Sunday, 17 December 2017

Saint Sturm's Day Misc 171217

A peculiar set of links

Usedom on the edge

There was a time when the Baltic was the centre of the world criss-crossed with trade routes bringing salt, herrings, furs, turpentine, masts, grain from one place to another. Last year I wrote about the Hanseatic port of Lübeck on the Ostsee / Baltic coast as a way station on the Alte Salzstraße. But the Baltic barely featured in my very expensive education, I guess we pitied the people of North Central Europe who had to take holidays on the Baltic Coast, which seemed pretty bracing if not positively bleak. As if an April day on the beach at Tramore or Duncannon was in some sense more easy on the chillblains. But the details of the geography were entire outside the curriculum. I read a rather intellectual (but short!) piece of about Borders as a reflection on the politics of hard/soft borders after Brexit. via MeFi where extra links. Until then I'd never heard of the island of Usedom which is a)  part of the Baltic coast and b) interestingly, divided between Germany and Poland. Don't forget that the whole of Poland was shifted West in the wake of WWII to please the Russians and discommode and displace the Germans. Honestly you wouldn't know where what who you were if you lived anywhere close to where Gregor Mendel was born.

So here's Usedom/Wollin as an Olde Mappe which rather exaggerates the islandness of it all. The real current island is much more embedded and connected with the coast, so that it is hard to see where the Mainland ends and Island begins until you zoom in to the places where roads appear to join the two. The explanatory cartoon below shows the tortuous coastline of today; albeit totally detaching the island from the continent for clarity. The pinkish slash about midway indicates the border between German & Polish Pomerania that would be Mecklenburg-Vorpommern \\ Województwo zachodniopomorskie.
I've taken the liberty of indicating Stettin = Szczecin on the upper map. Why? Because it boggles my mind how a town so far from actual Baltic could have become such a major player in the Hanseatic League. An indication of its importance / desirability is the fact that, after being founded by Wends in the late 700s, it was successive part of  Poland, Saxony, the Holy Roman Empire, Greater Denmark, Sweden, Prussia, Germany and most recently Poland.

For reasons of geopolitical importance at the 1945 time, the border between Germany and Poland was not set along the Swine/Świna the middle of three drains between The Stettin Lagoon to the South but through the countryside West of the metropolis of Świnoujście. Thus giving control of both banks of the thoroughfare to Poland. German traffic had to winkle 20km through the Peenestrom between Usedom and the mainland. Polish ships had the choice of wending along the Świna OR the Dziwna to the East of Wollin. This years-ago economic decision makes for a rather less defensible border between the two countries which meanders through the dunes and salt-marsh [R] until it gets its feet wet in the Baltic. Unless we're going to suffer Plexit after Brexit, I guess we don't need to worry about the defensibility of the DE-PL border here or further South.

Saturday, 16 December 2017

Saint Bob

I have an understandable interest in Bobs: Bob the Island - Bob the Point - Bob the Province - Bob the Builder - Bob the Asteroid - Bob the Socratic - Bob the Gypsy - Bob the Thunderer - Bob the Farrrrmer - and I see that Bob the Blob [R] is a thing. Now we are getting Bob the pain-in-the-arse aka Sir Bob or, here ironically, Saint Bob.  I'm all for excellence and salute the outstanding, and take my hat off to experts. Personally, I'm more for celebrating the ordinary. But too often celebrity gives a rush of blood to the head, and a loss of humility. In science there are Nobel laureates: by the prize they are acknowledged expert in something. Logic, utility and respect allows journalists to phone them up for a soundbyte when something notable happens in their field. They may well have other things they care about: their grandchilder; match-box cars; Manchester City; the local library; the planet [Sulston prev]; but they don't have locus standi to pontificate about those. Being a celebrity in one field doesn't give you bragging rights across the board.

