Thursday, 31 May 2018

My body spake, not I

Roseann Barr just uttered an outrageous racist slur on Twitter and had her back-from-the-dead Gig on ABC cancelled forthwith. Twitter is like an open mouth ready for foot. She blamed her medication: Ambien which is a neurotransmitter-jiggling sleep-inducer. Sanofi, the French MegaPharm which has made billions out of Ambien didn't issue a cease-and-desist because you cannot re-call the spoken word, the sped arrow, the past life, the lost opportunity . . . or the sent tweet. They did, however, point out  “People of all races, religions and nationalities work at Sanofi every day to improve the lives of people around the world. While all pharmaceutical treatments have side effects, racism is not a known side effect of any Sanofi medication,” they should know because the list of side-effects is long. And includes one which is exactly opposite to the effect for which people take Ambien:
  • SUBJECTIVE: trouble sleeping; discouragement; clumsiness or unsteadiness; confusion; depression; sleepiness or unusual drowsiness; daytime drowsiness; confusion about identity, place, and time; seeing, hearing, or feeling things that are not there; burning, crawling, itching, numbness, prickling, "pins and needles", or tingling feelings; dizziness, lightheadedness, or fainting; loss of interest or pleasure; memory problems; mood swings; nightmares or unusual dreams; sense of detachment from self or body; slowing of mental and physical activity; tiredness; trouble concentrating; double vision; drugged feeling; false or unusual sense of well-being; feeling of unreality; feeling sad or empty; lack of appetite; lack of feeling or emotion; lack or loss of self-control; lack or loss of strength;
  • OBJECTIVE fast heartbeat;  skin rash; swelling of the face; abnormal or decreased touch sensation; abnormal sensation of movement; appetite disorder; chest discomfort; chills; dry mouth; heartburn; hives or welts; itching ears; nausea; redness of the skin; redness or soreness of the throat; sneezing; stuffy or runny nose; vomiting;
  • BEHAVIOUR: binge eating; unusual excitement, nervousness, or irritability; 
  • BOWELS: abdominal or stomach pain; constipation; diarrhea; frequent bowel movements; 
  • PLUMBING: frequent urge to urinate; difficult, burning, or painful urination; bloody or cloudy urine; longer or heavier menstrual periods; bladder pain;  
  • BREATH: difficulty with breathing; wheezing; 
  • MOVEMENT: falling; loss of balance; balance disorder; difficulty with moving; difficulty with swallowing; joint pain; muscle aches, cramping, pain, or stiffness; swollen joints; 
  • VISION: eye redness; blurred vision; vision changes; 
  • HEARING:  earache; headache; hearing loss; continuous ringing, buzzing, or other unexplained noise in the ears; change in hearing; [see also falling / balance / dizziness above]
I put out a list of all the reported side-effects for infliximab two years ago. Totally different disease, totally different drug, totally different mode of action . . . but lots of overlap in the adverse symptoms.
HuffPo has an essay on the particular and peculiar cases where the Ambien Defense has been played by lawyers for people who have killed other people while under the influence. My Da, a sea-captain, never shirked responsibility for his own actions and neither for the actions of everyone under his command.

Zolpidem, sold as Ambien, seems to act as a GABA agonist: locking into the gamma-amino butyric acid GABA receptor to gee-up its potency. As with all oral medications that interfere with normal neurotransmitter-receptor relationships it is impossible to target the drug to only those receptors in the particular subset of neurons that you wish to influence. As you see from the list of side-effects above, GABA affects, at least, the brain, bowels, lungs/trachea, urinary tract . . . I tell ya, it's a wonder any drugs are approved as safe and efficacious.

Once, while he nodded on a chair,
At the moth-hour of eve,
Another poor man sent for him,
And he began to grieve.

'I have no rest, nor joy, nor peace,
For people die and die';
And after cried he, 'God forgive!
My body spake, not I!'

Wednesday, 30 May 2018


I'm too old and tired to get angry but . . . my shoulders do slump sometimes as I feel my vocation as a teacher being diminished by the needs of objective assessment. Science at The Institute is split into two streams - the Physical and Biological - which are weighted most unevenly. Youngsters don't seem to be interested in doing chemistry at Third Level and nobody really knows why; whereas biology is recruiting much better. It may be because we put 'Forensics' in the Degree title after CSI became super-successful on the TV. It may be because there are jobs for the boys-and-girls in "Pharmaceuticals", another word that appears as part of a degree title.  In any case, behind the scenes and without my involvement, my Department has been crafting a new degree to replace the rags of a four year course that used to be Chemistry and has gradually morphed into Environmental Science.

It was, accordingly, a surprise last week to be invited to a meeting with the External Panel which has over several months been reviewing the new course paying particular attention to the new modules which have been developed especially for the new degree. Large tracts of the old course have been preserved and all our courses have a common first and second year where the fundamentals of biology, physics, chemistry and maths are presented, examined and forgotten. We all forget 90% of what we learn over the subsequent day or two, so it's not surprising that students in second year claim they've never heard of X . . . and could we go over it again? There's ways of teaching, say, The Calculus, which make it rapidly forgettable. A couple of members of the external panel had clearly done some recent CPD [that would be continuous personal development] at the TLC [we all have a teaching and learning centre even if some places call it Centre for Enhancement of Learning & Teaching (CELT)] at their home institution.

I know this because, although the External Panel were very happy with the C for concept, the culture, the curriculum, the creativity and the content of the course they wagged their fingers and sighed over the Learning Outcomes.  Tsk tsk, they told us, you must never use the words knowledge, recognise or understand in college-level LOs because those words are not sufficiently high up the tree of Bloom's Taxonomy. No, no, no you must use Measurable Active Verbs [MAVs ??] like D for define, describe, detect, differentiate, distinguish. If you are in the realms of rocket science, I presume you can move on to the E for evaluate, explain, elaborate, estimate.

