International students

Flags are not unequivocally A Good Thing: national flags tend to get owned by extremists.  I grew up in Britain and the only people I knew who would sport the Union Flag without irony had fought in Korea or WWII or were either members of the National Front. I mentioned flags going up Vimy Ridge in 1917 with the Canadians and had some harmless fun thinking about what the Irish flag might look like if the Vikings had maintained a better toe-hold in Waterford. ANNyway, flags are not totally foreign to The Blob, so I make no apology for displaying a few on the left.  They are there because yesterday was International Day at The Institute. and this is about 1/4 of the nations that are represented in the student body.  NL TR ES OM KR IN as a clue to those who failed Vexillology 101 && are better at top-level internet domains.  It's a fair representation of the diversity although all continents are represent somewhere in our community.

Yesterday was just wonderful because of two anecdotes (which don't make a dataset). As I came back from class in the morning, I noted that India had acquired two noticeboards behind their husting and made some comment to the lads manning the booth.  Quick as you like one of them said "We have a lot of people in India" to which I replied that the Chinese were 6 meters South and they could manage with one board.  Another chap put his arm round the shoulder of his pal and said that he was from Pakistan but had thrown his lot in with the Indians because there were only 4 or 5 Pakistanis on campus and they had, this year, been snowed under with assignments and exams.  I was quite affected by this casual statement because people have been killed in Indo-Pakistani conflicts in 1947, 1965, 1971, 1999 with stand-offs and shape-throwing in 1986, 1987, 2001 and 2008, not to mention the perpetual simmering aggro over Kashmir.  I quipped that the (articulate, sunny [and probably Sunni too ho ho] and clearly intelligent) young man would be the next President but three back home in Pakistan.  It's not impossible to imagine that an Indian friendship forged in Ireland 3 decades before would open up the dialogue to avert a nuclear meltdown on the subcontinent in 2043.

Later on I was roused from reading a pile of lab-books by a blare of Latin American music and went out to the balcony to see the Brazilians showing that their hips move.  I was standing next to one of the porters and I told him my morning's tale.  After another set, he turned to me and said that this multiculturalism (nods downwards) was just berluddy marvellous and not before time.  So we agreed that bacon and cabbage was all very well but it was just great to have the option for kielbasa and chicken balti.  I think we both felt a certain pride to be working in an Institute that was enabling something so important. Tomorrow I'll have my last classes which include two pairs of French students.  They've been with me since September but return to their home college in Paris after Christmas.  They've brought a different way of writing their lab reports which I'm going to implement next year and have generally and in every way been étudiants formidables - they've been good for us all.  

Bon chance les mecs!

First catch your harebell

I've had two first year Biology lab sections to play with since September and I've had a lot of fun.  I think they have too.  On Monday morning after my first class I thought I'd check in to see what was on for Biology between 3 and 5pm that afternoon and I discovered that the material laid out in the manual was definitely not laid out on the bench. I believe standard practice under those circumstances is to shrug, apologise to the students and cancel class. We were meant to be looking at the anatomic structure of flowering plants, specifically comparing dicots [two seed leaves, leaves with netted veins, flower-parts in 4s and 5s - such as anenome (Ranunculus nemorosa), ash (Fraxinus excelsior), daisy (Bellis perennis)] with monocots [one seed-leaf, parallel-veined leaves, flower-parts in 3s and 6s -like bluebell (Hyachinthoides non-scripta), wheat (Triticum aestivum) and ryegrass (Lolium perenne)].

Eeeee when I were a lad, bluebells were called Scilla non-scripta. My first bio-mentor Mr Wilkinson told us that it was so named because the early taxonomists were trying to recreate the Utopian world of the Classics before the Dark Ages had obliterated 'civilisation'.  If some plant was mentioned by Aristotle, his successor Theophrastus Θεόφραστος (author of Enquiry into Plants Περί φυτών ιστορία) or in Apicius' On Cooking De re Coquinaria, however sketchily described, then "av Gud" the new scientists in Sweden and Germany would find it.  The Scilla of ancient Greece had a mark on the petals so distinctive that it had been recorded. Bluebells don't grow around the Mediterranean, but were the nearest match to Scilla in Northern Europe, so they were called Scilla-without-the-mark,  Not to be confused with the Scots' bluebell Campanula rotundifolia especially as the latter is a dicot.

