In Hock

. . . up to our armpits.

Here's and interesting graphic of per capita debt from howmuch.net which could do with some explanatory text from bigthink. It show that tax-payers in Ireland have taken on stupendous amounts of borrowing; half of which to bail out the banks in the financial crisis of 2008. The banks went mad shoveling electron-dollars from one hard-drive to another because the shovellers could convert their 'secondlife' dollars into real Porches, whores and sandwiches filled with whale filet mignon de baleine Balaenoptera physalus. But, unaaccountably, The Rules made by The Man dictated that we-the-people had to pick up the tab when the circus tanked. The bankers got to keep their Porches and productivity bonuses.  If your country doesn't feature on the poor quality pixellated pizza above you should check out the source above. This is a well-handy way of displaying the data because it shows that islands with rather small populations like Ireland and Singapore can have huge relative debt even when the absolute numbers fade in comparison to the USA because there are 100x more yanquidogs.

For years I have been commending the Norwegians for investing their share of the windfall from North Sea Oil and Gas in future-proofing their nation and big infrastructural projects. They also, according to me, paid off the National Debt. I have been contrasting this with Margaret Thatcher's use of the UK share to give massive tax-breaks to the middle class, distribute the public housing stock into private ownership,  ditto all the public utilities; kill the railways, build motorways and encourage everyone to have their own car. Those in a position to buy their own council house, buy British Telecom shares, or receive a 25% pay-hike for academics in Universities [meeee!] are now asset-rich while the subsequent generations are shanked. Moan Moan. Whether my analysis of Norwegian debt was ever correct, the country now has a per capita burden of $23K each. That's a lot better than Ireland or Japan, but a lot more onerous than Argentina $6,300, China $1,300 or Liberia $27.

Short changers 111216

Heartwarming commercial endorsements

• Miscegenation is OK
• Same sex marriage ditto
• Intergenerational aggro is normal???
• Intergenerational misunderstanding is common
• I don't think the old guys are gay.
• It's okay to hug The Other.

I didn't know about the association between Free the Gays and Subaru: reading matter

• Giving back to the dispossessed I plastic
• Giving back to the dispossessed II with shingles [you only need watch the first half: it repeats]

Cheesy

I'm on the last chapter /section of Michael Pollan's Cooked. He has some interesting things to say about cheese  a nun called Sister Noëlla who lives in Connecticut and makes a cheese called Bethlehem which is more or less the same as the Auvergne's Saint-Nectaire.  If you don't want to read the book - and it's taken me a month of elapsed time - you can hear Pollan reading some of the juicier excerpts at a foodie conference. Over the weekend, I as hanging out with Dau.II and her bloke and her grandfather Pat the Salt. We all got fed up with the TV rather quickly and Dau.II suggested we watch an episode of the TV series based upon Cooked that is available on Netflix: here's the trailer. The smiley face of Sister Noëlla makes a brief appearance. The films - we saw 1.25 of them and fell asleep over another (right after dins) - are gorgeous and complementary to the book rather than a précis of the text. The series has clearly been made in the tradition of David Attenborough - high  production values and tight editting so that you feel you're getting a mouthful of executive summary.

Pollan addresses a modern foodie dilemma: we are moving on from a century of Pasteurisation into a post-Pasteurian world where 'this milk is RAW' is taken to be highly complementary . . . and still rare. We gave up on raw milk 100 years ago because it was shown to transmit typhoid Salmonella typhi and Mycobacterium tuberculosis. These germs were susceptible to the brief heating and rapid cooling process invented by Louis Pasteur. The trouble with using Pasteurised milk to make cheese is that you have to employ a food-engineer add the Lactobacillus that are an essential part of the process. Traditional cheese-makers never bother[ed] with that - the bacteria and fungi just fell from the roof of the cave or came out from under the fingernails of the cheese-maker. Indeed, before Pasteur, they didn't even know that microbes were involved in the miraculous transformation. Needless to say, Sister Noëlla makes her cheese [Like St.Nectaire above R] in the traditional way a bit like I make sourdough bread. The wooden vat she uses is never washed - just rinsed - and has a slick white interior. There will be billions of bacteria on this surface ready to go forth and multiply as soon as warm milk is added.

