Saturday, 31 January 2015


We went to the English Market in Cork a week ago and looted a lunch out of there in the old-fashioned way - moving from stall to stall tasting a bit of this and being overwhelmed by the smell of that and talking to the stall-holders about what was best.  Very civilised and minimal packaging. Tonight the local Sub-titled Film Society, of which we were knicker-throwing founder members, is showing The 100 Year Old Man Who Climbed Out the Window and Disappeared, the film of the book Hundraåringen som klev ut genom fönstret och försvann by Jonas Jonasson. Really looking forward to this, as always. Last night we were 2/4ths of a team at a Table Quiz to support the local Protestant church and came 2nd after a last minute surge from Table 4. This is clearly the most exciting weekend of our lives since we went out to dine two nights in a row last weekend in Cork. Films? Food? - time to build on the theme and share some tasty short films about good food.  It will make a change from The Blob brim full with my opinions and louche approach to syntax.  If a picture is worth 1000 words, a movie might be worth more?
Okay, enough!  I've put on 10 kilos just watching.

Friday, 30 January 2015

The left hand of deathness

Since the start of the year a long time obsession with islands and archipelagos was given a bit of an airing -I, I, II, III, IV.  But I also seem to have been picking on left-handers a bit I, II, III. Not picking on really, but poking at the idea that left-handedness is something of potential interest.  Left-handers seem to rise to the top of several key professions: 6 of the last 12 President's of the US [3xL] have been southpaws including the present incumbent. There is pretty good data supporting the hypothesis that lefties do better at one vs one sports like tennis, boxing, and baseball: maybe 3x over-represented in competition. Some pundits have tried to rationalise this excess by invoking better spatial awareness because the wiring of the southpaw brain and its left-right cross-over is arranged advantageously.  But I think it's more likely that it is an example of frequency dependent selection.  Many (most? all?) natural human populations seem to support a little over 10% lefties.  If you're in the minority group you almost always encounter right-handers and learn to cope with their stance and heft from an early age.  Right-handers also have most of their matches against fellow right-handers and so can be disconcerted when their opponent is a mirror of normal.  This advantage plays in favour of left-handers but only if they are in the minority - as they become more common their advantage evaporates.

In skirting round the Edge of Leftness, I came across several uncritical references to the fact that left-handers have a dramatically shorter lifespan and there were ready explanations for this 'observation': that southpaws didn't fare well in a right-handed world and did daft, dangerous and non-dextrous things with scissors, knives and cars which finished them off early.  The data for this deficit stems from a study of death records in California carried out by Diane Halpern and Stanley Coren and published in the prestigious New England Journal of Medicine NEJM in 1991. In California everything is the in public domain and Halpern and Cohen obtained a long list of dead people, their age at death and their addresses.  They then contacted the grieving rellies to ask if the deceased was left- or right-handed.  They found the average age at death was 56 years for southpaws but a full nine years longer at 65 among right-handers.  This is a staggering discrepancy: the only way to reliably achieve such a shortening of lifespan is to smoke 120 (!) cigarettes a day - one every 8 minutes and they say it takes 5 minutes to smoke one.

It was so unexpected and so contrary of people's own experience, that lots of competent medical practitioners and statisticians rounded on the data and found a notable bias that had escaped the attention of Halpern and Cohen in their direct and obvious tally.  The issue being that old people had been born a long time ago . . . when customs were different.  In Victorian and Edwardian times, left-handedness was seen as a defect, a sin or worse and children were forcibly converted as effectively as the Conquistadors made good Catholics out of Aztecs, Incas and Mayans or with rather less success some Christians seek to make homosexuals love the opposite sex.  The Beloved's mother was forced by the Good Sisters to write and sew with a her right hand in the 1940s. So there was a notable deficiency of left-handers among octogenarians, not because they were dead but because they wrote with their right hand and were categorised dexter for the study by their surviving relatives.  As the 20th century meandered on towards a more tolerant and inclusive society, beating children into writing with their wrong hand diminished as an acceptable practice and the number of left-handers bounced up to the normal/natural 10-12%. Graph by Chris McManus via BBC. People dying in their fifties were thus more likely to be (seen as) left-handed than those who were older.

In the demolition of Halpern and Cohen's some nice analogies were bought out. The average age at which Harry Potter readers die is much less than readers of Charles Dickens but you don't (or shouldn't) conclude that Voldemort kills HP fans with The Dark Arts - no it's just that Pottering is really only a task fit for children.  Likewise you could, but shouldn't, conclude that creches are much more dangerous than parachute training school because the average age of death in the former is much less than in the latter.  I suggest that if it is completely clear that Halpern and Cohen were a) wrong and b) it was obvious to you, then you are deluding yourself with 20/20 hindsight.  More importantly, I exhort you (and more importantly me) to be more aware of the subtle bias and other unconsidered certainties that we just can't see.

Thursday, 29 January 2015

Plagiarism - not so easy

I've had occasion to talk about plagiarism before: treating it as a ritualistic box-ticking exercise; being destructively uncompassionate about it; exposing the folly of being dogmatic about it. I've also written about plagiarism - owning somebody else's ideas - where there is no written record. As I've said, plagiarism is a Bad Thing but it turns out to be quite hard to spot it when there is a bit of nuance in the case. We circulate a PDF called Credit Where Credit is Due which outlines policy on matters of plagiarism and gives help about how material that you cite or quote should be referenced. One of my colleagues had the bright idea to devote a session to the problem in the universal 1st Year Course called Quantitative Methods.  This course concentrates on allowing the students to get some practice at problem solving and is not a series of lectures; rather it complements a series of lectures on mathematics, statistics and computers that we deem to be essential prerequisites for science.

I was skeptical about the value of the exercises because they described a set of abstract anecdotes  which had to be binned as "plagiarism" or "not plagiarism". I thought the artificiality would make it too easy to spot the sin and it wouldn't really help much in the real world where the specifics would be different and so more difficult. But it turned out to be interesting because there was disagreement among the students and, I must add, disagreement between me and the official line.  Although I'm the first to admit that my moral compass is a little wonk. The following two scenarios caused the most difficulty/dissension for us; you might ask yourself which if either of them is okay.  [I hasten also to add that these are <citation/referencing alert> courtesy of the Library of the University of Leeds]
  • You use some sections from an essay you wrote last year for a module that you are doing this year
  • You use a direct quote and remember to put in the reference for the source and the page number, but you forget to put the quote in quotation marks.
These are both "plagiarism" but I'm not convinced and we more or less agreed that it would be okay if you put an appropriate flag after the first example citing your earlier original work. I find the second one to be disagreeably pedantic and uncharitable. It is so little different from a punctuation error that I had a sinking feeling about what level of correction I really should be doing.  Cripes, if I red-penned every spelinge errur, every misplaced apostrophe, every dangling modifier, every verbless sentence as well as every missing quote mark . . . well I wouldn't have time to write The Blob and then the sky really would fall.  In the discussion, it transpired that some course manuals require students to label diagrams "in block capitals" and are liable to lose marks if they fail to do so. Well really!? How is a rule like that going to inculcate a love of science, foster the spirit of enquiry, help students think independently? So I was wrong about the utility of the exercise, it generated some engagement and some creative ideas and clearly some original thinking.

The second exercise was similar in that it began to address the fact that plagiarism is not black and white and you can have both venial and mortal plagiarism. I cut up a sheet of paper with eleven situations (similar to those described above) into 11 separate pieces of paper.  The students were asked to read each paragraph and then sort them in order of most plagiar-sinful [1] to squeaky clean [11], I got them to do this in pairs.  Soon there was a buzz of chat as each couple discussed the merits of this case over that and I soon had eight lists to compare. When they twigged that I was gathering the data, one women jested that it was too difficult to think this out with her partner and she would just copy the same list as the people on the the other side of the bench . . . and suitably reference the fact.  I thought that was a pretty sharp deconstruction of the whole protocol. We also had an interesting discussion about how long the stolen sentence/phrase had to be to preclude independent origin as an explanation of the similarity: this is a central issue in aligning biological sequences in the world of bioinformatics.

