersed in a barrel of brandy for transport home to a state funeral.  On dit que the common sailors were so desperate for drink that when the barrel was opened on arrival in England six weeks later it was half empty.  I am very sorry to report that according to Andrew Warriner (no better man) this fine story is just a story.  Nevertheless the practice of drilling a small-small hole in any barrel of liquor and surreptitiously sipping the contents became known as tapping the admiral or sucking the monkey which latter phrase was not very flattering to the 'diminutive' English hero, is it?  Sailors are colourful coiners of foodie words and phrases: gannet (any hungry boy); scran (food); grog (rum ration); oggies (cornish pasties); growler (pie); babies heads (steak&kidney pudding); burgoo (porridge); lobscouse (ship's biscuit boiled with meat and veg); corned-dog (corned beef); snags or snorkers (sausages); toenail (beetroot); Spithead pheasant (kippers); kai (thick cocoa); all of which were eagerly scarfed up rather than being thrown in the gash (rubbish);

Sunday, 20 October 2013

Vajont October 1963

You know those Mensa IQ puzzles where they ask for the next couple of terms in a series: 1, 4, 9, 25, 49, __, __, or L, M, M, J, V, __, __, ?  Well what about Botox, Sarin, propylene, beer, __. ?

You will have noticed a tendency to track anniversaries on The Blob.  It's a way of limiting the choice of things to think/write about from the infinite to the dayinit. I'm interested in events at the intersection between the natural world and the folly, hubris or even malice of people. There were good reasons why Italians wanted to develop hydro-electric power in their Alps as their economy started to show green shoots after the debacle of WWII. There was pressure (political, economic, social) behind a plan to build one of the tallest dams in the world at the head of a modest valley carved by a tributary of the Fiume Piave.  The CEO of the local electricity monopoly had been Mussolini's Minister of Finance, so he was well-connected, and interested in money.

The dam was first considered in the 1920s, authorized in 1943, but construction didn't start until 1956.  They had, of course, done a geological survey to determine whether the walls of the valley were strong enough to hold this huge 260m high wall of concrete upright and some, more cursory, investigation had revealed some evidence of ancient land-slips further up the valley.  Construction was authorized and pouring concrete started.  Several outsiders sounded off about the instability of Monte Toc which loomed over the valley that was to be filled with water.  After the dam was built, the sluices were shut and the valley started to fill with water.  Some time later a farmer noticed that a 1700m long crevasse had opened up roughly parallel to the valley on a shoulder of Monte Toc.  The ever-increasing width of this crack suggested that a very large chunk of the local world was thinking about taking a plunge in the lake.  This was worrying but the company had invested a lot in the project and accordingly cast about for more data and solutions to probable future scenarios. With 20/20 hindsight, two significant scientific gaffes were committed.

The first error was to treat anecdote as data. They noted (N=1) that when the water level increased the crack had started to open. When they pulled the plug (N= -1?) and let out some water then the creep stopped. They therefore believed that the water level in the lake was driving any local land-slippage. The second error was to assume that one anomalous value was wrong rather than that it was the key to a new and much better paradigm of what was happening under-ground.  They had drilled four boreholes deep beneath the limestone surface to see if the solid rock went all-the-way-down or was resting on something far less stable.  Three of the holes' piezometers said "solid" and the fourth, which they put down to faulty instrumentation, said "wobbly".

Regardless of these data, the company was determined to filler 'er up and start to generate some return on their investment.  Any rock slide would just have to be managed: if and when it happened enough redundant safety features would have been installed, so that nobody would be hurt.  The company's engineers built a scale model of the valley with a mini-dam and dumped loads of gravel over the edge and measured what the resulting mini-wave got up to.  They concluded that biggest possible landslip would result in a tsunami 20m high.  So they drew a Plimsoll line 25m (25% extra to be sure to be sure) below the top the dam for the maximum safe height.  They then filled up the lake again and waited for what would happen.