Every year people die from eating unPasteurised cheese - it's the Listeria stupid - but I don't think that's sufficient reason to ban the stuff. Far more people die each year in automobiles and nobody is seriously suggesting these pleasure vehicles should be forbidden. Apparently Sister Noëlla saw off the local Food Feds by adding E.coli to a) her wooden barrel and b) a 'clean' culture of Pasteurised milk in a stainless steel vat. The latter was far, far more coliform than her stuff, because her stuff was a thriving mutually supportive community that could together resist attack from the interloping Black Hats. Vive le fromage, vive la microbiome, vive la France.

Mon pet du chou

Forty years ago as students we had a copy of John Seymour's Self-Sufficiency and aspirations about making food from scratch. It was more normal then before everyone out-sourced so much food-preparation to a factory in another county whence it came to a local shop in a neat box with cooking instructions [multiprevlier]. In the fall for several years I would make a vegetable chutney, sometimes in absurdly large glass jars, which was never anything like, or as good as, Branston Pickle [R next to an enhanced cheese sandwich]. My pickle required boiling up a lot of chopped veg with vinegar and then putting it in jars for as long as it remained un-furry. It was actually on the verge of repellent and I only ate the stuff out of a sense of duty to my craft. I hadn't a clue. I was learning it all from books because I was a long way from home, and even home was along way from traditional kitchen practice.

The final section [earliers] of Michael Pollan's Cooked is, not very well, entitled Earth and is about pickles and ferments. It turns out that I was mad to be buying vinegar and salt as way of lowering the pH and raising the ion concentration of the vegetables so that they would not seem tasty to 'bad' microbes. I should just, like a master of Aikido, have tilted the tables so that some microbes would make their own acetic and lactic acids as a by-product of partial digestion of the veggies and thus deter other microbes from getting in on the act. I've learned a lot more about LABs Lactic Acid Bacteria since I had to teach it at the Institute than I ever learned in school or poring over cook-books and Self-Sufficiency. LABs are a key component in the transformation of cheese, yoghurt, buttermilk and sauerkraut,

But, according to Pollan, the LABs are only a stage in the process of ecological succession that converts the sulphurous fibre of cabbage into crunchy and digestible sauerkraut and kimchi. The first step appears to be carried out by Enterics, from the gamma proteobacteria that also include E.coli, Salmonella, Vibrio cholerae, Enterics, despite their name, normally comprise only about 1% of the intestinal flora and we quietly ignore them until we eat out at a sketchy burger joint and spend the next two days talking on the porcelain telephone. As the enterics fade in their vigour, poisoned by the own waste, then Leuconostoc mesenteroides steps up to the plate to clean up the mess. They are the weeds of the microbial world: fast growing, adaptable and tolerant. As they convert the available sugars into lactic and acetic acid, first bubbles and then a positive fizzzz of carbon dioxide starts to emerge from the seething surface. When Leuconostoc has made life intolerable for itself and its children, then Lactobacillus planatrum presents itself as having even lower standards and starts to divide and conquer. You don't need to know this history of transformation, you can just leave things to happen in their own sweet way and wait until the bubbling and burping stops.

If you open the lid too soon you may encounter evidence of a transient member of the community, as sulphate reducing bacteria start to pump out hydrogen sulphide and your brew starts to smell distinctly funky: old egg sandwich in spades. But there is only a little sulphur in cabbage and the farty-effects only endure for a little while. As with presents coming up to Christmas, it is best not to peek into the sauerkraut vat too early. Interestingly the biochemical tool-kit for reducing sulphur can be carried by two wildly different groups of bacteria: 1) the delta proteobacteria like Desulphobacter and Desulphobacula and 2) gram positives like a Desulfotomaculum and Desulfosporomusa. These microbiologist desulpho-namers of bacteria seem to lack for desulpo-imagination.  Remind me next September to offer a research project comparing the sulphur-metabolism genes of these two very different groups: bet you there is horizontal gene transfer going on.