Someone suggested driving down the road to the garden centre and I thought of driving 40km home because the manual mentioned nasturtiums and part of the poly-tunnel is currently knee-deep in them.  Then I twigged (duh!) that the Institute is on a sort of campus with flower-beds and is just across the road from a river with its own bank. I asked if anyone had a trowel I could borrow, so I could weed some of the flower-beds and use the spoil for educational purposes.  Nobody had a trowel and I was about to go off and attack the earth with a plastic spoon from the canteen when a long-handled shovel was materialised.  Armed thus I set off boldly into the chilly outdoors and soon enough filled a couple of xerox-box lids with a gallimaufry of small herbs: a dandelion-like member of the compositae, a pretty yellow-flowered crucifer and something that looked like shepherd's purse (Capsella bursa-pastoris), which is also in the crucifer family, and at least 6 or 8 other species.  And a couple of species of grass to hold the fort for monocots.  Then I walked across the car-park and clipped some ornamental bamboo to show that monocots can be woody too.

Sure beats getting into a car and destroying the planet.

The lab was unexpectedly wonderful.  My two mature students got stuck in with scapels, cutting transverse section of the root and stem of their plant - which promptly exuded a white sap: further evidence of its similarity to dandelion (Taraxacum officinale) and made a beautiful prep stained the palest blue showing all the transport vessels.  At the other end of the lab, I explained that crucifers are so called because of their little cross-shaped yellow flowers and that the family includes mustard. I hypothesised (it's a science class, so you're meant to do that at every opportunity) that the leaves should taste a little mustardy.  The thought being the deed, one of the students promptly snagged off a leaf and scarfed it down chomp chomp.  It didn't taste of much except "grass".  She and her partner also produced an exquisite cross-section of the other dicot species, so we had two things to compare. Later on, Omnivore reported that there was a distinctly mustard after-taste.  Of course, it is streng verboten to eat anything in the lab, but I didn't care. Finding stuff out trumps doctrinaire regulations.  Good fun, a good day.

Cryptosporidium

Apicomplexan  protozoa comprise many different species of parasites of animals, including Plasmodium (malaria), Toxoplasma gondii (not to be confused with Toxocara canis the roundworm kids pick up from dog shit in sandpits) and . . . Cryptosporidium.  They are weird and wonderful but humans can definitely have enough of them. In my Env.Chem. course they made a small parochial divertissement in the section on drinking water treatment because there had been a notorious outbreak of Cryptosporidiosis in Galway in 2007.  I used this as a vehicle for two ideas which are dear to my heart.

One concept is about On Being the Right Size, after the famous essay by JBS Haldane: the physical filters in one of the city's drinking water treatment plans at Terryland were insufficiently fine (> 0.9 μm) to exclude Crypto from the outgoing water. The protozoan is not properly killed by chlorination and Terryland didn't have UV treatment installed, so they failed on that count as well.  Another plant further up Lough Corrib at Luimnagh near Tuam was more modern and better kitted out, so part of the solution was to divert some of that supply from Tuam to the City of the Tribes further South. On my recent visit to The West and Lough Corrib, I got lost in suburban Galway and found myself at the very gates of the Terryland treatment plant. That was something to tell the kids back in The Institute.

I should come clean and confess that I may well have been wrong in my explanation (carcinogens out of the kitchen tap) of what went wrong in Poulaphouca and Ballymore Eustace to cause the water rationing in Dublin a month ago.  I now think that the settlement tanks in the treatment plant just got overwhelmed by the extra peaty particulate matter which had been washed out of the uplands by a wet October following a long dry summer. The floc needed extra time to settle so it wouldn't gum the works further downstream, but as Irish Water runs their treatment plants at 98% capacity at all times there is no slack available and they just had to switch off the tap periodically. 

The other idea that I encouraged my students to address was the cost-benefitness of interventions in the real world.  Cases of Cryptosporidiosis happen every year in Ireland, some years worse than others, with a characteristic peak in the Spring:

Here the HSPC shows the number of cases for the whole country for 2004-2007. There were 609 cases in 2007, half of which were assigned to Galway, but there were a similar number in 2005 (570). Because the 2005 outbreaks were not clustered and didn't happen in the 4th biggest town in the country, they never made the news. After 2007, Dick Roche, the responsible Minister, announced that he would allocate €48million to upgrading the water-treatment plant at Terryland and maybe other plants in the area. I asked my students to reflect on whether this seemed a sensible way to spend a substantive chunk of the finite exchequer receipts.  Perhaps, I suggested, anyone suffering from Cryptospo-runs would rather have €80,000 for their troubles as a pro-rata share of the gum'ment loot. In Ireland we're rather well fed, Cryptosporidium is intermittent and most of us have built up some immune tolerance. In any case if we get really sick we're only minutes from a hospital which will gear up with suitable therapies to kill the microbe and rehydrate us.

