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.

Monday, 16 October 2017

Ophelia incommming

The L picture is a still from which tracks winds in real time all over the world; it shows the whole of the Atlantic. The site allows you to rotate the globe, so I can assure you that the zoom R of incommming Ophelia is the most exciting thing happening on the planet at this time. The arrow is to show the direction of travel. This Mother of Storms is about to travel through Ireland for shortcut.  Schools are all closed including (message at 2045 last night) The Institute, so I'm hunkered down at home. We spent yesterday afternoon battening down the hatches, reefing the tops'ls, and securing the raffle about the decks. We've made sure the life-boat has water [no electricity no pump] and ships biscuit and there is fuel for the wood-burning stove, so we can heat soup and make chapattis. I also took 20 minutes to fuel-up and sharpen the chainsaw and put that in the back of the car . . . before the news of school closure came through.  The blessing is that, in contrast to the Big Wind of January 1839, Ophelia is making her passage in daylight.

The Darwinday Storm of Feb 2014, when I had to cut my way back home through a fallen tree, is in the Ha'penny place compared to Ophelia which is said to be bigger than Charley 1986 and possibly bigger than Debbie in 1961.  Reading up about those big Irish storms of the last century shows that we have way more information now - see frighteningly beautiful maps above - than back then. The meteorologists 'lost' Debbie for a few days between the Cabo Verde, where it killed a planeload of people, and its arrival in Ireland.  No amount of information or preparation is going to keep trees upright if they are worked to their resonant frequency.  The other blessing is that Ophelia will pass quickly through on her flight to Russia and this time tomorrow we'll tidy up and move along too.

Sunday, 15 October 2017

Away with the fairies 151017

Very miscellaneous.

Saturday, 14 October 2017

The Outdoor Man

Another of my friends has recently pegged out. We first met him when he and M'sis were living on Erraid in 1997. Or rather we met his legs, because that’s all we could see of him poking out from under the Erraid tractor trailer as he welded its broken axle.  Getting to Erraid, an island, off an island, off the West coast of Scotland, was the trekkiest one day journey (from O.Fr jornee a day's march) we made with two small children. Taxi to airport; plane to Prestwick; train to Glasgow Central, shuttle to Glasgow Queen Street, train to Oban, ferry to Mull, minibus to Fionnphort, row-boat to Erraid, wheelbarrow for luggage to house. You may be sure that the Erraid community of candle-dippers and wiccans really appreciated having one good pair of hands about the place.

For the next tuthree years, “McAndrew” (because we encountered him in Scotland) and McSis would come to visit us in Knockroe for about a week.  He was kindly and avuncular with the girls but had little patience for kitchen chit-chat and catch-up. Sometime early on day 2 of any visit, he’d ask if there was something useful he could do, preferably outside, preferably with his hands.  We’d set him some task which seemed incredibly daunting to me and he’d quietly set to: scoping out the problem, thinking about it briefly, then gathering tools and starting work. He’d come in when called for dinner or if his hat bowled away on a really wet gale but otherwise quietly plugged away at the job. Very occasionally he’d ask me to supply some brute force – heaving up a bigger-than-one-man rock or holding the other end of a long timber – but generally he preferred to be unencumbered with ‘help’. Unless it was Dau.II, he was always happy to have 5-6 year old Dau.II pass him nails.

I’ll give a couple of anecdotes because respect is in the details.  In scrabbling about the farm, we had unearthed a huge flat kidney-shaped stone and conceived the idea of raising it on 3 granite piers to make a garden table.  The stone was really flat on one side but undulating on the other. McAndrew coursed around the farm locating three sufficiently long piers [they had to be down in the ground at least 15 inches and we wanted to get knees under the table too]. He then carefully measured the underside of the table-top, dug three holes, dropped in the table legs and back filled them so they were immovable.  The tops of the three legs were at slightly different heights, so that, when the granite table top was flipped over, its undulations would complement the piers and the table-top would be perfectly horizontal. And it was so.

On the other side of the lane from the house we own another 3 acres of fields in the middle of which are The Ruins a.k.a. Hickey’s after the last family to dwell in them. When we took over, only one building had a (corrugated iron) roof and we used that as a reasonably convenient, reasonably dry, wood-store. As well as a roof it had an ivy-covered gable-end which loomed ominously over the lane because the ivy had penetrated the fabric of the wall and lifted the stones up and outwards. This was a source of 3AM-screaming anxiety for me because our lane is used by hundreds of hill-walkers a year getting access to Mount Leinster and the surrounding uplands. The nightmare was that our wall would crush a group of boy-scouts as they adventured up the lane.

McAndrew did things rather than worried about them and he hunted out a packing-box and a beer-crate that together would just give him access to the topmost stones of the disintegrating wall. Let’s start small, he thought, at the top he thought and carefully lifted out one stone . . . pause . . . there was no roaring avalanche, so he stepped up again and removed another stone. By lunchtime the wall was down to shoulder level and he could put the beer crate out of harm’s way. He then removed the last sagging 8 ft of the roof: carefully, to keep the corrugated sheets for recycling. Having dealt like a dentist with the cause of the decay and dug back to sound foundation, McA then rebuilt the gable-end wall 8 ft back from the lane (and the innocent walkers) – the neatest, solidest, and most functional dry-stone wall on the property. He finished off the apex of the shed-wall with a hit-and-miss wooden curtain (like we built our woodshed last year) made of creosoted match-board recycled from the house’s original kitchen. That solution kept the wall to head-height and allowed draft to circulate through the wood shed behind the wall. It was triumph of recycling, appropriate technology and getting on with things. He was really happy with the result; I was delighted.

