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.

Monday, 11 December 2017

Top Ten Human Genes

Peter Kerpedjiev had an idea that required some moderately high-throughput analysis and got himself a full-page spread in Nature, Europe's premier general science magazine about The most popular genes in the human genome. This requires a mash-up of two sorts of data which are effectively orthogonal to each other - related but not correlated. Most popular is here defined by those genes which have appeared most often in the recent scientific literature. There's all sorts of other stuff we know about genes and their protein products: molecular weight; genomic location; which tissues they are expressed in; whether they are receptors or enzymes or signalling molecules or proteins that switch on other genes. You wouldn't expect that any of these things-we-know would tell us about the other attributes.

We had a paper in the 00s, for example, which showed that genes expressed in the liver (or heart or kidney) are scattered all over the genome. The long genes aren't all found on the longest chromosome.  Olfactory receptors are clustered in little groups, it is true, but there are lots of these OR clusters and toll-like receptors TLRs are all over the shop. We'd be mad if we only wrote papers about receptors and ignored enzymes. Kerpedjiev was curious about which genes/proteins occupied the collective time and energy of science and wrote a simple-enough script to snag this information for each and every one of the 27,000 protein coding genes we know about. It's exactly the same idea as I've been progressing with the Masters of Imm up in Trinity over the last several years from 2012 until they sacked me in 2016. I called it the Most Sexy Immuno-protein competition. We didn't aspire to be comprehensive because we couldn't write a simple-enough script without a lot of help. Nevertheless, we showed that some TLRs were stupidly more popular than others because science puts a lot of handicaps on doing original research: everyone - HoDs, funders, editors, reviewers and referees - is happier if you mullock along in the footsteps of others. Wenceslas science, we might call sing it.

A few proteins acquire legs and outstrip their trudging  rivals for the attention of scientists. Aled Edwards from Toronto did a similar study ten years ago in which he showed that the $1billion Human Genome Project had been effectively useless in generating new targets of research to ameliorate the human condition. Researchers found it easier to fondle each other's work than to strike out into the unknown. Working within the herd is safe but not very exciting. Going all maverick makes funders nervous and the results require too much effort to assimilate and tend to get ignored. I could ask you to guess which genes are most highly cited in the scientific literature, but even if you are full time in bio-science you likely won't have the breadth of interest to know them all, let alone put them in the correct order.

Well here they are [L]. I'm surprised that TLR4 isn't there but that's only because we discovered a minority interest TLR and so I think that TLRs are bound to be interesting to everybody and I acknowledge that TLR4 trumps our 'umble TLR15. But all TLRs are collectively a bit of a side-show. Even among the top 10, p53 is Eclipse first, the rest nowhere, but in a way that is reminiscent of Zipf's distribution laws for letters or Benford's for numbers. So who are these celebrity boys and girls of biomedical world?
p53 is the guardian of the genome a tumour suppressor which is found to be mutated in about 50% of all cancers. The implication is that, when fully fighting fit it is preventing the development of cancer.. Several of the other genes reflect the biomedical world's obsession with cancer - which affects the family and friends of the affluent white males in power in the West - rather than possible targets for infectious diarrhoea, TB or malaria. The million black babies a year who  succumb to each of those diseases can't afford to pay for drugs.  #2 is TNF whose name tumour necrosis factor says it all: it works to gee up the immune system to kill tumours. VEGF vascular endothelial growth factor is the source of another nifty insight to treating cancers. As a tumour grows through out-of-control cell division it demands to have more oxygen and glucose to fuel its energy demands. If we can suppress the develop the growth and development of the local matrix of capillaries then we can suffocate the traitor in our midst. EGFR epidermal growth factor receptor works on the same process from a different angle. If we can jigger the receptor of a growth factor, then we can also suppress growth. Note the GF in TGFB it's another target for growth factor control. Note the R in ESR1 the oestrogen receptor which is involved in ovarian and breast cancer and tell us the oestrogen has more role in life than just shedding an egg a month for 30 years.

I'll refer you to the original article for a really neat graph of the timeline of trendiness. When I was in college 3% of all the publications were obsessing with beta haemoglobin HBB, mutations in which led to the first genetic disease sickle cell anaemia. Hey, before President Richard Nixon signed the National Cancer Act in 1971 and diverted $billion$$$ towards the War of Cancer, biomedical science cared about black babies. You have to talk % impact because in absolute terms publications were a trickle back then compared to the tsunami of tosh today. I say tosh because the average citations for a scientific paper is less than one: more than half of all papers published bob up and promptly sink without trace effectively unread by everyone including the authors.
1980 280,000
1990 410,000
2000 532,000
2010 940,000
2016 1,259,000. Heck and jiminy there are even 13,000 pubs for 2018 out there - I guess mostly from the Journal of Clairvoyant Studies and Prognostics.

Sunday, 10 December 2017


I love watching or listening to experts. People who pwn a part of the knowable universe. Anything will do: people who collect match-books; people who know all about the Taft family; people who know where fish will rise; the man who knows all 6,000 genes of the yeast genome; a child who has trained her dog.