This is perhaps annoyingly glib, especially if you're reading this doubled up with cramps on the john or if you're over 30 and hail from Milwaukee.  In 1993 that city experienced a huge municipal water driven Cryptosporidium outbreak, with 400,000 people affected - about half of those served by one of the two treatment plants.  The population served by the other plant (which didn't take in water from Lake Michigan 2km away from a sewage outfall) reported no cases.  More than 100 people died - although, as I said to my chemists, almost of all of these had compromised (HIV/AIDS, immunosuppressive drugs, elderly) immune systems.  But it is foolish to count the cost of such outbreaks only in coffins, as we do for road traffic accidents.  After 1993, the CDC published a report fronted by Phaedra Corso on the costs to the community of Milwaukee from this massive cock-up in policy and its implementation.   This is a data driven exercise in guesstimation.  The CDC classified the 400,000 into mildly (1 day off work: 88%), moderately (needed doctor and A&E, 4 days off work: 11%) and severe (needed hospital admission, 2 weeks off work: 1% = 4000 beds); and plugged the data into a tot-up program (physician visit $45, ambulance $225, hosptalisation $6,300, lost earnings for patient and carer $80/day etc.).

This tells us that a lot of walking wounded have more impact (mostly loss workdays) on the economy than the headline cases (mostly medical expenses). It also tells us that the Galway outbreak cost in the region of  (600/400,000) * $96million ~= €300,000 (Inflation 58%; $1=€1.35).  Which is a long way adrift from the $48million cost of maybe preventing another outbreak.  Annual costs in the USA (1991 $) from water-borne illness are $21billion from 500,000 severe and 7 million less severe cases - $2,800 per case, but only $70 per head of population per annum.  Hilariously appropriate joke: Middle class parent receives bill for school fees with typo "€5,000 per anum" and says "Thanks but I'd rather pay through the nose as usual".

Part of the problem in water-treatment is that everyone from the WHO on down obsesses about fecal coliforms as if there are no other significant microbiological players.  Thus the EU parametric values are set so that 0 (zero!) colony-forming-units/100ml is the highest tolerable value for coliforms in drinking water.  Luckily what kills coliforms will kill most other diarrhea-inducing microbes. Which brings me to a timely essay in Nature last month by Boris Striepen which should serve to shift some of our cosy assumptions about what is actually killing small black babies every day.  A massive (N=22,500) study of third world infant diarrhea published in the Lancet in July 2013 obtained some data rather than woofling forward on obvious-to-all-thinking-people "knowledge". The data indicate that Cryptosporidiosis kills more than all the enterics combined and if we are to allocate resources on a strict utilitarian basis, we should sink as much research money into Crypto research as into HIV/AIDS - at least on the pediatric front. There are 20x more scientific papers published on malaria than on Crypto but malaria kills nothing like 20x more children.  You must read Professor Striepen's essay for some really nifty insights into how we might exploit the peculiarities of the life-cycle and biochemistry of Cryptosporidium to knock it back down into the cellar.  Rotavirus kills more but, as a virus, will be less amenable to such solutions.

Footless and fancy that

From the Aldi catalogue on special this week:  "Six footless glasses with different coloured stems in a glass vase - perfect for parties during the festive season". €14.99!!  Sorry?  In what way could such a product be perfect for parties at any season?  When the first five quaffers take out their glasses, the last one looks perilously close to tipping the beaker and making a puddle; and what sort of a party is it with only six people?  I suspect that this is driven forward by the cordless drill that was on ALDI special a tuthree weeks ago.  On dit que, and so does Rachel Botsman at TED, the average lifetime use for an electric drill is . . . 12 minutes.  These crippled champagne flutes can be re-purposed into something useful AND you can get 5 minutes more utility of your drill by drilling 6 holes in your dining room table.  Remove the table cloth first because it is bound to get all rucked up as the drill bit rotates.
Brought to you by harmless handy hints (HHH Inc.) for the real world.

Born on the 14th September

If you were an American bloke and born on the 14th September in any year 1944-1950, the bottom fell out of your world on 1st December 1969. You had 'won' the lottery to be drafted into the US military and quite probably sent to Vietnam.  The lottery was a way to make the Draft fairer and there was probably a belief that it would up the quality of the troops by including fewer of the dispossessed and more educated, better fed and more widely experienced young men.  My mentor for graduate school, for example, who was born a bit earlier than 1944 in one of the leafier suburbs of Boston had been able successively to defer his drafting by being in college, being in graduate school and being married.  His contemporaries in Black Roxbury or Irish South Boston with only a high school education, if that, had had to take their chances.