Bloom's Taxonomy is named for Benjamin Bloom the chair of a US committee tasked to help educators design curricula and assessments. The book of their deliberations was Taxonomy of Educational Objectives: The Classification of Educational Goals . . . there has been no film of the book and the clips on youtube are a) woeful and b) a long long way from going viral. I suspect because nobody really gives-a-damn; although LRC people talk Bloom's Tax up a storm.

Two helpful comments came from other members of the External Panel.

1)"Wouldn't it be great", mused one, "if you could write your learning outcomes in language you and your students could understand and then whack them through Google-translate into Bloomspeak at the appropriate level?" That's my sort of guy, slightly cynical, good crap-detector, clearly engaged. There are six levels to Bloom:
The small discs/layers at the top are built on the foundations below. The higher the step the more valuable and the more discriminatory: only Harvard students can do the Evaluate and Create stuff, the rest of us bumble along just trying to remember where we left our glasses.

2) the other comment was "You can't design unambiguous exam questions with words like know, recognise or understand". If you use measurable action verbs in the LOs, then the exams write themselves. There was a lot of sage nodding at that insight because it showed a clear way to close the circle of syllabus, learning outcomes, test, mark, label, dismiss. I've ranted and railed about the constraints this puts on teaching anything that matters.

It might have been the same guy who added a schoolmarmish argument against using understand in LOs. "If it only happens IN the student's head it's not an OUTcome, is it?". It took commendable self-discipline that I didn't leap across the Board Room table and assault him (verbally) "I will show and tell my students things next year that they will remember for ever and use with advantage but will never write down in an exam" -

  • how to do tabs and accents in Word
  • where (and indeed what) is my pancreas;
  • that you and your pet hamster have red blood cells of the same size; 
  • that not knowing something is okay; 
  • that demeaning somebody is not; 
  • how to make F for flapjacks (a skill whose utility is waaaay beyond Bloom)
  • that irony is different from sarcasm;

While searching for good video on Bloom's Taxonomy - fail! - I came across Azul  Terronez' definition of a teaching excellence: Great Teachers Eat Apples. There's more to it inside. Terronez advocates teaching children how to Listen. Too many teachers just drive on through the content without pause. If they stopped & listened they might try a more effective way of getting their stuff over. But for Terronez the medium in the message: by listening to students you give them respect. That respect will be absorbed and brush off on others.

Tuesday, 29 May 2018


Have you noticed how almost all Protestants have Protestant parents? It's because most people, most of the time, are not critically evaluating their choices; they are rather rolling with what is easy, normal and local. You can extend this reasoning to every aspect of society and our behaviour. In the Pub it's "Will that be the usual, sir?". We're still supporting Man.U. years after we stopped dribbling the ball
 and just dribbled.  I put it to you that we'd all be better off in a happier, more open and more tolerant society if more of us changed our minds more often. There's a word for it: Metanoia, which word-a-day is urging us to use more often: it is a noun from Gk μετάνοια A profound transformation in one’s outlook.

I am, because they are rare, much taken with people who are capable of changing their minds. A piece I wrote a while ago cited The Edge Question for 2008: What have you changed your mind about and why? As it happens both the leaders of the main political parties in Ireland - Leo Varadkar, [R below] Fine Gael and Micheál Martin [R above], Fianna Fáil - had a salutary change of heart (within a few days of each other) during the run-up to the Repeal the Eighth referendum about which I'll soon stop gabbling [backlog] - promise. I say salutary because a) they came round to Yes b) at a time when it was by no means obvious that Yes-Repeal was the The Wave of the Future c) It is a nice change for politicians to be leading from the front rather than rowing desperately in the wake of public opinion to secure another term at the next election.

For Varadkar, his volte face was achieved by listening to two of the many Difficult Cases which engaged the media at the time but also after Martin had announced that, for him, the Eighth Amendment was a cruel and unusual punishment which just didn't deal with the reality of crisis pregnancy in Ireland. I got the feeling in January 2018, that someone close to Mr Martin had bluntly told him that crisis pregnancies didn't only happen to women Out There. The alphabet soup of A B C D X & Y evidence / cases / anecdotes had all been available during all the years when Martin had been content with the post 1983 status quo, but suddenly he announced his conversion. Who knows? It doesn't matter why, it matters that his change of mind made a significant change in the tenor and impetus of the debate.  Likewise Varadkar.

In the spirit of David Attenborough, I'll show a picture of some endangered species, 31 Fianna Fáil TDs and Senators who nailed their No colours to the SS Love-Boat on 3rd May 2018:
These chaps [mostly chaps as you see despite pushing the five women to the front] will now be hoping that a general election is not called anytime soon. They have some overlap with the 32 TDs who voted against holding a referendum [full list at link] at all at all. And to be fair, there's also a good few Fine Gael and Sinn Fein pols who are adamantly No. Please remember their faces when they come round asking for your vote and ask them whether they've had any sense of metanoia so as to better to represent the will of people.

Monday, 28 May 2018

The Midwife of Chemistry

That would be Marie-Anne Pierrette Paulze Lavoisier [shown L at R], who lived through turbulent times in the French Revolution. She was married off at 13 by her father, a senior bureaucrat for the Ancien Régime. The early marriage was in the nature of a pre-emptive strike to side-step a proposal from a 50 year old paedophile aristocrat who was in a position of power over the father. The preferred bidder in the auction was Antoine-Laurent de Lavoisier a younger and more personable aristocrat. Antoine and Marie-Anne were married in 1771 and became one of the most famous married-couple teams in the history of science, with complementary skills and the habit of banging half articulated ideas off each other until a synergistic truth emerged. Yet she is often, literally, photoshopped out of the picture [eg]. I made an ironic comment "Lavoisier hears the doorbell" beneath one such portrait in my 2014 essay about le père de la chimie moderne as the French like to give their boy his puff. The English prefer to give the Father Of title to others like our own Robert "Up the Déise" Boyle or John "atomic theory" Dalton.