The next year we decided to recycle one of the wrought iron gates that had been thrown into a ditch on the property. Painted up it would make a nice entrance from the lane into The Ruins. That meant straightening the existing pier so it would hinge the gate and sorting out some recycled ironmongery to hold gate to pier and allow it to open. That required a lot of patience, WD40, a lump-hammer and a vice-grips. But the icing on the cake was finding another pier for the new gate to close against. I was useful here because the only suitable granite pier was 150 m away, so I was allowed to help push/pull/drag the stone on a sack-trolley up the hill to its new site. As with the legs of the stone table, you may be sure that when the jamb-pier was dropped into its foundation hole, the top was precisely level with the top of the gate. It didn’t have to be like that for function, but, for McAndrew, it could be none other.
That’s the thing about McAndrew, he made a difference to the things around him and by doing made other people happier. I learned a little from his confidence that the sky wouldn’t fall if you stopped thinking and just made a start; I have fewer nightmares now and do more about the place. McAndrew’s changes to the landscape will be there, unsigned but appreciated by those who use them, long after we are all gone.

Friday, 13 October 2017

Top Billing

In science, as among movie stars, it is so often about Meeeee! Back in the early 90s, I was working in a minority-interest field of science.  I was plugging away at the human genome, the aspergillus genome, the yeast genome, the candida genome, the drosophila genome . . . all before any of those genomes were delivered complete into the public domain. That's where I had two of the three big ideas I've had in science. We had a corner on a particular, peculiar way of looking at genetic sequences and were applying our technology to the genetic inventory of one species after another. The inside joke was that we should write a mail-merge program to write the same paper again and again only changing the name of the species, the tables of data, and a single sentence of the conclusions. The convention in bioscience is that the last author is the PI, the principal investigator, the Gaffer, the one who wrote the grant to land the money for everyone else's paycheck. The first author is often the youngest person in the lab; they are The Effective, the one who has done all the grunt work. As a youngster starting out , the number of first-author papers is what gets you interviewed for a permanent position. Anyone else involved in the project is shovelled into the middle ground. For us there were rarely more than 3 or 4 authors to be listed.

In biomedical science, later on in my career, it was rather different. I remember having a one-side-heated conversation with a post-graduate in the ophthalmic genetics lab one floor down. He was raging because he had been placed 5th / 8 in the billing for the lab's latest paper. He was convinced he should be 4th! I was amazed that someone would a) care b) be so precise in the algebra.  The other thing that used to annoy me when I worked in a hospital setting was that the consultant surgeon and often his registrar would get their names on the scientific papers when all they had contributed was some very delicate butchery to provide the samples which the real scientists had analysed. I said at the time that you should only get your name on a paper if you could present it at a scientific conference if/when The Effective fell sick at the last moment. You can do this if you've written a chunk of the text, or you're the boss, of you've heard & seen the results thrashed out at numerous lab-meetings. The surgeons are far to busy to attend lab meetings in the research centre so they often haven't a clue how their abstracted tissue is analysed.

Sometimes, the paper results from the collision of two different trains of research. Then you have two young turks, of similar seniority, who have both put their all into the project for the last several months. The solution to that is "joint first author". I know at least one case where, the most ambitious and, let's face it, ruthless of the two has gotten his [almost always a he] name physically first among the joint-firsts. Papers are usually cited as Smith, J.  et al. (20xx) so it does make a difference in external perception. So it's very much a case of "Eclipse first, the rest nowhere". In my own case, we were on a collision path when my old boss, who had moved to Nottingham, and my current boss in Dublin found that they were both analysing the same pair of organisms in essentially the same way. My oppo in Nottingham was much younger than me, just starting out and a woman-in-science. Of course, I let her take first-first place in the list of authors.  This helps explain why I am a nobody at The Institute while the other actors here cited are Rulers of Empires at home or abroad.

As I said in the hook at the top of this piece, the ambition, the chutzpah, the meanness are all present in Hollywood. The megastars in any film get top billing on the promotional material. Even if it means the order of names bears zero relationship to the mugshots in the back-ground photo. Actors have agents to fight their corner on this, because the order means money. If two monster stars are neither of them backing down, you can stagger the names so that one is leftest and the other is toppest [R] and let their agents fight over how many pixels higher or lefter their client finishes up.

Thursday, 12 October 2017

Homeless is Hopeless

"Homelessness is too often accompanied by hopelessness", that was one of the ideas floated across a packed theatre in The Institute yesterday morning, by Fr Peter McVerry the Voice of the Homeless in Ireland. He is a Jesuit priest who, many years ago was working with school drop-outs in Dublin. One day he found one of his charges, a 9 year old boy, sleeping rough. It was huge eye-opener for the good father as he realised that you'd be at nothing trying to keep kids in school if they don't have a home to go to after school's out. The event shook his certainties and he shifted his focus to set up what eventually became the Peter McVerry Trust. I mentioned him a couple of times last year [bloboprev] getting angry but not truculent about the unwillingness of the Irish government to build homes. For him anger is a driver for change.

McVerry was down with us to launch Volunteer Day at the Institute where students, and others, are encouraged to give a bit of time to Fairtrade; or horse-riding with the disabled; or meals on wheels; or the local hospice; or sorting books for Oxfam. He started off by explaining why he had given a life-time to others
  • it was the christian, or at least the humanitarian, thing to do
  • to express gratitude for the fortunate circumstances of his birth which gave him huge potential . . . if I hadn't joined the Jesuits as a young man. The obvious way to express his thanks was to give back.
    • He noted that these push-pulls had been widespread among the religious in his time. Sadly the implementation of humanitarian protocols had been completely un-audited and so had too often degenerated into abusive relationships.
  • every day he gets some rewarding feedback. Those endorphins are their own reward. Heck, they'd have to; because these guys aren't driving BMWs between their homeless-hostels.
To a hammer everything looks like a nail, you may say, but McVerry makes a good case that having a home is the prerequisite for a) health [TB is on the rise in Dublin rough-sleepers] b) happiness - rates of depression are higher in hostels than in age matched 'homed' people c) productivity - it's hard to apply for a job if you don't have a return-address and it's much harder to hold one down if you can't get a clean shirt together.  Yes, yes, not all homeless people are deranged drug-abusers: the PMcVT has on its books homeless students and homeless professionals. and only a minority of their client base has addiction issues. But these things are globally relative. In Ireland, contra Bangladesh, everyone has access to clean potable water; although we're unwilling to pay for it. Without clean water you don't reach adulthood in many cases; you're dead of the flux before housing becomes an issue.