Saturday, 9 December 2017

Birthday lies

It's The Boy's birthday today. In contrast to the arrival of his sisters I wasn't there, then. My maternal grandmother was christened Lily Valentine because she was born on 14th February 1893. Even back then Valentine's Day was a thing. I was glad she had that birthday because I still remember it and she's dead nearly 17 years. It's like being born on Christmas Day and getting called Noel. Actually, as I pointed out in 2013, not many people do get born on Christmas Day, especially in 'advanced' countries like the USA because of elective C-section. That allows you to pick your delivery date so it doesn't interfere with the school holidays or a vital business meeting at work. But also more positively, there is an up-tick of births on Valentine's and Paddy's Days for strictly romantic reasons. Follow the link to see if you were born on a minority bday. Later on I did analysis that showed quite clearly that births are not distributed evenly through the year but experience a boost in August and September. It can't all be because people get drunk over The Holidays 40 weeks earlier. It's more likely an evolutionary relic of coming into heat at a time the ensures birth at the best time for survival: mother and baby doing well. Sheep have a much more fluctuation in birthdays.

Years ago I signed up for a feed from and read the traffic there far more than I should. Quora is a stream of inane questions, interspersed with kids expecting adult strangers to do their homework for them but it is 'mostly harmless'. Occasionally something interesting pops up:
That was from Jérôme Cukier's answer to the question "What are some surprising or non trivial statistical facts about Facebook users". I'm one of the last holdouts against the Empire of the Zuckerclones but I thought one of the terms of service was that a) you have to use your own name and b) you had to be over 18. That's fatuous because unenforceable. Facebook also asks for your birthday, ostensibly so that their robots can send you an e-cake with pixie candles on the day and make you think that somebody cares. Well it seems that, in the rush to get registered, people put down any old date when asked with notably preference for the 1st of any month or 01/01 02/02 etc. dates.  Particular /peculiar chosen dates include 4th of July and Valentine's Day. You can maybe see the shadow of the [real] September births are up trend.  You should always take the results from questionnaires with a skeptical pinch of salt.

Designers of census forms please note. One of the anomalies thrown up was the existence of a number of teenagers who had endured multiple pregnancies. The most likely explanation was that ages like 76 and 79 had been tallied up as 16 and 19. Most of the time it doesn't matter much because that's what standard error is for. All those blips up and cancelled out by blips down and the Census finishes up correct with an allowable +/- error of estimate. Sometimes the errors are from laziness and ineptitude of the enumerators or the punters. Then again, sometimes it's because some people are a little hazy about the facts of life. Recent surveys have found 5 women in every 1000 who have been pregnant but have never had sex. The same source reported a few virgin fathers but that smacks of cuckoldry.  Similar transcriptional errors recorded in The Blob

Friday, 8 December 2017

Say Cheese

You can spend a lot of money on cheese or more modest amounts. Experts can tell the difference. Whichever, whatever, I love the stuff, since I was first exposed to different cheeses aged 8. I've had a good bit to say about cheese on The Blob
While it may be safe to eat the rind but it's not always safe to eat cheese. The main problem is Listeria monocytogenes. This Gram-positive bacteria grows well in the presence or absence of air. It is common enough in the soil, and so is spread by plants that have contact with the soil. We're still pointing at canteloupes because a 2011 outbreak of listerosis was associated with that fruit [map R]. That deadly incident dealt a serious blow to canteloupe farmers in Colorado and elsewhere in the USA, but it was a once-off as far as Listeria and canteloupes are concerned. It's easy to wash the fruit - ammonia or ethanol will do it - because it is big and nobody eats the rind so you'd be ++ unlucky to get sick from that source.

Another once-off food contamination scare happened in the run up to Christmas 2014 with toffee apples [L for cases map]. The problem with apples is that the Listeria can lodge in the holes at each end. But that's okay because most people [self is excepted because I eat apples pips and allll] leave the 'core'. The toffee-apple case was unfortunate because driving the stick up the apple's oompah transferred the Listeria to the anaerobic interior of the fruit, where it grew anaerobically.  But most of the outbreaks of listeriosis recorded by the CDC in the last ten years have been caused by cheeses of various sorts.  A useful graphic for the process of determining  which puka-puka people are part of the same event.
Listeriosis could be a case study from Risk Assessment. This is the idea where you have balance the likelihood of an event and its severity to decide what sorts of events are worth preparing for or acting to avoid. Risk is usually defined as the product of the likelihood and the severity. Salmonella and Campylobacter contamination of food is common but 'case fatality rate' is only 1% while Listeria is much rarer but 25% of contractees seem to die. This is why health professionals talk large about Listeria. But the talk is always in the context of small babies (and late stage pregnant mothers; the elderly and those who are immuno-suppressed including those with AIDS and those who've had a hearth, liver or kidney transplant. That's because the rest of us has an immune system which can duff up Listeria before it gets started and that's why Listeriosis is rare.

Listeria is also a problem because of the wide range of temperature at which is grows. It is happy to go forth and multiply at 37oC but will also grow and divide at 4oC. That's what your fridge is set to! Cooling food and left-overs is a really effective strategy for slowing the growth of E. coli, Salmonella and Campylobacter. But cold-loving  'psychrophiles' like Listeria and Pseudomonas won't be bothered by the chill. It would be stupid to throw up your hands and say "Why bother with a fridge?" because that controls the growth of the vast majority of food spoilage microbes.