The anomalous piezometer (20/20 hindsight here) showed that the whole huge slab of limestone and its attendant topsoil, trees and foxes was separated from the mountain by a layer of clay. When this failed it allowed a near frictionless slide downhill, so the mass traveled far faster and was far more massive than the simulations had considered possible.  Indeed there was more stuff (260 million cu.m) going downhill at 100km/h than there was water in the reservoir.  It was like dropping a walrus from a great height into a bath-tub. Instead of a wave 25m high, the mountainside slopped 50 million tons of water over the edge of the dam in a wall 250m high which wiped 4 villages and 2000 people off the face of the earth in a couple of minutes.  It's reminiscent of Lake Nyos.  The dam survived with only superficial damage and is still there to this day but they never filled the reservoir after the 9th of October.  It's all rather well covered in a National Geographic documentary.

One set of answers to the questions posed at the head of the post:
1,4, 9.25,49,121,169 (squares of primes)
Lundi, Mardi, Mercredi, Jeudi, Vendredi, Samedi, Dimanche (French weekdays)
150ng, 150mg, 150kg, 150t, water=25,000t (quantities that can kill a person)

Saturday, 19 October 2013

Oxygen of folly

Today marks the 25th anniversary of the implementation of the British Broadcasting Ban by their Home Secretary Douglas Hurd.  It was a rather desperate response to events at the height of The Troubles.  March 1988 had seen things escalating with the inevitability of a Greek tragedy.
  • 6th Three members of an IRA active service unit executed by an SAS active service unit in Gibraltar.
  • 16th Three dead and 60 injured in an attack by a loyalist gunman at the funeral of the Gibraltar victims in Milltown
  • 19th Two British soldiers killed while/for watching the funeral of one of the Milltown victims
The latter two events were extensively filmed by the television crews present and there were freedom-of-the-press issues about whether they should/would turn over their film to the security forces. June and August saw two very bloody bomb attacks on vehicles carrying British soldiers in Northern Ireland. Clearly something had to be done, and seen to be done, by Mrs Thatcher's government.  They were particularly fed up with the fact that, after each atrocity, the media would ask for a sound-byte from those believed to be close to the perps.  Tory Chairman Norman Tebbit, who had been injured and whose wife had been permanently disabled in the Brighton Bombing of 1984 said the media were giving the other side "publicity that they shouldn't have had". Mrs Thatcher, trained as a chemist, came up with the more memorable "deny terrorists the oxygen of publicity".

So Hurd implemented a couple of sections of 1981 Broadcasting Act, which proscribed the broadcast of the words of any members of ten 'terrorist organisations' including the acronyms IRA UDA UFF INLA UVF . . . was the Judean People's Front among them? I forget.  I make the facetious remark because the ban turned into a farce. Initially the voices-of-evil were replaced by subtitles but then dubbing took over. The words of Gerry Adams, democratically elected Sinn Fein MP for West Belfast, was too powerful for the public to hear but those of an actor could be dubbed over footage of him speaking. As trained actors were used in the dubbing, the rhetoric often became more powerful.  The dubbing got so good that occasionally nobody realised that there was a voice-over.

Apart from being fatuous in its implementation, the ban dug huge pits in the high moral ground from which the British addressed such global political issues as Apartheid in South Africa. The explicit acknowledgment that Sinn Fein's rhetoric was more powerful than the government's should have given them pause but the ban stayed in force for nearly six years. Once in place, it was difficult to step back from the position because that would seem to be seen to be soft on terrorism.  It wasn't rescinded until two weeks after the announcement of an IRA cease-fire in 1994 and British broadcasting returned to the status quo ante or same old, same old.  I won't talk about the shameful position on censorship w.r.t. events North of the border that was enforced by the Irish government and enthusiastically taken up by RTE.  But rescinding the broadcasting restrictions on RTE in early 1994 did help the Brits back across the line of sense.

John Birt, D.G. of the BBC, announced "We can once again apply normal and testing scrutiny to all sides in the debate".   I think many people would have greeted this with a hollow skeptical laugh at the time.  Do I think we're nearer to unbiased broadcast media now? Do I Fox!