But I was very impressed by and unaccountably proud (no credit to me of course) of another couple who thought they could best crack the problem by reassembling the page which I had cut up by lining up the slight differences - like an indenture - in the line my scissors had made.  That was so left-field clever that I predict a great future for them in science.

ANNYway, here's the data <huzzah! for data>.  No two lists were exactly the same (so if anyone had plagiarised the plagiarism exercise, they had put in sufficient spoilers to make it undetectable). What I show here is a correlation matrix.  Each cell contains a correlation coefficient CoCo between the order-of-sin calculated by two different couples. A CoCo runs from zero [no similarity at all between the orders] to 1 [exactly the same order and <plagiarism alert!!>]
What this tells me is that Teams E, G and H have very nearly the same assessment of what constitutes plagiarism; while Team B has a radically different assessment from everyone else. Now it might be that Team B knows something that the others are missing but I'll stake €5 that E,G,H are correct in a Wisdom of the Crowds way and that the Bs are a bit lost . . . or wholly dishonest perps who shouldn't be trusted with the petty cash.

Wednesday, 28 January 2015

In Code

A week ago, I was writing about 6 young scientists who had made a difference . . . by having an idea and implementing it in the real world.  I had heard about them because they had won prizes for the efforts.  Three of these prizes were top awards at the annual BTYS science for youth affair that happens in Dublin every January.  The fact that each of these prizes were for projects concerned with feeding, housing and healthing the dispossessed was probably not entirely coincidental.  I don't think it is outrageous if clever ideas that leverage social good are privileged at these events.  On the other hand, I don't think that science only has value if it has a bleeding heart.  In any case, thinking about prize winning young Irish scientists brought to mind Sarah Flannery who won in 1999 with ideas that were going to be more valuable to bankers and MegaCorp than to people living a tent in a refugee camp. She went to the same school in Blarney Co Cork as Richard O'Shea who won BTYS a few years later - hmmm, maybe teachers do make a difference?! I wrote this for the Home Education Newsletter about ten years ago.

Book Review: “In Code by Sarah Flannery with David Flannery”
This is the true story of 16 year old Sarah Flannery who won the 1999 RDS Young Scientist’s Competition for her new and original take on internet encryption.  It is an inspiration to all of us who seek to nurture the natural talents of the young. 

It is not altogether surprising that Sarah made her contribution to scientific progress in mathematics.  She comes from a math-able family and her father is a professional mathematician teaching in Cork Institute of Technology.  Some of her ability may have been in the genes, but her interest in maths was doubtless fostered by a father who was passionate about his work. He is also obviously passionate about education.  In one of the stranger episodes in the story, the Flannerys meet a millionaire who “…mentioned that all his children had been educated at home before going to university.  That was something I knew would impress Dad a lot – let’s just say Dad has very unorthodox views on education.”  One of the Flannerys’ unorthodoxies is that there is a blackboard in the kitchen – which is the sort of furniture you’d expect to find in the cliché home educating family.  And it seems that the blackboard is used by them all to explain things and to solve problems and puzzles.  A key formative event in Sarah’s education was enrolling in her father’s CIT evening class in recreational mathematics. This course is filled with the interesting aspects of maths; the anecdotes; the history; the triumphs and unexpected connections.  In other words, all the bits that are left out of the Leaving Cert curriculum because it is too full of the boring and the examinable. 

While this may seem ominously like the hot-housing of a gifted child, it doesn’t read like that.  Sarah has gotten serious about maths because her home was steeped in it.  It’s really no more surprising than the fact that so many catholics are raised in catholic homes.  What is engaging and compelling about the story is the strong feeling that her pursuit of excellence came from something near the core of her being.  She came across a problem in cryptography, and was engaged by it.  She read in ever widening circles around the subject in order to understand it more fully.  She had certain key creative insights that add enormously to the coherence and value of this branch of her chosen science.  She wrote it all up and cared enough about it to go the extra step of making the abstruse intelligible to other people.  The part of her “fifteen minutes of fame” that she most relished was when she was treated with the respect of an equal by professional mathematicians, some of whom, as competition judges, were obliged to give her and her work a good grilling.

And while maths is very important to her, don’t imagine that she is a one dimensional person.  She has other passions including that peculiar affinity many teenage girls have for shovelling horse dung.  Just a normal girl, who taught herself to program computers and read articles as thick with Greek as a brack is with currants.

It is obvious that some folks who go to school get a great “home education”: by which I mean that they are given, or make, the space to grow to their full potential. Who knows what Sarah Flannery’s full potential is, but she certainly achieved something remarkable before she voted in an election.
- x -
Update in Wikipedia: like Emer Jones, Sarah Flannery went off to Cambridge and is now a software engineer.

Tuesday, 27 January 2015


I know a bit about cycling in the city; in the early 1990s we lived 12km North of Dublin and I worked in the very centre of the city.  Bus-service was iffy and using a car to commute was only really an option at nights or weekends when it would take about 15-20 minutes.  On my 6-gear pink road-bike I could do it in 40 minutes - much quicker than the bus in those days before bus-lanes. So over 5 or 6 years I clocked 40,000km in the traffic = the circumference of the globe. I won't exaggerate the accident that put a stop to me gallop as a Near Death Experience, but several bones were broken and my poor bike was pretzelled. I remember writing to my pal Oisin who was a) mad about the bike b) emigrated to Canada when 700m of cycle-path was opened alongside Fairview Park on my commute-route.  For the other 11300m of my journey I was still compelled to weave and jink between moving cars.

They do things differently in the Netherlands where to can cycle from Rotterdam to Nijmegen more or less on a dedicated Fietspad [cycle-path] a lot of it along the top of the dijks separating the River Maas/Rijn/Waal from the roads and farmland below.  In all the major cities, the three main users of the streets - pedo velo auto - have their designated space.  Where possible cars are separated from bikes by little kerbs or plantings of bushes. It is cycle-heaven. Of course this is helped by the fact that most of the Netherlands is flat as a pankoek.  But it took a huge political and economic re-think to achieve this two-wheel nirvana.

In the aftermath of WWII, the Dutch economy picked up on a re-building boom and real wages doubled in about 15 years. The newly affluent bought all the stuff that was becoming available and this created more jobs and the economy grew as capitalism desires. Cars were high on the list of items to be acquired and the infra-structure of many Dutch cities was stretched or smashed to accommodate all the vehicles, market squares became car-parks, roads were widened and a comprehensive system of motorways was constructed to link all the major population centres at home and abroad. If you had a car, you could aspire to a home with a neat garden in the suburbs. The average commute distance grew from 4km in 1957 to 23km in 1975.  You'd have to be bike-bonkers to undertake a 25km commute every day, so cars must have been part of this equation (although the Netherlands, in contrast to Ireland also has an integrated and functional public transport system). This all came with a cost, however: in 1971 there were 3,300 deaths on Dutch roads, 400 of them younger than 14.

One of those tiny tragedies was the child of a journalist who helped start the Stop de Kinder Moord [stop the child murder] campaign, which took to the streets, the airwaves and the print-media to demand that something be done about the slaughter. The oil crisis of 1973 providentially added an economic push to the band-wagon and Car-Free Sundays showed city dwellers what it might be like if cars were excluded from city centres. Propaganda movie. In the famous case of De Pijp the children of a crowded inner city district of Amsterdam took to the streets [L - "more play-space"] demanding the right the play in the streets the way their parents had. In the movie-clip you can clearly hear an angry van-driver being told that his stroppy behaviour is "Niet gezellig" [not nice]; being gezellig is deeply embedded in Dutch social consciousness. They are packed like sardines: 400/ so need to be more sensitive to the needs of others than in Ireland 65/ or Ukraine 75/

This grass-roots movement took on the tyranny of the car and the whole society started off in a different direction.  Many cities restructured the street-scape to allow for permanent cycle-paths and in Tilberg, the leading light, cycle-use increased by 75% having fallen by 6% over each of the previous 20 years.  I'll repeat: in 1971, 400 children were killed on the roads in the Netherlands; in 2010 it was 14! Everybody cycles - young/old; fat/fit; suit/shorts - and nobody wears a helmet. You can cycle holding hands. You can cycle carrying a bed, an umbrella, your kids, or some flowers.
 I've spent about a year of my life living in the Netherlands mostly in big cities (Dublin is bigger than Amsterdam, they are none of them "big cities" like New York let alone São Paulo) including Wageningen, Utrecht, Nijmegen, Amsterdam and Rotterdam.  Each town is civilised with its little neighborhoods and I just love the streets, they are so neat, so accessible, so fit for multiple purposes . . . so gezellig.