Later with a rhetorical flourish the old chap (he's 74 but definitely not retired) asked us what was, for those directly affected, the hardest part of homelessness:
  • not the absence of a regular bed; 
  • not the boredom of endless days sitting around without purpose; 
  • not the hunger or junk food. 
What matters most to the homeless is the feeling that nobody cares whether they live or die. It is a strong policy in the PMcVT that
  • phone calls are always returned;
  • stories are always listened to;
  • respect is always shown. 
Even if there is no bed, no sleeping bag, no food parcel, you don't get the door shut in your face.

Challenged by change
And here's the thing, volunteers are generous with their time, yes, but they also benefit from the relationship. They are changed by the encounters with the dispossessed and if they can take the stress of dealing with such troubles, they are changed for the better; on the basis of what kills not, fattens, if no other. If you are the least bit open to The Other, then your certainties, your values, your prejudice will be challenged. Like US Army grunts who fought next to compatriots of a different colour, and came out realising that white people could be kind and some black people were real crap at the blues. For McVerry himself a key moment was when a young chap told him "The fact that god might exist depresses me" which McV took to mean that the boy felt he was always being judged and found wanting / sinful / bad: that his condition was his fault. The priest absorbed this and turned his face from the god of judgement [R] with whom he'd grown up towards a god of compassion.

Now let's be a bit critical of the PMcVT and its work: they're big enough. In 1980s Britain, the weekly satirical cartoon programme Spitting Image mercilessly guyed the royal family, celebrities and, in particular Margaret Thatcher's conservative government. A case has been made that Spitting Image, which had HUGE viewership each week, acted as a safety valve that prevented a revolution against the divisive changes that were being imposed on the British people.  If Peter McVerry and his Trust did not exist, maybe the government would be compelled to vindicate the constitutional rights of all its citizens. That would require a revolution, of course, we'd have to pay more tax, and the useless mouths of the quangocracy would have to find useful work outside the public service. I've been agonising about the ethics of the voluntariat since at least May 2014. But then you may not believe that the government is capable of organising anything more challenging than ordering posters for the next election. If homelessness hurts then you just have to roll up your sleeves and do what you can. For Peter McVerry, like fellow christian Martin Luther [prev], he can do no other.

Fr McVerry talked about how the people in his Trust, by giving time, respect, homes, support, food and hope to the dispossessed, receive as much back in self-esteem and a sense of worth. Thus give and take become an exchange. That resonated with me strongly because last week I'd seen a fascinating video about Proto-Indo European and what we can deduce about the culture of these our ancestors from linguistic analysis. It turns out the PIE word for give is the same as the word for receive/take! Exchange to mutual benefit is in our DNA. I barrelled up to him  after his talk and shared this insight to him, which meant I got to shake his hand - an honour.
The Peter McVerry Trust is in the middle of a fund-raiser:

Wednesday, 11 October 2017

International Day of the Girl Child

IDG? That would be today, 11th October as it has been for each of the last 5 or 6 years. I like girls, I shared a house with a couple of them for about 20 years and I was delighted to see them grow up straight and tall; becoming canny and independent young women. But, notwithstanding my Victorian father demeanour and insistence that they wear sailor-suits and sing a lot, Dau.I and Dau.II had a relatively easy time of it. With no brothers of similar age, they weren't made to do more than their share of the chores; I didn't insist that they marry a crusty farmer from up the valley; they got access to education even if it was not in school [how - result (whc applies also to Dau.I)]. It's rougher for girls in, say, Africa just because they are girls and the local culture doesn't seem to value or appreciate them. Which is damned . . . stupid, according to Caitlin Moran. Although our girls didn't go to school, I can see that for poor, disenfranchised, girls formal school is a way out of the poverty trap. Reading empowers especially if you don't have an iPad. Chess is good too.

Worldwide here are 1.1 billion girls - females under the age of 13 - and collectively they do 550 hours of housework every day: which is about 40% more than their brothers contribute. But wait, that's only 30 minutes each a day; doesn't sound oppressive to anyone who grew up on am Irish farm like our girls. But there are girls out there, from the First World, who can't boil an egg or sew on a button, let alone make a dress or make a soufflé; let alone let alone fetch 25lt water from a distant well before school and gather firewood on the way home, so I guess the average isn't really the useful statistic.

Much earlier in the year, girls around the world were asked to send in stories about how they triumphed in an adversity which was brought upon them because they had two X chromosomes. Today, at UN HQ in NY NY, they are having a symposium to hear these voices. Can't be there but can bring you some vids on the general subject
Well there wasn't much joy in any of that, eh. Clearly something is wrong with the world. But here's something you can do today. Find a girl, any example will do, give her a big hug and tell her that she is stonkin' wonderful. You'll promptly get arrested by the pedophile thought-police which will help the child remember the event for longer. Recognising your sacrifice on her behalf will ensure that she walks taller, and takes additional classes in assertiveness, which will be good for everyone she encounters. It's a plan.

