Sunday, 22 October 2017

Banana Sundae 221017

I hope this inspires you to make something self-indulgent to pile up between the two halves of a banana. I hope you have a banana!
What else is new:

Saturday, 21 October 2017

Pushing the boat out

We got the power back after Ophelia in time to make a hot-water bottle for bed on Wednesday after 56 hrs of darkness at night and washing in a bucket. Pals of ours on the Wexford coast were still powerless yesterday (Friday) evening which means they have missed the boat and will be bumped down the list by at least 48 hours. Why? Because Storm Brian is in the process of stomping through Ireland for a shortcut [see whippy winds, especially at sea R]. The electricians will work though rain-storms but draw the line at being on top of a cherry-picker in 100km/h winds. The prequel to Brian was a wall of precipitation that took 6 hours to travel across the island W to E. That's about right because The Weather travels at about 60km/h regardless of the speed of the component circulating wind. aNNyway, we had been looking forward to the launch of m'pal Russ's book about The Fishin' in Waterford Harbour. We set off as night fell and the rain was still hosing down; we had to cruise through a deep road-wide puddle before we reached the first bridge at the county borrrder and another before we reached the first village on our journey; so we bottled out and went home. Launching a book is one thing; to launch the car is another. Hardier, localler folk turned out in sufficient numbers so the Book Launch wasn't a total wash-out. In my Ophelia aftermath report, I mentioned the far more serious consequences of Hurricane Maria in Puerto Rico.

It turns out that one of the smartest members of my scientific Set has done good for herself and has joined the diaspora to work in Harvard Medical School. She posted a message to the bioinformatics listserv list to tell us-back-home about Harvard's response to Puerto Rico's woes. I complimented her and her co-workers for doing something rather than closing the emotional shutters in the face of a tsunami of disturbing thoughts and pictures.  Her e-mail included a
List of Urgently Requested Supplies; 
Solar panel charger for USBs; Phone battery chargers with USB and a wall charger; Inverter power units for cars; Portable water filter bag; Feminine hygiene products; Mosquito repellent; Sunblock; Sleeping bag; Baby wipes; AM/FM radio that can be recharged with USB port; Hand sanitizer; First aid kit; Plastic gloves; Disinfecting wipes; Flashlight or lamp (preferably solar or charged with USB); D batteries; AA batteries; Hat to protect from sun; Matches; Toilet paper.
If you have a drop of kindness left for the inhabitants of a distant sub-tropical land, you'll want to do something. Your far more likely to actually respond if the path-of-giving is clear. Since before my parents got married in 1950, happy couples have wanted to avoid getting 12 toast-racks and no bath-towels as wedding gifts. The solution has been setting up a wedding list service at the local department store to allow wedding-guests choice while ensuring that the happy couple get a useful cross-section of what they need to start a home together. Amazon has tapped into the well of well-wishing and will provide a similar service for other events: here's the Harvard list of essential supplies for Puerto Rico, you can buy (among a lot of other required kit)

  • a sun-hat 192/200 -- 4% donated
  • solar power bank 163/225 -- 27%
  • protein power bars 57/75 -- 26%
  • AA batteries 199/225 -- 11%
  • sanitary pads 150/225 -- 33%
  • sleeping bag 211/225 -- 6%

The fraction indicates the number of each product still required, the % is its reciprocal: the percentage of that requirement which has been fulfilled. Oooo, data! The project was only launched last night, so the giving is ongoing, but it's interesting what the first responders consider to be the most important items to ship out foreign. The item most seen-to-be essential is a box of rubber-gloves [76% fulfilled]; that might be because they are cheap or for more complex psychological reasons. I know that the charity sector [in Ireland at least] has suffered significant reputational damage in recent years [fraud, featherbedding, 4x4s]. The Irish response to this Irish problem is to set up a new supervisory quango under a well-paid CEO! But really wouldn't it be more efficient to give $7.69 to Oxfam / Goal / Trocaire and let their experts decide the optimum way to spend the money in San Juan? Heck, Oxfam would be able to negotiate bulk discounts from wholesalers rather than paying retail to Amazon.