Monday, 26 January 2015

HomUncle Wilder

If you have to undergo brain surgery you'd probably be better off under the hands of neurosurgeon Henry Marsh than in the charge of a second year houseman. It's all about the experience that comes from doing things again and again (and making some mistakes along the way). When Mr Marsh is pushing into the slobber that makes up your central processing unit, the chances are that you will be under only a local anaesthetic.  This is made possible because the brain has no pain receptors, but using a local is not just to make the anaesthetist's job less complicated. Such a protocol also enables the surgeon to get feedback and direction from the patient and so lessens the chance of a catastrophic cut with his hardware.  This addition to the care and cure of patients is largely due to Canadian neurosurgeon Wilder Penfield, who carried out some of the pioneering work in the field of mapping the brain. Although his mentor Otfrid Foerster also needs credit. It wasn't solely in the spirit of investigation, it also told Penfield whether he was getting closer to the seat of the lesion he was attempting to cure.  This was all a long time before CAT scans and MRI.  It is probable that his wandering off target to see the wider picture would not pass modern standards of informed consent.

While Penfield had the lid off, he systematically stimulated the sides along a fold in the brain called the central sulcus [Top L across Penfield's head] and got the patient to call out where s/he felt the tingle (sensory) or which part twitched (motor).  After many operations, where the responses among patients was accurately reproducible, he was able to produce a detailed map of the brain's view of the body.  It was not quite as you might have expected. For example, your body is represented upside down with the head down by the ears and the toes poked down between the left and right hemispheres. The picture is symmetrical with the left hemisphere dealing with the right side of the body and the region devoted to the dominant hand is usually larger. The other finding that is less surprising with 20/20 hindsight is that certain small parts of the body loom disconcertingly huge on the homunculus that represents us in the brain.  The lips, tongue and hands are much more important in terms of the number of neurons that support them than the shins or feet.
Anatomists sort of knew this before Penfield because you can do a neat experiment to work out the density of sensory receptors on various parts of the body.  Get your guinea-pig to close her eyes and poke her with either one pin or two pins a known distance apart; ask her how many pricks she feels.  Two pins can be centimeters apart on the shoulders and still be detected as one event while two pins 1mm apart on the lips or finger-tips can be readily distinguished.
Knowing this map clearly has implications for understanding the phenomena associated with phantom limbs.  And while it is true that the penis is over-represented compared to the lower limbs it is dwarfed by the sensory importance of the hands. So, ladies, it is just not fair to say that men think with their penises: like you, blokes rely on their fingers. Wilder Penfield was born 26th Jan 1891 >!today!< in Spokane, WA and died in 1966 in Montreal, he was a pioneer of the then unknown landscape beneath the skull.  Hats off . . . so he can make the first incision?!

Sunday, 25 January 2015

Dydd Santes Dwynwen

If your last name in Jones, Williams, Davies, Evans or Thomas OR you had a traumatic encounter with a huge man in a kilt after a rugby match (*) you may not feel like celebrating Burns Night this evening with neeps & tatties or in any fashion at all.  Those five surnames take up 18% of the Welsh telephone directory. Today is Sant Dwynwen's day the patron saint of lovers.  There is no evidence that she or her bloke Maelon Dafodrill existed - legends about them emerge from the dark ages fully formed and embellished with imaginative detail; not all of it lovely. She may have hailed from Angelsey where the ferry leaves for Dublin and Dun Laoghaire and may have been a princess. The celebration of the day has been given a boost these last 10 or 15 years by Bwrdd Yr Iaith (Welsh Language Board) and you can now buy cards in the Principality to send to your inamorata.  Now you know me, I'm all for increasing the cultural diversity of this our over-burdened planet but does it always have to be monetised?  I get a particular bee in my bonnet about Father's Day in the middle of June, partly because it often eclipses my birthday, but mainly because it is a totally artificial modern concoction with far less tradition than Mothering Sunday.  Make that zero tradition beyond a board meeting at Hallmark Cards a couple of generations ago.  Few people know about the Roman soldier called Atrium Marcus who is the patron saint of gougers who'd like to make a fast buck out of a gullible public.

But I would encourge you all today, from Kinsale to Kiev, to turn to your mate and try "Dydd Santes Dwynwen Hapus" but possibly not while eating breakfast, hmmm? a spray of chewed toast is not going to help your case.  But b'god the Welsh can sing!

(*) Q. Is there anything worn under the kilt?
      A. No, it is all in perfect working orrrder.


We are down in Cork this weekend to visit Dau.II and see if The Real Capital is really the gastronomic centre of Ireland or if they should cede that, along with everything else, to Dublin.  The population of Dublin is now about 5 times larger than Cork and so has great Harry Potter winner-takes-all Total Eclipse potential.  We drifted into town on Saturday morning to check out, not for the first time, the famous English Market which was visited by Mrs. Windsor, the Head of State of the island next door in 2011.  There is much to be said for this institution - it is still, amid some pretty high-falutin' delicatessen, a genuine market where ordinary people go to do their weekly shop especially that part of which involves meat and vegetables. It is the only place in Ireland that you can regularly have choice in the matter of awfully good offal
  • tripe, the washed lining of the stomach, is absolutely standard fare, in umpteen variations, on menus in Portuguese cafes and restaurants but is foreign to most Irish larders
  • drisheen, a variety of blood pudding, is claimed to originate from Cork but is nowadays only of minority interest in Cork or anywhere else in the country for that matter
  • crubeens, pig's trotters, are greatly relished by The Beloved's mother who prefers to wrastle with her food but is more or less universally rejected by anyone under the age of 50: the pale things look altogether too biological
  • pork bodice are spare ribs in a long rack and rarely seen outside a Chinese take-away
  • ox-tail which makes such exceedingly good stews because long boiling works tasty miracles on the connective and nervous tissue of the diminishing run of vertebrae - but it looks too much like anatomy for most modern tastes
I'm sorry to say we avoided all these challenges and bought some excellent olives served up from a barrel with a big wooden ladle; two balls of delicate mozzarella; a sesame seed loaf, a handful of neat dolmades ντολμάδες; some hommous and a little pastry au choix for everyone in the party (in case we didn't have enough to eat!).  Then we went home and made an excellent lunch from our multinational fare.  Yum Yum.

But today is Burns Night the birthday of Rabbie Burns the poet of Scotland.  Just as Poles, Greeks and especially Montserratians wear a green tee-shirt on St Patrick's day, a lot of people with only  a tenuous connexion with Scotland will try a morsel of haggis on this day in late January.  Haggis is made from the 'pluck' [heart-liver-lungs] of  a sheep minced and mixed with oatmeal, onions, suet, salt&pepper and stuffed into a stomach, preferably of the same sheep. Genuine versions of this dish are disconcertingly biological with strings tying off the base of the oesophagus and the pyloric sphincter at the other end.  But it is tastey enough and traditionally served with plain potatoes and boiled turnips "neeps & tatties"  . . . and single-malt whiskey.  We can't say fairer than Rab Burns:
Ye Pow'rs, wha mak mankind your care,
And dish them out their bill o fare,
Auld Scotland wants nae skinking ware
That jaups in luggies:
But, if Ye wish her gratefu prayer,
Gie her a Haggis!
Offally good!

