Saturday, 29 February 2020

Motion sensor

It [L] is me right thigh, patella downwards. It is a leg-selfie [you shd try it - it's the latest thig thing] to show an ActivPal accelerometer, [can this really cost $450 each?] wrapped in a micro-condom and stuck to the flesh with a transparent Tegaderm plastic film dressing [about 60c each]. The point of the condom and dressing is to stop the gizmo getting wet. The crude stick-man is to indicate which side sthould be kept upright - a bit like the glass icon on some packing cases. Anyway anyway, the reason I have this accelerometer attached to my leg is because I am being a guinea-pig for Sean and Cian, two of our Sporty students who are studying "physical activity and sedentary behaviour" among the staff at The Institute. It is, I gather, the first such study inAs I am almost permanently welded to the sofa [blob blob blobbety blob blob] at home, I'll represent the sedentary wing of the party.

We were told to act normal - the lads would not be impressed if I made it seem like I was a really active person. The ActivPal is taking a snapshot of the motion undergone by my right thigh every 15 seconds and storing it on board over a week. At the end of that time, I will report back to the boys and they will download the data for analysis. Every 15 seconds is a good compromise between data-heavy and often enough not to miss a key event. Actually it is quite likely to miss most of my runs up the stairs - I never walk up because I don't do trudge. I often twit the graduate students who habitually use the lift to go to the research lab on the second floor - travelling up by lift has a carbon footprint [costs about 2c a go but if you use it 5 times a day, 250 days a year] that's enough to buy a round a drinks. But I give them a right bollicking if I see them coming down in the lift. Back in the pre-Institute days, my lab was on the 4th Floor, and I always used to run up the stairs . . . and then be unable to talk for 5 minutes. My jog upwards was essentially anaerobic, so I needed that amount of time to suck in enough oxygen to function. In these Covid19 end-of-days days, there are additional reasons not to travel in a lift with Drs Hack, Sputum and Coffin.

The intrusive and ubiquitous nature of the data gathered by these ActivPal devices seem to me to have GDPR issues. It will be clear how many times I get up in the night for a pee - which coincidentally also takes a little over 15 seconds to empty a mammalian bladder; and of course how restless I am in bed; and of course it should record any bouncy-bouncy. It also occurred to me as I sat at stool, that the data readers should be capable of inferring that I was doing exactly that - Motion Sensor, indeed!

A final bit of advice, triggered by the mention of Tegaderm transparent dressings: as well as your torch, shovel, tow-rope and warning triangle, every car should carry a roll of cling-film. If you encounter or participate in a road traffic accident, then cling-film is the paramedic-preferred way of staunching bleeding wounds. It a) stops or slows the flow, b) is reasonably sterile c) allows the professionals to see the damage. I hope you never have cause to thanks me.

Friday, 28 February 2020

Family silver

Like I said, we were over in England sorting out family papers last weekend which is not something that you can pay someone else to do. You can pay someone to 'clear the house' and remove the largest fraction of it straight to land-fill. There is a very limited market for second-hand side-lights, second-hand crockery and second-hand books. There is no market at all for old photographs, old letters, and old theatre programmes. Me, I'm really not interested in the details of family history, so much of the effort is put in on behalf of an, as yet unidentified, archivist or biographer who will be able to put all my childish letters in chronological order and realise [and care] that the "Lucas" of "I got poked in the eye by Lucas" is now an elderly literary agent living in London.

My Sister picked Dau.I and me up from the airport and delivered us nearby at the end of our two days riffling through the mouse-shitty papers trying efficiently to triage them into keep / share / trash. About tea-time on Sunday we were done and I was in the yard packing the sistermobile. Neighbours passed the gate for their afternoon constitutional and quipped brightly
Neighbour: "Aha, taking the family silver, I hope"
Self (ironically): "Clank, clank"
And it was a tiny bit true: over the last couple of hundred years, my middle-class professional family has gathered a modest hoard of sterling silver trinkets, including an unconscionable number of sugar tongs some sterling, mostly EPNS, for  example. Sugar tongs [like cuff-links] are an absurdly specific, wholly redundant artefact: everything you can do with tongs you can achieve with a spoon; with a spoon you can also stir the tea and eat a squidgy bit of cake. This Smaug's Hoard of Glittery was reduced when my mother's gaff was burgled in 2002. We know the exact date this occurred now because I found letters from the local police and local victim-support about the event last w/e in a very miscellaneous box of papers & cards. The sugar tongs were also depleted by a rogue house-cleaner who was gaslighting my mother; but that's another story.  Anyway, here's a nice set of spoons for when Dau.II have company - they will make short work of the gateaux de kale, crème et chocolat.
The dinky tongs are too small for any sensible amount of sugar, so I'll guess it's for rock-salt.

Some of my collateral rellies did better than others. My grandfather's sister Lily had red-golden hair in her youth which she boasted came down to her from the 'red-headed cook' Sarah Auliffe who had a long-time liaison with The Boss and gave birth to three boys including Lily's father John, the 'natural' son who inherited The Big House in King's County. Lily married a wholly unsuitable cad and bounder who abandoned her and their daughter with unseemly haste before the girl started school. When we knew her she was living in a rather grand house on the sea-front at Buddleigh Salterton in SW England. She was living with an old buffer called Walter Bell - nobody every saw a marriage cert - and they clearly had no worries about money. Abundant cash and credit sat peculiar with Lily's thrift - I'm guessing times were hard after she was abandoned by The Rotter. She would order oranges by the crate because they were cheaper but half of them would be furry before the box was finished. Eight pints of milk were delivered each day because she liked 'the top of the milk' in her cornflakes. Walter died shortly after we got to be old enough to be aware of him: he spent his last toothless months subsisting on a diet of Complan <glark!> and whiskey filtered through a capacious walrus moustache.

But he wasn't always like that. He was young once and fit. How do I know? Because he won a prize! Here is the evidence.
That's nice. It makes you wonder how big the 1st Prize Seniors was, let alone the School-wide prizes: probably on a scale of the Jules Rimet Trophy. If you turn the cup round, it turns out to be solid sterling silver! [evidence as footnote] . . . except for a glass bottom so you can watch your horses while swigging mulled-wine at the local Hunt. Silver bullion is currently worth $0.60 /gram and the mug weighs 335 g, so its melt value is about €200. The unfairness of life is that such valuable trinkets rain down on people who already have wodges of wonga; while poor folk continue to have no milk at all for their cornflakes.

But life isn't fair! As my father repeatedly told us when we complained about some personal injustice. It might be tolerable if the Walter Bell fortune was acquired by hard work and an entrepreneurial spirit.  At clue lies in the fact that the house in Buddleigh Salterton where Lily and Walter lived was called Woolsington. Years later, I got my first academic job in Newcastle upon Tyne. We naturally flew home to Ireland through Woolsington Airfield which was better known as Newcastle International Airport. The Bells were strong farmers with an estate of roughish pasture in Northumberland. When coal-measures were discovered under a broad swathe of Counties Durham and Northumberland, the above-ground land-owners cried Payola! and didn't ever again have to worry about hoose, murrain, blackleg, Brucellosis. glanders, lung-worm, Pasteurellosis. And don't be coming up our lane to rob us: the mug is in England and the spoons in Cork.
Dau.I and I did some superficial research on what these marks: [lion rampant; serpent's head; dagger; J.E] actually mean. They shd zero in on a country; an assay office; a year and a maker. Standing lion probably means Glasgow, although that is a long way from Eton. Help needed, please send answers on a postcard.