Long haul, whole picture

As science gets more expensive, there is more scrutiny on the bottom line. More science-trained people are securing work vetting science and counting deliverables and ticking them off against the list promised in the grant application. To pass muster and secure future funding you have to acquire a reputation for doing what it says on the tin. Inevitably, you'll be less ambitious, less daring in the hypotheses that you undertake to test. And the turn-around time is important too. A project has to be launched, trouble-shot, carried out and done and dusted as a couple of publications within three years. In the last decade, to my certain knowledge, two of the smartest STEM women in Ireland's premier university have been pulled up short and briefly demoralised by being identified as "failing to publish sufficient papers". This was largely because they had been brave enough and curious enough to take on a big question beyond the current frontier rather than something safer and same-old same-old that would satisfy the beanocrats.

So it's rare to find someone who had spent a lifetime accumulating data on a single system. My brief foray into molecular biology at the bench was mentored and encouraged by a STEM woman Monica Hughes who was halfway through a lifetime working in cyanogenesis. It's an interesting conundrum. Certain plants produce free cyanide when they are damaged by herbivores. Cyanide is, as any reader of Agatha Christie knows, toxic. Its binding to an enzyme cytochrome C oxidase prevents the production of the energy currency ATP by the electron transport chain in the mitochondria of all eukaryotic cells. After a few bites of cyanide enriched clover, the cow don't feel so good and drifts off to eat something else. We, and cows, have developed an olfactory receptor that recognises CN^- and sends a signal "bitter almonds" to the part of the brain that integrates food, memory and behaviour. The conundrum is that plants also require a functioning electron transport chain and so cannot produce free cyanide all the time.

Clover Trifolium repens works it by having two different genes. One specifying the production of a cyanogenic glycoside [where the toxicity of the cyanide is reduced by bolting it to a sugar molecule] and the other to make an enzyme cyanoglycosidase which, on specific signals, cleaves the complex to release the free cyanide. The specific signals include physical damage to cells caused by teeth.

Monica had started off as a geneticist measuring the presence of the enzyme and the CN-glycoside in different plants, crossing them to work out how the genes are inherited and whether they are located on the same chromosome. There was a nice assay for the presence of CN using paper strips soaked in picric acid aka trinitrophenol TNP and put in a sealed jar with the sample. TNP is very similar chemically to TNT [prev] and also highly explosive. But a wee bit on a filter paper isn't going to go up with a whoomph. When exposed to CN, the yellow picric acid turns red and you can quantify the amount of cyanide present by comparing to standard colour strips. By cross-referencing parallel assays:

• unknown
• unknown + material known to have the enzyme
• unknown + material known to have the glycoside

you can see whether a particular plant has the glycoside, the enzyme or both. It has the potential for many a nice little hypothesis-driven research project. Frost damage also triggers the enzyme and so you expect that clover higher up a mountainside will be more likely to be missing one or other of the genes involved in the process etc.

My project was taking the knowledge of the system one level deeper by tracking the changes in the DNA that are associated with the 'normal' and mutated genes. A few years after my ineffectual and self-destructive <ouch!> foray into her lab, Monica undertook to sequence the genes involved because that was what you did in that era and that was where the money was available. But the research was still rather academic than practical - despite the Final Paragraph of successive grant applications which asserted how important this knowledge would be for agriculture.

Later still there was a more genuine pay-off and a lot more foreign travel when she started a collaboration with scientists in South America who were investigating a parallel system of cyanogenesis in cassava Manihot esculenta. For feeding the starving millions, cassava/manioc has a very important part to play because it is hardy and drought resistant and a generous source of carbohydrate . . . and cyanide. The starchy roots need a lot of processing before they are safe to eat and a deep knowledge of the genetics of cyanogenesis holds out the hope for breeding varieties that are large, succulent, able to grow on marginal soils . . . and cyanide free.

Then it turned out that certain active principles in cassava might have something to offer the world of cancer treatment. Think about that: if you were a policy wonk trying to map a future for [insert country here] as a technological Nation, would you nurture the career of a plant geneticist in order to develop a cure for cancer? It takes a life-time to build the accumulated knowledge that generates this sort of quite unexpected breakthrough. It just wouldn't be allowed now.