Saturday, 24 January 2015

Eleftheria terrae

I've been warning you about the imminent end of useful antibiotics as more and more pathogens become resistant to everything we have in the shot-locker.  It is decades since a really new form of antibiotic was discovered.  Big Pharma would much rather patent a me-too modification of penicillin than go out into the wide world and isolate a new bacteria killing bacterium.  One thing that puts a disheartening stop to any new frontiers gallop is the well-known fact that 99% of known bacteria cannot be cultured in the lab. We cannot make the environment on a petri-dish sufficiently complex to satisfy their fastidious requirements, that's why, for example, we call it Clostridium difficile.

Then 12 years ago Kim Lewis and Slava Epstein had a "b'god I wish I'd said that" idea and developed a product called an iChip (i as in isolation, Chip as in plastic sandwich for high-throughput data processing). Picture. This is what you do:
  • Dig up a trowelful of soil and wash off all the bacteria into a cup
  • dilute them so that each chamber in the chip has about one bacterium
  • seal the chambers with micropore filters that will allow soluble products in but keep stray bacteria out
  • pop the iChip back in the soil and see what grows
You can then take a pure sample of, say, 10 million of a particular never-before-cultured bacterium and plate them out with Staphylococcus aureus, the cause of MRSA and impetigo.  If the growth of S.aureus is inhibited you concentrate on that sample and try to chemically characterise the active principle.  Just like one of the early lab strains of E.coli was isolated from the back-passage of Andre Lwoff, so a lot of the soil samples came from the back-yard of Losee Ling, the Head of R&D at NovoBiotic Pharma, Lewis and Epstein's start-up company.

It turns out that this is a fruitful source of novel bacteriocidals, rather too fruitful in many ways because a lot of the Staph-killing products were detergents that killed everything, including human cell-lines. After a decade of bump-and-grind they have this month released details of a totally new way of killing gram-positive bacteria called Teixobactin isolated from a species they have named Eleftheria terrae. I've had cause to be snitty-snotty about the cultural shallowness of some American scientists when it comes to the naming of parts.  NovoBiotic have patriotically called their new bug Freedom [Gk] of the land [L.] but C.P. Scott, editor of The Guardian 100 years ago, was chilling "Television? The word is half Greek, half Latin. No good can come of it" in his deprecation of mixing Greek and Latin roots.  John Logie Baird sent the first (crap-quality) transatlantic TV broadcast in 1929, Scott died in 1932 before he had a chance to see how wrong he'd called it.

<geek alert>
Teixobactin (τειχω = wall) is a depsipeptide (new word for me): a compound made up of amino acids (some weird) in which some of the bonds in the chain are ester bonds not regular peptide bonds.  Like penicillin of old, Teixobactin prevents bacteria from forming a cell wall so that they leak out their innards and die.  But it's a totally different mechanism of interference in wall building and so will hopefully provide a few decades of tinkering about with the core idea to generate another family of related therapeutics.  Even now Teixobactin has huge therapeutic potential.  €5 says Lewis and Epstein get a Nobel Prize within the next ten years.

Friday, 23 January 2015

Young scientists: blooming marvellous

I was wending my way home through the near-freezing fog last night listening to Newstalk-FM and caught the end of an interview with the Nitrogenase Three from Kinsale, Ciara Judge, Émer Hickey and Sophie Healy-Thow, whom we met last Fall because they had made the cover of Time.  They were dropping in on the radio studio en route to an event with Michael D Higgins our diminutive but big-hearted President. They were explaining, ever so s l o w l y, that despite them not yet being eligible to vote they had discovered something new and interesting about the world  . . . and despite being told that their idea was nonsense because nobody [nobody adult, by implication] had done it before.  Why would we want to do the research if someone had done it before? was their perfectly legitimate response.  They won the  BTYS Young Scientists Top Prize in Dublin this time two years ago.

Let will serve to launch three other young scientist project
reports that I've had on the skids for the last couple of weeks.

James Roberts a student at Loughborough University in England recently won the James Dyson Award for Mom, a portable, inflatable incubator for keeping babies alive [L] in, say, refugee camps in Syria in the depths of Winter. As 150,000 children are born in such places each year with mortality between 15 and 20%, providing an affordable safe-haven for the newly arrived is clearly going to affect the quality of life of many families. Affordable? Maybe less so, at £250, in regions where families live on less than $2 a day, but still 100x cheaper than a regular maternity ward incubator in The West.  Cripes, I'll buy two and send them to Kurdistan.

A young man with handy hands who is interested in alleviating the plight of the dispossessed in distant places?  That had me dredging my memory for another BTYS winner Richard O’Shea, from Scoil Mhuire Gan Smál [School of Mary Without Stain or Mary Immaculate] in Blarney, Co Cork, who won in 2010. His contribution to human health and happiness is a biomass (dung and twigs probably) stove that is a) really efficient and b) virtually smokeless.  Lots of people in the third world die slowly [lung and esophageal cancer, bronchitis, TB, pneumonia] from smoke inhalation from cooking over a heap of sticks. Here he is [R with his two part stove and a Suit] wearing his school uniform and big smile. In this case, the apple falls not far from the tree because young Richard's parents met in Africa when they were both working in overseas development.  That's not to disparage in any sense his success, he clearly has it in him to a) care and b) do - but his parents maybe influenced the direction in which his talents drove him.

Emer Jones, BTYS winner from Tralee Co Kerry in 2008, was also probably influenced by her folks in that her father teaches engineering in the local Institute of Technology. Quotable Ralph Waldo Emerson said "Build a better mouse-trap and the world will beat a path to your door" Emer said something like Build a better sandbag and you'll have a door to your home to which the world can beat such a path.  After watching a documentary about poor people living in temporary accommodation following an earthquake, Emer started thinking and making a better sandbag, that wouldn't sag and collapse from the after-shocks.  Her final solution was a brilliantly "appropriate technology" solution to this third world problem. By driving two bamboo stakes crosswise through each sandbag she enormously increased the stability of the whole structure.  The protocol is so simple that nobody had thought of that before. Emer was only 13 at the time. Turns out that several years later, she clocked full marks on her Leaving Certificate and is now finishing up a degree in Natural Science in Cambridge.

With blooming marvellous kids [L Father Christmas agrees] like these walking tall in the land there is hope for the world.

Thursday, 22 January 2015

Furry bags of genes

Felis catus the domestic cat is handy for keeping down mice and less desirable for killing song birds but these are value judgements that we humans lay on the poor creatures according to how useful they are to us. An interesting and valuable project is being launched today here in Ireland that is based on the fact that cats come in a palette of colours and that those colours are largely determined by variants inherited in a 'simple Mendelian fashion".  The last phrase of jargon means that the genetics of cat coat colour is well understood and that you can tell which gene-variants a given cat carries merely by looking . . . with binoculars if necessary or even by microscopic analysis of a photograph that appeared on the front cover of Journal of Heredity. Almost all other species would require a blood- or DNA-sample to generate any genetic information.

This project is a good example of where a number of observations can be combined to yield some data. Q: "What is the singular of data?" A: "Anecdote".  You can't tell much by determining the genetic make-up of the cat next door; except to hazard a well-informed guess as to which of the neighbourhood cats were its parents.  But if you look at many cats, you can calculate what the frequency of the genes are in that population. This was first done in a scientific fashion by a student of J.B.S Haldane in 1947: A.G. 'Tony" Searle was tasked by the great man to sample the cats of blitz-damaged London as part of his PhD programme.  It turned out that there were a lot of stray cats on  bomb-sites and in SPCA shelters and, in short order, Searle had data on 700 cats.  That sounds like data but on another level it is also an anecdote.  It is just one dot on the globe with rather a lot of numbers attached to it.  A few years later, however, Searle was posted to Singapore and he dusted off his cat genetics tool-kit and found several hundred cats in the streets and bazaars of that outpost of empire . . .  