Thursday, 27 February 2020


We hosted a parcel of 16 Transition Year teenagers at The Institute at the end of Rag Week. I was tasked to help greet them and give them a tour of the research facilities and, at the end of the day, get them to fill out Evaluation Forms and take a group photo. I also got to coat-tail on their visit to the aeronautical engineering hanger, which I'd never been inside. That gave me a few opportunities for vicarious war-stories of The Boy's years in the airline industry. He went to school near Dublin Airport and a, perhaps unsurprising, number of his pals' fathers were airline pilots. It was through one of them that he got his gig as a ground-handling agent [bag-slinger, toilet-tankerer; plane-batter] for Ryanair when it was still a modest almost local enterprise. A month before he started work, one of his predecessors had failed to follow the SOP [standard operating procedure] for walking in front of propellors and had been minced down to the waistband for his carelessness.

That led to a discussion about the damage done to the machinery from such contact with flesh-and-bone. Thankfully, man-meets-engine is much rarer than bird-strikes; not least because birds are too dopey (and illiterate) to read the SOP.  That means engineers don't really have to design turbo-fan blades to cope with human contact but do so need to take account of bird strike. I explained this to the youngsters [rapt because the story was potentially gruesome] by saying that engine-engineers will order a bunch of chickens; fire up the engine in their test wind-tunnel then lob birds into the intake and assess the damage. Everything went well, I said, until someone failed to follow the SOP [defrost the chickens before throwing them at the engine] with catastrophic results for the fan-blades. There was a moment of palpable confusion as they realised that the unfrozen birds were dead. Whoa lads, I added, they're engineers not a class of unhinged sadists; how do you think they'd get ethical approval for using live chickens in a destructive testing assay? Which served as a seamless side-step into Ethics in STEM which would be unlikely covered at school.

Wednesday, 26 February 2020

Who gets promoted

I was away in Brexitland with Dau.I this last weekend. We were there to work [doing triage on the family papers for the third double-day session] but there were tea-breaks and transit time when we had nothing more fruitful to do than catch-up. These chats were not only phatic re-assurance of our mutual respect and devotion but also involved a certain amount of rational discourse, information transfer and data processing. She is coming up for working 2 years in the Dublin Library Service and she really believes in the service part of the title: ensuring that libraries are friendly and functional for a) teenagers b) people with a better tan than me c) BLTs d) the staff - not only the desk-jockeys, but also security, cleaners, trainees.

I've been 40 years working in Science but I never planned it that way my career was more a leisurely bumble than a train hurtling along the tracks to a real or imagined goal. But it seems to be different for Dau.I who has had a face in a book since before she learned to read and has had on-again off-again fantasies about growing up to be a librarian. It's peculiar and instructive to realise that there are completely different takes on A Life Well Led - none of them wrong and all of them suitable for at least some people and personalities. One of the clatter of books I am inching forward is Behave: The Biology of Humans at Our Best and Worst by Robert Sapolsky [whom we've met before: talking about pandemics which we all could with advantage re-read as COVID-19 refuses to get back in its box. Anyway one of the rhetorical riffs that Sapolsky indulges himself  in is to assert that you do well in school: to get the best possible University place: to get a position in the biggest corporation: to rake in the biggest salary for 40 years so that you can pay for the very best nursing home.

Anyway, anyway as a young librarian with ambition and reasonable prospects, she is mapping out the process of promotion and putting her advancement ducks in a row extending forward well beyond the time when Dublin will be 3 feet deep in sea-water. Getting this qualification will licence her to push thorough that innovation etc. She is also aware of who is currently elbowing their way to the top of the ladder; and how they are doing it; and whether they are casually if metaphorically stepping on other people's faces on the way up. You get to Grade 6 by serving a certain amount of time at Grade 5 and not annoying too many people. Competence in / for your new responsibilities is not always the primary criterion for promotion. Dau.I was telling a couple of anecdotes about colleagues who were snotty, snobbish, hierarchy- and status-obsessed knobs who shouldn't be put in charge of a child's tricycle let alone a branch library or Gender&Equality provision.

As she went on, I reflected that such prospective promotions should be announced to the Library Community the way that Banns are proclaimed in the parish church of three consecutive Sundays before a marriage. The purpose of Wedding Banns is to ferret out any proposed unions that involved bigamy, incest / consanguinity or other just cause or impediment why these two people should not be joined in holy matrimony. Promotion Proclamations could be done in a similar manner to allow [anonymous or otherwise] information to filter through from the community to Library HR Central before another utterly unsuitable unaccountable person UUUP is promoted beyond their levels of capability.

Tuesday, 25 February 2020

Shaken and stirred

The Boy went on a year-long young person's working visa to New Zealand, arriving just in time a couple of weeks before his 30th birthday in 2005. He worked briefly in recycling but spent the rest of the year in Christchurch airport checking passengers in for one of the regional airlines. It was a great life: fully-functioning knees; money in his pocket; multicultural pals;  great climate; sea on his doorstep. Christchurch was good to/for him but, to the hearty relief of his mother, he didn't fall for a Kiwi girl and settle down on the other side of the world. Four year after he left, Christchurch was hit by a 7.1 Mw earthquake and a much more damaging 6.2 Mw seismic event six months later. More damaging because many buildings were 'shook' from the previous event and also because the 22 Feb 2011 shock occurred at lunchtime when people were out and about downtown. 187 people were killed.
My view of earthquakes is framed by the events of  22nd April 1906 in San Francisco, partly because my grandfather was there, then. There, the ground moved; buildings were shook and fell down or bits fell off; gaslines ruptured and fires started; debris in the streets made it difficult for emergency services to get where they were needed. As everbode kno, the 'quake was caused by the relentless Northward movement of the Pacific Plate, grinding nad ju-d-d-d-ering past the North American Plate. In places like the picture L, the ground on both side of the join is rocky and once the shift is over its over. That's more or less what happened to the South of Christchurch where there is a range of hills separating the big city from Lyttelton. Parts of  the scenic route between these places fell down the cliff-face and other sections were rock-covered from above. This route was a regular weekend cycle for The Boy and his pals: we have parent-terrifying footage of their downhills. Four years after the bif Christchurch quake you could see nature taking over: Sumner Road 2015 the road has since been reopened wider & faster but it don't look as scenic anymore.

In the river valleys especially the Avon River wending its way through the Northern suburbs of Christchurch altogether more frightening, because uncanny, things happened. Those leafy residential areas were built there because the land was flat and near the city.  It was flat because it was a flood plain covered in a more or less uniform layer of run-off and silt from the hilly hinterland. For regular housing stock 1 or 2 storeys tall, you don't need elaborate foundations, with piles sunk in the soil until they reach bedrock. Building regs will normally specify a trench filled with concrete [rebar possibly desirable] and then lay brck and mortar or a wooden frame on that.
But that assumes that the subsoil will be more stable that ketchup.  In the Avon valley, the subsoil was sufficiently stable . . . until it was shook; at which point thixotropy [prev, Aberfan] took hold and the soil liquefied. The weighty houses and their concrete foundations settled into the sludge - unevenly. The car [R] is an image so widely propagated that we must assume that sort of event was uncommon for cars. Obviously [?] You can't allow people to live on in such areas, even if their homes sustained relatively little damage.