Tuesday, 10 October 2017

The Skipper

My father was born in London on 10th of October 1917. That was exactly 100 years ago today. I'd like to get a glass of champagne into his hand to recognise the full century but I can't do that a) because he died in January 2001 at the age of 83 a few months after we celebrated the parents' 50th wedding anniversary and b) with the cremation and all there is no hand. I wrote last July about how his restless and questing acquisition of knowledge finished him off in the end. If he hadn't felt the need to read all the Sunday papers, he might have had a free hand to steady himself on the way up to bed. With his hands full of newsprint he fell back down the stairs with more noise and commotion than he'd intended on his way upstairs. His children were assured that he was doing alright and that a full recovery was expected but five days later he was dead. So none of us got to say good bye. In Britain they are famously inefficient and drawn out over funeral arrangements and it was a full ten days before the Old Man had his final trip to a crematorium.

When I finally got back to work I had an insightful conversation with my boss about [not] saying goodbye to parents. His position was that, if I had failed to have The Conversation with my father, it was because at the time it didn't seem appropriate, so there was no point in beating myself up when the door clanged firmly shut on ever having that Conversation. I thought that was wise, or at least that it provided a ha'porth of solace. I miss him occasionally: usually when I dig up a nugget of information about the sea or maritime history; or when his grandchildren achieve something nifty.

A couple of days ago, I reminded my brother and sister that today was Der Hundertjahrfeier because its hard to know where to send the birthday card and I didn't want to let the day slip by entirely unacknowledged. I wrote last January about him being a stickler for time keeping; how he was late for his own funeral; and how the irony of such a final comment on a life-time's cultivated habit would have tickled his sense of humour. Sunday lunch was not only at 1 o'clock +/- 2 minutes, it had a comforting predictability: a joint or a chicken, vegetables, gravy and roast potatoes followed by pud. He would volunteer to wash the dishes but that meant that we three children had to facilitate the process: one to clear the table,  one to dry the dishes and one to put them back in their cupboards. He was willing enough for the chore but casually terrible as a plongeur! If something appeared on the draining rack that was really unacceptable, the drier would pass the offending article behind the Old Man's back to the table-clearer for another go through the suds. At Christmas there would be a huge to-do in one corner of the kitchen as he made bread-sauce <glarrk>. Nobody else in the family would eat the stuff, but it was an immutable tradition. The other food-error that he was never allowed to live down was when he was once tasked to make breakfast on a family holiday, but burned the toast, used lard instead of butter and tried to disguise the shambles with a thick layer of marmalade.

The Skipper grew up in and around boats in Dunmore East where his father was harbourmaster. He was interested in maritime history because he was a career naval officer through the war and afterwards at home and abroad.

He could paint [above - on the beach at Duncannon with sweaters: when shall we three freeze again?], leaving behind a huge collection of water-colours. He could also play the piano nicely but did so rarely; he preferred it if music from an extensive collection of classical vinyl was roaring through the house - no head-phones till much later. But the records that got worn out weren't Bach or Brahms but Tom Lehrer poisoning pigeons in the park Ottilie [Patterson]'s Irish Night The Ould Lammas Fair and Peter Sellers taking the piss out of Ottilie's jollitie. I dunno, I guess you had to be there and we were, we were. I will finish with a limerick, a verse form of which the Skipper was fond . . . but one which breaks the rules, another thing he felt able to do:
There was an old man from St Bees
Who was horribly stung by a wasp
When asked did it hurt
He replied: quite a lot
But I'm jolly glad it wasn't a hornet.

Monday, 9 October 2017

A sad loss for science

In science you can't cover everything, you just have to pitch in to an area where you believe you can make a difference. Because of increasing specialisation, after a couple of years of contributing and reading the literature; and a couple of conferences presenting your results and listening to what your rivals are up to, you know all the Effectives in your field. You also identify the make-weights who, however diligent and worthy, are not going to set the world alight anytime soon. Just after the turn of the century, I got a seat in one of the first labs funded by Science Foundation Ireland SFI to give the frontiers of biological science a really good shove.  I recently wrote about those exciting times as a way of giving tribs to a very smart woman, then a graduate student, now CSO of a biotech company. That lab worked (and worked damned hard) because of the intra-group chemistry. Including the boss, there were about a dozen really clever people, half Irish half Other, rocking up to work each day. If you hit a wall or had half an idea, you could always find someone to help you to a solution.

I'm really sorry to report that one of that band of brothers and sisters! is no longer available to help us thrash out the big questions. Mario Fares [R] died, far too young, over the weekend and will be buried tomorrow evening. It is a  huge loss to science: he was only 45. If we had in biosciences the equivalent of Erdős numbers, then I'd be particularly proud to have a Fares number of 1. That paper, which was published after our days together in the crucible of SFI, came about because Mario was extremely generous with his time in mentoring our graduate student in the the correct way to approach the analysis of positive selection in populations. The standard tool for carrying out such analyses was/is called PAML, invented, maintained and distributed by Ziheng Yang from UCL. I quietly boast that I am one of a select [N=384!] group who has found a bug in PHYLIP, another key software suite in the field of molecular evolution. Mario, de lo contrario, during his PhD in Spain took his data through PAML, stress-testing it against every option and parameter in the program. At the end of that journey, he understood PAML better that anyone on the planet except, maybe, Ziheng Yang. You couldn't ask for a more authoritative source for the down-and-dirty on this sort of analysis.

I met Mario the day he stepped off the boat plane in Ireland. He'd signed up to Ken Wolfe's SFI lab but flew in on the Saturday before he was due to start work. It was a drizzly, stormy, soggy, Irish day. One of his new colleagues picked him up from the airport and said there was a garden party down the country and asked Mario if he'd like to drive for 2 hours into the wilderness for his dinner. Back in those days we had a Summer Solstice cook-out up on our mountain and invited everyone down from the city. When Karsten and Mario rocked up at 3 pm, they were the only people to arrive. Everyone else had decided to stay warm and dry at home. We fed and watered the boys, played petanque à la irlandaise in the drizzle and then they drove back to Dublin - a bit of a wash-out.