Remember the Sumatran Tsunami of Christmas 2004? I was working in UCD at the time and so was Dr Chandralal Hewage.  Indeed, that community was so small that we were co-authors on a paper.  Chandralal originally hailed from Sri Lanka and, in the aftermath of the tsunami's destruction of the fishing industry, set up  a fund to buy a replacement fishing boat for any surviving fisher-folk to use. Because we knew Chandralal, the project was massively oversubscribed and within the next year fifteen 15! boats were built with the UCD logo [L at launch]. If the same thing happened today, they'd be more imaginative about the names of the boats.
Note: today its a twofer: check piece immed below?

Mind your mouth

Annie Dillard, Anne Fadiman, Anne Lamott. They are filed in my "mind" in the same bin. Maybe it is something so superficial as the fact they run variations on a common first name, but probably it's coupled with the fact that I started reading them at the same time. The other thing is that they write really well, I fact I've reflected on before in the case of Dillard and Fadiman. Now is the time for a bit of parity of esteem for Anne Lamott who is the most difficult of the Trinitanny.  I think the only book of hers I've read is Bird by Bird; some instructions of writing and life, which is both insightful and a stitch.  It's also holding its original price on Amazon better than Ex Libris [Fadiman] or Pilgrim at Tinker's Creek [Dillard].

Bird by Bird's title comes from an anecdote about Lamott's father and her younger brother who, as a teenager, was experiencing writer's block over a daunting essay on ornithology. The father's advice was "Bird by Bird, Buddy" in the sense that all great journeys start with a single step but that without that first step you'll spend the rest of your life unfulfilled on your sofa. Addressing a massive entangled problem by finding a small knot and tugging - just to do something - is what I have called a Javi Problem. Lamott, like many women, had an uneasy relationship with her mother whose was uniquely infuriating to her daughter. But their relationship softened a little when Lamott became a single parent in her mid-30s: granny and grandson were besotted with each other and that helped Annie-in-the-middle see more virtue in the older woman.

That boy Sam, features in a brilliant anecdote in Bird by Bird which I'll defy copyright by quoting here in full:
“My son, Sam, at three and a half, had these keys to a set of plastic handcuffs, and one morning he intentionally locked himself out of the house. I was sitting on the couch reading the newspaper when I heard him stick his plastic keys into the doorknob and try to open the door. Then I heard him say, "Oh, shit." My whole face widened, like the guy in Edvard Munch's Scream. After a moment I got up and opened the front door.
"Honey," I said, "what'd you just say?"
"I said, 'Oh, shit,'" he said.
"But, honey, that's a naughty word. Both of us have absolutely got to stop using it. Okay?"
He hung his head for a moment, nodded, and said, "Okay, Mom." Then he leaned forward and said confidentially, "But I'll tell you why I said 'shit.'" I said Okay, and he said, "Because of the fucking keys!”
I hope that makes someone go and get her book out of the library and read it. You might then be ready for an hour-long interview which is, by turns, confessional, insightful, laconic and funny. Her boy Sam became a father at a ridiculously young age [why a year younger than me] and Lamott wrote a book about the coming of the wunderkind called Some Assembly Required: A Journal of My Son's First son. Here Lamott reads sections with Sam to rein her in.

If you're not [yet] a fan, you might try 12 truths I learned from life and writing which is a) TED and b) only 16 minutes long . . . and nails world peace. Here's an even shorter piece [5 mins] anout how she got sober with the help of Jack "Why don't you come over and we'll talk" and God.

Friday, 20 October 2017


I love my work. Every day I find out something new - about science, about myself, about the students, about real life.  My mind is a bit like Lake Oroville [prev] now; I feel that it is reaching capacity: every bit of information added sends another over the spillway to oblivion. That's possibly why I think I'm learning new stuff all the time.