The NZ government therefore mobilised their geologists to survey the whole region to identify areas where it was  foolish to allow houses to be built. You can see from the map, that this is a mix of landslide risk regions in the hills to the South and all the alluvial areas near the Avon River. It can be quite specific: a distance of a few tens of metres can put you on top of completely different, more stable, geological strata. Kiwis live in a democracy not a poluce state, so the government offered householders the option to sell their houses and move elsewhere. In the process they acquired and demolished 8,000 properties leaving the suburban grid to revert to nature. You can't leave empty houses: they quickly get to look unsightly; they attract vermin and vandals; they become a fire-hazard; they hold back the succession to scrub and then woodland. You can't get a grip on liquefaction without movies:
We have a not dissimilar situation in Ireland where hundreds of homes were built on a back-fill of pyrite brought there by geologically ignorant or culpably negligent developers and signed off on by geologically ignorant or culpably negligent planners and buildng regulators. Dry pyrite is hard core, wet pyrite is sludge; it rains in Ireland. Because we live in an unaccountable plutocracy rather than a democracy, the owners of those homes are expected to make the best fist of the disaster as they can. There has been no suggestion that the state would buy those defectively planned, defectively regulated and defectively constructed homes because, well caveat emptor.

Monday, 24 February 2020

Tuberculous inertia

We have a peculiar relationship with TB in Ireland. It's almost as if the tuberule bacillus Mycobacterium tuberculosis infects our brains to ensure its own survival. Kill those badgers it insidiously suggests, so that we are distracted from changing the tuberculosis-friendly practice of bunching cattle close together in sheds for much of the winter. I was scathing about this in August 2016. Testing testing testing for TB-positive cattle is a major part of the income stream for rural veterinarians. Where would they scrabble for cash if we could cure the sourge?
Along with malaria and infectious diarrhoea, TB is the biggest killer [WHO report] of [small, black] people in the world today. In 2018 there were 10 million new cases and 1.5 million deaths attributable directly to tuberculosis infection. Worryingly 5% of those new infections were from antibiotic resistant strains. If you can't kill the bacteria with drugs, it would surely be a good idea to prevent the initial infection.

Yes, yes, we have a solution for that, in Ireland we used to routinely vaccinate young people with Bacille Calmette-Guérin (BCG) but that is no longer the case because the incidence in Irish people is so low that the Health Information and Quality Authority (HIQA) reckons it's not worth the money and hassle. Compare that answer to the community health management of HPV with Gardasil. I remember getting my BCG as a teenager in England. One afternoon in about 1969 the whole school was lined up with sleeves rolled up and given a scratch with an infected needle. The BCG was originally captured from Mycobacterium bovis and "passaged" in the lab for more than a decade until its virulence was attenuated to acceptable levels in the 1920s. It was still close enough to feisty fighty tuberculosis to make the immune system aware and ready to deal with any subsequent infection - before symptoms were apparent. It was all very similar in technological advancement, but with better ethical paperwork, to how Jenner and Jesty helped prevent smallpox 200 years earlier. Routine vaccination is definitely on the cards after cost-benefit analysis across much of the Third World.

But frankly, the BCG is not really very good. Far too many youngsters are vaccinated and go on to develop full-blown TB later. Like Dau.I getting MMRed as an infant and contracting mumps as a teenager. The immune system is remarkably varied and subtle with different immune cells servicing different parts of the body. The skin is exposed to a different cohort of potential pathogens to the lungs or the gut and so might well have a different set of immune effectives. In January, a group from the Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD [Darragh et al.] [exec summary News&Views]reported the results of their investigation of alternative routes for vaccination. Same old BCG was close to 100% effective in rhesus macaques Macaca mulatta IF administered intravenously! We've been scratching at the surface for the best part of 100 years for no better reason than that we've always done it thus.

Sunday, 23 February 2020

Sunday rounders

The largest piece of detritis delivered by Strom Dennis last weekend was MV Alta Celeste [above]

I R in England agane. Possibly the last time on this cycle of sorting family paperwork.

Saturday, 22 February 2020

Futility planting

My gloomy verdict on the fate of a string of small Indian islands brought to mind another island planting story which also had a gloomy outcome.
20 years ago, my sister lived for several years in a community on the island of Erraid; 270 hectares [almost exactly a square mile] of rock and moorland off the West Coast of Scotland, which, in a previous century, had a starring role in RL Stephenson's Kidnapped; you can walk to the island at low-tide. It was wonderful in the Summer with a private white sand beach [L] on the far side of the island from the village but the relentlessness of the Winter gales eventually got to my sister and she moved South to Severnside.

One winter they decided to plant some hundreds of trees - maybe Scot's Pine Pinus sylvestris - they order up the saplings, set to work together and planted the trees across the side of a bare moorland rise. They all died. With 20/20 hindsight they realised that they could have achieved their aim if they'd spent 10 or 20 years at the task. First to identify a fold in the ground that was sheltered from the bitter cold salty gales of West Coast winter. GPS was not necessary to identify such a sheltered spot; you just had to look where there was a clatter of blasted hazel, willow and hawthorn. A few birch (fast growing, hardy enough to over-winter in Finland) and a few Scot's planted in the lee of the existing brush would, with luck and good staking, survive to provide a taller shelter belt for subsequent plantings. This is what would eventually happen anyway with the natural succession from bog to boreal forest. But people can't wait till their grand-children are grown to make their mark on the landscape. So the protocol I've outlined is a way of ooofffing on the natural process to bring it along a little faster.

Our half hectare of forest, planted in 2007-2009, is doing very nicely, thanks. We planted whips of Scot's Pinus sylvestris, larch Larix europaeus, ash Fraxinus excelsior and larger stumps of oak Quercus robur as well as a gallimaufry of native trees. Active support took a while with us having to give the tiny trees an edge over the grass, but then they took off and many of the trees are now taller than our two storey home.

Starting a woodland is a bit like Aikido where you don't attempt to block the Ki of your opponent but rather divert its energy into a path that is of more benefit to you. Ah So's to you too, mate.

Friday, 21 February 2020

Finding another way

I cover human physiology in The Institute. My only qualification is that "I have a body". But, like much of the material I teach, I've learned a lot and do my best to make the content delivery interesting, true and engaging. Hum Phys is easy to understand if you accept that it is all about homeostasis: multiple interlocking systems to maintain things in equilibrium to quite precise tolerance. Unless you have haemophilia, you eke out a continuous dribble of Factor VIII - just enough to deal with micro-bleeds from knocks and cuts. Treating haemophilia with regular injections of Factor VIII is a bit like dealing with a chip-pan fire with a tsunami. Same with regular insulin injections for diabetes - it's not subtle but it's better than diabetes!

The way I structure the Hum Phys course is to start somewhere and cover each of several systems in turn doing my best to emphasise that all these systems  - nervous, endocrine, circulatory, immune - act in concert. At the end of each section /system I have been in the habit of setting and marking an assessment [usually a MCQ quiz] on the material just covered. I assure the students that it is much easier to accumulate marks in this limited fresh-minted arena than in the Final Exams in May when they are expected to know all the material and the contents of all their other courses too. Nevertheless, about 10% of the class seem unable or unwilling to learn the relevant material despite the notes, the lectures, the executive summary, the text-book, their pals, the internet.