Marie-Anne had been educated in a convent and acquired facility in Latin and English which was very useful to her husband when he set up a gentleman's hobby laboratory in his home. The Industrial Revolution was smelting away across the Channel in England and practical and curious men were in high demand. Without nailing the fundamentals of physics and chemistry, the bridges [Coalbrookdale], plates [Emma Wedgwood!], textiles, and steam engines wouldn't work safely and efficiently.  The reports, by the likes of Richard Kirwan, Henry Cavendish and Joseph Priestley, were written in English and Anne-Marie was able to translate them into French. But she was far more than a dull Google-Translate robot. She was able to critique and evaluate the science and the finished text was peppered with her observations and additions.

Come the Revolution and the Terror and both Marie-Anne's husband and her father were executed on the 8th May 1794 [19 Floréal II in revolutionary time]. She lived on for another 40 years, justifiably bitter about the treatment her family had received and watching her husband's rehabilitation, not to say beatification by the the French government. She played a very active part in that rehabilitation as she prepared for publication Lavoisier's Elementary Treatise on Chemistry - Traité élémentaire de chimie (1789), and the earlier Méthode de nomenclature chimique (1787). Even back then, without publication there is no science: it was she who ensured that the offspring of the father of chi=enistry saw the light of day. She was competent in technical drawing and her illustrations in the Traité and the Méthode greatly facilitated those who followed in Lavoisier's footsteps. Indeed she was formally trained in drawing and painting by no less a luminary than Jacques-Louis David, who was arrested during the Terror but manage to keep his head. The picture at the Mast-head was commissioned of David by the happy couple just before the Revolution and probably shows more of their relationship than has come down in print from contemporary writings.

Sunday, 27 May 2018

That's a lot of blaas

There has been a bit a changing of the guard down The Déise. The Girl Who Invented Herself has gone back to work in the Far East as VP Networks AsiaPac for Megacorp. Which leaves one less for the rota of looking after my venerable father-in-law Pat the Salt. For much of last year, I used to cover Sunday nights because I had no classes at The Institute on Monday morning. On Mondays we'd typically spend a couple of hours with the Heritage Club, playing bingo and chatting about the old times in Tramore. Then I did have classes on Mondays, so I haven't been hanging out on Sundays. Pat is quite sure that he not safe to be left alone: he's heard too many stories of old folk falling and breaking bones and lying in a heap for a couple of days until the postman can't get anyone to sign for a parcel.

I'll share one story here to clear it from my stuff-of-nightmares. In the 1980s we spent 7 years living in suburban Newcastle-upon-Tyne across the water. Early one Saturday, The Beloved and I went across the main road to Mr Patel's corner shop for milk. Almost immediately an ancient fellow came in and asked Mr Patel Jnr, who was behind the counter, for help with his younger brother. Jnr was non-plussed because there was no-one else to mind the shop. So we went up the street a piece with the ould chap to see what we could do. Turned out that the two brothers shared a nice neat Edwardian row-house. The night before, the younger (aet. 88) had trip-and-fallen and had been lying all night on the floor with a broken arm. The older brother (aet. 92) had been unable to lift him into the bed. He had rather sat vigil all night until the shop opened the next day; believing that the centre of our community would help with the lifting. It was beyond comprehension that they should call an ambulance for such a small task and they didn't want to bother the injured man's son who was a dentist out in the poshest suburb in the county. We set to making a pot of tea and used this to first moisten the sand-paper lips of the casualty and then start spooning the nectar in to start rehydration. The angles told us that the arm was broken for sure and we persuaded them that paramedics were definitely the best call. They were really reluctant because they suspected that, if the young-feller ever went into hospital, he'd never come back home. Anyway, the ambulance arrived, the paramedics came in and with shocking brisk efficiency sheared open the young-feller's tweed jacket and shirt to get a closer look at the damage. Half an hour later he was stablised, pain-killed, given another cup of tea and whisked off. We never followed up on the story . . . it was sure to be too sad.

The family agrees with Pat's self-assessment and with classes effectively finished I have time for elder care. The Beloved spends several days and nights a week two counties away, so we communicate by e-mail and phone:

TB: Can you mind Pat on the 20th while I'm in Dublin?
Me: Sure. That's the first official day of holidays. Will work for blaas
TB: Just how many blaas would 24 hours constitute ;)
Me: N = 415 at 24 hours minimum wage €9.95 and blaas at €2.30 for 4. That's a lot o' blaas.

To be more precise / graphic, that is about 3 x 20kg stack-and-nest crates full of the quintessentially Waterford white bap:
Movie-time  Walsh's  - M&D - Barron's - as gaeilge. And foreign johnnies from out-the-Déise might need some help on the pronunciation.

400 blaas is more than I could eat in a sitting. Heck, it's more than Takeru Kobeyashi could eat in a competition. Nobody except carers and junior doctors works for 24 hours on the trot. But that's a lot of bread (albeit at the pricier end of the bread market) for a little over half a week's normal M-F 9-5 work, such as I do at The Institute. You'd think a chap could live on the minimum wage if all he ate was blaas - obviously trading some of them for a scrape of butter and the odd tomato. But he probably can't live on the minimum wage because property / rental prices are wholly dysfunctional in this Our Republic. And we might pause to reflect on how we pay carers  at both ends of life the bare minimum: for thousands of families across the country the carers get nothing at all - only anxiety, hard work and hardship. The rest of us pay creches and nursing homes to look after our loved ones while we go out to work.  It costs a king's ransom and the workers at the coal-face of care get paid buttons. That's not right. It's not even sensible: these people are looking after our Most Preciousssses and we're throwing them crusts and apple-cores. Just wait for a case of The Revenge of the Crèche-Workers. We've already had The Frustration of Carers showing in Swinford, Co Mayo.

Sunday wind-up

Last Sunday in May.  Peculiar and ordinary:

Saturday, 26 May 2018

A Great Day for Women

The Repeal the Eighth Amendment referendum [above: interim results 1530 on Count Day] was all over before the count began because two exit polls published late last night showed a decisive win for - almost the mirror image of the numbers in 1983 when the Eighth Amendment was referendumed into the Constitution. Blob backstory:
TodayMay18 - May18 - May18Mar18 - Dec17 - Oct17 - Jun17 I'll shut-up for while now!