So did holders of Green Cards. Welsh-born Howard Stringer had stepped off the boat six weeks earlier when, in 1966, he was drafted into the US military at the age of 24.  He served a year in Vietnam and was decorated.  On his return he progressed his career in The Media and finished up as CEO of Sony.  He was knighted in 1999 and appeared on Desert Island Discs (a much higher accolade?) earlier this year.

After much thought, it was decided to write out all 366 dates of birth, put each slip of paper in an identical plastic container and draw out the days in random order.  The first number out was 258 (1st Sep) and so boys with that birthday were to be called up first.  You can get a vicarious retrospective frisson by checking your birthday against the order of drawing here.  Better, especially if you are American, ask your grandfather what his birthday was.  If you look at the sidebar of that page, you can read the harrowing (but long and unedited) stories of boys who were called up and went or called up and went to Canada.  Here's all the data displayed graphically:

Actual birthdays along the horizontal, random order number vertical, the first two dates identified at the bottom, also the evidence for the first cry of No Fair.  Those born in December cried foul because a disproportionate number of December dates had low (draftable) numbers and there was an apparent December deferment data-desert which I have outlined.  A Just-So-Story (in the ad hoc fallacy sense, not Kipling's) was put forward as a mechanistic explanation:  The lottery balls were added in date order (January first, December last) to a shoebox which was then shaken, they were then tipped into a literally and metaphorically transparent pick-one jar.  The objectors claimed that insufficient mixing left the last-added December balls on the top and so more likely to be chosen.  I wasn't there but this sounds like hooey because those December balls floating on the top of the shoe-box were tipped first (bottom) into the actual jar. A report from those who were there here.  A much better prima facie case for unfairness was for those born on 29 February who had a 4x higher chance of going to serve.  Post hoc that turned out to be a non-starter because 29 Feb was drawn 285/366th.  The following year, having drafted in the National Bureau of Standards, the method was modified to double randomise the dates.  Two draws were run simultaneously: one drawing out dates in random order and one drawing numbers 1-366 in random order and matching each pair of numbers.  Under this method the first drawn birthday was as likely to be assigned a low as a high number.  You can imagine that the contracts for supply of "plastic balls, hollow, identical, blue, 366 #" and "plastic balls, hollow, identical, red, 366 #" were put out to tender and Boondoggle Inc, of Peoria Illinois sold them to the Selective Service System for $50,000.

By the Mark Twain

It's his birthday today!  Samuel Clemens was born on St Andrew's Day 1835 in Florida, MO and grew up down the road in Hannibal, Missouri on the Mississippi River.  Four of his 6 siblings died in childhood and his father contracted pneumonia and died with Samuel was 11.  That sort of thing doesn't happen to families nowadays because of antibiotics, which we really under-appreciate.  Samuel had to earn a living for what was left of his family and his mother and worked as a gopher on the local newspaper before spending several years as a riverboat pilot.  Mark Twain as any fule kno is what the leadsman would cry when there was 12 feet (3.75m) of water.  Twain because 12 feet is two fathoms; "a quarter less twain" is 10-and-a-half feet.  More details including how each depth is marked (leather tags, red white and black cloth strips woven in) on the cord at boatsafe.  "By the mark twain" meant that for the moment the boat was safe from grounding, although with the ever-shifting silting and sand-banks, that margin of safety could rapidly shoal to nothing.  "No bottom" was defined as anything greater than "by the mark four" 24 feet, 7.5m.

Twain in Tesla's Lab

Clemens spent about four years in his early 20s as a pilot on the river, two years learning his trade and 2 practicing it until the Civil War put a stop to all civilian traffic on the river, and he always cherished his time there.  His younger brother Henry was not so fortunate as a riverboat pilot, getting killed when the boiler of the steamboat Pennsylvania exploded.  Clemens went Went West Young Man and worked, unsuccessfully, as a miner and, more successfully, as a journalist and writer, in Nevada and California.  Later on he moved East to New York and Connecticut where he was great pals with Nikola Tesla, Thomas Edison and other technologists.  But he's not really famous for his techie inventions (self-adhesive scrapbooks and improved suspenders) but for his writing - understated, ironic and vehemently anti-pretentious.  Reading, say, Moby Dick by his contemporary Herman Melville you know you're in Victorian times; reading Twain you are outside of time or for all time.  And he's so quotable:

• “It ain't what you don't know that gets you into trouble. It's what you know for sure that just ain't so.” which I've quoted before.
• A lie can make it half way around the world before the truth has time to put its boots on. 
• Every generalization is false, including this one. 