. . . and they were completely different from the cats of London. Not in the sense that they had extra legs or googly eyes but their gene frequencies were different. In post-WWII London, for example, Siamese cats were exotic and rare but in Singapore they were common as muck. Well, that's interesting: any scientist would start to ask questions:
  • What's halfway between Singapore and London? Ans: Kuwait
  • Will the frequency in Kuwait of, say, orange cats be the average of Singapore and London?
  • Would I expect the frequency profile in Kuala Lumpur to be  rather similar to Singapore's?
  • What about Australia?  hmmmm, maybe those cats would look more like London than Singapore despite geography?
  • Black cats in the tropics?  White polar cats with long hair?
Such questions spawned a cottage industry that covered large portions of the globe in the 1970s and 1980s.  In my callow youth, I was part of that project and it got me an education, lifelong friends and loadsa data.  The data that came in were idiosyncratically patchy: New England, Brazil, Scotland and the Netherlands were exhaustively covered but Africa and Spanish South America were blank.  It all depended on who was prepared to make a run for it in a particular region.

Aoife McLysaght, in conjunction with the Irish Times, is taking up the baton today to bring the field of cat population genetics into the crowd-sourced 21st century. By making it easy for Sean O'Public to contribute a genetic diagnosis of the family cat, they hope to get a mountain of data from across the country and see whether the 40 year old findings in Donegal have held up to the buffets of evolution.  Here's the lead article in the Irish Times which includes an embedded link to a simple web-form that will enable you, or your class at school, or your scout-troop to contribute. One of the questions will allow them to tie your data to a particular county.  This follows an honorable tradition in the footsteps of George Dawson Ireland's first Professor of Genetics who surveyed the country's human inhabitants w.r.t. their ABO blood groups back in the 1950s.  He went to the Blood Transfusion Board and lifted data for something in excess of 150,000 people (1:18 of the whole population) and calculated the frequencies for each county.  Like Searle with his cats, Dawson was gratified to find that there were slight but statistically significant differences in ABO frequencies in the West of the country compared to Dublin.

And what about Ukraine?  A parallel project would mobilise a lot of youngsters into doing some real science.

Wednesday, 21 January 2015

Don't do as I do, do as I say

Not owning a TV, my access to news is limited and parochial.  I get 30 minutes of Newstalk-FM on the drive into work in the morning and I get to hear whatever is floating the boat of Ivan Yates and Chris Donohue.  Often good copy for The Blob. A few days ago I was reading part of the backlog of Natures of which I have a substantial unopened pile and found an article about Jerry Brown, Governor of California. I was brought up all standing because I remembered a Jerry Brown, Governor of California, [R, 1976] way back in the 1970s and I knew my Nature-backlog didn't go back beyond 2014.  It turns out that, having been Governor [D] of the Golden State from 1975-1983 (preceded by Ronald Reagan) and having a shot at the Presidency vs Jimmy Carter/Gerald Ford in 1976 and Ronald Reagan/Jimmy Carter 1980 and against George W. Bush/Bill Clinton in 1992, he has been back as Governor since 2011.  He was born in 1938, so is no longer young but attracts a rather fanatical loyalty among his supporters.

The article in question was about Governor Brown getting agitated about climate change and eliciting some science from a couple (and Couple) of palaeoecologists Anthony Barnosky and Elizabeth Hadly who worked at UC Berkeley and had recently published a paper in Nature about climatic tipping points. Brown the consumate politician wanted Barnosky and Hadly to re-write their findings in words that politicians and voters could understand.  It was an transformative experience for the boffins because re-languaging forced them to re-consider some of their certainties.  It also showed them that they owed tax-payers an explanation for how the public's supportive $$$ were being spent.  And, surprise!, their Outreach statement had far more impact than their original scientific paper.

But in among the feel-good I found this WTF? statement: "One day they got a call asking for hard copies of the consensus statement that the governor could take to southern California for a meeting with President Obama and President Xi Jinping. They went to a printing shop, ran off two dozen copies, then Barnosky and his daughter drove the reports to Sacramento, a six-hour round trip."  Only in America could it seem normal that a six-hour car-journey was an appropriate way to get a PDF from A to B. I'm missing some info because Berkeley-Sacramento is only 125km. The Americans invented the interweb but they're wedded to their wheels. Neither is the irony of a gas-guzzler delivering dire forecasts about global warming lost on me.  That Governor Brown has some charisma.

Tuesday, 20 January 2015

The left-hand of benthos

When I was young, I was a fussy eater, but could be relied upon to eat enormous amounts of the few foods that passed muster (and pass the mustard). When the family ate out, which was rare enough in the austere 1960s, plaice and chips was an item on most menus and I could be relied upon to choose the familiar rather than trying something a) new b) more challenging; but, hey, I was only fourteen.  So I must have eaten a lot of plaice Pleuronectes platessa in my day.  I knew they were flatfish: hard to escape that knowledge as they were eaten skin-and-all, so were clearly not a fillet or if they were filleted it was clear that there was a black side and a white side.  Yum yum, aNNyway!  When I grew up and left home it was treat to buy a bagful of dabs Limanda limanda for half-nothing because Irish people at that time wanted their fish in big slabs - preferably salmon Salmo salar.  But they're wrong as well as boring in the choice.

One of the peculiarities of dabs and plaice  . . . and halibut Hippoglossus hippoglossus, sole (common or Dover Solea solea; Lemon Microstomus kitt) and turbot Scophthalmus maximus, apart from being moreishly tasty, is that they are flatfish which spend their adult lives on the sea-floor but start off as planktonic hatchlings being woofled around the ocean by the currents.  As fry (juveniles) they look like regular fish with eyes on both sides of their head (so they can see predators and take evasive action) but as they grow up a remarkable developmental transition occurs as one eye moves across the top of the head so that they both finish up looking more or less in the same direction.  Simultaneously, the now adult fish drops out of the water column and settles to the bottom, where it spends the rest of its life scarfing up crustacea worms and molluscs and growing to enormous size over many years.  The record for halibut is a fish 2.5m long weighing 230kg: that's a lot of fish-fingers. Clearly that's a double transition that needs to be quite well coordinated - a free-swimming fish with a blind side will soon be dinner for something else but there's not much to see if one eye is permanently embedded in the sand. The other coordinated change is developing a camouflage pattern topside and depigmenting the underside. 
Footnote: if you for "halibut fry"
all you get is pictures of batter.

All the species eaten above are right-eye flounders of the family Pleuronectidae which comprehends about 100 distinct species in total. They lie on their left side and have two right eyes. I say distinct species because the biological species concept of Ernst Mayr defines species as "species are groups of interbreeding natural populations that are reproductively isolated from other such groups". Species are thus the only biologically meaningful item in our classification schemes for making sense of the living world. Fish breed by shedding sperm and egg into the water and hoping that they make contact.  The developmental genetic instructions are likely to be fatally scrambled if sperm from one species meets an egg from a different species. But it turns out that, in the Baltic, viable offspring are found whose parents are plaice (Pleuronectes platessa) and flounder (Platichthys flesus).  Not only different species, but different genera (the classification level up) as well!  That calls out to be investigated.

It turns out there is also another distinct group within the same order Pleuronectiformes which are left-eye flounders Bothidae.  These lads lie on their right side and have two left eyes. There doesn't seem to be any genetic, developmental or evolutionary advantage to being lefty or righty and occasionally you'll find an individual of one species that has flipped the 'wrong' way. The completeness with which the roaming eye migrates varies among the species. Some flatfish can also change colour to match the background like a chameleon. And I should add that rays and skates of the super-order Batoidea related to the shark family are also bottom-feeders that hug the sea bottom, but become flat by spreading out rather than turning on their sides.  Evolution has many ways of cracking essentially the same nut.
More on Southpaws.