Once upon a time in Dublin, there was a band called The Boomtown Rats, who started as The Night-time Thugs until one of their number refused to play under that banner. They were very successful, in Ireland and abroad, in the early 1980s. You may remember I don't like Mondays - Banana Republic - She's so modern. You don't have to look very hard in those clips to recognise a youthful Bob Geldof before he went Global. In 1984, at the peak of his pop-stardom, he saw footage of a famine in Ethiopia and, with Midge "Ultravox" Ure put together a mammoth charity fund-raiser called Band Aid, "Do they know it's Christmas?" raised $8million. The following year they went, if not Global, at least trans-Atlantic with Live Aid, a media circus which shook $150 million "give us your fuckin' money" out of white-folk's pockets for people without pockets at all at all. No matter how tired you may be of hearing "Do they know its Christmas" again in December, I think we have to give the man credit for doing something about inequality rather than just sighing about it.

Shortly after that The Rats split up and Geldof launched into another career as ambassador against poverty, oppression and inequality, He recognised that, if left to their own devices, most people will spend their money on food, t-shirts and a Summer holiday rather than tithing [bloboprev] their income for the poor in Africa. A month after The Rats' last concert in 1986 Geldof accepted an honorary knighthood from the [Tory] British government for his services to fund-raising.  It was a peculiar arrangement: the Tory government were bullied into a cynical act of populist appeal because the Great British Public and the Great British Media seemed to demand that Geldof be recognised. Geldof, a citizen of a Republic, saw no inconsistency in accepting such an award from the Queen of the country next door. No inconsistency for the average Brit who thinks that Ireland is part of the Commonwealth because we speak English. And they could be forgiven for that belief given how much attention the Irish pay to British soaps, British soccer, Royal weddings and Britain's Got Talent.  For a while, in this century, Geldof was half of a mutual admiration society with British PM Tony "WMD" Blair. If he hadn't already gotten his knechthood, Tony "People's Princess" Blair would have sincerely secured one for him [can't find a picture of Blair looking convincingly sincere, so you'll have to imagine it].

In 2006, Dublin City Council got in on the process of canonizing the Blessed Bob by making him a Freeman of the City (whatever that means beyond a fancy scroll). My Alma Mater TCD was a bit slower off the mark: this Summer, Dau.I and I saw him a) looking scruffy and b) going in to get an honorary degree. The Freedom of the City is not showered out like confetti: they have been awarded quite a bit less than one every year over the last 140 years.
  • Freedomistas:
    • Initially to statesmen: Gladstone, Parnell, Ulysses S. Grant, Redmond; 
    • then to the Arts: Douglas Hyde, John McCormack and Hugh Lane;
    • then to the Church: Archbishop This, Nuncio That and Pope JP II; 
    • then all populist: Gay Byrne, Maureen Potter, and  U2; 
    • along the way they've been sporty: Jack Charlton, Ronnie Delany, Johnny Giles, Brian O'Driscoll.
In 1999, while she was still under house-arrest in Burma/Myanmar, they offered the honour to Aung San Sui Kyi, and she flew to Dublin in 2012 to finally accept it. At the time, ASSK was revered, only second to Nelson Mandela,  as the silenced, oppressed but dignified symbol of freedom. Things have turned pear-shaped for her since she was released, especially her recent failure to condemn ethnic cleansing among the Muslim Rohingya minority in Myanmar. From the outside looking in, it's either black or white. People who were falling over themselves to shower ASSK with prizes and honours were now fighting to throw the first stone.
Notable among the latter have been U2 and Geldof requesting and requiring the City to rescind the Freedom they gave to ASSK in her shiny-white phase. Geldof has been unhappy about the pace at which the City Fathers were acceding to his righteous indignation. In the middle of November Geldof [R with worshippers] brought himself, his scroll, his publicist, and plenty photographers back to Dublin to return the honour earlier accorded to him. The City Council, led by the Lord Mayor Mícheál Mac Donncha didn't like being chivvied by a publicity hound and this week overwhelmingly voted to accept Geldof's resignation  . . .  at the same meeting where they stripped the epaulettes off ASSK. Now Geldof is all upset and wants them to put the scroll back in his pram.