In 1803, at the very beginning of the 19thC, impossibly romantic Robert Emmet was executed after failing to achieve Independence for Ireland. His speech from the dock goes on a bit but finishes thus:
"I have but one request to ask at my departure from this world — it is the charity of its silence! Let no man write my epitaph: for as no man who knows my motives dare now vindicate them. let not prejudice or ignorance asperse them. Let them and me repose in obscurity and peace, and my tomb remain uninscribed, until other times, and other men, can do justice to my character; when my country takes her place among the nations of the earth, then, and not till then, let my epitaph be written. I have done." [one of many sources].

A case could be made that, with the result of the referendum, Ireland has ceased being a 19thC theocracy. With women now another step forward towards being treated as autonomous independent adults, someone more poetic than me might be in a position to write Emmet's epitaph. It might bring in the sad sad story of Sarah Curran, Emmet's fiancée who was disowned by her father, lost her lover, lost her first born after marrying another man and finally died of tuberculosis at the age of 26. She is far from the land where her young hero sleeps. We have, with respect both to the status of women and the effectiveness of healthcare, come a long way since 1808.  We might don rubber-gloves, take up some tongs, dust off and recolour Fianna Fáil's 2002 election slogan:
A lot done. More to do.
Sound byte from An Taoiseach Leo Varadkar "it is the same country that it was last week, just a little bit more kinder, a little bit more tolerant and a little bit more open."
Thank you from Together For Yes head office after polls closed but before the result. M'daughters, who have worked the streets and pounded the pavements of Dublin and Cork for this . . . well, they are delilah! I am so proud of them for finding belief and backbone and grit in themselves . . . I've been a little teary all morning. They on the other hand have fought A War with a wildly diverse demographic, the kind of people whom they'd never meet normally. They are, this weekend, 10 feet tall.
Chapeau! and, like Bonnets!

The Invisible Background

How do you run a democracy? You hold elections and referendums regularly and you ensure that everyone is free to vote as they choose and is absolutely not pressured to vote in a particular way. In Ireland, there is a moratorium on the broadcast media - wireless and TV - having any coverage on the matter at hand from 2pm on the day before polling until after the polling stations are closed at 10pm on The Day.  The Electoral Act on 1992 specifies that Polling Stations must be absolutely clear of partisan election propaganda: no hucksters outside the gates, not posters within 100m of the building in which polling is taking place. Officials ensure that only one person is in a polling booth at a time. Wives may not tell their husbands how to vote, or children their parents. A partisan tee-shirt or badge may be seen as election propaganda and we have been specifically discouraged from wearing any such in the building - or presumably within 100m of the gate. You may not take photographs inside lest you capture a voting slip in the background. This referendum, for the first time, the polling stations can emBraille polling cards so that the blind can cast their vote independently and unpressured.

Also it would be undemocratic to force people to travel long distances to vote, so you need to have a LOT of publicly available buildings to house the electoral officers and their ballot-boxes. For example, the rural Carlow-Kilkenny constituency has 200 polling stations while the urban county of Dun Laoghaire Rathdown can manage with only 38. As a matter of convenience, the network of National Schools [N= 3300] form the back-bone of polling stations and the kids are given a day off. It is a matter of history and demographics that almost all the National Schools are owned and operated by the Roman Catholic Church but that's okay because the political parties are none of them aligned with the church - partly because until recently "everyone" in the country was Catholic.

The referendum yesterday was about repealing the 8th amendment to the constitution to allow, in certain as yet unspecified but very limited circumstances, for abortion. The largest and best resourced institution which has a strong and clearly stated position on such an amendment is the Roman Catholic Church. Oh Oh! Would the facts outlined above given the Pro-Life No Repeal No Abortion position a home-team advantage? Would a truly independent Referendum Commission alert to possible bias re-think the location of the polling stations for This referendum?

What greets you at the door when you go to vote in a Catholic National School? A statue of the Blessed Virgin Mary and a photograph of Papa Francisco, just in case you haven't quite made up your mind. Now it's not deliberate, it's not a plot, it's just lazy, because even if you 'have to' use the National Schools, steps could have been taken to remove or cover the obvious icons of the Institution with arguably the most skin in the game. But that didn't happen because the Catholic Church, like the poor, is always with us in Ireland. It is part of the invisible background [I write about such unseens a lot]: most people, most of the time, just don't consciously see it there. But if you turn up to vote because you know it needs to be done; but you're still not sure (because it's complicated) as you approach the polling station; would a glance at the head of your church remind you, even subliminally, where The Cross should be put on your voting slip? In the last 'what society?' referendum where the Catholic Church had a position (on divorce), the result was as close as one vote per ballot box.

Friday, 25 May 2018

Normalising the extraordinary

Shortly after I returned to Ireland in 1990 to work as a post-doctoral researcher, my boss asked me if I'd fancy doing a bit of teaching; to keep my hand in, like. I was briefly excited by the thought that I could dust off my amazing course "Evolution: from (primaeval] soup to [hominid] nuts". But the boss was doing his version of that area of passionate engagement. "Would you, could you, teach FORTRAN programming to 3rd Years?". I could, I did, and at the end I assessed it, dealing with plagiarism issues along the way. I asked the boss how he'd like it marked because I was planning to give zero to the two students who had clearly learned nothing from the course.
"Whoa", he said, "have they made any effort and answered even the first part of the assessment?"
"They have"
"Then give them a scraping pass at 40% and give the best, who have answered all parts of the question and given it a little bit more by adding a bell or a whistle, 75-80%"
And it was so. That course dealt with a small infra-structural part of a geneticist's tool-kit, really only useful for those who were planning on doing their honours research project in our lab the following year. It contributed only 10% to the grade at the end of the year. Students got 4 5 6 7 or 8 out of 10 with almost all clocking 5 or 6.  The rather large range in ability had been had been normalised almost out of existence. Same for marking lab-books at the Institute: 4/10 for handing it up at all at all.