I wrote a few years ago about a brief 25 minutes when I gave back to Mario by acting as a sounding board for his latest Big Idea. A couple of years after we met, in the drizzle, Mario applied for a job at one of the other Irish Universities. Everyone encouraged him to do so because he was a great explainer and a really rigorous scientific researcher . . . and a walking genius! He applied believing it was a forlorn hope because, back home in Spain you only get places by being the protégé of a much bigger cheese. If you play your cards right and keep your nose clean, your mentor will secure you a suitable place. Mavericks need not apply. We have nepotism in Ireland, sure, but also an official level of transparency that often allows the best candidate to win through, regardless of who is his uncle. In that case, Mario was that best candidate and he went off to Maynooth for a couple of years. Before he left, I gave him some avuncular advice: in setting up his lab he shouldn't necessarily go for the cleverest candidates; successful scientists can be a bit driven and may be a a little too ambitious and such people can be a) a little wearing b) not the best pick for the greater good. If Mario were to pick one person who was good enough at the science, but had also coached a teenage football team or showed some other element of social competence then that might provide the social lubrication for really superlative science. That's the sort of group we had in the Wolfe SFI lab, which had eased Mario into the scientific establishment of a foreign country.

In any case, Mario was back in a couple of years with the offer of a permanent post in the Genetics Department in TCD; which Trinity people would regard as a step up. A short while after that he secured another job back home in CSIC-UPV in Valencia. Since then he appears to have juggled his commitments between both countries and getting paid by both institutions. The fact that the administrative burden of such a peculiar arrangement was taken on board suggests that he was really indispensable to both places. And now he's gone; several big holes, one in my heart, need to be filled.

Identigen clean up Switzerland

Identigen is one of the great successes of Irish biotech companies. I knew all the principals when it was founded as a campus company in TCD 20+ years ago. It span out of an academic research project that was using genetic fingerprints to trace the evolution of cattle. Two of the nicest young middle-class postgrads you could meet showed that they had the bottle to go out to the rawest parts of the Third World to gather and process bovine blood-samples. The academic project was a big success showing clearly that cattle have been domesticated twice: once up the Indus Valley and once in Europe [or more likely in the Near East with subsequent migration into the wilds of uncivilised Europe. The 'Indian' zebu cattle Bos indicus with the big dewlap and a hump on the shoulders are so genetically different from Euro humpless cattle Bos taurus as to suggest a separation of 200,000 years. That's waaaay before humans domesticated anything; so domestication must have happen twice in divergent undomesticated ancestral species. A case can be made that [some] African cattle have incorporated a third strain of wild cattle in their mix.

But one of the young turks in the Bovine Lab, working away on processing bovine blood samples to obtain genetic information, had the idea of monetising his hard-won lab-skills. He never finished his PhD but floated off on the idea that identifying individual cattle with a unique bar-code could help trace BSE aka mad-cow disease. That was the birth of Identigen. Getting the technology reliable and reproducible is only one part of launching a company; you then have to get alongside some venture capital; stabilise your burn-rate; scale up and start delivering product. The product here is information and their slogan is "from the pasture to the plate". Every side of beef is sampled as it comes through the slaughter-house, the DNA is sequenced for a unique code and that information is attached to the number on the ear-tag. If you-the-customer come down with food-poisoning or an as yet unnamed virus, Identigen can sample the container that held the hamburger and finger the farm it came from. If the problem is at source it can be remediated.

Many years later, I asked one of the directors if Identigen was profitable. He went all leery on me and answered "It depends what you mean by profit". I guess he meant that he was drawing a nice salary, as were all the Effectives, but the company wasn't coughing out payola dividends twice a year to its investors.

I was in the lab next door and a few years later we also developed some IP = intellectual property. We were working in the field of innate immunity and carried out some experiments which opened a door to the problem of antibiotic resistance. The results were preliminary but we had our own young turk who was ambitious and scientifically competent but more importantly was interested in money and the stuff that money can facilitate. We also had a medical consultant with wodges of folding-money in his golf-cart who might be induced to buy shares in a campus start-up. I had absolutely no interest in monetising my ideas and The Boss had a full time job and lots of extra-mural commitments already. I can't remember why or when the prospect of becoming share-holders in a new biomedical venture went tits up. But it never got off the ground and our tame senior medico never realised how close he came to being shaken down for some ca$h. We were capitalist wusses altogether.

Their entrepreneurial spirit has landed Identigen a 5 year €17 million contract to keep tabs on the quality, purity and provenance of Swiss beef and beef-products. For the next five years it will be much harder to get horseburger [bloboprev] in Zurich.

Sunday, 8 October 2017

Whacaccino go again

[You're getting this because of a weird blogspot glitch. I wrote an earlier version of this piece but when I pressed the [publish] button the thing disappeared from 'drafts' but failed to appear on the website. So I sat  down to recreate the post while it was still fresh in my 'memory'. An hour and a half later, I recd an e-mail from one of the handful of folks who get Blobs delivered, at their request, by e-mail a) saying thanks and b) attaching the whole text of the lost ms. Turns out that the recreated rewrite was pretty close [see alignment at bottom].  So apologies if you've seen something very similar to this before. Further investigation showed that the post, launched on 7th October was somehow published with a date of 28th September; probably because I messed up on 'scheduling']  
Mais revenons a nos breuvages!

