Shut out

The COVIDs are coming! Came to work yesterday = Friday as normal and was told that my Alma Mater TCD had fielded a case of CoViD19 and they were shutting down. There was nothing so dramatic, let alone timely, on the TCD website. . So I googled for deets and found:
"The relevant part of the University (Floor 4 of the Trinity Biomedical Sciences Institute), and the lifts in TBSI, have been closed as a precautionary measure and will be cleaned in accordance with HSE guidelines. The rest of the University is open and operating as normal.”
Most of the similar reports have shown a picture of the iconic Front of Trinity:

which is about as far away from the TBSI as possible while still being on the same campus. If you a) live in Dublin and b) want to avoid buildings where one CoViD+ perp has been identified, then get your search image from the more modern building at the head of the post. Dau.I works in the library about 200m East of the TBSI, I'll tell her to cross the street when she goes past the building <not>!

I know rather more than I should about this because I used to work there up until the end of 2012 and was having occasional meetings and teaching gigs up until about 2015. Right up-close-and-personal there: on the 4th Floor of the TBSI in TCD! Around about the time I ran out of TCD money and had to get a proper job at The Institute, a palomino left the same lab with a PhD to try the commercial world of research in MegaPharm.

I sent him an ironic e-mail "We escaped just in time"
To which he replied "My great timing! I was there yesterday! The TCD Postdoc Society organised a careers day and they wanted people who managed to escape to industry. I dropped by the 4th floor to say hi, to the old lab. The sick guy is from XXXX's lab. Today when I got to work I was told to get my laptop and work from home. No good deed goes unpunished!"

That helped me zero in on the perp to the extent that my old lab-mates were not in the front line of Assault by CoViD . . . or at least it will be a few days before they go symptomatic. I was tickled by the idea that they would be doing a blitz on the lifts. When I worked there I never used them! I couldn't countenance the carbon footprint of raising me up without any effort on my part: like a balloon. On the stair front, I don't do trudge, so I always run up t'buggers . . . and am utterly out of puff on landing. This story gives me a further reason to be lift-smug because CoViD emphasises that these vehicles are a perfectly designed incubator / propagator for spittle-borne infections.

Another of my TCD contacts is the lab manager for another of the laboratories on Floor 4 and I commiserated with her about the task ahead. De-contaminating a movable box with six clear, cleanable surfaces is imaginably 'easy' - just get in and souse the surfaces in bleach or fill the box with ozone. Cleaning a lab full of drawers, cupboards, shelves - all laden with bottles, beakers, plastic and metal gizmos and biological materials: that sounds like a nightmare unless you're going torch the whole place and have all your Effectives start their experiments again.

Trinity is a big business; with 2,600 employees and 18,000 students. They can't [yet] close down the whole place for one case, they have to be proportionate. This weekend several plane-loads of Italians are coming in to Dublin because they had tickets for the [cancelled] Ireland vs Italy six-nations rugger match. Insurance won't refund your money if you choose not to fly, and what's not to like about the prospect of a weekend mooching around Dublin without the distraction of the sporting fixture? It's going to be impossible to be up-to-date with CoViD19, so The Blob isn't even going to try. But it was hard to resist a comment on this chapter.

Star-struck by star-stuff

Tremendous coup at The Institute: someone persuaded Jocelyn Bell Burnell [bday tribs] to follow me down to Carlow to give a talk to local secondary schools about the fact that we are all made of stars. She is a national treasure and has done as much as anybody on the planet to recruit and retain young women in physics.  As a post-graduate student, she famously didn't get a share in the No-Bell Physics Prize in 1974 for discovering pulsars against the express orders of her boss . . . who did win the Nobel that year. The delicious irony is that, partly because she missed out on the earlier gong, she was awarded a Breakthrough Prize in 2018 that was worth $3 million - about 30x more than the might have been Nobel. JBB donated that money to establish a scholarship fund to facilitate unlikely people [like women] to do a PhD in physics. There is so much to like about her style! [R we gave her a biography of local boy John Tyndall]

Before she could scan the heavens for radio-waves, and in due course discover the first pulsar, young Jocelyn had to build her equipment. I'm ten years younger than her and in a different field but I was too late for the era which blew their own glassware to make the instruments with which they measured their tiny patch of the infinite universe. All pipettes and Petri dishes were glass however; everything washed after use and ready for another experiment.  It was left to planet-eating subsequent generations in Genetics to adopt use-once-and- throw-away economics. The Interplanetary Scintillation Array radio telescope was built of wires strung on poles across a 4 acre field near Cambridge, England and Jocelyn became practiced in driving those poles in with a sledge-hammer. No bottled water in those days, just hard graft and carry on.