Monday, 19 January 2015

Primum non nocere

"If the patient is going to be damaged, I'd rather
let God do the damage, than do it myself.
That's a very on-the-button dilemma for those "in charge".  When I was young and foolish, we didn't get The Boy immunized, either for MMR (measles-mumps-rubella) or DPT (diphtheria-pertussis-tetanus) and in due course he got measles (aged 2) and whooping-cough/pertussis (aged 12). When he arrived in Boston aged 5 and enrolled for a Community Health Plan, the medicos were shocked that a white, middle class child had contracted measles. We had some woofle-think arguments in favour of the no-vaccinate position but it basically came down to not wanting to take responsibility if he turned autistic from his MMR - preferring God-given blindness, deafness and more serious brain damage from his not-MMR.  20 years later, we had grown up and got the girls the full set of shots - didn't prevent Dau.I from getting mumps as a teenager though!

I got a late Xmas present from my mother Do No Harm: Stories of Life, Death and Brain Surgery by Henry Marsh, neurosurgeon. The title is derived from the Hippocratic Injunction primum non nocere [above all do no harm] which is not in the Hippocratic Oath and indeed seems to have been conjured up in the mid 19thC by Dr. Thomas Sydenham. The reason I have that header-quote is because it was advice or a musing given to Mr Marsh by his neurosurgical mentor. I've been ripping through it: the last book I finished Nate Silver's Signal and Noise took me 10 months. S&N was good stuff: chock-full of interesting and thought provoking material but I could put it down.  It's interesting that DoNoHa has no illustrations: the writing is so lucid that you don't need a picture to save 1000 words.  And this is not to say that the language is for reading-age=7; the horrendous tumours Marsh has dealt with are all properly labelled and acronymed and adequately described. I had to look up wikipedia, though, to find out why ITU is his preferred acronym but used interchangeably for Intensive Care Unit (answer: Treatment)

The neat little chapters each start with a medical war-story and use that as a springboard to further discursions on matters that engage the great man. Rather like the small but perfectly formed radio-essays by Alistair Cooke. Some of the themes:
  • Compassion vs Detachment. Surgeons don't operate on their own family because their judgement is sure to be clouded by their anxiety to Do No Harm.
  • In obtaining informed consent, you can tilt the discussion by saying that intervention may lead the patient to be disabled which guilts the family into believing/asserting that, of course, they will look after the damaged goods (forever!). That makes it emotionally easy for the medics and usually leads to them doing something OR you can ask "what would your boy want (for himself and for you)" which leads to a difficult and prolonged discussion to resolve the competing emotional needs of parents, siblings, wife, children and sometimes falls in with Hippocrates by doing nothing.
  • You should never allow anecdotal thinking to cloud your judgement - just because you've been caught once by a vanishingly rare concurrence of circumstances and killed or 'wrecked' your patient does not make those circumstances more common or likely.
  • After an explanation or a discussion, either brief or prolonged, nobody reads the multi-page informed consent form before they sign it.
  • Moral hazard abounds in  the National Health. If the patient or the relatives insist, an expensive and medically doubtful procedure may be carried out in order to prolong life for a few weeks or months.  As no new surgery can be carried out unless a post-operative bed is known to be available, 93 year old Mrs Doohickey's biopsy may block the prerequisite emergency admission bed for, and so condemn, a young wage-earner with school-age children.
  • Mistakes in surgery are usually mistaken decisions rather than slipping scalpels or operating on the wrong leg. In neurosurgery, the key is knowing when to leave well enough alone: going for the last tricky bit of adhering tumour is what rips the artery.
  • You never get any experience if you do nothing. 
  • Young doctors do not get sufficient experience if they are compelled to work less than 48 hours in a week by a European Working Time Directive EWTD. Young Marsh worked 1 in 2 as a trainee doctor: on top of a working week he was on-call (sleeping in his clothes) every other night and every other weekend to be available for about 120/168 hours.
  •  Experience is built on mistakes [L view of Mr Marsh's St George's Hospital from where much of his experience is laid to rest].
  • EWTD might result in more coherent decisions by doctors who are not woozy from sleep deprivation but it makes a monkey of continuous patient care: nobody really knows the base line status of patients in A&E or on the ward if they haven't been on the firing step for long enough to establish the base line.
  • Ethics is hard
Listening to Mr Marsh talking about his book to medical students at UCL is a long hour well-spent (it will save you having to read the book if you're very busy-and-important). In the final Q&A session he shares a favorite analogy to show just how crude are the surgical tools at his disposal: one of his standard slides contrasts a pin-head with the bucket of a bulldozer which he claims is in the same proportion as his finest 2mm micro-surgical probe compared to the 1µm width of a single neuron. In all my classes I emphasise these questions of scale to help students appreciate relative size - an essential prerequisite for getting a feeling for the organism.  You can find other reviews of the book in all the British broadsheets.  You should think about reading this book even if you don't have a brain tumour.

Sunday, 18 January 2015


You know you shouldn't pick at scabs but it's very difficult to refrain.  It's even poorer form to pick at somebody else's scabs, but sometimes you just can't stop yourself bringing up an issue which others would rather keep buried.  I'm here (or rather there - waaaay out beyond the orbit of Neptune) because of the Galileo/Marius priority spat 400 years ago.  You'd think we'd left all that ego and aggro behind in modern civilised gentlemanly science, but we haven't. Science is about discovering something about the Universe . . . which nobody knew before.  We could, with advantage, spend much more time verifying or replicating or contradicting other people's work but it's much more exciting to find the next new thing. And there's no money to be had for tidying up what we all already know.  This is part of the reason whyIt ain't what you don't know that gets you into trouble. It's what you know for sure that just ain't so.” can remain in textbooks for so long.

Mike Brown is an astronomer from Alabama who is currently on the faculty at CalTech.  His career choice may have been tilted by attending the  Virgil I. Grissom High School which was named after one of the more colorful astronauts on NASA's Gemini program. In the early part of this century, Brown was concentrating on locating objects at the edge of the Solar System beyond the orbit of Neptune aka  trans-Neptunian objects (TNOs) or Kuiper Belt Objects (KBOs).  Knowing that scientific credibility depends on having a three-letter acronym (TLA), Brown and his colleagues David Rabinowitz and Chad Trujillo called themselves “Three Guys at a Telescope (TGT)”.  Their business plan was to program the Mount Palomar telescope to take three consecutive photographs of the same patch of sky and see if anything had shifted in their three-frame movie.  Computers had cranked up the throughput, but it was the same fundamental technique that Clyde Tombaugh had used to discover Pluto in 1930. It took 2 generations before David Jewitt and Jane Luu (who won the Annie Jump Cannon award in 1991) from Hawaii discovered a second TNO called "(15760) 1992 QB1". The boys from CalTech had been massively successful, finding at least 11 TNOs between Christmas 2001 and Christmas 2004. On 28 December 2004, TGT found another object which they nicknamed Santa and decided to work on establishing its credentials (mass, diameter, orbit, atmosphere etc.) with a view to publishing at a major conference in September 2005.  In order to register for the meeting they submitted an abstract to the conference organisers in July. They were gutted to find that they had been scooped when a week later Pablo Santos-Sanz and Jose-Luis Ortiz of the Instituto de Astrofísica de Andalucía in Granada, Spain announced on 27 July 2005 that they had located the same object on some old pictures.  Brown bowed to this gracefully and conceded defeat on Santa "(136108) 2003 EL61", not least because he had discovered two other TNOs within a few weeks which they had designated Xena (the Warrior Princess) and Easterbunny (because it was found just after Easter). Clearly they were dredging the depths of American culture for name ideas.