I was drifting out of Human Physiology class last week chatting with some of the students about the overlap between the different courses they are being taught. We agreed that it was usually a Good Thing to hear the Human Physiology take on a subject and the Drug Actions and Uses version of the same information. One of them then launched into the fact (news to her; and to me) that Roaccutane, which is prescribed for serious acne, is severely teratogenic - it generates birth defects. That is most unfortunate because the girls who are experiencing the worse cases of acne are also approaching their peak of fertility. Roaccutane = isotretinoin is a derivative of vitamin A and works by reducing the quantity of  sebum produced in the hair-follicles; making them a far less hospitable place for bacteria, like Cutibacterium acnes and Staphylococcus epidermidis. A course of 12 or 16 weeks will often knock the problem on the head.  But you need to be super careful not to fall pregnant while this stuff is coursing through your veins. Responsible GPs insist on two independent forms of contraception and a pregnancy test before and during the course of treatment. In Ireland, of course, finding that you are pregnant while under Roaccutane treatment won't help a lot because of Article 40.3.3. of our Constitution.

Like Gardasil, and for similar reasons, some folks hold that Roaccutane induces depression and suicidal ideation but, despite the tragic anecdotes, there is only weak epidemiological evidence for such an association. The drug will also filter through into the prostate but the levels of Roaccutane found in semen are too low to impact on the fetus.  The most common side-effect <duh!> is dry skin because you are interfering to reduce the normal lubricants. Dermatologists are likely to claim that Roaccutane is wildly over-prescribed in General Practice, but they aren't at the front line when an unfortunate teenager with a boiling face presents in surgery.  In my day, you just sucked it up (no, not literally, ye daft bugger) or went through a bottle of Clearasil and realised that a) it didn't really adversely affect your ability to 'pull' - because unpretty much all your rivals were similarly afflicted b) all things, even pimples, do pass.

A fortnight ago, we had a couple of visitors from Finland, and I landed a free lunch out of it.  My colleague refers to events in the white tablecloth corner of the canteen as "a bit of rubber chicken with our guests". That's not fair, especially if you like mashed potato, which comes with everything. All the larger place-names in Finland are doubled up, like our Gaeltachts, because Swedish is present as a minority first language [about 5%] especially round Åbo /Turku in the SW of the country.  The majority live in a country called Suomi or, formally, Suomen tasavalta = Republic of Finland. The Swedophones call it Finland and themselves Finns. That label makes their Finnish-speaking neighbours a teeny bit uncomfortable because, in their language, Finni = pimple.

Thursday, 19 October 2017

Ophelia: there's rue for you

We were all hyped-up for Ophelia. It's just wonderful that, with Met Eireann and a network of weather satellites, we can see The Big Winds coming in orderly one after the other from the Atlantic. Ophelia was a little peculiar in that she didn't visit Disneyland on her way to Europe but headed straight NNE after being born near the Azores. It could only do that, gathering power as it went, if the water was warm enough to hype her up; and it was this year. Maybe in future years this will be one consequence of global warming. I've had a little to say, mostly wrong, about oceanic water temperature and its effects on weather in Ireland.

ANNyway we spent last Sunday reefing the tops'ls, battening down hatches, putting a concrete block on the wheel-barrow. We also made sure the Good Ship Powerless had sufficient water i n containers because without electricity the water stays in the borehole. Not much we can do about our 17 x 9m poly-tunnel [pic etc.]. If it decides to take off, and it's bigger than the Cutty Sark's mainsail, it's gone into the next county. When the storm was fizziest, I went out to see what went down in between showers of horizontal drizzle and noticed that the edge of one of the corrugated iron shed-roofs was lifting and rattling a little too rhythmically for comfort. Power had failed us by then so I couldn't drill a hole in the corner and tie it down. But, with PhD smarts, I attached a C-clamp and tied that off on something solid. Not before some of the roof-nails had been worked out by 3 cm, though. Whatever about a mainsail's worth of plastic from the tunnel, nobody wants to see sheets of corrugated iron taking off . . . or indeed coming in to land again.