Thursday, 7 December 2017

Mapping the intestine

I grew up in the Genetics Department in TCD where we were taught to 'treasure your exceptions' - that variety, difference, was where the interest was.  The rival department was Biochemistry and I characterised their whole endeavour as "They go to the abattoir and get a skip-load of calf thymus [see Right], run it through blenders and sieves, purity columns and filters to get 2 grams of active principle. They then write the paper as discovery of the mammalian enzyme for wuggawugganess". They ignored all the lovely, intriguing, interesting variability!! Not only any difference among the contRIPutory calves, but also among the different mammalian species which last had a common ancestor 60 million years ago.  Nevertheless, it was a similar bucket scale protocol that isolated insulin as a treatment for diabetes; so it wasn't a total busted flush as science goes.

Fast forward 20 years and I was employed in the Biochemistry Department, pushing different frontiers of science and realising that I'd have to eat my earlier sniffiness because my new colleagues were every bit as sharp as the lads from Genetics. The Gaffer was the Professor of Comparative Immunology and I brought an evolutionary / genetics view-point to the project. Which was to investigate how different species had different immune responses to the same insult, probably because each lived in a different ecological niche and was beset by a different cast of microbial thousands. OR to investigate how the same species reacted differently to different pathogens. OR both . . . although was going to be complicated to set up. In about 2007 our second grant application to the Department of Agriculture was for a comparative immunology study to measure the immune responses of chickens to a virus, a bacterium and a protozoan parasite. That would have addressed some of the subtlety of immune response. But as we costed out the trials, the replicates, the hands to run the equipment, their taxes and social security contributions the numb€r$ far far over-topped the limits set by the DoAg and we had to pull in our horns. In the end, 10 person years of solid work and €500,000 of tax-payers money made some modest contribution to understanding what happens when chicks are exposed to the bacterium Campylobacter jejuni. With the limited funding and clunky tools-of-the-day, we hauled out the caecum from a bunch of chickens - some infected and some not - and analysed its contents (count them bugs) and also measured which genes in the caecum were being switched on (and off) in response to the bacterial burden. We flagged a bunch of immune-related genes which were differentially expressed in infected and uninfected birds and were just delighted with ourselves.

The paper was published five years ago. Instead  of processing a skip-load of calf thymus to identify and quantify a single molecule that was in vanishingly small quantities [we're almost all water, after all]; we dissected out a lump of wet tissue from a single chicken and measured the concentration of some thousands of genes. That scaling up has been exposed as crude, medieval, against today's standards. A study in last week's Nature has analysed the genetic repertoire of 50,000 single cells from the intestinal epithelium! In my immunological day, we could process white blood cells with an instrument called a flow cytometer. This would flick cells left and right and count them according to what proteins poked out of the cell membrane. The current study un-glues the cells lining the gut and measures each one's genetic activity. That's a level of precision that is truly astonishing, which is why it is published in Nature,  but will look completely normal and even expected in 5 years time.  All those genes in all those cells makes this an example of Big Science: far too much information to read, let alone tally up or assess. without the help of some hefty compute power. The picture [R] is not a Rand-McNally map of the counties of Antarctica; it is rather the first step in the process of making sense of the gut-cell genes. The X and Y axes are the two most informative trends in a multivariate statistical analysis, the diagram shows that known cell-types - goblet cells (island to the L), brush cells (smaller island R) - are not only similar in shape and function (we knew that, it's why they have been given identifying names) but also have very similar genetic profiles.

But it turns out that we made some mistakes when lumping things in the same bin just because they looked similar. We've made this sort of classificatory error before with giraffes - rhinos - elephants and other species. Well it turns out that brush cells aka tuft cells are really two quite different cell types that have rather different gene expression profile [see R pale and dark] and probably therefore have rather different function although it's hard to tell them apart under the microscope. Tuft-1 seems to own neuronal development while Tuft-2 are more down with inflammation. That explains why these two quite disparate functions were associated with 'tuft cells'. We'd be wrong if we classified people-with-helmets as essentially the same: policemen and fire-fighters and motor-cycle couriers and construction workers do different things: the only thing they have in common is an occupational need to protect the head. Tuft-2 cells are all lit up with CD45 which had previously only been associated withe the T- and B-cells of the immune system.

This would be enough for normal people to rest on their laurels but there's much more. And you may bet that, after the flag-ship Nature paper there will be a fleet of filler-of-detail and explore-new-avenue papers over the next tuthree years. Here, as a taster, they show a quite different response to infection by the bacterium Salmonella and the nematode worm Heligmosomoides polygyrus. Whatever about the gene up-regulation profile, it seems that the complement of epithelial cells changes significantly under the two different assaults. Salmonella induces the development of more Paneth cells which then blurf out anti-microbial peptides; H. polygyrus otoh triggers the growth of goblet- and tuft-cells which mount an appropriate response to nematode infection. I think it shows that we would have been 'at nothing' with our blunt instrument approach to different infections. Treating great lumps of tissue as 'essentially the same' and measuring anything about their function rides rough-shod over the subtle cell-by-cell difference in response that is essential to the maintenance of homeostasis against pathogens. It's like you put the entire contents of the Etihad stadium, spectators, astro-turf, goal-posts and all into a blender. . . and are then surprised that you cannot identify the importance of the football.

