Sunday, 3 February 2019

a M M Marvellous party

M&Ms

Saturday, 2 February 2019

What's the Russian for schism?

A. схизма
. . . but it's exactly the same word in Ukrainian - indeed it's the same word in English except for the cyrillic / roman lettering. In the West we have heard rumblings of conflict on the far side of the continent as Ukraine and Russia throw shapes (and artillery rounds, it must be said) to determine who rules what. The Crimea having been annexed by Russia in 2014 despite being part of the Ukrainian SSR from 1954 until 1991 when Ukraine became independent of its larger Eastern neighbour. More than 50% of the inhabitants of the peninsula being ethnic Russians. Two Eastern Oblasts of Ukraine, Donetsk and Luhansk, with the highest proportions of ethnic Russians, seceded from the union in 2014 as  Доне́цкая Наро́дная Респу́блика and Луганська Народна Республіка. They are now reintegrated with a mixture of wall-paper, string, and hope. There are parallels with Brexit where half the people in the UK want to sever ties with Europe and return to a 1913 era Edwardian tea party on the lawn.The other half want to go back to 2013 when Brexit was but a fantastic pipe dream by the Edwardians.

Recently Πατριάρχης Βαρθολομαῖος Α aka Patriarch Bartholomaeus I has been throwing his weight into the scales of unrest.  Who he? Wot Weight? He is the 270th Archbishop of Constantinople and Ecumenical Patriarch of the Orthodox Church. That post has an office in Byzantium / Constantinople / Istanbul but can only be held by a Turkish citizen. Bart was born, ethnic Greek, on Imbros in 1940 when the island was politically part of Turkey despite being mostly inhabited by Greek speakers; so he ticks that box. Most of the Greeks of Imbros have since left and the island has been more closely integrated with the mainland - getting renamed Gökçeada to show this fact more clearly.

His weight is that of a feather against the soul of man. The Orthodox church separated from Rome in the Great Schism of 1054. One of the unsticking points was Credo . . . et in Spiritum Sanctum, Dominum et vivificantem: qui ex Patre ⟨Filioque⟩ procedit: whether the holy spirit proceeds from the father [the Greek position] or father-and-son [preferred by adherents of Rome]. Oh that Trinity, the cause of so much disagreement and bloodshed. [No! not that Trinity] The Orthodox church has many independent Patriarchs each with their own parish but the historical importance of Constantinople to Christendom allows Bart to be treated as Primus inter Pares - the first amongst equals - by his patriarchal colleagues.

There are fourteen Autocephalous [with its own head] Churches under the Orthodox umbrella:
  • Ancient Autocephalous Patriarchates.
    • Constantinople
    • Antioch
    • Alexandria
    • Jerusalem
  • Junior Patriarchates
    • Bulgarian
    • Serbian
    • Romanian
    • Russian (with adherents ?Junior-junior?):
      • Belarus
      • Latvia
      • [Ukraine]
      • Japan
      • China
      • Moldova
    • Georgian
  • Autocephalous archbishoprics
    • Cyprus
    • Greece
    • Albania
  • Autocephalous metropolis
    • Polish
    • Czech & Slovak
    • [America]
    • [Ukraine]
Not everyone, and certainly not the Russians, recognise the autocephaly of the church in America which was under the watchful eye of Mother Russia, in the same way as adherents in China and Japan. In 1970, Bart's predecessor promoted America to the First Division; an assignment still not accepted by the Russian Patriarch. And now since 5th January the Ukrainian church has been liberated from the over-view of Russia by Bart. It is impossible to believe that this last move is wholly independent of schismatic events in Crimea, Donetsk and Luhansk.
There is a small Orthodox community in Ireland that used to be mostly expatriate Greeks, of which there are less than 1,000 in Ireland. Since Romania joined the EU, many have fled West and there are now more than 10,000 here. Orthodox Romanians have been giving voice to their version of the creed to the discomfiture of the Greek community. You can catch some mighty Gregorian chant at their Dublin 7 church, formerly Victoria Kindergarten School [shown R].