But a series of unfortunate events revealed that the traces of CalTech's primary data for the discovery were in the public domain on the interweb and access_log records showed that someone from Granada had downloaded the numbers between the publication of the CalTech abstract and the announcement of discovery and establishment of priority by Ortiz.  The event-train was precipitated by Brown googling (as you do) "K40506A" - their official code for Santa. Caltech called foul, Granada said they had merely been verifying their discovery to make sure it was correct.  At The Institute, we are very strict on acknowledging sources and it looks like the Spaniards were a little slacker about this than we'd like to find among our students.  But then again, if I could read Spanish better, I'm sure I could find evidence that it was another example of Yankee-dog cultural imperialism. But if Ortiz is claiming by precovery, he needs to cede priority to people who took photos of Santa/Haumea from Palomar Observatory all the way back to 1955! Since Ptolemy and Eratosthenes everyone with two good eyes could see Uranus in plain-but-faint sight but it took the Herschels to recognise it.

Brown and Co. settled down and moved on after a while and renamed his three new planets with more gravitas: Santa to Haumea; Xena to Eris; Easterbunny to Makemake (Easter Island deity!).  Eris turns out to be the biggest of a current count of 1500 TNOs. But I don't think the wound really healed and ten years later Brown was after Ortiz again with "this hurts me more than it hurts you" head shaking post in which Brown finds Ortiz going a step beyond what the data is capable of supporting. I think it is not bitter-and-vindictive sniping: the TNO world is vast out there but small and exclusive here on earth and if you're in the club then you read everything by friends-and-rivals with care and attention. It's actually a rather good anecdote about how science makes progress by pushing out and rowing back.

The discovery of Haumea, Eris and other lumpy objects beyond Neptune led to the demotion of Pluto to a dwarf-planet or plutoid. Brown writes in an engaging gallop and if you can find his book "How I Killed Pluto and Why It Had It Coming" cheap, it's probably worth reading. You can hear Brown defend his position as Mike the Pluto-killer.  He'll have to be circumspect in what he says about Nibiru, lest he be taken out by the shadow government

I'm a little bit embarrassed to report that in a previous life beyond my two-week event horizon, I was onto the same story a year ago, from a slightly different angle.

Saturday, 17 January 2015

Paco el de la bomba

Francisco Simó Orts was a humble prawn fisherman from Murcia is SE Spain. After 17th Jan 1966 he became known and renowned locally as Paco el de la bomba, and eventually secured a fortune in the process.  On the fateful January day, while Simó was put at sea fishing, the USAF were playing with matches (tsk!) in Operation Chrome Dome.
This was part of a cunning plan to ensure cold-war ascendancy by maintaining fully armed B-52 [L] bombers continuously in the air within striking distance of the USSR.  Except where depopulated Alaska comes perilous close to depopulated Siberia, the USA is a long way from the USSR and it was at the edge of technical engineering capability to fly the heavily laden bombers such a distance on the amount of fuel they could carry. The cunning plan accordingly required mid-air refuelling.  Air-travel is, in terms of passenger miles, the safest form of transport that we are likely to encounter.  But if you are in the air for an infinite amount of time there is certain to be an accident.  If the engineering is pushing the envelope then it's more likely that something will go wrong, somewhere in the system. There were 5 military nuclear mishaps in 1950 alone, only counting those involving the USAF and only those over North America or the adjacent ocean. We know nothing of the parallel cock-ups that were happening in the USSR and may speculate that Things Happened further away from US sovereignty which the New York Times didn't need to know about. And it was all hideously expensive: in today-money, it cost about $10,000/hr to keep these monster planes in the air. B-52s have the same wing-span as a 747.

On the day in question, the B-52 required two aerial refuellings and on the second of these the plane managed to rear-end the K-135 stratotanker which blew up and carried away the left wing of the B52.  Remarkably 4 members of the crew were able to parachute to safety; everyone on the tanker died in the conflagration. The four surviving crew floated to earth: three drifting out to sea. Four armed-and-ready nuclear bombs also came down: three just outside the village of Palomares in Eastern Andalusia where two exploded, while the 4th drifted out to sea on its parachute.  It took 45 minutes for the last ditched flyer to be picked up - by Francisco Simó. 

The explosions on the ground had not initiated a chain-reaction but had nevertheless blurfed radioactive plutonium over at least 260 hectares of tomato farms, woods and residences. The cleanup required 6,000 250lt barrels full of grossly contaminated topsoil but areas with lower levels of radioactivity were simply ploughed to shift the glowing bits initially out of sight.  It has to be said that, although you can still find snails that cause Geiger-counters to fizz, there is no evidence of cancer clusters amongst the human population. That should give pause to people who still want to blame fall-out from Windscale for a cluster of Down's Syndrome in County Louth.

The US authorities were happier engaging in the tech-happy problem of locating the 4th bomb than in the tedious business of bagging and shipping tonnes of contaminated soil. In Franco's Spain, it was largely a public relations exercise. But finding the lost bomb before the Russkies sent out their own subs was a matter of high priority. The USN deployed two dozen USN ships and thousands of crewmen to quarter the sea-bed looking for a very large hot cigar. They invited Simó the eye-witness to accompany their search vessels, paying him 8000 pesetas/d [~= $130] which was much more than he got from shrimping. Nevertheless it took two months of fruitless scuba diving before they brought Bayesian statistics into the equation and realised that Simó's testimony pointed to a different, deeper, area of the sea-bed. On St Patrick's Day 1966, the DSV Alvin [L] located the errant bomb 800m below the surface and started lifting it.  Someone dropped the ball >!oops!< however, and the prize plummeted to the bottom again. It wasn't until 7th April that the bomb was secured safely aboard USN Petrel.

Sr. Simó was given a medal at the American Embassy in Madrid but felt hard done by and eventually secured the services of an American lawyer and former Attroney General called Herbert Brownell . . . or Brownell hunted down the contract from Simó in search of his cut.  The law of the sea says that, if a witness provides information that leads to the salvage of sunken ships, then s/he is entitled to a percentage of the proceeds; usually a token 1-2%.  As the bomb was bloat-valued at $2billion, Simó and Brownell made a case for a token $20 million.  The USAF settled out of court for an undisclosed sum.

Friday, 16 January 2015

A lot to be said for it

A few milestones have been passed on The Blob Science Matters since the turn of the year.  The gauche post below about micreabhitheolaithe ciotógach was actually the 800th to go up. 60,000 page views is in the ha'penny place but I'm still plugging away generating copy expecting to go viral like Justin Bieber any day soon . . . I'm working on the daft haircut. Obsessive record-keeping indicate that I've written half a million words since this voyage started on 6th January 2013: that's almost exactly midway between Lord of the Rings and Война и миръ, but without either War or Peace. Hang in there, it can only get better after Borodino.

micreabhitheolaithe ciotógach

I have something to offer! Only left-handed microbiologists who live in Ireland need apply, and I've titled the post thus to stop any idle butterflies flitting in from the interweb looking for a bargain.  In the process I've created an Irish googlewhack:
Your search - micreabhitheolaithe ciotógach - did not match any documents. 

It's all because teaching at The Institute has got into gear after the Christmas break and I'm back in charge of Third Year Food and Fermenation Microbiology aka F&F. We've got 5-6 weeks of isolating and characterising the bacteria that impact on our lives. After a month of food-spoiling Pseudomonas and another of food-making Lactic Acid Bacteria LABs, we're now getting down to Enterics - including Salmonella, Escherichia, Vibrio cholerae. All of these have a tendency to induce runs-in-the-family. The first day in any such venture is devoted to preparing petri-dishes [plates] full of colorful gloop that will either support or not support the growth of particular bacteria; or change colour in their presence.  Ten students in the room, 5 media to prepare, 5 batches of plates for future use: work in pairs, so.

