Friday, 22 September 2017


What's the opposite of stolid [impassive, calm, dependable, and showing little emotion or animation]?  A case could be made that it is stollid, after Cliff Stoll the author of The Cuckoo's Egg [reviewed] and occasional contributor to Numberphile. The Cuckoo's Egg came out in 1989 and is a nerd's thriller. From a tiny discrepancy in the accounting software on his mainframe computer in Berkeley CA, Stoll hunts down ring of German hackers who are trying to infiltrate US government networks to sell the goods to the KGB. It's a race, I read it on the edge of my sofa, rather than settled back on Stoll's [R reading his magnum opus  while immobile (rare enough for him) on a sofa]. Here's the story in 12 minutes to save you reading the book. This video is an example where Stoll plays it frenetic, fidgetty overwrought - ie. stollid. Nevertheless his exploits inspired me a few years later to make my own small-small forays into protecting the data of my users.

At the end of that tale, Stoll articulates a moral that is mightily important, and not just for science. You can ignore discrepant data and moving quickly on record more data that sits more comfortably with our current notions. Or, like Stoll and his missing 75c you can worry about it and then worry at it like a terrier, pulling the miscreant thread this way grrrr and that nnnggg until it unravels the whole tapestry of our certainty and gives us a new fresh view of this our world. We also need patience to see past the annoying, peculiar, different character traits of other people. They may be aggravating but may still have insight and speak truth.
Treasure your exceptions.
William Bateson (1861-1926)
Here he is reflecting on why the sky is blue, which we've known about since John Tyndall [bloboprev] explained it. And then realising that it's not quite so obvious after all. It is a lesson to us all to refuse to accept it when talking-heads and politicians say that such-a-thing is obvious or is clearly whatever.

Why did this all boil up to the execute section on my 'mind'?  Because I came across a recent contribution from Stoll on the Numberphile channel: here he talks about two different concepts in effective computation: iteration and recursion.

Iteration is when you induce your program to process line after line after line of data.  It is a threshold issue: when the length of your data-file is much longer than the length of the software to process it then you write the code. Otherwise it's not worth the trouble of writing a program and debugging it and scaling it up; it's quicker and more efficient to process the data 'by hand' with the help, if necessary, of your handy calculator. This is a relevant dilemma for my just-starting final year project students at The Institute. They can do a 'pilot study' analysis of some data but, without programming skills, they cannot scale it up to do a substantive piece of work.

Recursion is when your analysis spirals down [or indeed up] through successive depths of data. I saw this happen in a way that made me weak at the knees when I paid my pal Speedo to help me set up a big Unix box to service the needs of Irish bioinformatics. At one point he thought to tidy up his work by removing some temporary files. Not realising that he was at the root of the tree rather that on a peripheral twig he uttered 'rm -R' and deleted the whole operating system. That's -R for recursion. Thank foresight that we had made a back-up!

Much as I was gripped by The Cuckoo's Egg, I was super disconcerted when I watched Stoll giving a TED talk published in 2009 [the talk itself was earlier: TED Monterey 2006].  He roved the stage and gabbled off in all directions, butterflying off from one bright idea to another to the next in a thought sequence which was only related in his head. He had written his talk-notes on his left hand which he insisted on getting captured by the roaming camera. It was chaotic and ultimately disrespectful: you have to meet your audience half-way, rather than induce in them a lot of nervous giggles. My under-Mentor in graduate school Bob Tamarin [multiprev] explained that you wear a tie to an interview to show that you'll jump through that hoop because you want a) the job and b) to be taken seriously. The tie respects the conventions and makes everyone on the other side of the table comfortable. Making other people comfortable is the key to good manners.

At the end of his TED talk, Stoll's legs stand briefly still and his arms cease their windmill as he reads the inscription on the bells of the campanile atop Hayes Tower, in SUNY Buffalo. The sentiment sings to him and the respect it engenders quiets his troubled mind&body.
All truth is one in this light:
may science and religion endeavor here
for the steady evolution of mankind from darkness to light,
from narrowness to broadmindedness,
from prejudice to tolerance.
It is the voice of life which calls us to come and learn.