MCQs are a painless way of doing these assessments: they are easy to mark, that's for sure.  I have been inclined to believe that IF there are 5 possible answers to each question and you can therefore score 20% by answering at random THEN someone who scores 25% must know nothing.  This year on my final furlong I've decided that the form of assessment may be at fault. I did really well at exams, particularly MCQs: that facility got me where I am today. But cutting less academically inclined kids some slack, I thought that maybe exam anxiety or dyslexia was getting in the way and I've been giving a back-stop alternative asessment for those who are MCQ-averse.

After the 10% failed the MCQ on The Nervous System. I set them this more vocational [they are all Pharmacy Technicians] task and said that would get a passing grade plus a bit on that section of the course. I've got to make it at least as hard as doing the quiz but not so hard or boring that nobody puts in the extra effort.

MS is a progressive degenerative disease which has affected 3 of my good friends, two now dead from the condition. I find that there are numerous drugs and medications on the market to help with the symptoms or slow the progression of the disease. As you know, MS is an autoimmune condition in which the leukocytes attack the myelin sheath. I find that there are numerous drugs and medications on the market to help with the symptoms or slow the progression of the disease. Like with “cancer” our understanding can be complicated by the fact that several different diseases {primary-progressive; relapsing-remitting} are lumped in under the label ‘Multiple Sclerosis’.
Here is an annotated list of those MS meds.
Your task:
  1. Explain the symptoms and likely outcomes of MS (in general, or limiting your response to one form of the condition)
  2. Pick one of the drugs /therapies from the Mayo Clinic list.
  3. Describe its chemical structure, with a picture if possible
  4. Find out how much a course (probably life-time, so annual cost) of treatment costs
  5. Say what the target is: the molecule and the cell
  6. List the side-effects and give some sort of an explanation for why these other systems are affected by the drug – this might require some thinking
  7. Identify any contra-indications: people and conditions that should avoid this therapy
  8. Is this drug approved by the regulator in Ireland?
  9. Write the report: preferably on a single side of A4 paper.
This is one multicolour, scrappy-looking but informative and dynamic answer to Fall BackStop about the drug Fingolimod. I was impressed:
Hey Beatrice: That’s seriously good stuff. Defo worth the mark-up.
Hi Bob: I agree! Thanks, Beatrice
I was so delighted with this answer that I clapped my hands. I'm taking it to mean that Bea worked really hard on the assigned task, that she learned a lot, that she recognises that she had done good work and heck-n-jiminy might even remember something about the nervous system come May.

Thursday, 20 February 2020

Binning the gays

Last week was R&G week at The Institute [prev] and widely across the country. It used to be called Rag Week when [medical] students would take a week off learning the names of bone nodules and spill out on the streets for a bit of a jape joust [R]. Because they were students, some of them would get hammered and forget that they were meant to be raising money for cancer research. Over time the student body seemed to forget the charitable heart of the events and concentrate on the get hammered. I suppose rebranding it as Raise & Give week hopes to redress the imbalance. Good luck with that! But the consequence was that there were very few regular classes and several extra-curricular happenings. Truth to tell, everyone probably learns more, as well as having a better time, when the Syllabus and the Learning Outcomes are off-stage.

Fr'instance, I got to attend a two hour session on the ABCs of LGBTQ+ run by a registered charity called ShoutOut - it's tiny: two salaries and a handful of volunteers with a board of directors in the background.  It's kind of woeful that, with a student body the size of  Nenagh or Gorey, and two Equality salaries, and Athena Swan certification, The Institute needs to buy in expertise from outside. Then again, ShoutOut does this all the time and have their patter sorted and are therefore more experienced. To be fair I did attend a useful and interesting Internal workshop on Pronouns 18 months ago. That was also kind of woeful in that only six [6!] people turned up including both the Equality Officers. As I said then, LGBTQ+ ain't going to make like Levis and fade away; so it is worth investing in getting the facts and attitudes correct.

So what did I learn?
  • That you really should go to one of these workshops (I gave already) 
  • Then you'd know the difference between LGB [preference] and T [identity]
  • That I hadn't heard of most of the celebrities who were somewhere on the BLT spectrum
    • Q.Francis Brennan, who he? A.sexual
  • That Malta has by far the most progressive BLT legislation in the EU - while also being super-Catholic and paradoxically patriarchal wrt the status of women
  • Queer is now the widely accepted inclusive umbrella term for BLT
    • Gay is used for /by women (as is 'lads')
  • Bisexuals are, evidence-based and objectively, more troubled mentally but are proportionately under-serviced by the state. The Man has got as a far as accepting and resourcing G & L but is blanking other sections of the BLT community as, currently, a bridge too far. The sands are shifting, Gramps, and bisexuals will get more fair dues as you drop judgemental and try compassionate.
  • We were invited to list our senses of identity; as a prelude to talking about Gender Identity
    • I R European, evolutionary biologist, anglophone
    • BLTs tend to identify as BLT . . . rather than Irish, Liverpool, dancer, driver or dog-lover
    • Many people identify as '[grand]parent'. No adults identify as 'child' even if they are primary carer of elders
  • Gender Identity is about your internal clock
  • Gender Expression is about external appearance / how you are judged / viewed
  • Sex at birth defines the pronouns and is the first question asked about a new-born
    • AMAB - assigned male at birth is currently the best option especially if you identify as Male and look the part
    • Significant discordance among {assigned, identity and expression} spells a world of trouble ahead
  • Trans[gender] = 1% are those who experience this discord. Cisgender is the 99% rest of us.
    • BLT - sexual preference is a different, independent, axis to how you are/feel about yourself
  • People start to identify as their [assigned?] gender more or less when they get out of nappies - aged 3-4. No pants gives a chance to compare notes and start the process of appropriate social assimilation to whatever are the local norms.
  • It is vanishingly unlikely that Trans kids don't start the same journey at the same time. It is therefore invidious to treat the coming out of Trans folk (as teens or twentisomethings, say)  as an event that just happened in a rush. Let alone that it is a [fashion] choice and so flippable backable.
  • In the maternity hospitals of Ireland there are just two boxes M [__] and F [__]
    • 98.3% of neonates fit obviously and easily into one or other box - it just takes a peek down there. Or a karyotype can be quickly done to count the XX XY chromosomes
    • But 17 per 1,000 live births are intersex: there is some discrepancy in the arrangement of the external genitalia or other sex-defining characteristics - clitoromegaly, cryptorchidism, Kleinfelters XXY [list with N = 35 variations]
  • How come you/I don't know anyone who is intersex?
  • Because it is routine to carry out routine cosmetic genital surgery before the child leaves the maternity hospital. Usually The Man does trim and tuck to make a hole, because a pole is more work.
  • Because it is routine to carry out routine cosmetic genital surgery before the child leaves the maternity hospital WTF! We're not talking circumcision here. Ditto to polydactyly.
. . . I am too shocked to continue. But last night I dreamt about CGS, so I clearly need to further process what I heard Tuesday

Wednesday, 19 February 2020

Going going gone

The tragedy of the commons is that, in any interaction involving people living things, individual interests top community interests. If you accept Darwinian natural selection as a fact of life (and all scientific researchers do) then your success - and mine, and his - is measured by how much of a limited resource you can secure for your - and my, and his - growth and development and the propagation of your - and my, and his - offspring into the next generation. You may want to be neighbourly but your neighbour is, in evolutionary and economic terms, your bitterest rival. That view was born in the head of Charles Darwin, grandson of Josiah Wedgwood one of the greatest  magnates of the English industrial revolution. Of course, he'd map his capitalist certainties on to his interpretation of the natural world. It looks like the rapacious exploitation of the world's resources by a relentlessly growing population of human beings is set to turn this blue planet into a beige sump of foulness where only microbes exist. hmmmm, maybe we could try a different business model before it's too late?