I taught, in a desultory fashion, in that department for the rest of the 90s, because I was director and sole employee of INCBI, and that took up most of my time. Accordingly I was invited to attend end-of-year examiners meetings. They were barely objective and transparent, because the Faculty had rather clear ideas about the ability of the students and their marks tended to get massaged up and down according to these prior expectations. I've written a shocking story of how a belated attempt at 'fairness' and 'objectivity' screwed over two youngsters at a prestigious [pink panther] British university.

Anyway, the year after I stopped being invited to Examiners Meetings, a rather extraordinary event unfolded. The external examiner had read with care and attention all the answers to "The Essay Paper". He'd done this because that paper carried 20% of the marks for the final year exams. The task for the students was to write for 3 hours on any one of a choice of about 8 topics which required a broad sweep of knowledge from, and beyond, the set curriculum. The Extern held up one paper, cast a magisterial eye around the table "Who has read this essay? Could anyone round this table have written a better, more comprehensive answer in any amount of time let alone in three hours?". Sheepish affirmation that nobody could have done better "I can't, therefore accept a mark of 75% for this paper and suggest we give the student 100%" And it was so. After acing a PhD, the student went on to take his rather frightening intellect to work for McKinsey, the Machiavellian consultancy firm. I wish I had been there!

This all came flooding back last week because we spent Tuesday and Wednesday listening to formal presentations by our final year project students. There were 37 of them, so it was a bit of a marathon. It is the last thing the students do for/with us: they have finished their written exams. I always go  because it is important to Bear Witness to this important rite of passage. Arguably more important than dressing up all medieval for Graduation in November. Few agree with me: the students attebd the session where they are obliged to do their own perf and might come in for solidarity with their particular pals. To a close approximation, nobody from Tuesday comes in on Wednesday and vice versa. The Faculty rock up to the session containing their own project students but are mostly "too busy marking scripts" to spend 10 working hours paying attention to a lot of short talks. The Project Coordinator and I and two of our Young Turks were this year the only people who, having Been Present for the whole nine yards, could compare all the presentations and give a mark [/10%] for the performance. This didn't stop some of our Faculty insisting, from partial knowledge, that their student had given the best performance they'd ever seen. The double meaning of partial is rather clever here: 1) incomplete, existing only in part and 2) favouring one side in a dispute above the other; biased. Apart from that almost every student ends up with a mark of 5 5½ 6 6½ or 7. Me, I button my lip when my students come up for discussion . . . I've given them enough of a boost from marking their project report!

Thursday, 24 May 2018


This time tomorrow, we'll all be able to vote about the Eighth Amendment to the Constitution . . . the one which supposes that the cargo has equal weight with the vessel . . . even when this ideal will wreck the whole venture. I think I've nailed my colours to the mast; certainly I have been wearing my badge all week. It has triggered few conversations but the responders are about 1/3 Nil and 2/3 . I know which team I'd rather be on:
. . . once more with animation!: Some of my genes-in-common have been out as well. In Dublin:
or in Cork
Everyone really needs to get out and vote!  You'll look-and-feel really stupid if you're leaning one way or the other and the result is as close as the Divorce Referendum of 1995
Yes 818,842 No 809,728
To the nearest whole number that is a difference of 1 vote for every ballot box in the country! You can't get closer than that without getting into a Bush-Gore 2000 AD existential debate about hanging chads and the difficulty of black people in Florida getting on the electoral roll. Let us hope for clarity in the result tomorrow but it would be better to have a close  than a landslide Nil. That will make the hard cases easier to resolve by legislation. Despite the propaganda, we are still decades from abortion-on-demand in Tullamore. Finally, if you have 5 minutes,  I'll share some thoughts from the coal-face of crisis pregnancy. HotPress thought the video didn't add much to the message, so you might want to close your eyes and listen.

Wednesday, 23 May 2018

Food poverty

Money is money. The invention of money - a universal medium of exchange - created wealth partly because it made life easier. If you've ever tried living cash-free, in a LETS scheme for example, you'll find your fellow anti-capitalists are heavy on aroma-therapists and light on plumbers. LETS = Local Exchange Trading System. If you ever get help from your neighbour and they refuse payment, you'd better be prepared to have them demand your first-born at a really inconvenient (to you) time in the future. Those reciprocal favours are really important social glue but quite hard to assign a monetary value. I wish there was more demand for help with biology or statistics in the deeply rural community where we live. Then I'd be able to add value to the exchange. I'm glad my firstborn has escaped because when he spent some time with us 15 years ago he was requested-and-required to paint a concrete fence across the bottom of our neighbour's yard . . . and I felt morally obliged to help him.

In January I confessed to being too thick to understand the concept of fuel poverty as distinct from, well, poverty. If the government was going to eradicate it, surely they would give recipients money which it would be hard to ensure got spent on bags of coal. Old Age Pensioners, for example, get €9.00 / week extra as Fuel Allowance between October and March. But that just gets added to Pat the Salt's General Account. Fair enough: four pounds of butter inside might be as valuable as bales of briquettes outside: not least because he doesn't have an open fire-place!

Now the idea of Food Poverty has sailed over my horizon and I sense that this is as equally suspect as Fuel Poverty in that all poverty is fungible (= mutually interchangeable). There is no Euro in a purse that is for dinner and another that may only be spent on heating. They have at least defined their terms. You suffer Food Poverty if you are
  • Unable to afford a meal with meat, or vegetarian equivalent, every second day;
  • Unable to afford a weekly roast dinner (or vegetarian equivalent); and
  • Missing one substantial meal in the last fortnight due to lack of money.
All three must apply to count as Food Poverty. We know that it is harder to eat well if you are poor. Salads are more expensive than hambugger and frozen pizza. Eating crap is bad for you but it is also bad for the state, which will have to treat and manage your obesity and diabetes, so it is worth putting money into getting proper food on the plates of all out citizens. But I don't find Food Poverty to be helpful either a) in the debate or b) in the solution. This is not denying that hunger is a problem among the poor, especially in dog-eat-dog societies without a welfare state. Check out this thread explaining the difference between being poor and being broke. Broke is better.