Thursday, 21 September 2017

Daughters civilize their fathers

Before they left home, my daughters wouldn't let me off if they thought I was talking nonsense or saying something outrageous. It made me more careful about what I said because it's humiliating to be called out by an eleven year old who obviously has a better moral sense and higher ethical standards than you do. By stopping my gob about certain matters, I adhered to and eventually absorbed their standards.  It seems that I am not the only father who has become less of a grumpy old bear with sketchy values by the schooling of daughters.

Paul Gompers, an economist from Harvard, and Sophie Wang, his graduate student, carried out a survey of hiring practice and economic success among a large large number of business start-ups and the Venture Capital firms who funded their rise. Weirdly, and it transpires interestingly, they also surveyed the hiring-and-firing decision-makers whether of not they had daughters. That question or the comparison of those data do not spring fully armed from the head of Zeus. It is asked because someone has a hypothesis - probably based on an anecdote and an insight.

It turns out that a) having a daughter makes you 25% more likely to hire women to work and make money for your company b) having made that admirably inclusive decision your company is going to do 3% better year-on-year than equivalent blokes-only firms. HuffPo's take on the story. As one who has two daughters in the work-place who will be looking for challenging jobs in the future, that is good news. Turns out that these good things flowing from girls-rule households include more liberal political view among congressmen, and more compassionate sentencing from judges with daughters. You can read the original paper IF you come from any of 200+ developing countries - including Vatican City, Liechtenstein, and Singapore which are not associated in my mind with extreme poverty. The rest of use have to pay for access.

It's sad that we have to make an argument of utility to achieve equality of opportunity for women in the world of banking and finance. But if it is shown to be profitable, more women will get the high flying, high paying jobs. That will promote diversity and diversity has to promote a certain bendiness and resilience in the face of challenge. If more and different solutions are put on the table then the problem is more likely to be solved.

Wednesday, 20 September 2017


I have a twin sister. In utero, I had a much better placental connexion and weighed in (or weighed out?) about 50% heavier than her in the midwife's scales. But, normal boy vs girl development being what it is, for all the years that mattered she was about 2 years ahead of me. She was educated in the Arts Block [French and Linguistics BA Edinburgh, as you ask], and worked for several years in the publishing trade. It was, in other words, a long way from Science that she was r'ared. But you can't keep a curious mind from asking scientific questions. A tuthree days ago, she sent me this:
  • Here's a mind bender. A woman 5 ft 6 1/2 in tall is walking on open ground at 500feet. Her shadow is 112ft6in long. It's 14 September in northern hemisphere. What time is it? 
That's interesting because it makes you think about which of these data are essential for cracking the puzzle and which are mere padding. Height above sea level, for example, is not relevant and it is only in the metaphorical sense that women throw a longer shadow than men. And we have to deprecate the use of imperial ft and ins because they make the math a bit harder. I straight away converted everything to metres and recalled the Mnemonic of Trig SOH-CAH-TOA. What we need to calculate is the angle on the left of the diagram above formed between two lines ended at The Sister's head and feet.  By extraplolating these behind her to the sun we can calculate Sol's height above the horizon. I've induced kids to use similar trigonometry to estimate the height of trees.
So here we have the sides opposite and adjacent to the angle so we can solve for tan θ = O/A = 1.67m / 34.3m = 0.05 which gives an answer of 2.78 degrees. The sun goes all the way round - 360o - the earth in 24 hours or 1440 minutes. Throwing the shadow in question, the sun is 2.78/360 * 1440 = 11 minutes before sunset. Which was at 19.24 on the day and at the place where the experiment was carried out.

This is an example of where the calculations are extremely sensitive to the stated conditions. Not in a chaos-theory sense where Hurricane Irma is triggered by a herd of locusts throwing up dust in Mauritania which blows out to sea in a wisp of a vortex. But if you think about it, the angle subtended by my sisters head a moment before sunset is infinitely small and her shadow is infinitely long. Thus a one minute difference about that time will make a huge difference in the shadow length and therefore [what we are driving at] the estimate of what the time is.  As it was, I was ten minutes adrift in my estimate.
Shadowfax is the name of Gandalf's horse and has nothing to do with this at all.