What do you call a dentist who doesn't like tea?
Why do Communists only drink infusions? 
Because proper tea is theft.
I've been having a fare amount of tea anxiety recently. Me, like George Orwell, I'm a simple chap, and because of the culture in which I was brought up, I like a nice cup of tea [R source] When I was young and full of vim, I made tea by spooning leaves into a mug and brewing the stuff hot and strong. When the restoring cuppa was finished, I'd often spoon out the soggy tea-leaves and eat them too - rrrrroughage!  Now, however . . .
The sixth age shifts
Into the lean and slippered pantaloon,
With spectacles on nose and pouch on side;
His youthful hose, well saved, a world too wide
For his shrunk shank; and his big manly voice,
Turning again toward childish treble, pipes
And whistles in his sound
. . . I make my tea weak. So weak indeed that it is more like making mystical passes with a tea-bag over the cup than actually brewing tea.

I have no time at all for 'infusions' of chamomile, rooibos, ginger&goatsblood, bedtime, woowah-lift, fennel. These are not tea. I am with Wikipedia for the definition: Tea is an aromatic beverage commonly prepared by pouring hot or boiling water over cured leaves of the Camellia sinensis, an evergreen shrub native to Asia. I'd even make a, not really strongly argued, case that these infusions are potentially hazardous because, while tea and coffee have been extensively investigated by biochemists and medical science, we know much less about the chemical contents of random herbs and bushes that you find behind the potting shed.  While I'm moaning about misnamed beverages, I'll have a swipe at almond, soya, oat milk. I'm sorry but these are not milk any more than chamomile is tea. What evolution has developed as a miracle elixir for raising mammal-pups, the food engineer has to imitate with chemistical emulsion. Compare:
  • Soy milk
    • Filtered Water, Whole Soybeans, Cane Sugar, Sea Salt, Carrageenan, Natural Flavor, Calcium Carbonate, Vitamin A Palmitate, Vitamin D2, Riboflavin (B2), Vitamin B12.
  • Milk
    • Milk
Quite apart from the semantic objections, here is a list of reasons why soymilk is dodgy. To ring the changes in an exciting life, on Saturday, at home, if it is going, I'll have medium-large cappuccino. I don't do Starbucks, so I don't know the difference between cappuccino and latte, and I may be getting the latter. This Saturday coffee ritual was a cause of huge amusement to our Polish pal Tadek who stayed with us for two winters 10 years ago: "Hej Bobek, saboda, kawa har har har" then he'd make me keep him company eating chunks of cold pork fat because we were men.

Occasionally, coffee will be off-menu and the current replacement is Macaccino which is a combination of three completely different plant-products:
  • Carob is the bean from the carob tree Ceratonia siliqua which in Order Fabales included with peas, beans and the locust tree.
  • Maca from the root of  Lepidium meyenii a member of the Order Brassica / Crucifer which includes mustard, kale, radish and cabbage.
  • Lucuma is from the fruit of an Andean tree Pouteria lucuma, Order Ericales, the heathers, but  also including tea, persimmon, azalea and blueberry.
As you see these ingredients are not a million miles from recognisable food-plants but each will have its own pharmacopoeia and who knows what will happen if the raw ingredients are dried, powdered and mixed with hot water?  Part of the effort to push this beverage out on the market so that some entrepreneur can build a ranch-house with a hot-tub overlooking the Pacific coast, is to present a lot of dubious claims and hype on a web-site. I've been to and been snowed under with data, which I love because data-is-analysis but also presented with dubious claims and assertions Dense superfood nutrition  - boosts immunityadaptogen energy - healthy fatty acids etc. But there's also a sort of patronizing gloss to the snow-job. Here's Aaron telling how to make a cup of his product. How difficult can it be to spoon powder into a cup and add white emulsion and hot water, that it requires an instructional video?

But we haven't time to be drinking hot beverages all morning when there are data to analyse. Aaron has employed some real biochemists to digest the proteins in his cocktail to their component amino acids and reports their concentration in mg/10g powder. This is has the ring of truth because two of the twenty protein-constituent amino acids are missing. The amides Asparagine Asn N and Glutamine Gln Q aren't in the list because when you do a proteolytic digestion you destroy the amide bonds as well as the peptide bonds and convert these amides to their equivalent acid: Aspartic acid Asp D and Glutamic acid Glu E. I give the three-letter and 1-letter abbreviations [prev] in all cases. What's troubling is that Cysteine Cys C is nowhere to be found in Macaccino. That cannot to be true and must be a piece of slack-bob editting. Elsewhere on the site, an infographic of the benefits of particular amino acids appears. Cysteine appears there <whoop whoop internal inconsistency alert>; but Serine Ser S is missing and they've invented a 21st amino acid called maganese. Thinking from those errors and inconsistencies that the whole list of ingredients might be a bill-of-goods,, I compared the relative concentrations to the proportions found in UniProt the database of protein sequences. The graph of that analysis [R], show that the proportions are 'within the normal range' and that Arginine and Glutamic acid are higher in Macaccino than you might expect. As well as being an essential component of all proteins, Glutamic acid, serves us as a neurotransmitter. If the marketeers at Macaccino were scientifically literate <harrumph!> they might seize this information and add it to the miracle-grow benefits of their product.

You will have seen Michael Pollan's advice about food "Eat food; mostly plants, not too much" [multiprev]. Here is The Blob's recommendation for beverages "Keep it simple, stupid".