In 2013, Mandate and Unite, the two big trade unions, commissioned a report on Food Poverty, and summarised the data in the peculiar map below. They chose to scale the size of the labels by the absolute numbers in each of the 26 counties. Dublin's 112,300 is bigger than Leitrim's 3,400 . They must believe that the geographical location of food poverty is somehow useful or informative.
The Journal picked up the press release running the story under the same map and drew this conclusion "The map shows Dublin fares worst with 112,300 people suffering food poverty. Larger counties like Cork and Galway follow close behind, with 50,500 and 25,300 people in need of assistance respectively." That jangled my crap-detector alarm because it implies that cities have a worse problem with food poverty than small towns and rural communities. It might be true: you might have a bucolic image of peasants at least being able to have some drills of spuds, fruit in the hedgerows and snaring a rabbit or two for Sunday dinner. But I thought it called for some analysis.
County FoodPov Pop County FoodPov Pop
Carlow 5,800 56,875 Longford 4,300 40,810
Cavan 8,000 76,092 Louth 12,500 128,375
Clare 12,400 118,817 Mayo 14,000 130,425
Cork 50,500 542,196 Meath 18,900 194,942
Donegal 18,700 158,755 Monaghan 7,000 61,273
Dublin 112,300 2,137,639 Offaly 8,900 78,003
Galway 25,300 258,552 Roscommon 6,900 64,436
Kerry 16,000 147,554 Sligo 6,800 65,357
Kildare 20,200 222,130 Tipperary 16,300 160,441
Kilkenny 10,500 99,118 Waterford 11,800 116,401
Laois 8,800 84,732 Westmeath 9,300 88,770
Leitrim 3,400 31,972 Wexford 15,500 149,605
Limerick 18,500 195,175 Wicklow 14,000 142,332
These data are remarkably, almost absurdly, well correlated: r = 0.98 which is more clearly indicated in a scatterplot:
The take home from this is two-fold. 1) the food poor are always with us: the number of people who suffer is very close to 10% of the population in every county except Dublin. 2) in the Capital, (the lonely dot in the top right corner of the graph) there is about half as much food poverty as elsewhere. In other words is would be better to scale the labels the other way round: Dublin's Food Poverty is only 112,300 while Leitrim's is3,400. Did I mention FoodCloud? I did, last December. One of our active neighbours signed up for this a couple of years ago and is the contact for the local ALIDL store. They will call her to say that they have 50 turkeys, or six boxes of tiramisu, or some really weird exotic cake which no normal Irish person would buy. She will drop by after work and load as much of the At Sell-By Date food as can fit in her Nissan Micra and then drop it all off at a couple of Traveller halting sites, a few households of indigent Romanians and the young chap with epilepsy. For people with no spare cash and probably a generous shaking of debt, this appearance of food, even peculiar food, is viewed as manna from heaven. That's a lot sounder that carrying the unsellable food out to a dumpster and locking the trap-door.

Tuesday, 22 May 2018

A new form of divination

I R 5 today!! On 21st May 2013 I posted an interesting historical document about how the genetic code was worked out and why UUU is given pride of place in the codon table. On 22nd May, I sank back exhausted (maybe because I was busy marking exams . . . or dagging sheep). On 23rd May 2013 I went all peculiar on myself and wrote about underwear. Since that date, I have posted something on The Blob every day, an unbroken stream of sense and nonsense. It looks like I put nothing up on 19th July 2016 but that was a cock-up on the scheduling front and whatever I wrote & posted that day was attached to an earlier date.
Insofar as normal people blog, they blog about their lives; The Blob has become my life, like the . Richard Herring, comedian and commentator has written something every day since 2002 on his Warming Up blog. He does it to prevent writer's block. For me it's so I know that I did something today. It is also a record; eventually everything I can remember will be captured here. The real benefit is in the nature of "if you want something done, ask a busy man": because The Daily Blob has now become a tail wagging the dog 'necessity', I am kept in a state of mental alertness. A Blob a Day before breakfast works as well as a cold bath at that time works well for Protestants: invigorating, cheap and effective.

To celebrate/mark 365*5+1 (for 29 Feb 2016) = 1826 days, I have discovered / invented a new form of divination to tell us what will happen in the future. You may forget scrutinising the tea-leaves or your Daily Mail horoscope or watching a yak butter lamp guttering in a Tibetan cave. What you need to do is click on to the Protein database and ask that Oracle for guidance. I entered:
"1826 [slen]"
and picked the most meaningful [Wiz! you couldn't make this up] of the 2213 proteins which Entrez delivered as being 1826 amino acids in length:
>XP_015453711.1 protein Wiz isoform X2 [Pteropus alecto]
That's a DNA-binding protein called Wiz Widely Interspaced Zinc Finger Motifs from Pteropus alecto the black flying fox: the GoTo fruit-bat.
With the help of Wa-Kan-Tanka, the Great Turps Substitute, I believe [alleluia] this tells what the future holds. The thing is that proteins are made of 20 different amino acids, each of which has it's own single-letter code.  The Oracle writes messages in this code and those who seek can find the true answer to their questions.
  • I know this message is for me because it starts off flagging three different mammalian species all of which have featured in The Blob: seal Phoca vitulina,  rats Rattus norvegicus, hare Lepus europaeus
  • Then we have: a aasgl glass a Harp feed a day repeated. I take as a  recommendation to remain mildly liquored up with Irish lager.
  • Then: Verdict, harsh, harsh, real harsh. Like the Sybils or the Oracle at Delphi this Word of Wiz can seem obscure but ultimately has meaning to those who seek the truth. It is clearly a salutary warning that more than three glasses at a sitting may have head-achy consequences
  • Finally: He's easily a sage [or saggy?] silver piss-pot must be warning that as I age [silverback] I may become awkwardly incontinent, especially if I drink quantities of lager shortly before bed.
Well that's me warned!. I am mindful of Mark Twain's advice about writing (for a living): "Write without pay until somebody offers pay. If nobody offers within three years, the candidate may look upon this circumstance with the most implicit confidence as the sign that sawing wood is what he was intended for".  I am indeed sawing more wood every day - it will be a long cold Winter