I am in my last weeks teaching at The Institute and one good reason for going is to make room for a younger person who will be a more attainable role-model for young women in science. I don't imagine any of my students look at a silverback like me and think "with hard work and good luck I could become that person" but they could do that with a few of our younger, fitter lecturers. There must have been an element of that when the schools talk was arranged at The Institute. Somebody had the bright idea to invite Aoife Ryan a PhD student from DIAS to talk about her work and the journey that brought her there. She wearing the hi-viz jacket because that is the 'lab coat' for radio astronomers and, like JBB, Aoife Ryan had to go out and assemble her own measuring device. Things have moved on in 50 years, wooden stakes have been replaced by plastic poles and the receivers are more sophisticated /expensive / sensitive, but the repeated history was striking. She couldn't have done this on her own because the field is too big and the ambitions are much higher, The LOFAR [Low Frequency Array] telescope, indeed, is bigger than a country as it patched together sites across 2000km to the other end of Europe. The Irish field is in Birr, King's County; just up the road from my home-place.  LOFAR ias centred on a site in Exloo, NL but has stations in UK, DE, IT, SE, FR, PL and LV, as well as Ireland. Birr Castle is a particularly appropriate location because from 1845 to 1912 it housed the largest telescope in the world, a record currently held by LOFAR.

What do you do with such a mighty, and nifty, piece of appropriate technology? Aoife Ryan is using time on LOFAR to study solar storms which spew out electromagnetic pulses. The Sun and fluctuations in its activity affect and surprisingly wide range of events on Earth 150 million km away. We're all hoping the next Big One won't be pointing directly at us like the Carrington Event which fritzed out the electromagnetic comms world, such as it as in 1859, 161 years ago this August. But  we lived simpler in 1859 and 1959: cars ran without on-board computers; people wrote and sent letters; at a pinch folk could cook on an open fire if all the power stations blew their gaskets. A world without electronics will be far more compromised than one with COVID-19. A roomful of teenagers listening to someone in their 20s being so brightly enthusiastic and so clearly accomplished - some of them must be marking their ambition cards to think "I could do that, I could be that person, let me at it, get out of my way . . . the Universe, here I come"

More Women in Science

Iced

. . .  by ignorance. You know more about dry-ice (solid carbon dioxide) than you think you do.
1) it is cold - you have to get CO₂ down to -78°C before it freezes. It is therefore useful for shipping stuff cold - biological samples or high-end meat. Regular ice leaves puddles behind.
2) it sublimates - avoiding the liquid transition between solid to gas that most other chemical compounds experience. When sublimation happens a white cloud fills the air and wafts across the floor - this makes good theatre in talent shows or for Macbeth's witches.
If you have read The Blob from the beginning and can remember it all a) you're doing better than me b) you'll know that CO₂ can be deadly: it killed 1700 people and countless animals when Lake Nyos erupted at midnight in 1986; it can also terminate mice inhumanely; one of my colleagues wasn't killed by the stuff - but it was NDE close.

Some clever clogs in Russia obtained a 25kg boxful of dry ice and threw it in a swimming pool for a birthday jape. What could possibly go wrong? It should be okay because the swimming pool is outside and CO₂ is a) gas b) heavier than air. If everyone stays standing and there is the slightest breeze and/or the ground slopes away in any direction then there will be calm after the foggy sublimating excitement. This argument is similar to that where short people [aka children] were disproportionately killed when the Syrian government lobbed the nerve-gas Sarin into the rebel-held suburb of Ghouta in August 2013.