Data of reproducibility:  In my day job I often have to align two protein sequences. I use Clustal [here] designed and created by Des Higgins [multiprev] and others or T-Coffee ditto by Des and Cedric Notredame [Prev].The Blob has used clustal to align text [pledge allegiance] before.
CLUSTAL O(1.2.4) multiple sequence alignment
WhacI  MeImasimplechapbecauseofthecultureinwhichIgrewupLikeGeorgeOr
WhacII MeImasimplechapbecauseofthecultureinwhichIgrewupLikeGeorgeOr
WhacI  wellIlikeanicecupofteaRcreditsWhenIwasateenagerandknewnobet
WhacII wellIlikeanicecupofteaRcreditsWhenIwasateenagerandknewnobet
WhacI  terIwouldputaspoonfuloflooseteaintoacupstiraddsugarandmilkdr
WhacII terIwouldputaspoonfuloflooseteaintoacupstiraddsugarandmilkdr
WhacI  inkitdownhot-and-strong-Oftenenoughonano-wastejagIdscoopoutt
WhacII inkitdownhot-and-strong-Oftenenoughonano-wastejagIdscoopoutt
WhacI  hesoggytea-leavesandeatthemtoorrrrroughageNowhoweverIdrinkmy
WhacII hesoggytea-leavesandeatthemtoorrrrroughageNowhoweverImak-emy
       *****************************************************    :**
WhacI  teasoweakthatmaking-----apotismorelikemakingmysticalpassesov
WhacII tea--weak-Soweakindeedthatitismorelikemakingmysticalpasseswi
       ***  ****     ****      *  ******************************* :
WhacI  erthewate----rthaninfusinga------nything---
WhacII thatea-bagoverthecupth-anactuallybrewingtea
        :: *        ***        *..          ***

Shorts Sunday 081017

I really must get up to the Faroe / Faeroe archipelago, The Blob has only looked at the islands from afar. Despite the isolation and windy weather, some 65,000 people are hanging in there with their own distinct language and culture. They are making an effort to bring a cascade of $$$s and €€€s into the island by giving the region a higher profile. If you want a sentence translated into Faroese you type it in here, wait a few seconds and you call will be routed to a real islander who will say it back  in her/his native language. How cool is that? Don't, like me, try "Let us kill more whales" though, they are fed up with that old cliché and a nice lady will refer you to where you will be lectured about regulation and sustainability. via MeFi where some interesting commentary about bandwidth and infrastructural support in Faroes vs Shetland and other remote parts of the UK

Saturday, 7 October 2017

Worrying moment

I find it very difficult to be out on the town and buy a cup of tea or coffee. I know that you're paying for the waitron, the warmth and the seat out of the rain, but it just seems a big difference between 3c for a tea-bag and €2.00 for a tea-bag in a cup of hot-water. Cappuccino is somewhat different, that requires kit and skill that are beyond my pay-grade. aNNyway, my office at The Institute has a window! that looks out into . . . The Canteen. Proximity makes it convenient if I want to nip to the boiler and get some hot water to throw onto one of my tea-bags. I bring a handful of these things, as required, from home. I always bring 'lunch' to work, which is usually two slices of home-made sourdough on either side of a slab of cheese, with lettuce or rocket, if we have any in the garden. In my first week, I established that the rule was that hot water was free. Well sometime in the second week of term, a notice appeared above the hot-water boiler:
If you are bringing your
own tea/coffee
milk, spoon, cup
these need to be paid 
for at the till
I was there, with my septic mug with one of my tea-bag, the place was super-busy so I went ahead, filled up and slunk back to my desk. There was no way I was going to pay 20c for hot-water. When I got home that evening, I hunted through the kitchen closets and wider through the sheds looking through boxes of stuff for a 'spare' electric kettle . . . to no avail. The next day, I filled a couple of 500ml water bottles and resolved to drink cold water - which I basically never do. But over-night, probably through the medium of a nightmarish dream, I'd had time to reflect on the peculiar syntax, punctuation and fonts of the previous day's announcement. I went to check the wording at a slack time in the during and providentially found one of the caterers trick about with the machine next door. This lady patiently explained that the status quo ante applied, the new sign was to put a stop to the gallop of people who brought a tea-bag, yes, but used a company cup, wasted a disposable company spoon, and took an aliquot of company milk.

It boggles my mind that anyone would think that the cup and the milk etc. were sort of 'free'. Then again, the sugar, bucketfuls in sachets, is 'free'; as are the loathsome one-use plastic tea-spoons. I've reflected on my dubiously flexible ethical code; especially w.r.t. small-small spoons on/from airlines. But it seems wrong and sort of self-destructive to be looting the cutlery from your place of work . . . unless you feel really hard-done-by and exploited there. Cripes, I could walk off with a dinner plate every day, until I had a service-for-twelve and then sell it on Ebay. I think I learned this sketchy moral code from my Reasonably Honest father.

Friday, 6 October 2017

Feet of clay

I've lucked out in my career in science. Richard Wiseman maintains that we make our own luck. That lucky people [like my Mum and The Beloved] are in some sense more open to The Other and that risk-taking sometimes falls out better than the status quo. Louis Pasteur had a slightly different take on the matter "Dans les champs de l'observation le hasard ne favorise que les esprits préparés." = chance favours the prepared mind. In 1989, we resolved to return to Ireland after more than a decade abroad. I went round my small-but-perfectly-formed network of contacts in Dublin looking for work but only one of the fish was the least interested in biting. He encouraged me to apply to EMBO and the EU for research grants. We got the EU money as a retraining fellowship and that placed me in a field of science that was just starting to go ballistic. By 1992, the joke was that, if you could spell bioinformatics, then you could command a salary of $60K from MegaPharma. And indeed one of my lab mates ditched her PhD, went to work for Glaxo, and never looked back: she probably owns a yacht now. Ireland was punching way above its weight in the field, and indeed a case could be made that the word bioinformatics was first used [not by me, but by my boss] in a grant application out of Dublin. I know I'm not stupid but for years in the 1990s I wasn't the smartest boy in the room. All those early adopters are now full €100,000 professors; heck, many of their students are now professors.