Monday, 21 May 2018

calcium is vital

More than 35 years ago I resolved never to sit another written exam again, ever. I devoutly wish that I didn't have to set and mark any exams either, but that change would be far too radical for The Institute. Nevertheless, I operate an, almost effective, No Child Left Behind policy: I make it very difficult for students to fail. To do this, I try to deconstruct the examination process and make it transparent. Listen up!: I don't like mondays marking; I want to make it as easy as possible for me; I don't expect long literate essays, least of all from my Polish students; I am likely to examine any idea that can be compressed into a list of at least four bullet points. One such feedback-loop is recalling the four functions of bone:
  • muscle-attachment and movement
  • protecting soft tissue: skull, thorax
  • calcium reservoir
  • making blood cells in the bone marrow
Calcium Ca is the third of the physiological cations (positively charged molecules) after sodium Na and potassium K. Clearly, especially according to the Milk Marketing Board, Ca is important for bone strength, the matrix of which is calcium phosphate. But calcium's physiological importance pre-dates vertebrates and all living things are avid for the stuff which is generally in short supply in the environment. It was therefore  a nifty trick to solve the engineering problem of movement by making the rigid struts out of calcium phosphate . . . so you could truck your own supply of calcium about so it was available for nervous and muscular activity. Why calcium is used as a trigger for nervous transmission and muscle contraction is lost in the mists of time but so used it is. Nerves and muscles have evolved so that they need just the right amount of calcium to be available and so homeostatic mechanisms have developed to ensure that this balance is just right like Goldilock's porridge.

The key is that there are two complementary hormones that control the amount of calcium circulating in the blood. You have a gland in your neck called the thyroid [prev], it is pink but it has cells of at least two distinct types, so distinct that someone named the minority type the parathyroid gland - not glands even though there are four clusters of parathyroid cells embedded in the thyroid but producing a hormone, memorably called PTH parathyroid hormone. These cells are not yellow despite being coloured so for clarity in the cartoon thyroid in a mnemonic picture at the top of this post. Other cells of the thyroid proper make another hormone called calcitonin. When blood calcium falls below a threshold, PTH is released. There are cells embedded in bone called osteoclasts which are sensitive to PTH and dissolve the calcium phosphate matrix and leach calcium into circulation. When blood calcium is too high calcitonin is released which triggers activity in another sort of bone cell called osteoblasts whose job it is to scavenge calcium and phosphate from the blood and build more bone with them. It is, like all normal Hum Phys, exquisitely finely balanced . . . until it isn't: clearly something has gone wonk if you suffer from osteoporosis. So this is what we know in the world of bullet-point learning:
Blood calcium Too low Too high
Hormone PTHcalcitonin
Gland ParathyroidThyroid
Bone cell osteoClast osteoBlast
Bone matrix Crush Down Build Up
Blood calcium raised lowered
Geddit? PC TB
For me and my expensive education, I associate osteoclast with iconoclast - an image breaker but that won't be helpful for my pharmacy technicians. There you are: two likely exam questions knocked off in one Blob:
Q1. Describe how calcium balance is regulated in human physiology.
Q2. What are the four functions of bone?
In the belt-and-braces way that is so typical of the effect of hormones, PTH affects not only the osteoclasts in bone but also the gut which is thereby primed to absorb more calcium as it passes through. And remember that vitamin-D's other name is calciferol and that it's also involved in calcium balance. But for answering Summer Exam questions for Human Physiology, let's keep it cartoon simple.

Sunday, 20 May 2018

No means Yes

Repeal the Eighth News.
You have to give tribs to the opposition for getting their message out on the face of Ben Bulben just round the corner from where William Butler Patriarchy lies buried  . . . or not buried - probably not.
Until it was removed [CENSORSHIP!! no fair etc.] the sign was seen by the plain people of Donegal and Sligo as they horseman passed by; then got another bite at the publicity cherry when the Yes side expressed outrage on Twitter and in the press. But there's no point in getting angry if you can get even; and the Irish way is to pffffft deflate the pretensions of the other side rather than punching them or setting fire to their homes. The power of photoshop has been mobilised to change the message
  • Does my bum look big in this? NO
  • I ViNO
  • kNObs
  • ☑ YES ☐ NO
  • BONO
  • NO country for young women
  • Did I leave the gas on? NO
  • Vote yes: NO more exporting women for essential healthcare.
Some of these responses are by local cartoonist Annie West who summed up the response to the marriage referendum. Thisall should remind you of the ironic response to breadmageddon during Storm Emma this Spring.

Backstory of Repeal: The Dadical- Sorosgate - October 2017March 2018 - Current Position

Sunday very Sunday

What have we in the bran-tub today?

Saturday, 19 May 2018

River runs 19 May 18

There's beauty in the silver, singin' river.

Let's hear it for Kiwis

They [here = The Man, Auntie, the Beeb] must think we are plug ignorant. . . probably because we are. Take the BBC's Missing Country Quiz to find out how little you know. The deal is that a four-colour map [it's a theorem: bloboprev]of some part of the world is presented in which one country has been dissolved into the [white] sea. Your starter for 10 shown R. If you think this must be a trick question because it's obvious, then you won't need the help which the BBC provides by reducing the possible answers to a MCQ N=3. Here is it Portugal, Italy or Greece.