These reflections sprang out of a good news story on the BBC about Vaan Island [R as tropical paradise?] off the coast of Tamil Nadu where India looks across the water at Ceylon. It's good news rather than good news because it is making a small-small step towards saving a wonderful (and valuable) marine ecosystem from obliteration but the intervention does not seem to scale up. In 1972 dry Vaan was 27 hectares in size, in 2016 it was reduced to only 4 ha. which is half the size of our 19 sheep farmlet. In 1986 the Indian government created the Gulf of Mannar Biosphere Reserve, which included 21 of these barrier islands. Since then, two of these tear-drops have been eroded to buggery and Vaan will probably join them in oblivion by 2022. A single big storm may be enough. The problem is, of course, erosion: the islands are basically sand-spits with a top-knot of vegetation covered in a dusting of guano. Where am dat place? Here:
In Ireland we have had some success in maintaining and restoring coastal sand dunes by a) keeping excessive numbers of people, their picnic rugs and quad-bikes off the dunes and b) planting grasses whose roots discourage the sandy soil from blowing away in the wind. Often it is appropriate to install wind-breaks of paling fence and mats of sheepwire to provide physical support until the vegetation gets a foot-hold. These restorative projects are not a quick-fix and need years of support and maintenance if they are to become self-sustaining.

For Vaan and the other sandy islands of the Gulf of Mannar, the erosion is not so much from the winds of the tropical storms that beat in from the Indian Ocean but the relentless suck and heave of the waves. The sea-bed is covered in meadows of sea-grasses. The roots of these monocot plants interlock to hold the sea-bed surface together. But when an enormous beam trawler passes by, scarfing up the shrimps and bottom feeders, the sea-grass meadows take a pounding and the next storm scours off what's left. That exposes the beach directly to the waves. This cycle will repeat itself until there is no island left. It would seem sensible to create a fishing-free zone to allow the meadows and their attendant animal life to recover. But 100,000+ people depend on the fishing for their diminishing livelihood, so it would take a brave politician to implement the restriction of fishing by all those voters.

Without the trawlers - yes yes without the people too with their expectations and demands - the shallow marine ecosystem might recover and propagate on its own. But if that ain't gonna happen, then you can weep and do nothing OR set about to re-plant and transplant sea-grass from dense stands to places where the meadows are gone or threatened. That is what Edward Patterson & Gilbert Mathews and their co-workers from Suganthi Devadason Marine Research Institute attempted [original pub].  With great care they dug up three species of seagrasses, Cymodocea serrulata, Thallasia hemprichii, and Syringodium isoetifolium, from one area and transplanted them to places which were going a little bald. They used 1m x 1m plastic squares [above L] covered with a loose network of jute strings as anchors to support the transplanted grasses until their roots 'took'. At best speed with perfect weather, a pair of scuba-planters were able implant 80 plastic quadrats a day. I'm assuming that the quadrats are not anchored shoulder-to-shoulder but in some sort of checker-board - allowing for the established transplants to do some in-filling. Let us generously suppose that the day's work blocks out 800 sq.m. of regenerating meadow.  But Mathews & Co. have identified 45 = 45 million sq.m. of degraded sea-grass meadow in the bay. You can do the math: it will take somewhere North of 150 years to remedy the damage using this method, even working under optimal conditions 7 days a week, 50 weeks a year. A day's work under-water will be swept to oblivion by a single pass of a trawler. It doesn't scale up. lads. Vaan is doomed. Sorry.

Tuesday, 18 February 2020

Does he take sugar?

Sing!: Yer toe-bone's connected to yer foot-bone; yer foot bone's connected to yer ankle bone . . . dem bones dem bones gonna walk around,. The deeper I get into genetics, development and human physiology the more peculiar the connexions become. Take vasopressin: a hormone distributed from the posterior pituitary which, as it says on the tin, compresses blood vessels to keep up blood pressure. The same hormone has an alias - anti-diuretic hormone - which promotes water retention in the kidney . . . which keeps up blood pressure. I'm covering this next week in Hum Phys as a classic case of homeostasis (and redundancy). Lecturing to pharmacy technicians on Hum Phys mentions a lot of drugs; most of which have a quite extraordinary range of side-effects. Take infliximab for example; or rather don't! unless you're real sick. What that tells us is that the normal function of the drug-target is remarkably varied and wide-spread.

What about TAR syndrome? That's Thrombocytopaenia with Absent Radius. It's a genetic disease caused by mutations in a gene RBM8A or deletion of the portion of chromosome 1 which houses that gene. Thrombocytopaenia is the absence of platelets, which brings its own clatter of problems, but it seems absurdly specific that the same lesion should absent the radius but not the ulna; the other bone in the fore-arm. Because the radius, which could be considered the foundation of the thumb, is absent the thumb is opposable but often smaller than optimal function requires. And the hand, lacking half of its supports is canted at right-angles to normal. Your thumbs are one of your most under-appreciated assets: try opening a jam-jar, writing a thank-you letter or whacking a home-run into the crowd without 'em!

Why do I know so much about this rare [1:200,000 live births] disease? Because yesterday I met one of the bus-load of Irish people with the condition. Nice young chap, doing his Leaving Certificate next year and wanting to be a forensic scientist: must have been binge-watching CSI on the telly, like far too many youngsters. His parents asked if they could bring him round to The Institute to test the waters and see just how hard, or easy, studenting in science might be for a young chap with plenty of determination and ambition but a bit short in the arms. Is that an unsurmountable deficit? I would have preferred, if having brought him from home, the parents had buggered off for a coffee rather than hanging around being useful.

In first year science, students typically will take physics, chemistry and biology. I did 50 years ago and we're still in those parallel-and-never-meet ruts in the 21stC. That because we bin science in that way and have done for about 200 years. "Keats and Shelley were the last two poets who were at all up to date with the chemical knowledge." Because in their day, a chap could be expected to know all the science that anyone knew. Since then, the amount we know collectively has ballooned into a monster that not even Wikipedia can fully cover; hence the specialisation.

As we're starting first year microbiology next week, we have a bunch of already poured Petri dishes and some stock strains of bacteria to play with - E.coli, Pseudomonas, the usual suspects. I suggested that I could get the chap to streak some plates and see how they grow. It's no more difficult than writing your name: the other hand its important for holding the Petri dish or paper steady while the dominant hand scribbles. Well he made a total hames of it the first time, but that's okay. He tried a tuthree more times and seemed to be making different mistakes each time, but that's okay too. If his life depended on it, I'm pretty sure he could learn to streak plates efficiently and reliably. But I don't think we'll have, or make available, the extra resources of time and consumables to get him where he needs to be. That's not discriminatory because we don't give any of our students time and consumables and practice to get to do anything really well - because we are obsessed with content and getting through a demanding syllabus of repeating dead white men's experiments.