As I was leaving Newcastle in the 80s, The Suits decided that Departments were really old fashioned and the whole University should be restructured as a collection of Schools. Uproar! Nobody will make me talk to those cads in Biochemistry. My integrity has been impugned. I am a Zoologist not a Biologist. What will happen to our secretary, photocopier, coffee-room, students . . . Funnily enough exactly the same thing happened 10 years later when I was working in TCD, with exactly the same muttering over coffee and prognostications of doom.  Monica otoh was entirely phlegmatic about the change: I've been around for a long time, I started in a school, then we were departmentalised, now we're to be schooled again. It won't make a bit of difference to my science. If that sounds like a heads-down, self-absorbed, egotistical response don't be fooled. When she was prevailed upon to be Head of School, Monica stepped up to the plate and carried out this thankless task with tact and efficiency. The best head I've ever known, was the assessment of one of her team when I met him at a conference. Chapeaux bas!

More women in science.

le Brave des Braves

"The Bravest of the Brave" aka Le Rougeaud from his ruddy complexion died this day 201 years ago. Maréchal Michel Ney [R at the height of his powers] came from Sarrelouis / Saarlouis on the border between France and Germany. The town is currently in Germany but has been shuttled back and forth between the superpowers to East and West over the last 500 years. Michel was born in 1769 into a family of francophone coopers who were also fluent in the local dialect of German. You had to be bilingual if you wanted to have a working business or needed to argue the toss with your neighbour about his over-hanging apple tree.

Trained to boredom as a notary and civil servant, he ran away for a soldier's life at the age of 18 and joined the French Hussars. Not having blue blood or an escutcheon, he was excluded from the officers' mess in the army of Louis XVI but he achieved promotion through the ranks because he was bright and willing and carried himself with confidence. When the monarchy fell, the new egalitarianism allowed him to win his commission as an officer. He travelled all over Europe from Lisbon to Moscow over the course of the next 28 years. In the Peninsula War he as c-n-c of the rear-guard as La Grande Armée retreated from Portugal to the Pyrenees, he dextrously won time for the rest of the French so that the retreat didn't disintegrate into a rout. Ney was conspicuously courageous in his leading from the front like my name-sake and distant rellie who died at the head of his regiment at the crossing of the Nivelle - almost the last engagement of the Peninsula war. He fought at Borodino [prev] and was the 'last frenchman to leave' Russian soil, again leading the rear-guard in the holocaust that was the Retreat from Moscow in 1812.

As leader of the Marshall's Revolt, Ney was instrumental in persuading Napoleon to throw in the towel and go with dignity, but no army, to exile in Elba in April 1814. Ney then swore allegiance to the reinstated monarch although his position was always that his loyalty was to La France rather than to the personality at the top of the pyramid.  A year after arriving at Elba, Napoleon was on the move again beginning the 100-days campaign that culminated at Waterloo on 18th June 1815. When the news arrived in Versailles that Napoleon had landed on french soil, the government dispatched Ney to stop his previous Chief and turn him back.  In a super-romantic encounter at Auxerre, Dan O'Herlihy Ney is unable to shoot or capture Rod Steiger the Emperor and rurns his coat again.  Here's take two [2002] of the same episode.

Ney was a key figure in the Waterloo Campaign, unable to follow through at the Battle of Quatre-Bras [16 June 1815] and leading a super-romantic but unsupported and ultimately ineffectual cavalry charge at Waterloo [18 June 1815]. Ney had 5 horses shot under him on the field of Waterloo. Running out of horses, he led a final hopeless advance of the infantry with the words "Venez voir comment meurt un maréchal de France!" but Death was not interested in taking him at that time. There are those who put much of the blame for the outcome of Waterloo on poor Michel's shoulders.  But the Waterloo Campaign could not have been won. There is no way that Europe was going to come to any accommodation with France with Napoleon as head of state. Losing Waterloo - which was in Wellington's own words "A damned close-run thing" - would have deferred defeat until the next battle. Napoleon, ever the optimist, was on a hiding to nothing, as we say in Ireland.