Friday, 1 February 2019

De Mother of De Bride

When my correspondent G got married on a Summer Bank Holiday weekend 30 years ago in Carbally Co Waterford, the family rowed in to do the catering. Ham and salmon; potato salad; green ditto; hummus bi tahini; cake and ice-cream. Monstrous portions, lovely weather, tipsy aunts, riotous children: a great wedding. Despite the absence of any form of mean-spirited portion control, there was still rations of food the following day. The left-overs were laid out on trestle tables in the farm-yard and we all nibbled our way through mighty hang-overs to a state where we could face another dhrink. The toilets backed up from the septic tank and had to be rodded out. The following following day, it was the same: folk were still trenchering through an apparently undiminished food mountain making sandwiches from cold cuts. Then I turned over a slice of ham to reveal (m'eyes were better then) a couple of neat rows of blowfly Lucilla sericata eggs. Quiet word with the chatelaine [no point in frightening the horses] and the rest of the spread was quickly and discreetly condemned to the bin. No harm done.

It is an ill wind that blowflies nobody any good! Lucilla sericata does get a bad press because it flits between the kitchen and midden with sticky feet - without even getting as far as laying eggs. But it has a useful side as well; as was brought home to me by some of our Pharmacy Technician students. They had been formed into groups, each  to do a small independent research project, summarise their findings in a poster and present it all at an academic meeting later in the year. There's €250 riding on the best poster from The Institute and more prizes at the national meeting. The Faculty from the PT course were each assigned to mentor a poster-group and mine elected to write about the uses of leeches and blowfly larvae in wound debridement. Most PTs choose to work in community pharmacies but others go for work in a hospital pharmacy where they deal almost exclusively with medical professionals rather than anxious parents and dithery ancients. One of the jobs of a hospital pharmacy is to feed the leeches Hirudo medicinalis! These lads are closely related to the earthworms that rummage through my compost heap but they depend on a blood meal rather than deco posibg vegetation. You can pick up leeches if you wade through the water where they live - which was all over Europe and much of West Asia.

They are in hospital pharmacies for their saliva which is a rich stew of anti-coagulants: to stimulate the blood flow y'know. If the surgeon clamps a couple on after a microsurgical finger re-attachment, then these secrations keep the blood circulating in the area and promote healing. Very retro, not to say medieval, but they are in some circumstances the best tool in the box.

In the bed next to Jimmy with accident chopping kindling, old Mrs Doohickey is nursing some weeping sores on her lower legs: her diabetes doesn't help but the primary cause is an antibiotic resistant tuberculosis infection. Because she's old and quite crocked up (the diet of cigarettes and  biscuits doesn't help) her immune system just isn't clearing up the wound. The nurses have to change the dressings twice a day and the smell is funky. Part of the problem is that the resident bacteria are working away underneath a thick biofilm of dead and dying cells - both Mrs D.'s and her spongers' and what's left of her immune system is overwhelmed. Bring on the dancing blowfly larvae! These aren't on the inventory of the Pharmacy but can be ordered up from a convenient supplier. The larvae come cleaned! so that they don't make things worse by adding more microbes to the soup. It is also required that they are applied to the gaping wound under a maggot-proof dressing - nobody wants t'buggers crawling out between the sheets and dropping to the floor like a scene from the Great Escape. Amazingly, the larvae = maggots prefer the soupy elements of the lesion and eat everything back to sound tissue which is then able to start the healing process. Surgeons are taught debridement in med school - cleaning up ragged wounds so that the can be sewn up but the scalpel or more usually a curette is a rough bludgeon compared the delicate rasp of the larva's mouth-parts.
  • What about The Mother in the title? 
  • Where do you suppose the eggs come from which hatch into larvae and debride the mess? 
  • Do you always answer a question with a question?
I bet you're glad I didn't include pictures of suppurating sores. Instead I slapped in some nice thumbnails of a Spotted Wood Breacfhéileacán Coille Pararge aegeria, a handsome and still reasonably common Irish butterfly.

Thursday, 31 January 2019

Davy Jones

I spend quite a bit of time mulling over End of Life Issues intubation - nursing homes - DNR - funerals - disposal of remains. I hope not too dismally.  In any case, I was much taken with a link on TYWKIWIDBI about drilling 5cm air-holes in coffins . . . so that they sink smartly and don't go all Bob the Casket and drift ashore.