Tuesday, 19 September 2017

Anonymous shopping

In the world of teaching biology, I can be a gun-for-hire. When I started at The Institute, my boss waved an absurd list of courses that I would be required to teach [human physiology; remedial maths; 2nd Yr physics; 1st year biology and chemistry; environmental chemistry of water; food microbiology].
Yore 'avin' a game, guv'nor, I said.
No I'm not he replied this is what we need you to do, so I did.
In the 1990s, I was contracted to tool all over Ireland, with occasional forays across Europe, to teach short courses in bioinformatics and molecular evolution. It was tremendous fun. Along the way I developed a module for becoming a power-user of PubMed, the database of bio-science literature. I dreamed up a list of bizarre things to hunt for on PubMed, at least partly to show the wonderful breadth of human research curiosity.
  • Vending machine injury
  • Vacuum cleaner injury
  • Vasectomy and prostate cancer
  • Vesalius
  •   . . . and vat's jvst ve Vs
I was reminded of that because a comment on the blogosphere pointed to a an article tallying up the count of peculiar deaths occuring each year in the USA. That was interesting in itself because if you were required to put these potential killers in order of body-count, I bet you couldn't:
  • Vending machines
  • Dogs
  • Txtn while drivn [prev]
  • Autoerotic asphyxia
  • Roller-coasters
  • Falling from the bed
  • Terrists
The comment appeared under a flag on Metafilter pointing at a FastCo piece on the latest convenience startup. A couple of ex-Googlistas, Paul McDonald and Ashwath Rajan, are trying to launch a series of teched-up retail boxes called Bodega which will spring up at a location near you. Bodega will sell a short range of essentials and undercut the Mom-and-Pop store on the corner. Real convenience stores have a longer inventory and overheads like people-who-say-hello and will hold a UPS parcel for you. Bodega intends to cherry-pick the fly-off-the-shelves items and leave the competition high and dry. Retail is a dog-eat-dog world where the whole enterprise is predicated on a race to the bottom on cost. When I first knew them, Pat the Salt and his late and much lamented wife, my in-laws, ran a grocery in a village in the middle of County Kilkenny. Not a hamlet but a long way from a town also. That distance, demographic and geographic, meant that 700 inhabitants, with maybe 700 farming families for a hinterland, were supported by a national school,  two churches [RC and CoI], a creamery, an expensive petrol-station, 7 pubs and 7 shops.

It was pretty harsh.  In order to differentiate themselves from the competition, they started baking a big ham each weekend and selling it in slices through the week. It was an instant success, everyone came to try it out and and all resolved never to turn vegetarian. But it didn't do enough for the bottom line because the clients would buy their few slices of ham and then duck round the corner to get their tea, sugar, butter, milk, bread and baked beans from Mrs Doohickey who know their mother really well and had run her shop forever. After several years on the downward slope they sold up and tried something else. The Garda Sergeant's wife, who had an account, owed them a huge amount of money which she had no intention of ever paying . .. the trollop. Google maps suggests the premises are now a chipper: sic transit gloria hami.

To honour of the rapacious enterprise of McDonald and Rajan, I note that today is Talk Like A Pirate Day. All aboard the SS Amazon, me hearties.

Monday, 18 September 2017

The Filth

Charles Darwin spent his post-Beagle years largely recumbent, initially fathering an extensive squad of children [N=10 over 16 years] and then on the sofa downstairs reading through an extensive correspondence [average 2+/day in, say, 1872] and firing off suggestions about what to do next. He also read loadsa books of course and had the habit of dismembering big volumes so he could read them section by section. I think there are probably as many books published in Britain every day as the entire output of 1872.  In my restless search for copy, I have to rely on my own efforts, searching the blogosphere and my own, particularly unexciting, life at The Institute. I have, nevertheless, two 'correspondents' who send me links on a regular basis and I appreciate both link and sender. Not too many, mind, G - I don't want to direct all your mail to the spam-box.