Friday, 18 October 2013

Moby Dick

Moby Dick, or The Whale was published in Britain on 18th October 1851 when Herman Melville, the author was 32 years old.  IF you've only read the picture book version OR only seen Gregory Peck in the film ANDIF you are not totally spoiled for discourse by Twitter THEN you'll find much of interest in reading this great Victorian faction drama-documentary.  Melville had run away to sea 10 years earlier shipping on the whaler Acushnet before jumping ship 18 months later in favour of making love to a beautiful cannibal-girl on the Marquesas Islands.  He wrote up the tropical paradise part of his adventures as his first novel Typee.

Mais revenons nous a nos baleines. Apart from being a ripping yarn: "Call me Ishmael . . .Buoyed up by that coffin, for almost one whole day and night, I floated on a soft and dirgelike main. The unharming sharks, they glided by as if with padlocks on their mouths; the savage sea-hawks sailed with sheathed beaks. On the second day, a sail drew near, nearer, and picked me up at last. It was the devious-cruising Rachel, that in her retracing search after her missing children, only found another orphan", Moby Dick is also an extraordinarily detailed (135 chapter, 360 page, 200,000 word) treatise on the theory and practice of whaling.

One particular part has lodged in my head since I read it with some difficulty of understanding as a 14 year old boy.  They used to say about pig-butchery that they used everything but the squeal, and 19th century whalers were like that about their 'fish'.  Because it was published in Victorian England, there are some rather elaborate circumlocutions, so that 14 year old boys and women (the poor delicate things) could only with difficulty figure out what-in-heck was going on.  I've made some editorial changes in the first line of Chapter 95 to help you, dear reader:

"Had you stepped on board the PEquod at a certaiN juncture of thIS post-mortemizing of the whale; and had you strolled forward nigh the windlass, pretty sure am I that you would have scanned with no small curiosity a very strange, enigmatical object, which you would have seen there, lying along lengthwise in the lee scuppers. Not the wondrous cistern in the whale's huge head; not the prodigy of his unhinged lower jaw; not the miracle of his symmetrical tail; none of these would so surprise you, as half a glimpse of that unaccountable cone,—longer than a Kentuckian is tall, nigh a foot in diameter at the base, and jet-black as Yojo, the ebony idol of Queequeg. And an idol, indeed, it is; or, rather, in old times, its likeness was. Such an idol as that found in the secret groves of Queen Maachah in Judea; and for worshipping which, King Asa, her son, did depose her, and destroyed the idol, and burnt it for an abomination at the brook Kedron, as darkly set forth in the 15th chapter of the First Book of Kings."
...and a certain something in the next paragraph requires elaborate circumcision:
"Look at the sailor, called the mincer, who now comes along, and assisted by two allies, heavily backs the grandissimus, as the mariners call it, and with bowed shoulders, staggers off with it as if he were a grenadier carrying a dead comrade from the field. Extending it upon the forecastle deck, he now proceeds cylindrically to remove its dark pelt, as an African hunter the pelt of a boa. This done he turns the pelt inside out, like a pantaloon leg; gives it a good stretching, so as almost to double its diameter; and at last hangs it, well spread, in the rigging, to dry. Ere long, it is taken down; when removing some three feet of it, towards the pointed extremity, and then cutting two slits for arm-holes at the other end, he lengthwise slips himself bodily into it. The mincer now stands before you invested in the full canonicals of his calling. Immemorial to all his order, this investiture alone will adequately protect him, while employed in the peculiar functions of his office."

You may forget the latest cool-sloganed tee-shirt, this is the butcher's apron fashion accessory everyone will want.  Moby Dick, indeed.  You couldn't make this up.

Thursday, 17 October 2013

Drowning in the dhrink

Pretty much everything can kill you if taken in excess.  And lots of things that we know to be toxic are used therapeutically in certain limited situations.  Botulinum toxin, strychnine, and deadly nightshade (Atropa belladona) all have their, suitably dilute, place in medicine.  I've mentioned Botox before in a guesstimation exercise to see how much it would take to kill you - a vanishing small quantity: about 150ng. [ng is a billionth of a gram].  And over the months of 2013 I've looked at the lethality of Sarin [maybe 150mg or a million times more concentrated than Botox] and  propylene [150kg or million times more than Sarin and then only effective if you ignite it] and finally carbon-dioxide [150tons or about 1000 times more that propylene].  I was thinking of floating a company called LD50, Inc, but CeeTox has already cornered the market.