Cue Master & Commander soundtrack.  The EPA in the US has some restrictions on the practice but basically asserts that everyone has the right to be buried at sea - not just Pat the Salt. So long as
  • the launch is 3 nautical miles = 3,000 fathoms = 5.5 km from the low-tide mark
  • no wreaths esp. plastic wreaths
  • no tombstones, mausoleums
  • casket to be weighted (no lead!!) and bound with six (6) bands of stainless steel, chain or natural fibre rope, holes drilled in the top and both ends [see pic R]
  • The event is reported to the local office of the EPA within 30 days.
I can't imagine what the EPA is going to do with the information on the Burial at Sea form, except file it. You may be sure I was hopping from one foot to the other until I could find out what the score in in Irish territorial waters because burial at sea sounds like a cheap and cheerful option . . . unless a force 6 gale blows up as the mourners leave harbour. It turns out that there are no regulations (yet) about the practice - only guidelines.  A couple of years ago a woman was sea-buried but reappeared on the beach many months later and caused work for the Gardai and the state pathologist - who found this body has been post-mortemed before. Nobody wants that sort of hassle so let's all resolve to do it properly. As far as possible by following The Guidelines:
  • 50 miles off the coast!
  • No embalming and no MDF cheapo coffins
    • no oak mahogany or iroku either - they last too long
    • holes drilled prior
    • robust for launch impact >!kersploosh!< and indeed impact >!baDONG!< on sea-bed several minutes later
  • 100 kg extra weight - steel chain recommended
    • No lead Pb, copper Cu or Zinc Zn
The 50 mile exclusion zone indicates a weekend trip at least - bring plenty of rum and ship's biscuit.

Wednesday, 30 January 2019

Crispr: the craic is mighty

Someone who loves me and thinks I spend too much time bloggin' and not enough reading gave me a copy of A Crack in Creation by Jennifer Doudna and Sam Sternberg. Doudna is in line for getting a Nobel Prize for her invention of a gene-editing technology called CRISPR-Cas9. Sternberg was her graduate student, is now a professor at Columbia U, and can tell a story better than most scientists. He's not exactly a ghost writer because he gets full author credit. But you get the feeling that when publishers hunted down Doudna to write a popular science book about her journey, she turned to her most literate friend and brought him on board. After a few style-and-substance quirks that had me fling the book to the other end of the sofa in a pet, I settled down and read it through to the end without skipping much. I'm a scientist; I've known about CRISPR for half a decade; I know it is important; I know it is ethically controversial; I know that there are fortunes to be made; but I couldn't have explained how it works. To be honest, I'm not now better able to explain it after reading this book.

That is partly because the methodological explanation is at the start when I was aggravated by the stylistic yo-yo of alternating between over-simplifying the easy stuff and making unwarranted Curse of Knowledge assumptions about the trickier concepts. The Curse of Knowledge is when you've learned something (hard) it is impossible to unthink that knowledge to understand how an absolute beginner approaches the problem. I'll give you an unscientific example: on p232 "linkages between class and genetics would ineluctably grow from one generation to the next". In a popular book relentlessly or unavoidably would do just fine; ineluctably is a college-boy word. Next page exacerbate is used rather than worsen. I'm a college-boy - I've had to edit my fancy vocabulary [herbivore - salient - indelible] so my students know wtf I'm on about.

If you want to know how CRISPR works you could do worse than listen to Paul Anderson a high-school teacher from Bozeman Montana as he explains the system. I use his channel in my Human Physiology classes - his animations are better than I can do with words and static pictures. MIT, an institution with $ignificant $kin in the CRI$PR-CA$ game (and load$a money for propaganda), has produced their own video with fancier graphics than Bozeman's but gaping holes in their story. MIT don't trouble to explain that CRISPR is an acronym [clustered regularly interspaced short palindromic repeats] but tell us <yawn> that A pairs with T and C pairs with G. Every word in [clustered regularly interspaced short palindromic repeats] is a key clue to how the system works and what is its potential. No surprise that Jennifer Doudna was invited to address TED-Global in London in 2015, her technical explanation isn't as good as the high-school teachers perhaps because she's too close to it. WIRED's Biologist Explains One Concept in 5 Levels of Difficulty isn't what it says on the tin (he's hopeless with the easy stuff and seems to know less than the experts) but advances the discussion in useful directions. One could wish that youtube presenters would consider not-Anglophone watchers and Enunciate Clearly: problem not pro'm; ability not abil'y. tsk!