It would be terminally foolish to dive into a swimming pool buried under a fogging blanket of carbon dioxide; but 3 people at the birthday party elected to do that and had no more birthdays. Sad really; really sad, so young and full of promise. It is possible that alcohol was involved because a) it was an adult birthday party b) that has a huge capacity for making people do things that seemed a good idea at the time.

Hate

St Greta of Thunberg was addressing the plain people of Bristol at the end of last week about the end of the world as we know it. Several blokes from the local area decided that the most appropriate response was to shoot the messenger. That is, of course, a metaphor; the actual responses spattered the target: some worse than mere shooting, other peculiarly graphic. It's hard to say which was the least objectionable contribution to public discourse.

• Can someone grab her pigtails and ms trunchable her over the fence
• Crush the bitch
• milkshakes at the ready
• i would borrow a fire-engine and spray the lot of morons with water-cannon
• She should be burnt at the stake!
• Her parents need to slap her with a brick.

Your task is the match the comments to the face.
And the names: Anthony, Ash, Kevin, Kev, Max, Stevie
And test this hypothesis: the degree of hateful violence is correlated with the presence of alcoholic bevvies in the profile picture - presumably a key attribute of the perp's identity.
Answers in The Bristol Post. Ramifying comments on Mefi.

Wot are we like?

Logistics

As you see from the above, I was in The Institute's aircraft maintenance hanger with a bunch of teenagers who were having a day of science and technology. Someone has donated a miscellany of aircraft, aircraft parts and aircraft extras which more or less fill the space. I like the warning sign [above], it is so retro: like the old films where the pilot calls "Contact" and a guy in overalls heaves at the propeller to start the engine. Normally the hanger is where our student aircraft-maintenance engineers get practical experience, but as it was half-term, no one was there to answer our [many] questions.

I did the best I could to satisfy their curiosity and interest. After I regaled them about bird strikes, one of them asked about a little triangular window in the side-windscreen of a Cessna 335 II light aircraft. It didn't really look like the one shown R but the function was the same.

When The Boy realised that he had no future working in Ryanair, he slung his hook to seek his fortune elsewhere in the airline industry. After a bit trouble and a bit of travel he secured a position in the logistics wing of British Airways, operating out of Heathrow. LHR is one of the busiest airports in the World shipping not just people but also stuff which needs to get somewhere else in a hurry. The company was in the process of transforming itself into a fully automated, containerised shipping service and before he left, he was well paid but very bored. On average in an 8 hour shift, he was actually working about 20 minutes. Unless you call scanning a series of progress monitors to make sure the robots were shifting the containers through a massive, multi-level hanger.  Before that it could be quite exciting: like the time 8 tonnes of fresh shrimp [from BKK to JFK vis LHR] missed its connexion and had to be <fizz, fizz> dumped. "Useless if delayed" indeed. That was a loss to someone or their insurance company of about $100,000. In those early days, sometimes the connexion would be so tight that someone (often The Boy) had to trot out onto the tarmac to hand deliver a small package to the crew of a departing plane. It may be a fantasy but I got the sense that the envelope was handed up to a triangular window in the cockpit.  As the cockpit of a 747 is 7.5 m high, I suppose they used a rather long cleft stick.

Less than a week after I was reflecting on the problems of getting stuff from one place to the other, I came across a related story of shipping human organs for transplant.  As ever, interesting and informed commentary on MeFi.  The journalistic point is made that dozens of kidneys a year get lost in transit or delayed in logistics centres or shipped to BOZ rather than BOS. You surely know someone, quite possibly yourself, whose checked bags got sent to the wrong airport and may or may not have been repatriated eventually. I bet everyone is happy to see their used underwear again, but if you had to take compo for the loss about buy this year's boxers, then it wouldn't be the end of the World. Not quite the same if it is a well-matched kidney that has travelled 3,000km to find a new home. But if you look at the numbers of AWOL organs as a percentage, it looks more exceptable

15 years ago, I was working in an immunology group in St. Vincent's Hospital. One strand of research (not really mine) was to study immune function of and in the liver. In those days, StVs was the Irish centre for liver transplants and our students were on 24/7 call to collect liver samples from donor or recipient when a match was made and the recipient was called in to obtain a new lease of life. I've forgotten much of the detail, but back in the day phrases like ischaemia or hypothermic machine re-perfusion would trip off me tongue. The transplant team used to have weekly meetings doing triage on the waiting list of people with liver-failure. They tried to apply rational, equable, criteria for the decisions about who would live and who would die.