Today (or it may be yesterday, parallel stories are reproducing on the interweb) being the 199th anniversary of the Great London Beer Flood, let us reflect on how lethal 3-5% dilute alcohol might be. In 1814 the Meux brewery, at the junction of Tottenham Court Rd and Oxford St in West London was celebrating its 50th year. The demand for Meux products was mighty and they had acquired a vat capable of containing more than 500,000 litres (500 tons) of porter.  This megabarrel was say, 7m diameter by 14m tall and built of enormous oak staves bound with iron hoops. which was how barrels of any drink - water, wine, whiskey, beer - was stored then.  And suddenly at 6pm it wasn't stored there any more because the whole thing explosively disintegrated.  The resulting tsunami rocked neighbouring vats off their foundations and they shattered as well smashing a hole in a brick wall to loose 1.5 million litres of beer on the neighbourhood.  7 people aged from 3 to 53 are known to have drowned as their basement homes flooded.  But as most of the victims were the dispossessed living in the St Giles Rookery there may have been more.  Anyway it took about 150 tons of beer to kill each of these unfortunates - proportionately the same amount as carbon dioxide killed 1700 people in Cameroon.  You don't have to get cirrhosis or drive drunk to have an excess of beer kill you.

Needless to say their surviving neighbours ("tsk, those slum dwellers") behaved in a most unseemly manner, filling every available receptacle with free beer and even stooping to lap it from the very street. 

Wednesday, 16 October 2013

Quaternions 170 today.

There are a few, well-churned, stories of how a creative insight came to someone in a flash at a particular place and a particular time.  Henri Poincaré (1854-1912) was a French mathematician known as The Last Universalist (le dernier grand savant universel).  As I quoted J.B.S Haldane earlier "Keats and Shelley were the last two poets who were at all up to date with their chemical knowledge” so Poincaré knew all the then available mathematics.  Einstein was writing his key papers before Poincaré died and after his death things mathematical went exponential so that no single brain could retain it all.  As well as making major contributions to several different fields of mathematics, Poincaré was also a philosopher of science with a notable interest in the where ideas spring from.   In his 1908 book Science and Method he describes one of his own experiences getting onto a bus in Coutances in Normandy: "At the moment when I put my foot on the step the idea came to me, without anything in my former thoughts seeming to have paved the way for it, that the transformation that I had used to define the Fuchsian functions were identical with those of non-euclidean geometry." I can see that I'm going to have to come back to Poincaré later, because he is really so interesting.

Poincaré will be always with us, but not the fleeting anniversary of the discovery of quaternions by Ireland's own polymathematician William Rowan Hamilton: that comes but once a year.  I've mentioned him in passing before acting a bit of a groupie over the Ordnance Survey team that was mapping Ireland in the the 1830s. Hamilton was born about 50 years before Poincaré, so he had much less difficulty mastering all the mathematics then available, because he was quite as smart and there was much less maths.  He was appointed Professor of Astronomy at Trinity College Dublin at the ripe old age of 22; the position came with a house at the Dunsink Observatory NW of Dublin.  On 16th October 1843 he went for a stroll with his wife along the Royal Canal, and as he passed under Broom/Brougham Bridge on the tow path he had an amazing revelation about mathematical relationships, which he hastily scratched into a stone on the bridge:
i^2 = j^2 = k^2 = ijk = -1
NUI Maynooth hosts an annual pilgrimage walk from Dunsink Observatory to Broom Bridge or you can just go out on the Maynooth commuter rail and descend at Broombridge.  When I was last there 20 years ago, on pilgrimage with a friend of mine who had a degree in Mathematics from Cambridge, the area was all derelict rough meadows filled with old bedsteads and piebald horses.  Now, as you see from Google maps, the Celtic Tiger has passed through depositing now derelict rough sheds and warehouses.