If a 7 minute video is tl;dw for you, you can skip to the fact that this technique has the potential to precisely remedy the genetic damage that causes cystic fibrosis or retinitis pigmentosum or thalassaemia <etc.> and leave all the other genes unchanged. Parents who bonk bonk love each other very much but are carriers for one of these diseases can have children "of their own blood" but no chance of developing the disease that dogged their ancestors. You'd have to be a hard-hearted god-botherer to be against such tilting of Fortune's table IF the precision and reliability of the edit could be guaranteed.

But what about cosmetic changes [getting rid of all those Irish freckles] or smoothing out natural variability so that everyone has faster reflexes, nobody is on the autistic spectrum. If you can change such factors reliably and cheaply (which is a probability) then people who don't or can't or won't avail of the opportunity to change themselves and their children may get excluded. Me, I'd rather cherish and support The Different because diversity is intrinsically interesting: when conditions change [think End of World issues like carbon footprint] then maybe slower more deliberative folks will be an asset while the rest of us run around like headless chickens. We need to think about these ethical issues because genetic editing is at the gate and a lot of rich people have invested a chunk of their money in the technology and want a return of their investment.

Did someone mention money? In her book, Jennifer Doudna [L above] absolutely avoids talking about the Patent Law dispute her Institution, UC Berkeley, [and her pal and co-inventor Emmanuelle Charpentier [R above] of the Helmholtz Centre for Infection Research in Braunschweig, Germany] is fighting with Feng Zhang [sandwiched above], the Broad Institute and its parents Harvard and MIT. Berkeley & Co. want exclusive use and licencing of the whole field. Broad & Co. hold that their boy was the first to make a usable product out of CRISPR . . . perhaps while Doudna was agonising about the ethical issues and holding workshops to discuss them. The US Law is currently supporting the case from The East Coast while the Europeans are favouring The Californians - perhaps because Emmanuelle Charpentier is Euro-french. That split decision will play havoc with the development of CRISPR-tech because drug-companies work best in a Global Village - bigger population and a uniform playing field = more profits. I hope Doudna, and indeed the other two, makes a fortune out of these ideas and that they share it with all the people who inched the idea along the way. And watch the Nobel space!

Tuesday, 29 January 2019

Trust Axis

Week 3, term 2 ✓.  25% of my hours this term are on the remedial maths axis. That's not to say that all the people in the room need help because their math-anxiety is overwhelming: some appear to be both competent and curious about the edges of my competence in, say, MS-Excel. I can usually amuse such students if I ask them to plot a pair of unlikely variables against each other and maybe calculate a correlation coefficient. In class on Friday, I looked over the shoulder of my willing-and-able Magyar-Irish student, to see a map of early 20thC Central Europe! It was a long way [110 years and 2,000km!] from the class assignment, but he said he was making a pie-chart of the ethnic diversity in the Austro-Hungarian Empire prior to Sarajevo 1914. Well, that's at least as valuable a question as my madey-uppy dataset of Iron and Zinc concentrations. His graph [R] was particularly interesting to his Polish-Irish neighbour who hadn't previously appreciated that 5 million Poles had sworn fealty to Erzherzog Franz-Joseph the Last. Imagine how interesting it must have been living in Vienna or Budapest in 1910 - so many languages, so many cuisines, such a variety of dress and dance and song. Hark! the strains of the contemporary march "Die Bosniaken kommen".

Voices off: Don't mention the Axis! That's the next War. Sorry, lads, I've started on Axis [look at the post heading f'chrissake] but a very different beast altogether. If you've been reading The Blob since it was born 6 years ago then a) you are in a very small set b) you might be forgiven for thinking that The Institute has but one teacher - by the name of Bob. That is not true of course but reads that way because of an early policy decision to preserve [a thinly veiled] anonymity and therefore allow me considerable freedom to tell it like it is. Thus The Blob has reported on events in my classrooms and labs; on visiting speakers and other public events; on some of the absurdities of management; on what I read in the papers . . . but decided I wasn't going say anything negative about my teaching colleagues or the secretarial staff or the technicians. There have been times when I've been disposed to write about these people because they had really annoyed me, disrespected the students, or failed spectacularly to do their job: but I've held fire. De collega nil nisi bonum, eh?