All that preamble is by way of acknowledging a Guardian report on micro-plastics in the drinking water which was sent me by G a tuthree days ago. Microplastics are the new environmental bugaboo, not because they are unsightly but because they are invisible and we have no idea a) about how we are going to clean them up or b) about how harmful they are. Microplastics are defined as particles smaller than 5mm and larger that 1 micrometer µm = 1 micron = 1/millionth of a metre = 1/thousandth of a mm. Smaller than that we are talking about nanoparticles. E. coli is about 1µm across and 2µm long and a human cell is on average 30µm in diameter.

On microplastics on the beach, here's a nice imgur photo-story [and R for a sample] about beachcombing  on Tregantle Beach near Plymouth, UK, for the cohort between microplastics and my bailiwick of ropes, buoys and fishboxes.  It takes a particular and peculiar dedication to sift through 35 bagsful of beach detritus to find all the Smarties-tops, or Lego flower-parts.

The question is, Guardian readers, whether you should be really worried by the fact that 72% of your UK drinking water is contaminated with microplastics? First off, note that 28% of such sources had NO microplastics.  Of the rest, the contaminated, the average discovery was 4 particles per 500ml. Now there may be a long tail here, with some taps spouting 100s of microplastic chunks but I don't think 4 is enough to concern you/us. You could, for example, decide to go out and purchase a 1 micron mesh water-filter and sustain a disfiguring facial injury from a car crash on the way to the store.  That's not likely but it's a terrible outcome and Risk Assessment requires balancing that against a more common event (assault by microparticle) which has no known effect. No known effect is not the same as no effect! But the risk assessment helps put your worries into perspective and that should help formulate a rational course of action.

On the stuff-I-put-in-my-mouth front you should know that the FDA in the USA has allowable levels of contamination in the various food-products that pass through its labs and our guts. The plain people of Ireland thanks the US government for carrying out these time-consuming studies for the free[-loading] world, because, according to my calculations, our Food Safety Authority spends more of its time drinking tea than analysing it. The FDA's Department of Sanitation and Transport publishes a long, and fascinating, list of the levels of allowable 'filth' in food products.  Here we go with an excerpt:
  • Ground Paprika : hazard and action level
    • Mold Average mold count is more than 20%
    • Insect filth Average of more than 75 insect fragments per 25 grams
    • Rodent filth Average of more than 11 rodent hairs per 25 grams
The FDA recognise that it is impossible to keep insects and mice out of food-stores while noting that we don't want to pick earwigs and weevils out of the rice before we cook it. 50 insect wing fragments in your paprika? Meh! You want to look at your bacteria-laden tea-towels and pot-scrubber before your start to worry about evidence that your food is edible to both humans and rodents. 1000 insect frags, and you may take notice - it is evidence that hygiene standards in that food-processing process are dodgy and should be investigated and, probably, changed.

Sunday, 17 September 2017

Sporting life

For several years in the 90s I taught courses in Finland. It is about the only time I went to a sauna; as a sort of hats off (and kit off, of course) to the host country. Far too hot to be comfortable, really. I found the Finns had a very sharp laconic sense of humor, often quite dark. One chap referred to another as "about as useful as wet toilet-paper": with the accent and delivery it took me a while to twig this phrase as a synonym for utterly useless. Here's a pretty and peculiar [both] aspect of Finnish culture - keppihevonen - in which girls gallop over jumps astride a hobbyhorse and perform a fair imitation of dressage.
  • I've mentioned wife-carrying, another Finnish sport, before.
  • But maybe not [English] shin-kicking.
  • Worm-charming is another English all-the-family sport
  • Quintessentially British at this time of year: conkers.
  • Mountain unicycling, anyone? You've got to have a cotter-pin loose for that sort of thing
  • Paragliding.  It boggles my mind that I was in 2002 able to master the task of getting my canopy airborne above me and then launch into space.
  • Previous coverage for out-there passtimes.
Here's a another form of fun: playing a power-hose on a 130 tonne fatberg [2013 prev] under ground in East London. Metafilter used a come-on-and-click title Congestion backs up London Tube for a quarter of a kilometer to a predictably witty rich seam of comments.