Ophelia tracked up the West coast bringing down trees and whisking away the roof of a community school in Douglas, Co Cork. The Education Minister closed all schools and colleges on the Monday and most bus & train services were shut down in anticipation. In the end, it wasn't as bad as it might have been. 3 dead, 360,000 without power, 50,000 without water. Both those including us for the last 46 hours. Living remote, we are the last people to get power restored: those darned sewage treatment plants, hospitals and old folks homes getting priority. It's fun (for a while) cooking on a wood-stove and washing in a bucket. The Beloved is going to do triage on the freezer today. A lot of our neighbours are going to get lamb-chops, if they are getting soggy, even if they are vegetarians. I was comparing notes with one of my colleagues at work who lives in Athlone. He reported the most exciting news as the car (empty) of a neighbour of a friend of his cousin had been flattened by a tree. Then he mentioned another neighbour who works for a multinational which has offices in Puerto Rico. 200 employees of the Puerto Rice branch are unaccounted for after Maria. One flat Nissan Micra is a bit of a First World Problem.

When I went to work on Tuesday, I packed a fuelled-up new-sharpened chain-saw in the boot of the car along with the PPE clobber: hard-hat and visor, chaps, boots, gloves, ear-defenders. But the damage (maybe 12 biggish trees down over 40km of back-roads) had all been tidied away with just leaves left on the road. Those farrrmers, nothing they like better than getting out in the dark with a 4x4 for headlights and a chain-saw for macho. For us, apart from deadwood branches and twigs, a big ash tree Fraxinus excelsior fell out of the ditch and I've been doing manly things after work with the chain-saw gathering Winter fuuuuuuelll.

OPHELIA: There's fennel for you, and columbines: there's rue
for you; and here's some for me: we may call it
herb-grace o' Sundays: O you must wear your rue with
a difference.
Hamlet by Wm Shagsper
All in all we didn't rue Ophelia too much because she didn't get get real mad and make us over-much sorry from her passing through. The Hardy Boys and Girls from the ESB, have been putting in 16 hour days restringing electricity cables and got to us last night after 2100hrs and the power came on again. Two and a bit days without power is okay if you have a car and a job to go to, the use of your legs, and are reasonably continent in the toilet department. Failing any of those and it would be tedious. The contrast between my getting up this morning and the deliberate schedule (lighting the fire in the dark for hot water for starters) of the previous two days put our carelessness about the benefits of modern convenience into perspective. I heard a story on the wireless a few days ago about the bliss of a farming lady being brought a cup of hot tea in bed by her daughter after the Shannon Scheme came through with rural electrification in the 1950s. Before that, it was too much trouble because the cows needed to be brought in for milking before the fire could be laid to heat the kettle.

Wednesday, 18 October 2017

Homage to Catalonia

Title is Homage to George Orwell [prevoblobs] who was fighting there in the Spanish Civil War. Ever since I read H2C as a teenager - along with every other word of Orwell's that I could dredge up - I've flagged the Catalans as the Good Guys. The last hold out against the grey tide of fascism. I was schooled to adopt a less black-and-white view of Spanish politics when I got to be good friends with Pepe Malpica 25 years ago. There were good people on both sides of the barricades who were  sincere in their beliefs and anxieties. After such hideous internecine warfare comes to an end, you, me, we have to move on and the Spanish adopted a collective amnesia, so that after three generations the wounds are healing.

I don't really have a locus standi on the independence referendum that was carried out in Catalonia two weeks ago. It's the same sort of thing as Brexit, about which, as a horse European born in a stable in Dover, I have strong feelings. I believe in SS Europe The Good Ship Europa, especially the aspiration to equilibrate upwards: the belief that a larger market and free-movement would generate so much extra wealth that the poorest outposts of the continent would no longer be dispossessed. Poverty is not just about money, it's about culture and different ideas, and sharing. I found out last week that, in PIE Proto-Indo-European, the word for give was the same as the word for take. Back then on the steppes of Kazakhstan exchange was an essential part of life.
And please note, as did my pal Russ, that "believing in SS Europe" would stretch my politics further right than I feel comfortable about. Big red face on those nautical metaphors.