The day after that stormy Council meeting, Joe Duffy, RTE's self-regarding talk-show host, in one of his periodical fits of righteous indignation, "interviewed" the Lord Mayor. Which amounted to him hectoring that Civic Dignitary for being a Sinn Fein Republican and for daring to express his contempt for an Irish citizen who accepted a gong from a foreign power . . . especially that foreign power. Clearly there has been a bit of needle round the Council table and Geldof is not everyone's cup of tea. Simple people want life to be simple: Saint Bob is, or was, Good; Sir Bob is definitely Bad; Unscrolled Bob is . . . heck I neither know nor care. 

Friday, 15 December 2017

I haven't a clue

Somehow along the way, my teaching portfolio at The Institute has acquired a bunch of maths & stats classes. You can't call a first year class Remedial Maths - it really wouldn't look good on the prospectus. But heck'n'jiminy, many of the students require it. Every year I have a pre-quiz which inter alia asks for their grade in Leaving Certificate maths. The median (most common grade) is a D at Pass level. This is the bare minimum and an absolute requirement for entering 3rd Level Education. The optics being important we call this one hour a week practice in mathemactice Quantitative Methods or QM. A tuthree years ago, the Sporty side of my department renamed the euphemism QM as a more aspirational Research Methods aka ResMet; neither curriculum nor content changed underneath the rubric.

Whatever foundation we lay in Yr1 ResMet, someone else has to construct the edifice of ResMet2 in second year. I don't know if it's a mix&match policy (to spare any one group of students from really disaffected teaching?) but I've never landed the same people as they progress to Yr2. That's why I have to learn 100+ new names and faces every year. ANNyway, I've just finished marking the Exam for my ResMet2 class, which finishes at Xmas. Everyone passed (+40%) Yay! and the range was 46-88% [alphanonymised results R]

Early in the year, I was in a 1to1 with a student and asked him to guesstimate the size of something (area of Ireland, population of Poland, number of cornflake packets in a shipping container, I forget). I could see the shutters come down as he said:
"I'm sorry I haven't a clue"
"Yes you have William" I cried, "is it 10?"
"Is it 1,000,000?"
"There! You do have a clue: it's somewhere between ten and a million"
I think I might have been getting a little shouty towards the end, because my triumphant final shout raised a muffled titter in William's corner of the room. Relief, probably, that they were not being subject to a Socratic grilling. The same initial response came out a fortnight later, but William attended every class and knuckled down to learning what was required. He got 86% in the Final Exam.

Across the room on another week, I was expanding on the attributes and prevalence of the Normal, Gaussian, Bell-curve, Distribution to try to make the business of calculating the area under the curve more relevant . . . and  therefore more accessible. After listening to as much of this as he could bear, with scrupulous politeness, the student, let's call him Rob because that's his name, put up his hand - "Bob, just tell me what we have to do here". With much chagrin, I apologised for being off with the fairies again and told him the steps for completing the task and pointed out the relevant paragraph (with added screen-shots) in the manual. For the rest of term, even when Rob was absent, I'd pause in my explanatory gallop if I saw the over-load shutters trembling "I'm sorry Rob,  I'll stop now. You don't need to know all that, you just need to know how to do this task - both the mechanics and hopefully a suitable interpretation of the P-value that the mechanics generate." And, as everyone passed, to a certain extent, it was so.

Thursday, 14 December 2017


Pat the Salt, aged 92 spent the weekend on hospital a month ago. A typical refugee in the HSE, he went in for a chest Xray [pneumonia? pleurisy? weak-in-the-wind?], spent the night on a trolley, was found a bed and eventually occupied that for three days until he was discharged as well enough to survive at home . . . he has a home unlike 8,000+ people in Ireland today. He takes a modest pharmacopoeia of meds twice a day and these have been supplied in a 'blister-pack' to help ensure that he doesn't miss or double up or forget one of his drugs.  His daughter brought the blister pack in along with the script and the receipt from the pharmacy but the hospital staff refused it because they didn't know where it had been or come from. They preferred to buy new drugs to match from the hospital pharmacy. Out of sync drugs in a half blister pack are effectively trash. It all seems a waste.