But ya know what was the most depressing aspect of the morning? Everyone talked for him (parents) or over his head at the parents (us) or at him but nobody found time to listen to him. But at least I had one positive idea to share. There is more to forensics than swatting flies off body parts found in a bin-bag in a shallow grave. It is routine now to get DNA sequenced: to identify the sex, race and relations of that bin-bag-body; to identify the bacteria in a sputum sample; to check for HIV status. Someone has to be the whizz who knows what to do with DNA data. But DNA data is just data. You don't need to know how to streak a Petri dish; or dissect a dogfish; or operate a microscope - data is data and on a computer science degree you're good to go so long as you can hunt-and-peck across a keyboard - one finger ,or a toe, or a pencil in your mouth will do good enough. I spent 20 of the last 30 years doing little more than writing code to analyse genomes; it was good fun and they paid me to do this - what's not to like about that for a career?

Monday, 17 February 2020


Dau.I, the librarian, decided I needed to be weaned off 90 minutes a day of Newstalk FM on the wireless of my little red Yaris. The recent consolidation of a national library service makes it really easy to get whatever book you want delivered to whatever library is most convenient - regardless of which county authority issued the library card. Because she works in the system, she had a clatter of talking-books on CD delivered to Tramore library for me to collect. 11 hours of commuting got me through Erebus by Michael Palin which quickly got better than I expected. Then I started in on Sapiens:A Brief History of Humankind by Yuval Noah Harari, that would be קיצור תולדות האנושות in Hebrew. Harari is a Professor of History at the Hebrew University of Jerusalem, not scientifically trained. But we won't hold that against him because Science is A Way of Knowing - not the only way to make sense of the World and our position in it.

What Professor Harari wants to do is force his readers listeners to question their cosy assumptions and comfortable certainties. I'm right beside him on that because unconsidered certainties and their pernicious influence is a running theme on The Blob.

One of the earliest examples of a codified way of life is the Codex Hammurabi: a series of rules and regulations that was promulgated by the said Hammurabi, King of Babylon in 1776 BCE. It is a long list of prescriptions for lex talionis = retributive justice. Reading through the list of accidents, misadventures and crimes makes me grateful that I have little enough experience in that domain:
209. If a man strike a free-born woman so that she lose her unborn child, he shall pay ten shekels for her loss.
210. If the woman die, his daughter shall be put to death.
Whoa! The Perp gets off with a free pass but his chattel daughter gets offed?  If he takes his misogeny down-market and kills the unborn child of a slave, he only needs to pay money. The idea that he might strike the daughter of a 'superior man' is too uncomfortable to contemplate, so doesn't appear anywhere in the code.

Prof Harari goes into the social hierarchies and legal remedies of long-ago Babylon in some detail and then switches, with convenient symmetry 1776 CE to address the "we hold these truths to be self-evident" of the US Declaration of Independence. The juxtaposition might make you pause to question how these two sets of self-evident truths can be so diametrically opposite . . . except in the sense that neither code recognised women as competent adults. And what about us: are we justified in being smug about gay rights; tanned rights; women's rights; children's rights. Just because the convention in our section of society holds these truths to be self-evident does not, with my critical thinking hat on, necessarily mean that they are true for all times and places. Why lookit, our section of society thinks it is okay for two people to batter each other in the face to entertain a paying baying crowd.

Sunday, 16 February 2020

Sunday Sixteen

Phew, what a week! 12/02 we had Darwinday, 14/02 (it happened every year: one-two) we had alentine's Day. Now it's 16/02.
  1. Meet the scientist - Sarah
  2. Meet the Storm - Ciara
  3. Make the Montecristo - Esbieta
  4. Thar she blows - Kilauea
  5. Lì lei soffia - Etna
  6. Rutherford meets Race - Wireless
  7. Mellivora capensis meets Canis mesomelas - Python
  8. Age meets Youth - Depression
  9. LNWR meets MR - Viaduct
  10. Meet Mr Bayes - Probability
  11. Running the edge - Kilian
  12. Maps meet data - Pasture
  13. Pie rants climate - Sydney
  14. Façade rencontre Metro - Bâtiments
  15. Fermette rencontre pente - Legumes
  16. Hannah bends rules - RI-Xmas
From Link 12, a shocking amount of cattle burping up their Methane footprint
My chiroptobessive friend Emma sent me "a gorgeous bat to make you happy!" Most would think that it was a peculiar expression of condolence, but it's good with me. The bat-wrist is the knob halfway out along the fore-edge of  the wing. There are, just like us, five digits radiating from that stump: metacarpals [palm bones] and three phalanges [knuckle-bones]. Evo-devo is a curious mix of inertia and wild departure.
Further to link 13 above, my colleague David at The Institute alerted me to additional functionality at Windwatcher (where I get all my incommmming storm pictures]. Here's M2.5 particulates for 14 Jan 2020 at the height of the Australian bushfires in the News. [prevticulates] What is a huge <coff> <coff> problem in Melbourne is an everyday story of country folk choking in a miasma of cook-fires, coal-burning power-stations and badly-tuned diesel vehicles across swathes of India and China.

Saturday, 15 February 2020


Money for nothing and the carts for free

My late lamented gaffer Neil taught me a lot, while letting me analyse my data in the way I saw fit. Being thrifty but not mean; several colourful turns of phrase; where the other bloke's rights end; eating what's put in front of you; it's okay to buy second-hand books - heck, you might be agreeably surprised. In his last years he discovered Ebay and the last time I visited, he was up and down the cellar stairs gradually flogging off the books he'd bought during our field-trips in the 1980s. Wheeling and dealing, buying cheap and selling dear, was a lot more interesting than holding down a regular job. It helped that he'd been an early adopter of the collecting bug and amassed boxes of comics and coins when they were of little interest to anyone else. Much later the became valuable because so few had rated them when they were available. It also helped that his long-suffering wife was happy to go out and work for the City and bring in a regular income.

In 1982 the Commonwealth of Massachusetts realised that their land-fill capacity was finite and they'd better do something to monetise the trash of their affluent society. Their Beverage Container Recovery Law required all retailers to add a redeemable 5c deposit on bottles and cans. It did a little to lubricate the recycling movement but the tax on each can or bottle wasn't enough to make a sufficient incentive to return this recently chugged Sprite bottle to the nearest store. The bottle would, accordingly, be popped in the nearest City trash barrel. Neil's research and business ventures required at least one trip to the Post Office most days. On his way back home he would rummage through the trash, like a homeless person rather than a solid tax-paid burgher, and pluck out the discarded bottles and cans which he'd then redeem at the Star Market. The return on his time riffling through the waspy trash-bins would often cover the cost of the postage; he was never stung. Or if he was, he never complained. His point was that, although a single 5c deposit wasn't worth troubling about, over a year he could make several hundred $dollar$ of found money.