Organ transplant is at the sexy pinnacle of the surgical hierarchy, perhaps over-shadowed by brain surgery but definitely a cut above tonsillectomies and removal of unfortunate tattoos. Part of the reason is because it is technically challenging and so only the steadiest hands and quickest reactions to adverse events need apply. But I think its éclat also hinges on the process being intrinsically more expensive than whipping out an appendix. One problem with the economics of health care and indeed the economics of government is that it is rarely expansive in its overview. The liver transplant team is making a hard choice between Hilda Doohickey, mother of six children vs Sean Masterman chairman of the local GAA Cumann. But they never think that they could disband the whole transplant unit and devote the money to

• safe-sex education for teenagers
• addiction centres
• mental health support
• a really good system of home help for the elderly
• pelvic-floor surgery for urinary incontinence
• speech therapy for kindergarteners

All of which are in the unsexy bin of caring for the least of our citizens. Does a just and fair society need heart transplants?

Vergüenza naranja evitada

Orange shame avoided

Thank heaven for a leap-year: without it we wouldn't have made marmalade in February, let alone in January when Christians get the task done. When my marmalade-mate 2014 - 2017 Aoife announced last year that she was completely Out of breakfast preserves, I replied tartly that my marmalade days were behind me. Why would I get washerwoman's hands and spatter-burns all up my arms to supply all my friends-and-relations and various hangers-on at work with marmalade when I could drop into Tescaldidl as necessary and buy a serviceable jar for €1.80 the pop? I demanded with bitter irony. But Aoife is nothing if not dogged and when she repeated her call to marmaladey arms <ouch>, I was prepared to say yes. Then my mother died which consumed all the January weekends and February was almost done before Aoife found a window of time to plunge into the centre of Dublin and buy the oranges from Sam Dennigan. Because it was late in the Seville Season, there were several blue furry oranges in the box, which 'Sam' helpfully swapped out from another crate, not failing to chid her <tsk tsk> for not coming in January.

On Monday night [24/02/20] when I came back from yet another trip to England, I called by Aoife's gaff to collect the oranges. The following evening I did another triage through the crate finding a couple more blue furries but several others which had been up close and personal to the write-offs but were, like the curate's egg, good in parts. When I did that Tuesday triage, I cut the oranges in half to make sure they didn't house a world of spores in a dried out husk waiting to change colour. These edge-of-sell-by items I piled into a large saucepan and cooked up sufficiently to deter further fungal invasion. I was therefore one pan ahead of the game when I sprang out of bed at 0600hrs on Leap Day.

Inventory for making marmalade [R]:

• Seville oranges: must be orange; 
• large saucepan: may be orange, here yellow
• cold plate for testing: should be orange
• cooked peel; is still orange
• tea-cup; can be orange, here red

The great thing about about Deli O'Smith's recipe for marmalade is that it separates in time two processes essential to the gelling of fruit preserves. First you release the gelling agent pectin from the skin, pith and pips then you add sugar [the acid is already there in citrus fruit] which binds with the pectin [and increases the viscosity with dissolved solids]. Other recipes for marmalade try to achieve these two processes in the same time frame. That, dodgy, method is much more like to result in disaster: the sugar is caramelising then blackening on the bottom of the pan before sufficient pectin is in solution for the gelling reaction.

This year, because of the triage, I twigged that cutting the fruit in half allowed a more efficient packing of the pan, so that the ratio of water to orange was more fruity. Between 0600 and 0645, therefore, I had filled our two biggest, tight-lidded, saucepans with halved, cleanish, blemish-trimmed fruit, filled the gaps with ~2.5 lt water and set them to simmer for 3 hours.