Then again, I went back to classes in Grad School in Boston after the 1982 Summer vacation just as the Tylenol Murders were sweeping the USA into a panic of epic proportions [prev]. Thereafter all meds were retailed in tamper-proof packaging and nobody else, so far, has died from cyanide adulterated drugs. You wouldn't rummage about in the dumpster behind CVS pharmacy from free drugs because you couldn't afford them from front-of-shop . . . or would you?  Actually, I don't think this is possible because pharmacies are super careful about disposal. It is getting increasingly difficult to go dumpster diving for food as well: partly because of FoodCloud and partly because of padlocks. And First Responders pretty much have a policy of not accepting food gifts from the public; or rather accepting gratefully and putting the cookies straight in the trash.

I'm a bit of a bargain-hunter. It goes the with beach-combing, I guess. I'd rather buy a book for 0.01c than for €8.99 and have been known to buy books simply because they were too cheap to refuse. But not anymore, I'm done with stuff and am down-sizing the library: 95% of which has been acquired below retail cost. I wrote a while back about book warehouses and the 0.01c trade. Part of me is surprised at myself that I would give house-room to something whose provenance is so murky. What if the previous reader habitually failed to wash hands after going to the bathroom? I am shocked at how much food, bought in The Institute canteen, goes straight in the waste bin . . . but I don't reach in a fill up on cold french-fries. So I guess I have standards. The Beloved has standards too: she washes new bought clothes before she will allow me to wear them - it's the coliforms from the sweatshops, silly. And money is indeed filthy lucre.

Here's a nice essay on how items that are returned to US stores [brick and on-line, both] are dealt with. Amazon, CostCo and Walmart have sale-or-return policy for pretty much everything - including underwear [R a sea of knickers pic Holly Andres]. These big-box stores also have to deal with lines of merchandise that just aren't selling [quick enough - turnover is king]. So they sell them as pallet-loads to entrepreneurs who have bigger warehouses; more employees with rubber gloves; and better contacts in the bargain hunters world. via MeFi where comments are instructive and diverse. Many of the secondary buyers are prepared to pay folding money for a pallet, or a container full of stuff without seeing any more than the label, let alone handling the stuff.

Did you know about Mystery Boxes?  It's a thang: you pay $10, $100, $1000 for a Mystery Box on Ebay and then film yourself being disappointed that the vendor saw you coming. Here's Lucas, who is moderately funny about dropping 3x $20 in the post and getting trash in return. You're on your own watching dopey people $pend more: there's hundreds of these vids out there. Then there's Storage Wars on the TV.  Making and selling shite that nobody needs is what The Economy aka The Despoilation of the Planet is all about.

Wednesday, 13 December 2017

Bugging the blood pressure

In between Blobs, I teach science in The Institute: a shadowy college of further education in the Irish Midlands with links to Opus Dei and the Illuminati. It's coming up for five (5!) years now but the one course that has been mine through all that time is Human Physiology. My only qualification in this area is that I have a body, some curiosity and a preference for making sense of the world. Everything you need to know about Human Physiology is homeostasis:t he remarkable, and energetically costly, maintenance of things in equilibrium at a set point. Our core body temperature holds at 37oC +/- 1 degree through a remarkable range of external conditions: bouncing starkers from a sauna to a snowbank does Finns no harm at all and the thermometer popped up a Finnish rectum stays steady at 37 throughout. The remarkable properties of dissolved carbon dioxide and the bicarbonate ion maintain the blood pH at a constant level of acidity. Circulating glucose, circulating sodium, circulating calcium are some of the substances whose set-point maintenance we understand well.

One definition or explanation of senility (the process of growing old, not necessarily associated with dementia or dribbling) is the breakdown of these precise regulatory mechanisms, so that the swings about the set-point are less subtle. Hand-tremor is a good example of this: when you young chaps hold a pint steady at the end of your arm, about 30 different muscles are acting against each other to stop the booze slopping down your shirt. This handy life skill, which you take for granted, is a bit of an ask for Pat the Salt my 92 y.o. father in law. One muscle will contract and its oppo will over-react, so his hands are less steady than they were when he was your age.