The end of Marshall Ney is too sad. Ney was a soldier's soldier but detested by politicians of all stripes and was about the only name on a list of traitors: as defined by those who had thrown in their lot with Napoleon. There is a distinct sense of Voltaire's quip "Dans ce pay-ci, il est bon de tuer de temps en temps un amiral pour encourager les autres." about another another country and another time when a senior officer - Admiral Byng - was shot by his own side in questionable circumstances.  At Ney's trial, his lawyer had a cunning plan for evading conviction because Sarrelouis was then part of Prussia and so the French court had no claim on a foreign citizen. But Ney was unbending in his loyalty to France "Je suis Français et je resterai Français!" Poor chap seems only to speak in exclamations! Condemned to death, he was shot [L by Jean-Léon Gérôme] outside the Luxembourg Gardens in Paris on 7th December 1815. Of course he faced the firing squad with open eyes and gave them the command to fire! Chapeaux bas!

A Russian officer who expressed delight at the end of an old enemy was stripped of his rank by the Emperor Alexander Александр Павлович I. That kind of romantic chivalry about warriors on the other side is still about. There's a famous story about the William Callaghan, the Captain of the battleship USS Missouri, who in April 1945 insisted on giving an honourable burial to the top half of Setsuo Ishino a kamikaze pilot who had just crashed into the side of his ship.

Real numbers

I was trying some humility in my appreciation that not everyone at The Institute had the benefits of my very expensive education; not everyone has had the opportunity or inclination to row for work or pleasure. The humility comes from realising that, as I grew up: I never birthed a calf, changed a diaper, dug a grave, butchered a rabbit, drove a tractor, laid one brick on another . . . although, in fairness, I could do several of the other things on Heinlein's list of Attributes of Humanity. I picked up some skills later: I hefted my first dead body when I was 17 and working in the local hospital; I was catcher at Dau.II's birth; I've written a sonnet; and built a [low] wall. I figure that many of my students must have skills that I don't possess: on the sports field or using their hands or working in the material world.

If the education we transact at The Institute is to mean aNNything at all, being A Good Pair of Hands must be part of the parcel. We want to turn out youngsters who can saw a plank into 3 equal-sized pieces; who can reliably carry out some industrial or analytical protocol even if it's repetitive or 'boring'.  There is no point in having a bunch of book-l'arning in your head with no possible application in the real world.  I've come to believe that we are so driven by the content of our courses that we lose sight of the process. Indeed 'curriculum' [the running, the process] is now synonymous with syllabus [the facts]. I crashed home on my again this week as I had my end of term maths quiz for 1st Year QM. After the Midterm quiz, I had a ranty post-mortem 2015 and 2016 in which I pointed out where most of the class had gone wrong. In almost all cases this occurred where the real world met mathematics. It is an interface on which the whole of Edward MacNeill's brilliant book Mathsemantics is based.  So I put in Q1 Volume of 44 blocks? and Q4 Period of pendulum? questions again to see if everyone anyone had internalised my passionately expressed explanation from 6 weeks ago.

I also dreamed up another nifty Reality Station question: Q16. If a baby is 0.5m long and 3.5kg heavy at birth, what weight do you expect her to be when she's fully grown at 1.50m? This can be written as an equation - if that helps:

0.5m ∝ 3.5kg == 1.5m ∝ Xkg

where  ∝ means 'is proportional to'. And the obvious answer is to stop thinking and treat  ∝  as equal to =, and solve for X which yields the  answer that an adult woman weighs the same as a 10kg sack of potatoes which you or I can carry with one hand.  

But how, in the biological world, does weight increase as length increases? As we are 90% water and barely float in the sea, our volume in litres is more or less the same as our weight in kilograms. If we increase our length by 3x over 15-16 years we probably/surely increase our width and 'depth' in the same proportion: babies don't start off flat and fill out as they grow. Although the proportions do change as we grow up [prev and prevlier] - babies' heads are massive [see above L] compared to anyone's who can read - we could begin to guestimate the answer by treating us as a cube. A Rubic's Cube illustrates the relative proportions rather well: the new-born is represented by a single Rubic's unit, the whole puzzle = the adult. The length / width / depth increases by 3x . . . so the volume increases by 3³ or 27x. Starting weight is 3.5 kg, end weight 3.5 x 27 kg = 94 kg. That's a little heavy but it's in the right ball park and could be a first approximation for a model for the relationship among animals of different sizes as to their height and weight.