The next stage of the process, when the pulp, the sugar and the fishes of chopped peel come together in a final rolling boil, is best carried out in a wide jam-pan with sloping sides to maximise the surface area and hence the evaporation of liquid. A modest simmer won't do the trick. With all that sugar and protein, the liquid will at some stage in the process boil up [and over if the pan is too full], so it is better to split the pulp into a couple of batches and do them in sequence. Not least because if the first lot isn't setting you can add a touch more sugar (and/or a squirt of lemon juice; whose acid helps the pectin to set) the next time. In the Deli O'Smith protocol, this stage of the process takes not more than 30 minutes. You can do it by the clock or check by putting a dribble on a cold plate to see if it will set there. You have to have faith, sisters, because over-cooking will set the marmalade more chunky and less spreadable: less is more. otoh if you want a darker brew you can/shd cook it off a bit longer. Always, the last jars poured from a batch will set harder than the earlier top skims.

Just about the time the two 0600hrs saucepans were finishing their 3 hour simmers, the rest of the household started to wake up and demand breakfast. Dau.II, who had arrived the night before and is ever up for a colourful cook challenge, put herself on the task of scooping out the pulp, and processing the skins coarsely through a Spong hand-cranked mincer to generate the "fishes" of peel in the final product. The pectin-rich pulp was simultaneously [many hands make light work] pushed through a fine pored conical sieve.  Each panful of fruit generated about 4 pints = 20 fl.oz = 570 ml and my rule of thumb is to add 1kg of sugar per pint. That is on the low side of settability but if you add more sugar it just gets sickly sweet and the bitter grown-up bite of the Seville's gets lost in the wash.

A couple of hours and several cups of tea later, we had boiled down four or five batches of (2 pint pulp + 2kg sugar) and aliquotted them into oven-sterilised jam-jars. That would normally be a job well done and a cause for cake or at least a round of scones as a marmalade vehicle but we were still expecting Aoife's party to follow her oranges down from Dublin and get cookin'. Apart from anything else, we were running short of serviceable jam-jars. Undaunted, we filled up the two largest saucepans again with clean halved Sevilles and set them to boil. Not a moment too soon, the jam-jar cavalry arrived from the Big City and by the time we'd all finished a Leap Day lunch that couldn't be beat, we were ready to process the next batches of bubblin' Sevilles.

The joy of doing things again and again before you forget what happened last time is that you get to know the process. Like medieval swordsmiths who, after decades of deliberate practice, knew the temperature of the steel from its colour, so we could tell when the marmalade was ready to pour from the texture of the boil. No real need for a cold plate, let alone a jam-thermometer. The other positive outcome of repetition is that you can ring the changes - we are not machines after all. Confident that we'd mastered the basic process we made i) a small batch without fish ii) a batch with extra fish iii) a small batch with cardamom and then . . . we . . . were . . . done. It was full dark before we screwed tight the last lid and I for one had been on my feet for 14 hours. The days total was just over 70 pots of the warm South. I hope my ActivPal accelerometer was impressed or at least recording. In the end all that's left is a generous handful of pithy, seedy, compost [see R]

St David's Miscellany

1st March 2o2o St David's Day

• St.David's: smallest UK city.
• SwissTopo: the National Mapping Agency is trying to catch their cartographers random fish, marmots etc.
• Dead: Freeman Dyson physicist, thinker and crap-detector [bloboprev] Hans Bethe's opinion.
• Dyson's last publication on Edge
• Luxembourg: where the trains still won't run on time, but from today you won't have to pay for sketchy transport service.
• Alaska: the state's largest solar electricity farm.
• Nick-nack paddi rice: Seed-savers on a massive scale in India
• Balkanic: Le Temps des Gitans
• Gitanos: Ederlezi [prev]
• Copper: cookpots - making them.

Finally, in my January troll through the family archive, I discovered the address where we lived in Kingston, Ontario 1956-1957. This time, I dug up a postcard sent from Aerophort na Sionainne / Shannon Airport and address to little me aged 2¾. That's a relief, clearly I did exist before I got my PhD and started sciencing seriously.