For those with elementary maths, Hamilton's formula plainly does not compute because it violates the convention that minus x minus = plus, so there is no way two identical things can be multiplied together to make -1.  But Hamilton's equation has a bunch of such assaults on this agreement i x i = -1; j x j = -1 etc.  For those who have a tiny bit more maths, the Quaternion times table shown on the left violates the principle of commutativity.  The elementary maths chaps are leaving for a strong cup of tea at this stage because they can't remember ever being told about commutativity.  A commutative relationship is one where the order of application doesn't matter.  Regular multiplication and addition are examples of commutative transformations:  3 x 2 = 3 x 2; 7 x 6 = 6 x 7; 15 + 5 = 5 + 15; etc etc. the times-tables are much easier because of this symmetry, as is adding up a long column of numbers - the answer is the same if we start at the bottom and add from there or if we start and the top and add downwards.  Non-commutative operations include minus and divide:  5 - 3 .ne. 3 - 5 and 3/5 .ne. 5/3. [.ne. - not equal]
From the table it says that i x j .ne. j x i .  It does matter which order you multiply the elements in quaternion mathematics.  You can, idly, use the table to verify Hamilton's bridge-scratching "ijk = -1" (it's the same as i x j x k = -1) can be processed in two steps:  i x j = k ; k x k = -1.

"So far, so what?"  I hear you say, and for 100 years that was the consensus.  Quaternions were a clever game that mathematicians used to play with, trying to discover inconsistencies and mapping the results onto other weird branches of mathematics. Then it turned out that they were an extremely powerful, compact and useful way of representing 3-D movement, particular turning.  Where did we need to mobilise that insight?  First in space travel, controlling the yaw, pitch and roll of Gemini, Soyuz and Apollo with minimal expenditure of fuel.  Latterly, quaternions are key to being able to write code for computer graphics that is compact enough to execute in real time.  Without William Rowan Hamilton's insight 170 years ago there would be no Lara Croft, and the world would be a far duller place for 13 year old boys.

Tuesday, 15 October 2013

Potential energy

Today is Ada Lovelace Day.  This annual reminder about the fact that there are women working in Science, Technology, Engineering and Mathematics (STEM) has been running since 2009 but I only heard about it on Sunday. Check out Aoife McLysaght in today's IT.  We really must change  
ST[XX]EM << ST[XY]EM 
into something more like  
ST[XX]EM = ST[XY]EM
There's a huge reservoir of creativity and talent that is just not being tapped. I checked out the ADA website and the founder, and discovered a link asking for inspiring essays about inspiring women in science.  So I thrust The Blob's views on Barbara McClintock, Lynn Margulis, and Jocelyn Bell Burnell at them.  I've called that all-too-short list an occasional series. As it's exactly 3 months since the last entry, and for the day that's in it, I'll write a few words here about Cliona O'Farrelly.  She is a scientist and a woman and a mother. I mention the last qualification because this attribute had a significant impact on female professionals of her generation and none whatsoever on their male contemporaries.

She is now Professor of Comparative Immunology in TCD.  When she was appointed six years ago, she was not the first choice of the chaps on the committee, because her publication record was solid but not stellar.  First they offered the Chair to a high-flyer from Foreign, who had forgotten to ask his wife, a professional in her own field, and family if they wanted to up-stakes and move to the edge of Europe (rotes Gesicht zu Hause).  Then they offered it to a local man who used the offer to blag himself a better position at the place he was then working (and good for him).  Finally, and possibly with a sense of desperation, they offered it to a woman.  Maybe it wasn't exactly like that, my memory is woofly, but many professional women who read this will hear a small ring <ding> of truth.

I'm sure that one of the reasons she made it to the short-list is that she is a great teacher.  She's not a narrow specialist, but has many interests including things beyond science.  She is thus able to draw her explanatory metaphors from a much wider experience than the specialist scientific literature.  I remember going to one of her seminars a decade ago; the pictures for her talk came with her on a CD. This disc was put into a Mac computer which dutifully ate it up and choked.  Nothing anyone could do would either release the CD or bring the Mac back to life.  Only marginally daunted, she carried on with her talk, which was mainly about the work her molecular evolutionists had been doing on computers, showing the multiple sequence alignments with vigorous horizontal sweeps of both hands, the conserved sites with precise vertical chops, and the Hidden Markov Model with similarly appropriate theatre. Eee, it were great! So clear, such fun.  Every year she visits her local girls-only secondary school to talk to them about science - careers in science ostensibly - but really, passionately, about science.