Now think about blood pressure; that has to be maintained in a wide variety of conditions. Asleep, your heart has it easy: pumping blood on the flat. When you stand up, immediately, your heart and arteries have to up their game for some metaphorical fell-running, the system is now being asked to pump blood up a 1.5m to 1.8m hill between ankles and head. Me, I now have to be careful springing out of bed in the night. Unless I meet the problem halfway by sitting on the edge of the bed for a moment, I am likely to feel a touch of faintness, a prelude to crashing to the ground in a heap

Obviously, the problem of normal blood pressure maintenance features largely in my Human Physiology course. That way my colleague, a real pharmacist, teaching Drug Actions and Uses can look at all the interventions that are possible when blood-pressure goes too high. BP is a regular cash cow for MegaPharm Inc. I'll get round to some of these drugs and how they work later - it's a fascinating insight into how scientific research works. Ignore the drugs and abnormally high blood pressure: that's a very modern problem. Let us rather look at how BP was kept UP in normal life for the super-thin, marathon-running, hunter-gatherer who came down from the trees and started walking upright 4 million years ago. Those chaps, and we are their descendants, were designed to keep blood pumping uphill to the head, without that you can't make decisions while running down a wildebeest.

There are two ways to increase pressure in a closed system: you can make the volume smaller or you can add more fluid . . . or both. And you can also increase cardiac output: make the ticker beat more frequently or with more force. Making the system smaller is largely about peripheral vaso-constriction, your small arteries are all surrounded by rings of muscle, contract these and blood pressure will increase. A nifty way of increasing the volume is to have the kidneys retain Na = sodium. These sodium ions suck water back from the kidney tubules to stop the salt from coming out of solution and forming crystals. That's so elegant a working solution! Sodium is maintained in equilibrium in the blood because we need it for muscle contraction and nerve signalling, using it to attract water is a secondary feature. Everything is interlinked, sometime in quite unexpected ways.

Hot Press, we had it all wrong. Or at least our understanding of sodium balance and blood-pressure as a physico-chemical problem to do with hydrostatics was laughably simplistic. Actually it's all in the microbiome innit? I've had multiple occasions to write about the intestinal flora / microbiome - the 2kg / 100 trillion cell / 10,000 species menagerie that we tote around in our guts . . . with out-stations up the nose, down the uterus, in yer armpit and all over our skin. It seems that, although salt intake is very closely related to blood-pressure (and this is why we are begged to use less salt in our food) some people don't seem to respond to dietary salt in that way. A group from Charité-Universitätsmedizin Berlin wondered whether the connexion between high salt diet and high blood pressure might have a microbial dimension.  The News & Views about the study from Nature 30 Nov 2017 [paywalled] is by David Relman a leading light in microbiome studies. Apparently the excess sodium leaks across the intestinal epithelium and inhibits the growth of one species of the normal flora of mice called Lactobacillus murinus. Apart from being rather sensitive to salt, these Lactobacilli metabolise a dietary amino acid tryptophan into indole. Indole leaks back across the epithelium and prevents the development of a class of key immuno-inflammation white blood cells called TH17 lymphocytes. These lads have a tendency to blurf out a pro-inflammatory cytokine called IL17 (hence the name of the cell). IL17 is a small molecule that promotes inflammation which is an essential part of fighting off infections and pathogens and one of its effects is to  annoy the inside of arteries so they swell up . . . which increases blood pressure. You will have gotten lost on the roller-coaster of consequences, so here it is in tabular form:
Who designed such a Heath Robinson brown-paper and string system? Mrs and Mrs Evolution, that's who. It worked fine when we were all hunting about the Serengeti. Salt was in desperate short supply back then - there were fights at the salt-licks because everyone needed enough sodium to service their muscles and nerves. Now otoh it snows salt, so it's no wonder that the carefully crafted regulatory system are thrown all ahoo.