A similar calculation stopped me drinking in 2012, when the recession began to bite on reaserch funding and I was reduced to 1 day a week paid work in Dublin. Up until then a couple of bottles of old red biddy [prev] at €5.95 were part of the normal weekly grocery cart. That's a glass each, 5 nights a week and well below the threshold for alcoholic dependency, let alone falling down or getting a cringeing hang-over. It added up nevertheless to a little less than one month's salary in my new dire straitened circumstances . . . so I quit. Teetotalism is part of the reason that Dau.II can survive and thrive working only 3 days a week.
Did someone mention grocery carts? Ya have to check out Murray Siple [life] and  his amazing film Carts of Darkness about racing grocery carts full of bottles down the hills of North Vancouver at 70km/h! That is insane - if you are going to spin off coming round a corner too fast then you really don't want to land in a bed of breaking glass. Then again it adds a certain [artery severing] edge to the pursuit of rush. There is an underclass of alternative types - Big Al; Geordie; Fergie, Little Al; Bob, Max; Buckles - who are taking advantage of the market in 10c deposit beverage containers. Like Neil 30 years ago, they gather up other folk's discards and make a modest living returning the bottles for redemption. If you live behind a tree under some cardboard packaging, then your outgoings are so little that 2-3 hours of scavenging like a latter day hunter-gatherer can support your humble needs. Go Carts! indeed.

Friday, 14 February 2020

One Planet Development

Gweithgareddau’r Cyngor Un Blaned - One Planet Council is a quango managing sustainable development in Wales. One Planet Development offers a transition to a more sustainable way of life, by providing a way for people to live and work on their own land, with measurable social, economic and environmental benefits. Seems that there is a clatter of crusties living across the water in Pembrokeshire. Cob houses, bender-tents, vardas [as R for Romani], are being used for shelter and everyone shits-in-a-bucket - not the same bucket, or at least not all at once, I guess.

Such people have been with us (or against us?) since the 1960s when long-hairs with no obvious means of support and no strong ties to bricks & mortar began to replace Romani and Traveller folk as they were bullied and hectored and cajoled and encouraged to give up their peripatetic lives and become settled. If you know who to ask [anyone whose dog has a bandana round its neck?], you be able to find a squat or a hidden village, or a roiling community of alternative people who have decided that they prefer life without television, this year's sneakers, holidays in Barbados and a cubicle job to pay for all The Stuff.

I came across Un Blaned in a tiny homes youtube video which opened a window on the life of Grannie Emma, who lives in a round house built of straw-bales and mud, with ash-poles, butyl rubber and sod for the roof. You can see the ends of the ash-poles [R] which support the deep over-hang of the roof: necessary to cast water far from the mud-plaster walls. One of the many nice things about Emma's house is that although it is off-grid it is fully compliant with the planning process and building standards. The Welsh government is committed to  pushing the envelope of what is normal and allowable for the Principality's housing stock because they have embraced sustainability. Or at least they are prepared to let some citizens live the alternative dream; so long as they "are required to meet their basic household needs (food, energy, water, waste assimilation, and money to pay for IT/communications, council tax, clothing, and transport) from land based activity within a 5 year period". The state does want people to be free to live in unsuitable unsustainable houses that will be blown down as soon as the big bad wolf Storm Ciara huffs and puffs. It requires a reasonable level of sound architecture and engineering, so that the roof don't leak and the walls stay more-or-less vertical.

Last year and the year before Un Blaned persuaded some of the prior approvees to have Open House [and sell a few home-made scones] and invite a sustainable number of visitors to try the compost t'ilets "of various levels of sophistication". A number of these locations seem to be associated with Lammas Ecovillage, Glandwr, Pembrokeshire. Interested? Save the date for 2020: Mon 27th July -- Sun 2nd August 2020. The Book: The 'One Planet' Life: a blueprint for low impact development - a snip at £32!

Thursday, 13 February 2020

corona codona

In my butterfly life flit flit flitting from one bright scientific blossom to the next, I spent far too much time on the flitting and not enough time actually finishing the task on any one flower. I'm sorry if that's far too graphic an image of a grizzle-bearded silver-back helping out in the fertilisation of angiosperms. But in the early 1990s I was locked into a lab for 10+ hours a day trying to make sense of synonymous codon usage SCU, a field which was then both obscure and select and of no earthly use to anybody. I was locked into SCU because I got a bit obsessive and started to make contributions that were a) published and b) noticed in that small community and success became its own reward. SCU is the study of which triplets of DNA are used to encode for amino acids in the process of translation. GGU GGC GGA GGG all code for glycine and you'd expect [null hypothesis, we say] that each of these codons is used with rough equality. But they ain't, in many species GGU is used much more frequently than you'd expect by chance. And the other amino acids have similar distortions from random codon usage. As we got better at doing these analyses we became proprietal about doing the analysis right [i.e. like we did it] and on at least one occasion we savaged a group who intruded on the territory with a half-cocked analysis of SCU in Aspergillus nidulans.

My [and others] cerebral ponderings and analysis showed that for many microbes, there was a characteristic set of 'optimal codons' which were preferentially used, especially in genes which were in high demand. Decades later, these pioneering studies turned out to be essential for the efficient use of biotechnology in biomedical research. If you want a vat Bacillus subtilis to make a lot of human insulin in a useful example of genetic engineering; then you'll get more if you modify the human gene to incorporate many B. subtilis optimal codons. I was moderately chuffed by this vindication, although I had long before flit flit flitted off to an entirely unrelated field of research.

Because I'd moved off and away from SCU, I missed the contribution of Peking U Med School Wei Ji's team to the field  [PMID] in which they used SCU to identify a couple of snakes as probable intermediate hosts for the currently scarey Corona virus 2019-nCoV.  My pal Des "Whales" Higgins had to draw my attention to the paper; or rather its rebuttal. Now that snake connexion could be an important insight. If we know the source of a new virus that has leapt the species barrier, then we can carry out appropriate remedial action. You don't want to go slaughtering millions of  innocent chickens. Condemning chickens was appropriate in Hong Kong most recently in 2011 [NYT]. There, then, a single carcass positive for H5N1 bird 'flu precipitated the slaughter of 10,000 ready-to-eat chickens in an attempt to create a cordon sanitaire round the site of infection. In the same jurisdiction in 1997, 1.4 million birds were killed and incinerated rather than barbecued and eaten. H5N1 is the harbinger of doom: of 573 cases identified by WHO 2003-2001 336 died - nearly 60%. 60% mortality was the worst that the black death [bloboprev] could achieve in the 1340s.

IF it's snakes that Corona virus 2019-nCoV has escaped from, then a very different policy should be implemented - bounties [bloboprev] on snake heads, for example. But it just ain't so. Back in the early 90s one of the Effectives in our SCU lab was a canny chiel from Dundee whom we called Bobbo. I think he was studenting in Dublin partly because his granny lived in Ballyhale, Co Kilkenny. He had a brilliant early coup identifying a case of mix-and-match among HIV strains. It was /is going to be much harder to find a molecular therapy against HIV, if its RNA wouldn't stay in one place. That wasn't luck except in the sense that hard work and smart thinking makes you lucky. We now call him <respeck!> Professor David Robertson Head of Viral Genomics and Bioinformatics at Glasgow U.