Wednesday, 6 December 2017


Hello? What's not to understand!?  How much clearer do I have to be while unconscious? To a hammer everything looks like a nail; to an ER physician every body cries for intubation and CPR. Almost every time, the person in scrubs wins the dispute. The story, presented as case notes in the NEJM, and picked up by George Dvorsky at Gizmodo and then liked by Neatorama, is that an old chap presented at a Florida ER department a) unresponsive and b) with a signed DNR tatooed on his chest. The ER team intervened aNNyway, because that's what doctors do: decisions, especially those which result in direct action, become [as in are fitting to, but also as in create] a successful medico. But they also had the humility to send a note to the hospital ethics committee. The ethics committee decided that the tattoo was a clearly expressed wish and that it was silly - and wrong - to search for the next-of-kin especially as the old chap presented with no ID.  When my friend and mentor Lynn Margulis had a stroke, her daughter had to fight to get the medical team to heed her mother's clearly expressed terminal care wishes. NEJM

I've been to end of life issues before, and before that, and written a living will; but I haven't gotten the dnr tat yet. They're very expensive, tattoos, maybe I should get a permanent marker and draw a DIY DNR. That way, if I get "tattoo regret" - yes it's a thing - then I just have to scrub regularly or wait to exfoliate. The current advice is don't call the ambulance when you or your aged loved one has their last crisis. If you do, the professionals will do what they do intervening to save lives, even if if means breaking ribs during CPR or stuffing tubes in every orifice and making new holes to take yet more tubes. It is a living for the paramedics, nurses and doctors but it can be ghastly for the Principal on the gurney and eye-wateringly wincing for the attended loved ones. The trouble is knowing which is the last crisis, because most of us would like to see Mum back in her own home patched up for another while.  The last death - at home, in bed, a blessing - I was involved in, the family had to push back quite hard to prevent the corpse being taken to hospital to be pronounced dead. Most deaths occur in hospital and outsiders (GPs) are getting out of the habit of writing death certificates. You can't get the locus or the Care Doc to sign off, it must be the deceased own doctor. Shucks, nobody says that death is easy but it's going to happen for sure; so let's not make it more difficult than it needs to be.


That would be Independence Day in Finland. You might give a Finn a hug or find yourself a sauna to celebrate. It's special because Suomen tasavalta, Republiken Finland, the Republic of Finland is 100 years established today.  Some nice projects have been rolled out in tribute: 100 Finns each one a a year older than the next via MeFi where there is some commentary. Sadly the project to give Finland a real mountain (it is one of the flattest countries in Europe) ran into a sand of bureaucratic red tape. I've had a bit to say about Finns and Finland on The Blob. Check out:

That's all for now. You may take your hat off and sing along with Maamme.

Tuesday, 5 December 2017


You know what they say about women in the professions: they have to be twice as good to get half as far as their brothers. Here on The Blob, I write about a very mixed salad of topics but one of the themes is women in science, of whom I've written 60 short biographies. I do this because I want more women in science because they are another county heard from, and more diversity means more and more creative ideas about how the world ticks. I hope that some of them will be read by a teenage girl who might thereby aspire to be a top chemist or nanotechnologist. It embarrasses me when I hear, for the first time this late in my life, about a woman who has made a key discovery in science. Take Nettie Stevens, for example who surfaced in the blogosphere last week, she discovered sex-chromosomes right at the beginning of Genetics . . . never 'eard of her. Maybe my old prof ,George Dawson, who was huge fan of Barbara McClintock, mentioned her but her name rang no bell. With my training in genetics and interest in history, I shd have flagged Dr Stevens - tsk!

But today we're down with Elizebeth Smith Friedman [L in hat], peerless cryptographer in two World Wars.  I have a little bit more excuse there because her work was politically sensitive and for a variety of reasons was kept under wraps. Her work was also appropriated by some of the men around her. Jason Fagone discovered her a tuthree years ago as well as a treasure trove of her personal and professional papers and has just published a biography The Woman Who Smashed Codes which has been gathering rave reviews.  Easily confused with A Life in Code: Pioneer Cryptanalyst Elizebeth Smith Friedman by G. Stuart Smith. Except that Smith's April 2017 biography is trailing at 565,000th on Amazon while Fagone's September 2017 book is 1,700! Poor Mr Smith must be chewing his beard in frustration at the Harry Potterness of it.

Elizebeth Smith was the youngest in an extensive family of Quakers and grew up on a farm outside Boondocks, Indiana. She got a degree in English Literature and was all set for quotidian career as a small town school teacher until she got married. That was one of the sunnier options available for women born in the 1890s. But she yearned for something more interesting and, quite by accident, found herself deciphering Shakespeare for an eccentric millionaire on Riverdale his extensive estate outside Chicago. "Deciphering" rather than reading or studying The Bard because her boss was certain that Shakepeare's works were written by a cunning cryptographer Francis Bacon who had left clues to his identity in the texts themselves. Although it is hard enough to crack things that are obviously encrypted, it turns out to be easy to find hidden messages in documents that are not encrypted . . . if you are prone to confirmation bias or delusion. You should filter 'quite by accident' through the lens of all those people you know who are lucky because they make their own luck. It turned out that the US government of the day, in one of their isolationist phases, had essentially no cryptologists on the payroll, so they rolled up to Riverdale as and when needed.  One of the other Effectives there was a young chap called William Friedman and he and Elizabeth clicked over the codes and soon got married. In 1920, they shipped out from the Midwest and settled in Washington DC, she working for the US Coastguard.