Strange Maps had a commentary on the prospects of succession in Catalonia which included the map at the head of this post which was created by redditor bezzleford.  I love that map: the flags [multiprev], the borders, the quirkiness of the displayed data, the unexpected findings and the new information.  The snapshot doesn't flag the changes to the map of Europe where a region has already achieved its independence.  Think Slovenia, the first of the regions of the Former Yugoslavia to go it alone.  They achieved this aim in a mere 10 Day War  of succession in 1991, at least partly because the central government in Belgrade was stacked with Serbs and there were only a handful of Serbs in Slovenia.
It was bloodier, longer and uglier in, say, Bosnia which I still associate with Srebenitsa, pogrom, and ethnic cleansing. And part of the reason for that is because the territory of Bosnia and Herzegovina was and is ethnically and religiously heterogeneous. Bosna i Hercegovina aka Боснa и Херцеговина is now separated into two autonomous regions with a yellow cherry on top called Brčko. [map L]. The red area is now an autonomous region of the country which calls itself Republika Srpska or Република Српскa. It is a separate auronomous entity from 'the rest' of the country Federacija Bosne i Hercegovine aka Федерација Босне и Херцеговине. It looks like a desperate example of gerrymandering but actually closely tracks the ceasefire line at the end of the Bosnian War. This wiggly line is known as the Inter-Entity Boundary Line Međuentitetska linija / Међуентитеска линија. Although there are two constituent parts of the country, there are three constituent ethnicities which fall out on consistent religious and linguistic lines:
Group % Pop Religion
Bosniaks 51% Sunni Islam
Serbs 31% Orthodox
Croats 14% Catholic
There are three official languages, too, but they are essentially the same as variants of Serbo-Croatian. The Serbs preferring to write theirs in Cyrillic. The two blue exclaves at the top of this map don't make sense until you realise that they are just across the border from Croatia. And what about Brčko, the yellow hinge between the two flanges of Srpska?  There, the demographics between Serbs vs Bosniak-Croats are more nearly equal and it is currently run as a sort of condominium. According to the Guardian 3 years ago; it is a beacon of multicultural hope . . . a bit like Lebanon was before it collapsed into its own civil war 30 years ago. It will come as no surprise that Srpska appears on bezzleford's map with more than 50% of the inhabitants favouring independence. They have to sort out Brčko first, I hope they are less black and white there than they were in Sebrenitsa

Just about 15mm NW on the Eurosplit map above is another purple (>50% wanting out) enclave called Veneto which wants to pursue its own dreams independent of the rest of Italy. Where does that leave Friuli-Venezia Giulia [L. zoomed in and coloured red]? An exclave of Italy, is where! This map also identifies where Slovenia SVN and Croatia HRV fit w.r.t Italy, Austria AUT and Bosnia Herzegovina BiH. While self-determination is all well-and-good some consideration should be given to how your self-determination impinges on other people especially neighbours. Ireland isolated by Brexit, Friuli isolated Venexit, Brčko maybe disolated by Srpska in the future.