In October last year I had a "difference of opinion" with two of the other lecturers about the conduct of final year research projects. It was quite surprising to hear this first coming at me by scuttlebutt through intermediaries and very surprising when it came up and was minuted in a Faculty Meeting a few days later. But it didn't surprise me that one of the youngsters had chosen a Jacques Bonhomme open-forum approach while the other had preferred a tittle-tattle SoS snark of snake route. Each fellow was naturally behaving to type. Predictably these events caused a mild shit-storm of indignation - who would be next for trial by innuendo??  There was a bit of an enquiry as to whether there was any substance in the allegations: if there is going to be bad-mouthing in the scientific community, then it would be scientific to have the allegations both fact-checked and evidence based. Last week we had the next Faculty Meeting, when I was expecting the issue to be put to bed. But it never happened. That was partly because a far bigger management shit-storm blew up which took a lot of deliberation to decide about. But it was also because I didn't feel righteous enough about the disagreement to insist on another difficult discussion eating into everyone's dinner hour.

When I got home in the evening The Beloved and I talked over the non-event and I said something about being spineless nice to people because I liked to be liked. I had for example dropped in on Jacques B, whom I like and respect, the evening before the meeting to say "I just wanted to reassure you that I don't intend to get all shouty tomorrow". He had apologised (twice) and I didn't want the poor chap to lose sleep worrying about an Ordeal by Faculty let alone the far more frightening jihad by Baobab al Antiquam. TB said that, in her life, she found it easier to take adverse comment if it came from someone she trusted. That sounded a little redundant to me because I thought that 'trust' and 'like' were essentially the same; while she seemed to be claiming that they were on orthogonal [independent, at right angles as L] axes. If they are really independent, I said, we should be able to fill the bottom-right and top-left corners: people whom we trusted but didn't like much and/or people we liked but didn't trust. YMMV but I was scabbling to find examples.

For about 10 years I was the father of teenage girls, who were thankfully triple-M monogamous and minimally moody through the walking-out process. A couple of weeks ago, I was talking with another father-of-girls and asked "Is D still going with that Most Unsuitable Bloke From Enniscorthy MUBFE?" Apparently not, he'd been dumped a while ago (and good riddance). I then asked The Dad if any of the parade of dated lads were liked by the parents  - even if they were considered to be unsuitable for their daughters. Didn't get a coherent answer to that one but it seems possible:- young feller who is polite, helpful, deferential and funny but also feckless, spendthrift, and far too frequently drunk. People are complex and interesting because they are multi-dimensional.

Monday, 28 January 2019

A medical first in Ireland

In this months issue of the Irish Medical Journal IMJ, three doctors from Tallaght Hospital record a peculiar case of self-abuse. Young chap had presented himself to hospital because his arm was all swollen, painful, red and hot - tumor, dolor, rubor and calor - the four classic symptoms of inflammation. The patient revealed that, to cure a back-ache, he had elected to inject his own semen intravenously every month for a year and a half. A comprehensive search of the medical literature revealed that no similar case had been reported since records began. A bit like the Darwin Awards for people who have offed themselves in extravagantly silly ways [examples], such stories get quite a bit of traction. I felt I had to share it with you even at the risk that several readers might try a copy-cat self-treatment for a real or imagined illness. Semen is, after all, free and readily available [to chaps anyway] and in all sorts of metaphorical ways is deemed to be 'potent'.

Searching the medical literature through Pubmed is an essential part of medico-scientific research: you need to know if anyone has been there before - they might have a helpful remedy. The current investigation reminds me of my training set of pubmed search terms which included "vacuum cleaner injury". Don't go there if you're squeamish and don't read Deadspin's 2018 Year in Review list of objects retrieved from people's orifices. Don't compare and contrast 2017's list: same picture different inventory.

This report is only vaguely related [even in my 'mind'] to the widely misunderstood tale about Irish poet laureate WB Yeats and his monkey-gland potency injections - which probably never happened. In that story, I used Yeats as part of the back-story on experiments where youthful blood is injected to old veins in an attempt to live forever. This treatment has gone commercial at least partly because blood-transfusion falls under medical regulators' categorization "generally recognised as safe" GRAS. Ambrosia Inc. will sell to Patriarchs 2 litres of young blood delivered for $8,000. It's not clear how that $8K is divvied up among the donor, management, share-holders and lawyers.