Robertson, who has been immersed in the evolution and recombination of viral genomes from 25+ years, doesn't acccept the conclusions of Ji et al. but points rather to bats as the most likely reservoir / vector for the current Wuhan outbreak. Lancet paper by Lu et al. rushed out says 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China. Two days after Robertson, Kristian Andersen rowed in with more data and a different analysis but the same conclusion:
a) don't worry about snakes
b) don't eat bats - no matter how nicely they are presented in the bush-meat markets in China

Wednesday, 12 February 2020

DarwinDay 2020

Most years since 1982, the centenary of his Death, I have been celebrating Charles Darwin's birthday 12th Feb 1809 by baking pizza or a slab of flapjacks or purchasing a few dozen donuts and taking them into work. 20132014 - 2015201620172018 - 2019. With retirement looming, I suspect that this will be the last year I'll take anything extra into work on Der Tag. I seem to be the only person among my acquaintance who can reliably remember the 12th of Feb, so I suspect that nobody will notice next year when nothing un-toward happens. Rap it! Baba Brinkman! And . . .

Tuesday, 11 February 2020

Hawking the CV around

My tempestuous affaire with my ex-student V from Tamil Nadu continues. He has 6 years of post-secondary training in Pharmacy back home, which count for nothing over here. In some cases, there is mutual respect for the qualifications and licencing between two countries; but often there is skepticism at best. When I applied for a driving licence in Massachusetts in 1980, I showed them my British quals and was required to take an exam on the local practice and rules of the road. The exam was a multiple-choice quiz with ten random questions, of which I had to get 7 correct. They would be happy to let me off on the highways of Massachusetts if I was ignorant of 30% of the regulations! Knowing just how crappy is public transport in Ireland, V wants to drive a car. But the authorities here will cut Indians no slack at all. It is as if they cannot drive at all and applicants must sit the theory test and take many lessons from a licenced training school and pass the on-road test and then spend 2 years sporting N for Novice plates on the back of the car. I've banged on the door of my local network to source a competent colour-blind driving instructor.

V's current plan is to get work, any work, in the bio-med-pharma-drugtrial arena. His latest wheeze is to start at the bottom as a Pharmacy Technician, learn that aspect inside out while earning more than he'd pull down in India on the minimum wage here [much higher cost of living, though!]. In parallel, he will be getting his TCQR Third Country Qualification Recognition; which involves paying €1,500 and sitting an Equivalence Examination. This is quite Hard Chaw: after all it is designed to show equivalence with the 6 year Pharmacy degrees that are offered at Irish Universities. As with the Driving Licence, the PSI want to maintain standards of competence. Try this sample question:
Granulocytopenia, gastrointestinal irritation, gingival hyperplasia and hirsutism are possible adverse effects associated with:
a. Carbamazepine
b. Lamotrigine
c. Phenobarbitone
d. Phenytoin
e. Valproate

 Anyway, anyway, the eternally optimistic V has an interview today to work as a Pharmacy Technician in one of the community pharmacies in town. So this is what I advised:
"I will convey my full skill" may not be the right approach. If you can, try: humility and willingness to learn the Irish Pharma business because you appreciate that, although the drugs are the same, the dispensing and distribution, payments, customer engagement and sex-ratio are completely different in our two countries. In Ireland, as you know, pharmacy is heavy on women (although The Pharmacist / boss is still more likely to be a man). What Irish workers in the field worry about is men from 'abroad' bringing Patriarchal values from home and applying them in Ireland. We have experienced this in the PT course - which has a +95% F ♀ enrollment - where chaps from abroad are insufficiently respectful of their female colleagues and/or expect them to do all the work in the lab. Remember your honoured mother and how you would want/expect her to be treated? But definitely do not go the other way and be all hand-wringing and humble and deferential. But you are a kind, smart, well brought up (thank your mother) old (26 is nearly pensionable) man. I hope they recognise that. Good luck, Tuesday,"

Monday, 10 February 2020

Death and The Man

Justice is about the balance of rights. Law is about who can afford the biggest lawyer. Justice is also about right and wrong, of course, but life is rarely black and white so we need to weigh competing rights to come up with bargain that seems fair.

We've just had an election. In the last week of the campaign Marese Skehan [appropriately L], a radical candidate from Thurles standing in the Tipperary five-seat constituency, died in her home and precipitated a constitutional crisis. The 1992 Electoral Act has a section dealing with such an eventuality:
(b) the returning officer shall forthwith give public notice that all acts done in connection with the election (other than the nomination of the surviving candidates) are void and that a fresh election will be held,
(c) all the proceedings for the election shall be commenced afresh, but a fresh nomination or consent shall not be necessary in respect of any candidate who stood nominated at the time when notification of the death of the candidate was sent to the Minister,
You can see where this article is coming from. If a mainstream [lots of adherents] political party is running a single candidate in that constituency, then that party needs a chance to replace the deceased candidate with someone who can vote in the next Dáil. Without that replacement, a chunk of citizens are being disenfranchised.

But an enormous investment of time, logistics and political momentum is tied up in the election and its dynamics. Pulling the poll and starting over in Tipperary would be unfair for the same reason as it is deemed unfair to report ongoing exit polls on election day. You don't want to have people leaving their couches or X-boxes to vote only in response to a surge to the Left in their constituency. Running the Tipp election two weeks later when the results everywhere else are known would put all sorts of undemocratic pressure and focus on those voters. Nevertheless, James Seymour, the returning officer, following the requirements of the 1992 law, did exactly that. Several of the still living independent Tipperary candidates lawyered up because it suited them not to wait: few have infinite quantities of stamina for the campaign trail.

But - phew! - the constitutional lawyers in the Attorney General's office slapped a Constitutional argument on the table for business as usual:
Art 16 3 2° A general election for members of Dáil Éireann shall take place not later than thirty days after a dissolution of Dáil Éireann.
Any conceivable rescheduling of the election would have slipped Tipp beyond the 30-day pale and so become repugnant to the Constitution. And solutions like postponing the whole election nationally or having the vote but delaying the counts would still have been caught under this proviso.

It is surprising, given how political candidates are disproportionately older, maler and over-weighter, that these awkwardly timed deaths don't happen more often. On 3rd October 2011, the Nobel Prize committee announced <taRAAAA!> that Ralph Steinman was to share the Phys&Med Prize with Bruce Buetler and Jules Hoffman for their work in innate immunity. The committee were unaware that Professor Steinman had died on 30th September. It is a fixed rule that Nobels cannot be awarded to the dead. But the committee went ahead with the nomination anyway despite a bit of red face about their due diligence. You can't, after all, be phoning candidates a minute before the announcement to check if they are still with us. Apparently Steinman, dying of pancreatic cancer, had joked with his family about holding on for the few days to see if he'd be nominated.

And yet, and yet . . . you have to ask what the response would have been if Simon Coveney, the Tanaiste and standing in Dau.II's constituency, or some other magnate of the political establishment had keeled over and pegged out on the campaign trail. In 1948, Eamonn Coogan TD [FG] died on the hustings and the election in Carlow-Kilkenny was postponed by 4 days. Fine Gael were able to get two of their candidates over the line, so everyone was happy. I, for one, am sorry that Ms Skehan didn't get elected [182 posthumous 1st preferences suggests I'm not the only one]: she was by all accounts a thorn in the establishment's vest: tirelessly campaigning for women's rights and the dispossessed. 
Ar dheis Dé go raibh a hanam dílis