Tuesday, 12 December 2017

Learning academic writing

Each year at The Institute - ir's coming up to five years in January - I've been supervising final year research projects: sometimes a handful, sometimes a dozen, one year 16! The kids have a choice of doing this task in the lab "all wet" or with me using computers "dry" to reveal the pattern and process of evolution. The 'Binfos' are a mixed bunch - some, like me, known to be inept at the lab bench; some slackers looking for an untaxing option; and every year tuthree who are really the best students we have - curious, motivated, self-starting and independent. I love 'em all! Not least because of the mix - getting our least academic students to fulfill their potential and a little bit more is just as rewarding as having an adult discussion about the evolution of 'flu viruses or the epidemiology of  Huntington's Disease. Whatever the level, these are all original research projects - finding out something about the world that nobody else on the planet knows. That's a pretty rewarding challenge for someone who has just got the vote.  How do we know that nobody has been there before? Each student is requested and required to carry out a review of the scientific literature on some part of the natural world. Sometimes, especially with our rocket scientists, I will be bullied into 'supervising' a project which is driving the student. Otherwise, I'm allowed to let my butterfly mind flit over the meadows of knowledge looking for a pretty flower to investigate. It must also be admitted that I'm not above whoring out my Effectives to answer questions posed by colleagues and collaborators. That can work out really well, and at least one student has parlayed that relationship into a Master's degree elsewhere.

It's nearly the end of term and by 1700hrs Friday 8th, all our students, wet and dry, had to submit a first draft of their Lit Review. I then had a really interesting half-week's work reading, critiquing and returning them. This year the reviews were all serious pieces of scientific research, neatly capturing a variety of different topics. Even the essays submitted with a "this is crap, but I'm drawing a line under it here" warning were on-message, coherent, unwaffly and full of interesting stuff. So I've learned a lot, and we should all be collectively proud. In a number of cases, the LR has thrown up potential avenues for research that I had not thought of.

I won't pretend that all the work was written in perfect grammatical English: we have two Polirish this year and they are quite mean with their definite and indefinite articles. And don't get me started on the apostrophes scattered like confetti at a wedding. But this is really the first substantive [5000 words] piece of academic writing they've ever submitted. Accordingly I've had to explain some of the basics of communication.

They read, they write, I read, I come across a strange word. Now I had an expensive education, some of it involving Latin, so I can often make sense of long words. But sometimes I'm totally foxed so I Google it up and find a definition there. That's not really good enough. The Lit Review should aspire to being self contained, so I push the students to include a Glossary.

Glossary - should include all the words that only appear in your report, which you wouldn't expect your bff or another Binfo to know; because you're the only person on Campus who has read what you've read. In some cases, that will be an essential addition for the readability and utility of the report. Remember that the report goes off to an external examiner who is a generalist. S/he may not be able to spell Blast, let alone Huanglongbing or Sporolactobacillus. The glossary also serves as a memory aid: that three letter acronym TLA which you defined some place earlier in the report; I've forgotten what it means. All those should be in the Glossary.

They read, they write, I read, I come across a strange idea which I'd like to follow up. If it's come from the literature, there should be a citation embedded in the text which will kick forward to a list of references.

References.- Everyone should use referencing software like Endnote Mendeley or Zotero to match the citations to the references because it is part of the training. But the result has to be fit-for-purpose which is to allow the reader to follow up one of the statements to the source. In the old days of print this required: Authors, initials, (year), Title, Journal, Vol, pages. Back in 1977 I could write Smith AB 1975 NAR 213: 410-417 in my notebook and hunt out the relevant volume in the library. The students of The Institute are submitting a hard copy, so all this info shd be included for that reason. In the modern world of epub and full text, for any biomedical paper, it is handy to include the Pubmed ID like PMID: 8441625 because I can easily get to the source then. Referencing software operates on a GiGo [garbage in garbage out] principal and some of the kids have driven the software so that itmangles the author name or the citation, or doesn't include page numbers - it is part of the learning experience to sort this out.

As our reading gets so cluttered with hypertext links, I like the idea of being forced to think that a written essay is a mode of communication. To reflect on what must be done to ensure than your reader is not misled and is empowered to follow your thoughts forward into the unknown.