Several years later, I met one of those Stars at a conference just after he'd landed a new position in a different country. He'd ridden into that job, as is entirely normal, on the back of his previous successes and was now experiencing imposter syndrome. I felt a rush of empathy because I've often enough been there myself [example]. I braced my pal up, telling him he was a walking genius and when I got back to my desk sent him a copy of The Flying Saucer chapter from Surely, you're Joking Mr Feynman.  The tl;dr version is:
So I got this new attitude. Now that I am burned out and I'll never accomplish anything, I've got this nice position at the university teaching classes which I rather enjoy, and just like I read the Arabian Nights for pleasure, I'm going to play with physics, whenever I want to, without worrying about any importance whatsoever.
Within a week I was in the cafeteria and some guy, fooling around, throws a plate in the air. As the plate went up in the air I saw it wobble, and I noticed the red medallion of Cornell on the plate going around. It was pretty obvious to me that the medallion went around faster than the wobbling.
I had nothing to do, so I start to figure out the motion of the rotating plate. I discover that when the angle is very slight, the medallion rotates twice as fast as the wobble rate--two to one. It came out of a complicated equation! Then I thought, "Is there some way I can see in a more fundamental way, by looking at the forces or the dynamics, why it's two to one?" . . .  The diagrams and the whole business that I got the Nobel Prize for came from that piddling around with the wobbling plate.

I was reminded of all this by a rather wonderful video about Euler's Disc in which two math geeks play with a spinning disc and record various bits of data as the thing wobbles its way to a stand-still. I don't think there is a Fields Medal [prevliers Wiles <not>, GrothendieckVillani],  getting incubated in there but it's a nice mix of trying to make data-gathering reproducible, forming hypotheses and testing them against the real world. That's a succinct definition of what science is about.  Another inviting aspect of the discussion is their embrace of error rather than trying to sweep it under the carpet. I wish we could do more such real experiments at The Institute where there is no Correct answer because nobody in the room knows what the outcome of the test or experiment should be. That's when real science starts.

And was my pal really burned out and ready for the scrap heap? Was he, heck! You can't stop clever people from having ideas and soon after our conversation, he embarked on a couple of new ventures; one a scion from his earlier work and one in a totally different field. Those feet of clay turned into the solid foundation of new work. If I had anything to do with this, it was only that I choked back my Brit repression and more or less told the bloke that I loved and admired him. That might have been so shocking that he woke from his existential nightmare.

Thursday, 5 October 2017

taxonomy of darkness

I remember a profound conversation I had with The Beloved in the Summer of 1975 sous le pont d'Avignon. We had washed up on the banks of the river as we hitched back from a visit to my sister in Aix en Provence. We'd been into town and seen the gob-smacking Palais des Papes, bought something to eat and sat down close to the [remains of the] bridge to eat. I launched into a rather one-sided discussion about what was the most sensible way to classify the living world. You could, I suggested with rhetorical flourish, bin all god's creatures which flew together and keep another mental container for swimmers; another for those that perambulated upon the face of the earth and maybe another box, with a lid, for things that lived beneath the surface.  But that, I suggested, was rather arbitrary: locomotion is only one attribute, and what do you do when adults and young have a different mode of transport? Adult locusts can fly, their earlier instars merely hop shuffle and scurry. Contrariwise, adult barnacles are a lot more sedentary than their free-swimming young. I concluded (would he ever shut up, TB was probably asking, I'm trying to eat my dinner) that it was best to start your taxonomy on certain fundamental similarities: between whales and bats and aardvarks and tigers, for example. They have very different habits and habitat and diet; are very different in size and life-span but nevertheless:
  • all have hair-follicles
    • from which have developed mammary glands
  • all maintain a set core body temperature
    • have a high metabolic rate to service the energy to do so
    • have lost the nucleus of their red blood cells to carry more oxygen
  • all have seven cervical vertebrae
  • many of them have limbs with five digits; at least as embryos
  • all have three teeny bones in the ear to transmit sound
  • all have a clear common pattern of embryological development
That last is key.  You cannot easily tell the difference, among mammals, among a week-old embryos. All 5000+ species are built from the same bauplan, we just have extras on the facade, the roof-line and the windows, but developmental inertia dictates the basic structure. A radical change in the early stages of development and you have a starfish, the nearest relative to vertebrates. You can extend these sorts of arguments out from mammals to embrace a wider taxonomy of other vertebrates; other animals; other eukaryotes and find places of primroses, mushrooms, algae and bacteria. Scientific taxonomy is based on evolution: the things that are hardest to change tend to be deeply embedded in the tree of relationships; 'trivial' differences are out on the terminal branches. We're really close to chimpanzees, less so to whales and much less so to sharks.

This all came to mind as I followed a story about using social media to locate crime scenes. Europol have to look at a lot of deeply distressing pictures in order to break up paedophile porn rings. It is the nature of the beast that, while you can tell that abuse and exploitation have occurred, it is impossible to say where these dreadful things happened. It's a bit like trying to carry out a murder investigation without a body. Some bright spark in Europol had the idea to fuzz out the people and post some pictures of hotel rooms on Twitter to see if anyone recognised the place.  Clearly you don't want to focus on the colour of the carpet or the wall-pictures because these get changed and upgraded in hotels that aren't total flea-pits. But the over all structure of the room, the position of the bed w.r.t the window and the en-suite and the light-fittings, are much more likely to be diagnostic because they embody more structural inertia. Twitter is huge and the number of people who holiday in Mauritius AND use Twitter is considerable and soon enough a match [R: scene-of-crime above (with person blanked out) / promotional material below] popped up in the Marlin Creek Hotel on the island.

Europol didn't appear to know that there was a parallel investigation going on in North America at TrafficCam. If you are nerdy about such things and can blow up the details in the pictures, then you can check out the electrical sockets which are madly and maddening diverse across the world. You couldn't do this location matching with Irish Pubs, they all have the same clutter.