I won't be sending the Quiz Link the Dau.II the Sporcle Queen lest she take it up as an insult to her knowledge of the naming of parts about the world. The last question erases New Zealand from the map. This may be the whole point of the quiz, because erasing the Kiwis from the cartography geography is a bit of a meme. There's a whole website devoted to flagging missing cases. Here's Murray from Flight of the Conchords a) looking older b) phoning head office about being lost in limbo. The woman at the other end of phone is Jacinda Ardern Te Pirimia o Aotearoa. Who is clearly a good sport, as well as being Left, young (b 1980), cool with cannabis, down with the gays and pregnant. The fact that she was brought up a Mormon and now isn't shows that she can think about fundamentals: anyone who changes their mind as an adult is okay with me. Jimmy Carr having an anti-heckle with the PM on NZ TV. And I'm down with the haka too.

Friday, 18 May 2018

Go easy on the antibiotics

Does MRSA put the frighteners on you? What about CRE?
Q. How do they make up these acronyms?
A. [Pick-an-antibiotic] + [R-for-resistant] + [pick-a-microbe]
You shouldn't worry unduly about these nightmare superbugs because you have probably been exposed before and your immune system is primed to deal with them as they present on a dodgy burger served by someone with poor food-hygiene. Your Aunt Jenny otoh going in for a hip-replacement really should worry because she is likely to come out in a box on account of there being a lot of MRSA about (up 30% of Irish noses) and Jenny is old and her immune system is slowing down. She needs a bit of help over-coming nosocomial (hospital-acquired) infection and we've squandered the antibiotic discoveries of Alexander Fleming and others by using them as growth-promoters in battery chicken factories.

That's bad, especially for Jenny, but largely in the past: we can't turn back the clock and limit the use of antibiotics to 'vital' treatment. Turns out that dosing infants with antibiotics may also pay forward in deadly coin by limiting the effectiveness of vaccination.  I say this because of some evidence about the interaction of antibiotics and antibodies in mice. Here blogged. Here the original Elsevier pay-walled paper. Remember that almost all of biomedical research works on the model of if it's true for mice it is quite possibly true for humans. First we'll have the Elsevier executive summary for the tweet-and-manga generation:

I'll develop that a bit because it may be important. What the group from SAHMRI, Adelaide have done is treat mother-mice and their offspring with oral antibiotics ampicillin and neomycin for different amounts of perinatal  time and then measure the quantity and diversity of their gut flora. Not surprisingly the flora took a hammering under the antibiotic regime [L]
  • graph A at Day 21 the untreated NOABX pups have about 10,000x more bacteria in their guts than their ABX antibiotic treated litter-mates [it's on a logarithmic scale]. A week later, the effects of the bacterial holocaust are wearing off and the ABX mice have only 10x less bacteria. This is just counting bacterial bodies. 
  • graph B shows that the Day 28 flora in the ABX group are recovering their numbers but are seriously adrift wrt their diversity. After the antibiotic treatment, certain species of the remaining bacteria get off to a flying start, seize all the best places in Café Coliform and leave only crumbs for the less assertive competition.  Exactly who gets gets there firstest with the mostest is a little unpredicable - it is chaotic [sensitive to initial conditions and random chance] at the start of the race.
The gut-microbe situation [imagine a human home with a septic infant who has been treated with augmentin] will get back to something approaching the status quo ante in time because the sibs, the parents and the family dog will be liberally sharing their bugs with the wean as s/he recovers. That's all very academic, and you might be tempted to cry So what? Particularly if you haven't read my report on how gut Lactobacillus is a key cog in the chemistry of maintaining blood pressure.

Blood pressure is important but Lynn and Co from SAHMRI are in the business of controlling pathogenic infection in children. If you don't survive to adulthood because you've been whacked by infectious diarrhoea, malaria or TB, then a healthy blood pressure in middle age is moot. They are convinced that vaccination is a key element in boosting the immune response to pathogens. What if, they wondered, the normal gut flora is an element in ensuring the efficacy of vaccination. Many vaccines have adjuvants, like Alumina, which work by geeing up the immune system to recognise the added pathogen but nobody really knows how adjuvants work. IF there are 10,000 species of bacteria in the normal gut each making several thousand proteins contributing to several hundred biochemical pathways ANDIF this complex eco-system is managed by our immune system (so we don't die or have persistent coughs or spend hours on the toilet) THEN maybe the normal flora is relevant to the response to vaccination.

Team SAHMRI did a lot of parallel experiments testing the response to BCG [TB]; meningococcus B (MenB); meningococcus C (MenC); pneumococcus conjugate vaccine (PCV13); and the INFANRIX Hexacombination vaccine (Hexa) which contains antigens from hepatitis B, diphtheria, tetanus, pertussis, Haemophilus influenzae B, and inactivated poliomyelitis virus (IPV). All of which are routinely applied to tiny Australians. They found that, in almost all cases, after vaccination there was more immunoglobulin G aka IgG circulating in the antibiotic-free mice than in those treated with antibiotics before vaccination. I've shown the data for menC [L] which shows neither the clearest nor the noisiest difference between IgG concentration in NOABX vs ABX.  Production of pathogen-specific IgG is known to be a key element in the immune system's response to infection. There is lots more belt-and-braces experiments described in the paper including a rescue of the flora in ABX mice with a fecal microbial transplant FMT, which has been shown to be so effective against C.diff. But I won't overwhelm you with details - you'll have to pay Elsevier for them. This-all suggests strongly that a course of antibiotics in first months of life may adversely affect the subsequent response to vaccination. Ho hum parenting is so damned hard: you take the kidder to the doctor because she has ear-ache and she gets a course of antibiotics. You-the-parent would never think that this action to spare your baby pain will be responsible for a gruelling bout with the whooping cough two years later because the pertussis vaccination didn't take.

Full disclosure note: David Lynn did his PhD in St Vincent's Hospital under my co-supervision. My supervisory style was similar to the way we allowed Dau.I and Dau.II to educate themselves at home: "shut up and get out of the way". You can see how effective this strategy can be, because The Boy Done Good.