The Coastguard was the front-line in the Prohibition War as The Mob tried to import illicit liquor in almost unimaginable quantities. You'd have to wonder what sort of a democratic decision the Volstead Act was if there was such a demand for illegal booze. The Hoods made rendezvous on and off the coast by wireless and because that was open-mike, they conversed in code. And Elizebeth was able to crack these with reliable regularity even as the Opposition increased the complexity of the ciphers as part of the arms race. Between 1925 and 1931, she worked the entire gig with only one other (female) employee. After that Uncle Sam recognised the value of the work to the extent of sending her more hands for work and training. These were almost all men but such was her demeanour and no-nonsense efficiency that “Many times I’ve been asked as to how my authority, that is the direction and superior status of a woman as instructor, teacher, mentor, and slave driver, even to commissioned and non-commissioned officers, by these men was accepted,” she said. “I must declare with all truth that with one exception, all of the men young or older who have worked for me and under me and with me, have been true colleagues and have never been obstructionists in any way.” [source]

Elizebeth was definitely of sterner stuff than her husband William, who later on suffered stress fractures in his mind. He was working to break Japanese military ciphers during the war when failure was likely to result in thousands of extra US casualties. But like Alicia Nash, she added his care and attention to the list of tasks which she had to address on a daily basis. Whenever she felt like slacking off or taking a holiday, some government department or other would rock up to her door with an unsolvable conundrum and she often found it easier to solve the puzzle than Just Say No. We only know what we know because the Friedman's bundled up their entire archive and donated them to a local library. This was after the NSA had descended on their home and seized wodges of their papers in a security sweep in the 1950s. But for the Friedman's proactive stand, everything would have been boxed up and shipped to a warehouse in Area 51, Nevada.

What I find interesting is the kind of Arts Block creativity was what was looked for in code-breakers back then. They recruited for the Enigma project by having potential cryptographers do the Times crossword. You were in if you could knock that off in 5 minutes; or if you knew the complete works of Shakespeare by heart. They were looking for creative people who could see connexions between disparate things and recognise patterns. It's true that maths is all about recognising patterns as well and so the Enigmatists were also looking for math-whizzes form Oxbridge. Now cryptography is almost all brute force - persuading a massive computer to find prime factors of enormous numbers: no role for quirky cross-referencing there. Whatever her original training, I am owning Elizebeth Smith Friedman for STEM.
If you like Fagone's style you might enjoy this essay about another extraordinary woman 'solving'  gunshot wounds in Philadelphia.

Monday, 4 December 2017

The road to mutton quad

Sunday last I went on a bit of a journey down the rabbit hole and came up in a happier place. Saturday we were at a family Thanksgiving dinner that couldn't be beat at Pat the Salt's, with his collaterals (not many left) and descendants.  We were specifically doing family, solidarity and gratitude that one of our number was now in remission from cancer.  The family that's in it is famous for the vast number of unexpected guests who are catered for so Saturday was a mill of chopping and mixing, braising and stirring and finding enough chairs for 17. It wasn't until Blob-launch on Sunday morning that I realised that 300 people had been shot to death in an Egyptian mosque.  It reminded me of how we used to behave in Europe when different Christian sects killed each other over whether the deity was three-in-one or just three. Arnaud Almaric's way of separating the nontrinitarian Cathar goats from the orthodox 3in1 Catholic sheep at Béziers on 22 July 1209 was neca eos omnes, deus suos agnoscet - kill them all, god will acknowledge his own which I've cited before .

It turns out that, in solidarity with the atrocity in Sinai, the Library of Birmingham decked itself in the colours of the Egyptian flag. Why ever might the city fathers do that? Because B'ham is home to the largest concentration of Muslims in Britain. 22% of the Metro 2 million identify as Believers, edging out non-believers at 19%. Christians are still the majority at 46% but not in the majority, if you get my meaning. Especially not if practice is accounted: only 800,000 = 1.4% English people attend the Church of England regularly.  The Brummy Library otoh is the largest public library in the UK having been opened only 4 years ago right in the city centre adjacent to the Civic Offices. In the plaza outside is a lovely simple sculptural tribute [below] to John Baskerville the typographer who lived on the site  causing the current building to be named Baskerville House. The sculpture simply prints virgil in massive 'type' of bronze letters on white Portland stone plinths. The word is flanked by two mutton quads = em quads = big spaces which have "Industry & Genius" carved on the side of one and John Baskerville on the side of the other:

Why Virgil in this context? Because Baskerville (1706-1775) was  famous in his day for producing an edition of the Eclogues which happens to be a favorite book of Pat the Salt despite the fact that he never learned Latin before he ran away to sea in 1939 aged 14. A tributary chunk:
Dicite, quandoquidem in molli consedimus herba.
et nunc omnis ager, nunc omnis parturit arbos,
nunc frondent silvae, nunc formosissimus annus.
Classics MIT translation
Say on then, since on the greensward we sit,
And now is burgeoning both field and tree;
Now is the forest green, and now the year
At fairest.
John Dryden paraphrase
The trees are clothed with leaves, the fields with grass;
The blossoms blow; the birds on bushes sing;
And Nature has accomplished all the spring.

If we could have more birds n bushes and fewer guns n mosques, I feel we'd ALL be happier.