With two years of Institutional experience, I'm getting less terrified of the autoclave - the industrial pressure cooker that sterilises the media and so I make a point of handing off responsibility for loading, setting, timing and stopping it onto the students. Indeed I formally appoint each student in turn either Autoclave Liaison Officer ALO or Assistant ALO AALO; sounds like a sit-com. Everyone wants to get through this infrastructural plate-pouring necessity as quickly as possible - the exciting stuff happens next week when we start streaking samples out and analysing the results.  When the autoclave has been through its 15 minute sterilisation cycle, the bottles of agar are ready to pour but still piping hot, so you need gloves to lift the bottles out . . . or wait 30 minutes for the cool-down. There is drawer in the lab marked [heat-resistant gloves] and there are 6 or 7 hefty industrial-quality leather gloves in there but only one will fit a right-hand. Our students are no more cacky-handed than the general population, so this asymmetry of supply is not to accommodate them. It's because the right-hand gloves of each pair bought has been worn-out through use, turned ragged and thrown away. That's about right: 10% of people are southpaws, citeog, лівша, sinistrorso [It. note the similarity to our sinister], gauche [Fr. another loan-word in English with neg. assoc.].  Indeed, almost all languages diss the left-hand of darkness and associate left-handers with clumsiness, stupidity or consorting with the devil; except Greek where αριστερόχειρας means elite-handed from the same root as our aristocracy.  Hmmm, that's interesting.

ANNyway, if you, Dr Left, have a drawer full of surplus-to-requirement right-hand heat-resistant gloves, don't put them up on e-bay. We'll swap as many left-hand gloves for your righties and we'll pay the postage . . . both ways. It's going to be easier than I thought: there is a trade where the left-glove wears out quicker that the right - welding. So much so that you can buy a left+left pair of welding gloves [L!].  It's going to be much easier to find a welder than a left-handed microbiologist.

Thursday, 15 January 2015


Storm Rachel came roaring through here last night.  It started sounding buffetty around 2000 GMT and so I started tuning into Alan O'Reilly's CarlowWeather twitter-feed, which may drop 140 word sound bytes but also a rash of great data-rich pictures.  Ireland is hiding in the SE corner of this picture below the skirts of a classic anti-cyclone storm clipped from CarlowWeather.  Looks dynamic, no?  Even in a static picture!
Here's two consecutive clips from's rainfall satellite showing the squall-line whisking across the country from the West heading for the Irish Sea and Britain. If you've ever hung laundry outside in Ireland, you really need to tune into this site which gives the rainfall over the previous 4 hours at 15 minute intervals. It says: stair-rods; cats&dogs; incommming in, say, ten minutes.  So you can be like Francis Drake and finish your cup of tea before departing outside to save the sheets from getting an extra fresh-water rinse.  The rain-radar has also helped choose when to do field work for science.
 This is what things look like this morning.  It gives you a sense of how big an anti-cyclone is: Ireland is 500km from N-S.  15,000 homes are without power, including 1300 in Tullow Co Carlow where CarlowWeather monitors the meteorological situation and shares it with the world (Cheers Alan!). The storm is still whupping the NW of the country, so as one problem gets fixed a tree will fall across wires somewhere else in the forest.  RTE reports that several mobile-phone masts have ceased transmitting.

It's two years and four days since the Real Rachel (Rashers-the-dog) left us.

Wednesday, 14 January 2015

Litter in yUK

I spend over 2 hours over the weekend watching (entranced) a UK parliamentary committee hearing.  It wasn't exciting in a car-chase sort of way but it was just great because you could see that people were being compelled to change their minds by the quality of the evidence or the quality of the discourse or both. And the subject of all this engagement?
If you haven't got time, you can read the executive summary in the Grauniad, but you'll miss a lot of the to-fro and the interesting nuance. The deal is that an all-party committee of MPs meets in a room in Westminster and asks interested parties to come make submissions and subject themselves to questions from the parliamentarians.  In the panel is the Tory MP for Harrow East, Bob Blackman, whom we've met before being (dis?)respectful of St Nelson of the Mandala. On the other side are representatives of BigTobacco, MacDonalds and the people who make McDonalds' packaging, the Chewing Gum lobby, Our Lady of Incpen and bizarrely David Sedaris the humorist and commentator.  Sedaris is there at his own request because he spends several hours a day, after he's done his quota of writing, picking up trash in the second most ritzy community in England (Horsham in Sussex, as you ask, second after Winchester).  If you do gird up your loins to watch, note that Sedaris, Tobacco and McDs have the first hour and then are rotated off to give the other experts a chair. What I like is that the boogies of Tobacco and Fast Food Megacorp have articulate, well-informed and reasonable spokesfolk who see off the superficial certainties of the MPs and force everyone to think a bit about how to achieve the aim of Less Litter, rather than scapegoating the low-hanging burger-tray and feeling smug.

The California State Legislature, facing a drought crisis far more serious than a bit of litter in the hedgerows, want to fine their citizens if they waste water.  But it turns out that this, in the best conceivable case, can only save 3% of the water they have left - there are bigger fish to fry. As it happens 3% is the amount that fast-food packaging contributes to the litter-stream, so demonising McDs (where the poor people go to eat) is both unfair and minimally productive. It turns out (whoop whoop data alert) fast-food restaurants contribute an average of £9,000 per premises per year in cleaning their local environment, and they don't ignore cigarette-packets or sweet-wrappers as they pick up the stuff their own customers have left on the street.

The quango KBT, Keep Britain Tidy, decided a year ago that they were too clean to talk to Big Tobacco and the Local Government Association also holds this complacent attitude in their Local Government Guidance on Tobacco Control.  Tobacco is profitable and they know they have a crap PR image to counteract, so they're prepared to put money to encourage their clients to tidy up after their fix but nobody will engage with them. And if you think about it, as 80% of the cost of cigarettes goes to the government in tax, you'd excuse The Gaspers from saying "I gave already" and let The Government clean the pavements and provide stubbable litter bins. Obviously you can't look at tobacco solely through litter-tinted spectacles: we probably all want to discourage people, especially the young, from smoking; and pricing, taxing and rules of engagement can impact on this side of the problem. But it was salutary to watch the Tobacco-Guy patiently adopting the high-moral ground. If you'd rather watch Thank You For Smoking (92 minutes) that's fine (and damned funny) too, but over-dramatised.

Chewing gum has a case to answer as well: it costs the UK £50m/yr or 8% of the environmental cleaning budget to remove chewing gum warts from the street (nobody dares look at the underside of the tables in Jolly Fastfood).  But the Wrigley's rep was keen to do her part on behalf of the industry and at least local and national government will talk to them and have a mechanism for accepting their financial and problem-solving contributions.

A solution of hypothecated tax (a tax that is ring-fenced to deal with a particular problem) to which the MPs kept on coming back was roundly dismissed by the panel of interested parties.  If you directly add a tax/levy on something, there is evidence that you may paradoxically increase the amount of it that you find in litter because punters will think "I've paid already to have someone clean this up".  The story is analogous to the famous case where Israeli creches fined parents who were late in picking up their darlings.  It was wholly counter-productive as parents told each other you could pay a little more and get an extra hour at work/shopping.

But the best copy in the committee hearings comes from David Sedaris, who is clearly highly engaged, not to say OCD compulsive, about trash. He cited a Red Bull ad showing a newly stoked consumer casting the empty tin energetically over his shoulder and said that Red Bull and Lucozade [R] were major contributors to his trash-bags.  He held his ground when he was questioned for suggesting that the poor generate more litter and said that Tesco [cheap] bags outnumbered Waitrose [dear] bags by dozens:1 and he'd yet to find old opera tickets or macadamia nut cartons.  He also suggested that the authorities should set up road blocks and fine anyone who was driving a car with a spotless interior. More seriously, he reckoned that a series of ads exposing litterers to ridicule might make them wake up to what they were doing to the environment we all share.

For sure, litter is less important than genocide or human trafficking but it affects us all and desensitises us to worse crimes and public order offenses.  Part of the solution is education and in my educational institution I never see anyone except me picking litter off the floor in the corridors and class-rooms. The goddammed discarded cardboard coffee cups are everywhere and often still half full. Litter-people will have to take care or Conscience Girl will get them.  That's the stick; but there is carrot. Yesterday, I picked up a scrap of paper from the main science corridor at The Institute and found that it was a multiply-folded €5 note. Win! First homeless person I see gets it.