That-all only deals with geographic divisions. Many of the self-det movements are driven by an unwillingness to help neighbours less fortunate that ourselves.
  • Barcelona wanting to dump Andalucia; 
  • London [which is a 12% entity on the Eurosplit map] wants to ring-fence itself from The Tanned Other; There is a vulgar substratum of English yobs who really believe that wogs begin at Calais.
  • Lega Nord (full name Lega Nord per l'Indipendenza della Padania), which includes Liga Veneta wanting to ditch "Africa", which they consider starts just South of Rome. Padania is more or less cognate with Cisalpine Gaul which Julius Caesar left when he crossed the Rubicon on his march to supreme power.
Other self-det movements are pushed by a sort of romantic vision of history being used as an aspiration for a still rosier future. Last weekend there was an apologist for Catalan independence talking with Marian Finucane on RTE1 about how being a Catalan wasn't a matter of language or genetics but was a sort cultural sense of being. He mentioned that the Catalan 'spirit' had been stifled, if not actually crushed, by 300 years of Castillian misrule. To which Finucane chirped up that 'we' in Ireland had been similarly oppressed for 800 years by our larger neighbour. In her wobbly little noddle, I know that she was referring to my protestant ancestors. It's only a step from there for her to invite me and mine to go back where I came from to preserve the holy fantasy land of Ireland for Caitlín Ní Uallacháin and young subtle Conchubar, dancing at the cross-roads; Niall of the Nine Hostages tucking into colcannon, and Waterford winning the All Ireland. This is the most egregious sentimental nonsense: I have far more in common with a white man from Boston, a scientist from Turkey or a middle class professional mother of two from anywhere on the planet than I do with half the people whom I meet on the road home from work.
Patriotism? The last refuge of the scoundrel.
Samuel "Dictionary" Johnson

Tuesday, 17 October 2017

Learn by doing

In my time at the digital coal-face, I've learned how to program computers in Basic, PL/1, Fortran, Cobol, Pascal, C and Perl. I've done this in all possible ways: by the book, in formal courses, on my own or embedded in a lab. The best way has always been to a) have a project that needed to be completed b) access to i) time ii) a computer iii) a colleague. The colleague didn't have to be better at the task or a mentor; better be the source of half an idea towards the solution to intermediate problems or a willing ear. Book learning is a useful asset, but lectures are more or less a waste of time. Just DO it!

When I started work at The Institute it was about 5 years since the bottom fell out of the construction industry in Ireland. The undergraduate years were leavened with a really interesting cohort of grown-ups who had missed out on college because they were technically competent and a good pair of hands and had been sucked into the celtic tiger tornado more or less straight form school. They were great to deal with because they brought something to the table at lectures and had a very direct idea of why they were embracing 4 years of poverty in college. I caught up with one of these blokes last week when I saw him having a late lunch in the coffee dock. Turns out that he was back in college for a few days to run some samples through the HPLC; because they needed to be processed but also because he needed to be able to add "can drive an HPLC" to his CV.  He could do this because he is currently between jobs, which a cause of some anxiety, but he wasn't going to fret at home if he could be twirling the dials in the lab.

I suggested that, while getting down and dirty with the instrument was sensible if it didn't cost too much, it would be silly to go an an HPLC Course; if such a thing was on offer. All technical instruments are different; heck, each brand of HPLC is different, but they are designed to be used, if not by idiots, at least by technophiles. I reckoned that a couple of days would be enough to be able to blag "HPLC Effective" onto his CV. What he couldn't work out when he was hired by Chemicals Inc., he could ask about, or read the S.O.P. . . . or even peruse the manual.

That all reminded me of a family legend about G [prev] when she was young before she became a wife-and-mother she took herself off to London to seek her fortune. This was in the 80s and there was bugger-all in he way of work in Ireland. She decided, after some earlier experience working in a factory in Germany, that office work was easier on the back and paid better too. So she presented herself for interview at some financial institution as a secretary, typist and all round effective.
"Are you familiar with the Wang?" asked the office manager
"Of course" replied G
"Can you start Monday?"
"Of course"
So she started the next Monday and her desk was a Wang 1200 console. She leaned across confidentially to her neighbour and asked "How does this yoke work?". By lunchtime she had made a friend and made enough inroads into 1980s word-processing so that she didn't let the side down. Technical things, if they are designed properly, are easy to use. If they are not so designed, they don't clutter up the market for very long. I'm sure that,, at the time, secretarial schools were willing to take folding money from you to teach you "How to WP with the Wang 1200". All the pupils would have found it excruciatingly patronising and slow. Those being funded by their employers would be happy enough to have a week off real work. Those paying their own nickel would less happy about the time-wasting but hoping that the course qual would get them work.