All of which are also attributed to a wild array of different people.

• Pilgrim's Progress, about a man that left his family, it didn't say why. I read considerable in it now and then. The statements was interesting, but tough. Which might well apply to Moby Dick.
  
• It ain't those parts of the Bible that I can't understand that bother me, it is the parts that I do understand. 
• Often, the less there is to justify a traditional custom, the harder it is to get rid of it. 
• The more I know about people, the better I like my dog.  
• The difference between truth and fiction is that the latter must always be credible in order to work.
• Irreverence is the champion of liberty, if not its only defender.  
• Many a small thing has been made large by the right kind of advertising.
• It may be called the Master Passion, the hunger for self-approval. 

 You'll find his books in any good library: Europeans try Innocents Abroad; Atheists - good copy on Mormons in Roughing It.

Escherichia

The bog-standard bacterium, it's a pity it's so hard to spell.  It looks forrin dunnit?  I couldn't possibly look at the word long enough to remember that the first consonant cluster is sch and the last ch.  So it's almost always written E.coli. The reason we call it Escherichia coli is becauase it is named for its discoverer Theodor Escherich whose birthday (29 Nov 1857) falls today. He died of a very interesting stroke: he had a headache, began speaking several different languages on ward-round and succumbed the following 1911 day at the age of 53.  He was much too modest to name the common enteric bacteria of childhood runs after himself and it wasn't until 1958, more that 100 years after his birth, that the unspellababble name really stuck. I mention childhood 'looseness' because in his day he was the Top Gun in paediatric infectious diseases, writing the definitive tome on intestinal diseases of children as well as books on Diphtheria and Tetanus. He studed in Paris under Jean-Martin Charcot eponymous co-discoverer of Charcot-Marie-Tooth syndrome, which I often use as an example in bioinformatics courses because it sounds so exotic and intriguing. La Leche League should raise a glass of milk to Escherich this day because he instigated a high-profile campaign to promote breastfeeding and its benefits for the intestinal flora.

But if I was looking for mere birthday tribs, like 16th June, there's plenty of choice for 29th November: CS "Narnia" Lewis, Christian "Red-shift" Doppler, Jean-Martin Charcot (cue Twilight Zone theme), António "lobotomy" Moniz, Jacques "Président" Chirac.  Of all these Wikipedia has chosen to front-page an unregenerate Nazi SS-Obergruppenführer Artur Phelps possibly because he was at one time Kurt "Bundespräsident" Waldheim's boss. 

And rather than talk about looseness of the bowel when it is infested with some varieties of E. coli, I'll rant on a bit about the looseness of nomenclature when it comes to assigning names to bacteria. The Venn diagram at left is culled from a paper describing the complete genome sequence of a strain of Shigella flexneri, a cause of dysentry.  The numbers represent identifiable protein coding genes that can be identified in three strains of related enteric bacteria.  All of these chaps are Gram-negative gamma-proteobacteria, and one reason we assign them to the same group is that they all have a common core biochemical functionality controlled by about 3000 genes but they all have wildly different extra attributes.  Shigella, for example, has 175 genes which are not so much different from the other two strains, as completely absent from them: these include iron uptake genes and some enterotoxins.  It's not clear why Shigella should be separated into a different genus while the other two strains are lumped into the same species. 

In the course Fermentation and Food Microbiology (Food& Ferm or F&F) we've spent a chunk of time investigating "Enterics" which are bacteria like Escherichia found in mammal guts and Salmonella typically found in bird guts but also Erwinia carotovora which as the name implies eats carrots.  One of our tasks has been to differentiate these boys from Pseudomonas and Bacillus using tools very familiar to Theodor Escherich 100 years ago.  Core to these tests are the Gram stain, which reveals half the microbiological world as pink and the rest purply-blue; the catalase test which fizzes (or doesn't) and the oxidase test which turns purple-maroon (or doesn't).  These are routine and dead easy to carry out on any bacteria that you can grow on a Petri dish - so that's what we do. You-the-bacteria get to be called Escherichia or Salmonella or Shigella based on the tests that we can carry out rather than on the key attributes (production of enterotoxins; sensitivity to antibiotics; dependence on available iron) that we can't measure easily but which might have serious epidemiological, medical and therapeutic consequences.  It's like looking for your car-keys under the only street light in the dark alley between the night-club and your vehicle.