Sunday, 3 December 2017

Science in the everyday

This video, sent to me by The Boy's friend Eoin, is almost a definition of science. Observing / discovering something approaching magic, here a screw-driver floating in the air, he then thinks about how this could work without the intervention of pixies, forms a hypothesis, tests that thang, modifies the design in subsequent experiments to help work out the detail, makes other related systems to see if the phenomenon has wider applicability . . . and also gives previously unconsidered examples (golf and tennis balls) in real life to show that it's not just lab true. If you teach science 'dry' with white-board and powerpoint, you need to sit down and fire up some video like this.

And this illustrated explanation of the Fermi Paradox comes from The Boy recommending WaitButWhy. The blog is a sort of cross-over between science, philosophy and chat. Here's one which gives all a normal person needs to know about the brain - skip the first part about flatworms and frogs? And here's one I sent to a palomino who has a teenage boy exploring The Teen Condition: Quote
2) Don’t be such a dick to your parents, you entitled little shit. You live in a world where 99.9999999% of humans care more about how their hair looks than whether you live or die, and then there’s this person, or two if you’re lucky, who’d give their lives for you.

Here's Prof David "Numberphile" Brailsford talking about the rise of PDF.

I mentioned water-hammer before. Here's an engineer talking about it with equations and practical ways to mitigate it.

Ovo-tech = industrial processing of eggs. A food engineer's gloopy dream.

Pushing the envelope in figure skating - if everyone is doing triple, someone will attempt the quad [see also yest]

Water, you say? When the Panama Canal opened in 1913, hundreds of hectares of old growth tropical hardwoods were flooded where the stood. The anaerobic conditions have helped preserve the timber for 100 years. They are now being harvested.

Shared Space at Vox: the idea that removal of road-signs will make the interactions of cars, bikes, walkers, buses and wheelchairs paradoxically safer. One aspect of it is that, if there is a forest of signage you don't see any of it. No signs means that each actor has to take responsibility for their own safety / killing power and slow down. Needless to say, a single anecdote of a blind person killed is largely over-riding a huge amount of data showing the signless streets are safer.

Whalefall. It's a thing, here acknowledged by someone from the Arts Block.

Sunday song 03Dec17

I believe in singing together. You really should know about MILCK.

Saturday, 2 December 2017

True self, finding of

I wrote a few years ago about my neighbour who, though born a sheep-farmer with hectares attached to his patrimony, became in his middle years a stone-mason . . . and found thereby fulfillment if perhaps not unalloyed happiness. I noted there Bill Bryson's epiphany that, despite being born in Dumpy, Iowa he was at heart a European whither he went as soon as ever he could.  But these boys are the exception; almost all of us get trammelled by our class and culture, education and upbringing and plain geographic inertia and finish up growing to look uncannily like our parents. For people like me, the expectation is that you go to University because your whole class is going there like a platoon: exchanging the school uniform for another set of cultural and clothing norms. Damned difficult to kick over the traces and become a hair-dresser, lumberjack or carpenter. Likewise it's hard enough for the son of a chippy to land a middle-class job teaching in The Institute.

This is why I find stories of people, men and women, who reinvent themselves as adults so inspiring. When I was failing-to-thrive in my second year in college, I talked about dropping out to become a carpenter, but only got as far as looking wistfully through the window of a place in Temple Bar, Dublin called Rough Deal which made kitchen tables and similar robust items of practical furniture. As my only qualification was having made a remarkably uncomfortable chair out of a tea-chest, I doubt if the shop would have entertained my fantasies. I'm not a carpenter, I'm more of a generalist, a bodger in a few fields but insufficiently focused to make a living from any of them.

Here's a wonderful story about a boy from Sydney, one of the indigenous dispossessed, who by accident became an ice-skater and is now shaking the world of figure skating by its diamanté lapels. A very large part of skating is about physics - you spin slower if you throw out your arms & you need to be close to the ground - and there is a certain amount of being the right size to succeed. When Harley grew too tall to be a likely soloist, his coach made him try mixed doubles. Nobody in his orbit, nobody in Australia, could be found to match his style but the networked themselves to Moscow and tried out with Екатерина Дмитриевна Александровская. He is tall and has ears like sails, she is short and has a blond pony-tail, together they are MAGIC. It's insane what they expect girls to do in this circus: zing at 40km/h across a cold hard surface 2.5 metres high and upside down, supported on one hand by a chap she'd never heard of two years ago. Here's just one clip: Gdansk 2017. What I find amazing is that they can travel in parallel at turbo-speed without looking at each other - they just know whether the other is. And reflect that, when they met they were monoglots: she Russian, him English. The throwing each other in the air, the spins, the jumps, the stops, they're just razz-ma-tazz; the key thing is the trust, the empathy and the courage of young Екатерина.

Friday, 1 December 2017

Do you feel safe?

Are you deluded? Duleek, Co Meath was in the news again this week because a local lawyer is saying that their CCTV surveillance system [screenshot R] is illegal because it doesn't meet the requirements of the Data Protection Commission DPC. This is Duleek, not Detroit, so you might think that having CCTV on every corner might be exaggerating the lawlessness and gun-crime that goes down in Co Meath.
The Duleek Everyman position is that
cctv makes the local people feel safer
they can afford the purchase and installation costs
the monitoring is done in the local police station
nobody else has locus standi to complain. The lawyer said that anyone who goes down Main Street, Duleek and indeed the whole population have a civil liberty place to stand on for their objection. We the dissenters have a right to privacy: to sneak into the pub during lent; to meet our [consensual] adulterous partners; to cross-dress in purple . . . without it being recorded and pored over by our neighbours. Even if that neighbour is Garda "Curious" George Doohickey. One of the unsavoury info-bits that fell out of the Garda whistle-blowers scandal was that some Gardai habitually used Pulse, their central computer system, to provide material for coffee-break celebrity tittle-tattle or to check out prospective girl-friends. The Gardai are not, after all, a random selection of the population: they are probably top heavy with [reformed] boy racers; folk who like to be in charge; folk who are curious about the human condition and the peculiarities on humans in general. Swimming coaches, priests and scout-leaders are self-selected in a different way. Most of us gravitate to a place where we feel comfortable, where some need is met, even if not expressed. So having my private life monitored by the Gardai doesn't allay my concerns.