Saturday, 16 September 2017

The Ginger Man

I pretty green in 1973; but at least I had the gumption to leave home and country to go to college. Travel broadens the mind and I really needed to be exposed to different vistas after more than ten years being institutionalised by my very expensive education in England. On the ferry from Liverpool, I had brought a 20 lt volume box of volumes mostly Penguin paperbacks which I considered essential to civilised life. It turned out the at least two of these not particularly racy [for 1970s England] books were on the Index Librorum Probitorum and banned in Ireland. I had, for example a copy of La porte étroite by Andre Gide. I've written before about how another of these banned books, The Ginger Man by JP Donleavy, or rather my laughing at one of these, brought me and The Beloved together. It is accordingly with a certain sadness that I note the passing of Donleavy [L last year at his 90th bday with Glen "Once" Hansard] at the beginning of the week. There was a time when I read The Ginger Man ragged; riffling through it to find favorite passages and slapping the open book's face down on the kitchen table to acquire some accidental butter stains. I read a lot of his other books but they seemed a bit tired and derivative after Donleavy's first and most immediate book.  I will acknowledge that I cannot remember reading his Fairy Tale of New York but do rate The Pogues song of the same title.  The Ginger Man itself inspired Brian Cadd's song of that name.

I wrote him a letter in about 1974, offering to come out to his country mansion and interview him for the TCD student newspaper (with which I had absolutely no connexion or affiliation). Donleavy, quite sensibly, didn't reply to my letter.

Donleavy must have been an engaging chap, he was certainly a great boozer and intimate of Brendan Behan. You get a flavor of this listening to him on Desert Island's Discs DID in 2007. I've had occasion to mention DID as the ultimate tribute of respect from the British Establishment (=BBC): better than a medal, better than an honorary degree. I must ask The Brother, who has landed all three fish. Somewhere in his interview-with-music JPD offered the suggestion that some of the 45 million copies of the book have been so good for the morale of the sick that they have recovered "You don't die in bed if you have read The Ginger Man". That is likely to be confirmation bias, selective attention or cherry-picking. So many copies out there and everyone dies, most of us in hospital beds (or on mere trolleys in Ireland, there being insufficient beds). If every sick person receives ex officio a copy of The Ginger Man, some of them will recover and that connexion will wing its way back to head office at the publisher; the unmiraculous copies of the book won't be noticed under the hospital bed, let alone tallied up.

Nevertheless, I will share a nice story that was going the rounds when I started working in St Vincent's Hospital in 2001. In 1990, Ireland did surprisingly well in Italia 90, that year's World Cup soccer tournament. An elderly lady was occupying a hospital bed for her last journey surrounded by her anxious family. As the time for a crucial Ireland match approached, she told her sons and daughters to go off and watch the match in the common room "sure don't be worrying about me". After the game, her rellies trooped back somewhat sheepishly having had their priorities exposed. "How did we do?" murmured the old lady
"We won on penalties" they chorused
"I'm feeling much better, so; is there a cup of tea to be had?"
The restorative power of tea (and soccer) worked its magic, she was soon discharged and lived on for several more years.

It is strange and peculiar how sporting events can be so inspiring for people; even those whose nearest approach to a football is sitting on a sofa all Saturday afternoon working through a slab of tinnies and shouting at the ref. The case has been made many times that Ireland's somewhat limping progress through Italia 90 was the catalyst for the rise and roar of the Celtic Tiger.  On 3rd September this year Waterford and Galway met in the All Ireland Senior Hurling Final. Waterford, of all Ireland's cities, has had the roughest time through the recession and could do with a boost. Galway with a critical mass of IT companies is doing much better.  It was mental in Waterford in the run up to the key weekend: every house was dressed out in blue&white  Pat the Salt was compelled by his carers to buy a large flag although he has no time at all for GAA having grown up in Wales where Rugby is king. When Waterford went down GALWAY 0-26 WATERFORD 2-17, I wrote to my pal Paul who used to hurl all over Galway in his youth "Thanks a bunch Paul, you and yours have screwed over any chance of economic recovery in Waterford this decade"