When COF came to TCD, she found a catch-as-catch-can Transition Year work experience programme.  If you or your neighbour or your cousin knew one of the faculty members then you could ask them to take your teenager under their wing for a week.  Each youngster, as they came in, would have a session with the Safety Officer, a tour of the building, and other infrastructural essentials. Taking in such would-be scientists is paying your taxes to the aspiration that Ireland has a future as a technological nation.  Like taxes it is an imposition on your time and resources, so it is easy to shirk the responsibility.  COF codified the program so it happened on two specific weeks in the year.  Positions had to be competitively applied for, all the Faculty had to contribute and a program for the whole week was formalised. Half of the available hours were actually in laboratories experiencing work and half were group activities, tours, demonstrations and lectures - and the Safety Officer could efficiently give her talk to 18 people at once. It was great, not least because I was asked to devise a scientific scavenger hunt round the campus. I love treasure hunts.

Before TCD and after Harvard, she was for a decade the Research Director at the Education and Research Centre in one of the Dublin teaching hospitals.  The ERC had several  purposes but one of them was a place for consultants to park their graduate students while they were in theatre or doing rounds of the wards or rounds of golf.  Accordingly COF had an important role mentoring not only her own research group but also these orphans.  In the lifetime of any doctoral training, there will be at least one moment of despair, when the work is stagnant, the ideas have dried up and blown away, the avenues of advance are all obscured by thickets.  One of her mentoring SOPs was to fish the student out towards the edge of the Slough of Despond and get them to go through their first lab books with her.  Even for one at the lowest ebb of self-esteem, it is a revelation to see just how plug-ignorant and clueless you were when you started.  You cannot but feel better when it is clear that you have learned so much, and that your toolbox is so much better filled with sharper tools now.  Sometimes that helps and sometimes so does an ultimatum and a quite brutal shove and when that seemed necessary she didn't shy away from it.

The purpose of a PhD programme is not really about generating results, although that is a key deliverable for the funders. It's much more of a training in how to reason, how to marshal evidence, how to present data and how to solve problems . . . regardless of what those problems, or that data, are.  Even at this top level of formal education there is a wide range of abilities, some students are stellar and some are nearer our good green earth.  It's easy to supervise the ad astra chaps; they are as smart as you or smarter, they get up in the morning raring to go, they work all the hours that the day sends and they have ideas in their sleep. If you are brilliant and successful yourself you may never have to draw your students from the per ardua cohort.  COF sees her role as getting each of her people to fulfill their potential: to go as far as they can . . . and a little bit more. So it's not a doss or a doddle, no PhD can be that and be worth having, but it is clear to her that a good PhD contributes to progress as well as a brilliant PhD.  The narrow path blazed through totally new territory has to be braced and supported by work that comes after and builds in the same direction.  Exactly the same rules apply, over a shorter time-scale and a broader range of ability, to final year undergraduate projects.  Mobilising all this, especially per ardua, potential takes time and effort but the cost-benefit analysis is definitely positive. There can seem sometimes to be a relentless enthusiasm about Professor O'Farrelly, but that doesn't mean that the process is cost-free.  Such commitment to the necessary infrastructure upon which the high-fliers climb for launch is essentially  invisible - it should at least be acknowledged.  Rewarding it would probably be too much for society as we currently arrange things.  Nurses, primary school teachers, refuse collectors (do I mean mothers here?) are also often invisible and all get paid buttons.

So, as an alumnus of that institution, which makes me a sort of psychological share-holder, I think TCD got a good deal in their third choice. 
The Blob's women in science: Florence Nightingale - Barbara McClintock - Maude Delap - Cliona O'Farrelly - Lynn Margulis - Rosalind Franklin - Jocelyn Bell Burnell