We have a rural area neighbour phone-watch txt-alert system to which we contribute €10 a year. It seems to be mainly a way of cementing prejudice against the travelling community: Hiace vans are responsible for a disproportionate amount of the alert-traffic. As blow-ins to the rural place where we've lived for 20 years, our movements will be under disproportionate scrutiny when neighbourhood watch gets tooled up with cctv. In 1998, we got a special visit from the local Garda sergeant because a) two strange dogs had been worrying sheep b) we were blow-ins so the most likely owners of the dogs.

And what about the middle, financial solvency [they can afford the purchase and installation costs], condition? The burghers of Duleek have a pub-quiz and a raffle and a €100-a-plate fund-raising dinner and deter the hoods from rifling their nice outer suburban execu-homes . . . so the hoods go off to the next community where the pickings may be thinner but the risks are less. A slow hand-clap for NIMBY indeed.

And what about the feeling safer? The obnoxious and stroppy Newstalk presenter Paul Williams conjured up a graphic image of a widow beaten black&blue for her pension as if that alone was sufficient justification for cctv at the end of every bohereen down the country.

UCD Law Lecturer TJ McIntyre takes that apart as well.  The desire for surveillance is driven by an up-spike in rural crime which mapped quite well to the recession. As the financial pinch hit, burglars had to travel further and more frequently in search of their ill-gotten flat-screen TVs. But the crime rate was starting to tumble before the cctv arrived. You don't need thousands of €€€s for cameras and recorders you just need to wait until the economy picks up. Cost? between €1K and €3K for a 4 camera domestic system. But that's a noddy system, Duleek's 24/7 14 camera installation appears to have cost €50,000.  Which would be a fair price to pay (shared out among 3,000 Duleekists) IF cctv had a significant effect on deterring crime.  One of the DPC issues is proportionality: "Other uses may fail the test of proportionality. For example, using a CCTV system to constantly monitor employees is highly intrusive and would need to be justified by reference to special circumstances". The DPC wants operators of cctv to go through a check-list to make them weigh the cost-benefit of their surveillance toys. cctv is okay if there is a demonstrable good to be achieved and little collateral intrusion into privacy.  If the operators cannot marshal the evidence in this equation, then they shouldn't be allowed a license. If they cannot be bothered to answer the questions because they are smug in their uninvestigated certainties, then they are breaking the law. Here's an example of an intrusive technological solution to trucker fatigue that might be better solved by paying the drivers a living wage.

In certain, quite narrowly defined places - car-parks and shops - cctv seems to work. They reduce crimes and anti-social behaviour (parking across two slots?) in car-parks by 50%. The extreme example of this is the Bold Street car-park in Derby - billed as the most secure such building in the world. It used to be a hang-out for pan-handlers and low-lifes. Since the installation of cameras and other security measures in 1998 there have been no reported crimes. In the UK, some figures suggest that cctv reduces crime by a trifling 4%.  Civil libertarians reckon that you can achieve better cheaper reduction with low-tech non-intrusive measures like better street lighting.

Which brings me to my final point. If you feel safe - you've paid all that money after all - then you'll feel confident and maybe do daft and potentially self-destructive things. There's a cctv right outside the pub, so it will be quite okay to ridicule that fat chap's tattoos as we all spill out on the street at closing time? Don't think so.

Thursday, 30 November 2017

Nous sommes désolés

The young and symmetrical Prime Minister of Canada Justin Trudeau has been apologising on behalf of the State for oppressing The Gays through the second half of the 20thC. Inclusivity is in the air, and Trudeau said sorry for how LGBTQ2 Canadians were treated before he himself reached adulthood - he was born in 1971. I am trying to keep track of the fragmentation of gender identity and got as far as LGBTQ last Tuesday. Super-trendy Trudeau has stolen a march on me with his ABCDE2.  It stands for Two-spirit which has been appropriated by some of the First Nations to describe their citizens who don't fit a M and F dichotomy. I gather that it would be an impertinence for white folks to so describe themselves because their white privilege prevents them from experiencing the oppression meted out on Native North Americans, let alone NNA2s. Heck m Canuck, I bet NNA is now no longer acceptable in polite company, in the same way as the demonym for dark Americans changes so often as to wrong-foot almost everybody. When first encountered by French trappers, two-spirit folk were called berdache but you want to be really careful using that term outside of historical anthropology texts. Tim Minchin on the language of prejudice for minorities.

You may be sure that whatever the state of Canadian Law, different people are subject still to all sorts of prejudice and discrimination across the provinces of Canada.  The first step is to sort out the current situation and Canada has not been behind-hand in legislating for equality. Apologising for the sins of our fathers only works if you absolutely believe in the sincerity of the person uttering the words. I think I believed Gordon Brown British Prime Minister when, in 2009, he uttered a similar apology for the shameful treatment of Alan Turing 50 years earlier when Brown himself was still in diapers. I would not have believed his predecessor Tony Blair who was far to conscious of the cameras. What stuck in my craw about Turing was several years of political grand-standing that eventually secured Turing a retrospective pardon for his crimes and misdemeanors. Rewriting history with its whiff of whitewash is not the same as a sincere apology. The pardon allowed for a preening smugness and a delusion that those who secured it for Turing would have behaved better than their ancestors at that place and time. An apology otoh looks forward and carries the intention, however poorly executed in reality to do better in future with living people.  There is even talk of a compensation package as if ruined lives and lost pension rights (it was mostly public servants who were directly financially affected). That could be unseemly: do the surviving dependents get a claim; how much can money heal emotional wounds etc.
Catching the wave of Canadian right-on-ness on Metafilter led me to another sorry-fest from young Trudeau just after he was elected the second youngest Canadian PM in 2015.  That was flagged on MeFi as "The real value in the apology lies in a re-examination" and was about the shabby treatment of a shipful of immigrants from India to Canada who, in 1914 aboard the Komogata Maru, were held in limbo in Vancouver for 2 months before being sent back to India. On arrival back in the Subcontinent, they expressed their dismay and dissatisfaction at being unable to travel within the British Empire. In the ensuing riot, 19 of the landed passengers were killed by security forces. Trudeau apologised for a too nice application of the Law as it stood back then and for the series of unfortunate consequences of that legal stance.
I liked very much that fact that Navdeep Bains, the Minister of Innovation, Science, and Economic Development, was sitting directly behind Trudeau in his trademark bright red turban. Doubtless Trudeau, who is very much Optics-aware, made sure of the seating arrangements. When CBC cameras cut to split-screen Trudeau's continuing bilingual apology with grainy monochrome footage of turbaned chaps on the Komogata Maru [see above for screen-scrape], there was Bains as the bright proof that Sikhs and other minorities and immigrants have a sky's-the-limit future in Canada. That should give hope to all the Syrian paediatricians who are living tents somewhere. That bright red slash of colour may remind you of another symbol of hope: The Girl in the Red Dress from Schindler's List.  If you haven't had enough already of Trudeau fils, you might check his 2000 eulogy for Trudeau père.

Wednesday, 29 November 2017

Charter of ye Forest 1217

This month is the 800th anniversary of the promulgation of the Charter of the Forest [facsimile and transcript] by William Marshall, Earl of Pembroke (and a token handful of bishops) on behalf of the infant King Henry III who had just succeeded his father as king of England, lord of Ireland, duke of Normandy, Aquitaine, and count of Anjou. Henry was a boy of 10 years and needed someone to act as regent until he attained his majority. Remember that all folks grew up earlier back then - Henry V was having a near death experience in battle at the age of 16.  This is the same William Marshall who ordered the construction of the Hook Lighthouse on the Wexford side of Waterford Harbour. So he got around.

800 years ago is 1217 and the CoF is a sort of codicil to the Magna Carta signed by King John, Henry's father at Runnymede in 1215. Hindsighters hail the Magna Carta as the cornerstone on which the edifice of democracy was built but they should note that its terms were repudiated by both King John and the Barons who had compelled him to accept its diminution of the rights of the Crown, annulled by the Pope and ignored until the Baron's War ground to halt in 1217. Some of its clauses were reissued in the peace treaty of 1217. The CoF was added as a separate document to push back some of the royal creep of the acquisition of lands and rights by King Richard [the Lionheart] and his brother King John.  Note that 'forest' then had a special legal meaning as a special domain for hunting that was outside the remit of Common Law - a sort of private club where only the owner [usually the King] could play with his rich and well-connected pals - think Golf Club, another institution designed to keep the riff-raff at arm's length.

These two Charters were a long way from democracy as we have it today except insofar as both political systems protected the rights of the rich to get richer. The starting point of the CoF, what everyone agrees to be true, is what pertained in the reign of Henry II, [Good King Henry Chenopodium bonus-henricus above R] father of Richard and John and granbdfather of Henry III.

What's fascinating about the CoF is its insight into what mattered to people back in those days and the words used [full glossary] to define concepts that are now largely irrelevant. Not everything though: a cord of wood is a stack of branches 8ft x 4ft x 4ft as it is today wherever there are English speaking wood-burning stoves.  Here for example are some of the sorts of commonage:
  • common of estovers the right to gather fuel wood, sometimes ‘by hook or by crook’ 
  • common of herbage a special dispensation for grazing sheep without surcharge
  • common of pasture the right to graze waste
  • stinted common of pasture restricted to certain times of year
  • common of marl the right to dig clay, chalk, sand 
  • common of mast or pannage,the right to graze swine on beech mast and acorns 
  • common of turbary the right to dig turf for fuel 
turbary rights are still held across Ireland today; but the recently acquired respect for the planet is preventing owners of the rights from vindicated them by cutting and burning turf.. But nobody is allowed any more to keep a pig in the back-garden let alone take it for walks in the woods to fatten up on acorns.  The glossary is so rich and evocative of a time distant but still recognisable - especially if you have read any Thomas Hardy and tie string round your trousers legs under the knee to stop mice running up there.