Thursday, 31 March 2016


One of the questions which Gardner asked of the stakeholders in his enquiries about The University in the 21stC was "What one book would you give to all the students at graduation?".  He found that was really revealing about the interviewee and where they stood on what mattered.  It's rather like asking what is the book that you would preserve through Armageddon to stand as a beacon and foundation for any civilisation to arise from the ashes. Richard Feynman was famously able to take post-apocalyptic truth down almost to a a tweet "I believe it is the atomic hypothesis that all things are made of atoms — little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another."  I think that requires far too much base-line knowledge to be useful.  I'd put put forward "Mathematics for the Million" (1937) by Lancelot Hogben an extraordinarily comprehensively and accessible history of maths.  You can buy a more recent edition for 40c on Amazon.

Last year when library at The Institute was shedding some stock to make room for new books, I picked up The Mother Tongue . . . by Lancelot Hogben.  It's a bit schoolmasterish but gives an insight into where English came from; with asides about other European languages. We're not the only ones to have borrowed words [beef, pastry, craic] from our neighbours: French canife was absorbed from gothic knife, Irish seomra is clearly ripped from French chambre. If Hogben can write a killer book on maths, is he really qualified to write about language?  Well [duh!] yes, he can write books about language because he invented one Interglossa which was at one time a rival for Esperanto.  There's a revealing moment in Mother Tongue when Hogben takes time off for a swipe at Esperanto for retaining accusative case endings like Latin.  Well really, he says, it's always clear from word order which is the object in a sentence.  Interglossa: a draft of an auxiliary for a democratic world order, being an attempt to apply semantic principles to language design [phew!] was published as a blue Pelican paperback in 1943. The guff about democratic world order is from Higben being one of a group of high-profile leftist scientists in the 1930s, many of whom were formally members of the Communist Party. We've met JBS Haldane before, and JD Bernal in passing, Sinologist Joseph Needham was another who needs to be visited.

As it happens, Hogben's rep as a scientist is in neither linguistics nor mathematics but as an endocrinologist.  He was the man who put Xenopus laevis the African clawed toad on the map as a standard model organism. While working, briefly and in political pain, in South Africa he injected urine from a pregnant woman into one of his toads and noted that it immediately started to ovulate!  This procedure was developed as the Hogben Pregnancy Test and was the gold standard for several decades - it's the progesterone in the pee, silly.  You have to ask what combination of circumstances caused him to think the experiment was a good idea.

Back back to the Mother Tongue which is a germanic language overlain with Norman French, Latin. Greek and everywhere the Brits colonised: bungalow, chutney, gong, pyjamas, hammock. But little words are still patently from the same branch of PIE as Frisian, Dutch and Swedish.  Try reading this:

Se ealda man beneothan tham treowe neah thaere brycge wuneth on tham huse uppan than hylle begeondan tham streame mid his hunde and twa cattum. His wife is nu dead. He ne haefth bearn and friend ne cumath oft to his dore. On tham gearde behindan his huse beoth twa gaet feawa henne and beon. he maketh ciese to etenne of tham meolce fram his gatum and baecth his agenan bread. Hogben helpfully strips off the endings which we have shed in modern English.  For the things that really matter, we are still speaking Olde English from 1000 years ago.  Alexander Pope expressed the sentiment.
Happy the man, whose wish and care
A few paternal acres bound,
Content to breathe his native air,
                            In his own ground.

Whose herds with milk, whose fields with bread,
Whose flocks supply him with attire,
Whose trees in summer yield him shade,
                            In winter fire.

Wednesday, 30 March 2016

Stinks and bangs

It's two years since my gaffer from grad school left us bereft. As a child he had a couple of near-death experiences doing daft boy-things: crushed pelvis when he fell off the running board of a running truck and fell under the rear wheel; left hand blown to ribbons when one of his bombs exploded prematurely.  That sort of thing happens much less rarely nowadays because kids are glued to their devices rather than out testing the reality of the world.  No matter how graphic the graphics, nobody dies in Grand Kill Zombie Apocalypse IV.  I suggest that this is a Bad Thing; early experimentation teaches care and attention and a handiness with physical things. We need 'a good pair of hands'; we need a lot of them indeed if we're to have a future as a technological nation.  It's not going to happen if we protect children too much from making mistakes. Robin McKie has a passionate polemic about this quoting from his own experience of blowing up his bedroom and Alec "DNA fingerprinting" Jeffries growing a beard to hide the burns on his face.

Today is also the birthday of Robert "Burner" Bunsen, unless it isn't: he was definitely born in March 1811 but not even he was sure if it was the 30th or 31st.  No matter, he grew up when Chemistry was at its most exciting. The first synthesis of an organic compound (urea) was carried out in 1828 and Bunsen grew up into a world where everything was waiting to be discovered.  Nowadays 500 new compounds are being developed described and named every week; but it's not possible for a teenager to make a wholly novel contribution; the frontiers have moved away from a cupboard in a bedroom. Wolfram maintains that the frontier is present for youngsters in the world of big data. But that's not direct 'good pair of hands' reality. Bunsen's career was notably peripatetic: born a son of the chief librarian at Georg-August-Universität Göttingen, he held faculty positions in Göttingen, Kassel, Marburg, Breslau, and Heidelberg. Nobody doubted that he was smart - he was awarded his PhD at the age of 19! - but he was also notable for the rich network of collaborators and correspondents that he built up.  He was famous for the quality of his teaching and his students, including the dreadful Fritz Haber, loved him.

His earliest work was assisting at the birth of organo-metal chemistry, especially compound of arsenic which were notoriously smelly, toxic and in some cases unstable.  His position at Kassel was inherited from Friedrich Wöhler, the chap who carried out the laboratory synthesis of of urea. Bunsen continued the great man's work on compounds of  tetramethyldiarsine [L] which had been named cacodyl [foul-smelling oil] by the great Swedish chemist Jöns Jacob Berzelius. Bunsen noted "the smell produces instantaneous tingling of the hands and feet, and even giddiness and insensibility. It is remarkable that when one is exposed to the smell of these compounds the tongue becomes covered with a black coating, even when no further evil effects are noticeable". He spent years living in a miasma of garlicky pongs which might have prevented him getting married.  More importantly, one of his cacodyl experiments exploded [I did mention 'unstable'] on him and destroyed the sight of one eye.  One of the developments of all this basic science was an effective antidote to arsenic poisoning.

He's known now for his eponymous Bunsen Burner which was the first widely available, controllable, safe, clear, hot, flame for use in laboratories.  But in his day, in collaboration with Gustav Kirchhoff, he was known for his work in spectroscopy - the analysis of the wavelengths of light absorbed and emitted by different compounds. They appreciated that you could only get good crisp results if their samples were of high purity, which they had the determination and application to achieve. Bunsen knocked off the distinctive spectral lines of lithium, sodium and potassium.  Afterwards he noted that mineral water from a spa at Dürkheim produced spectral lines in the blue range of the visible spectrum.  In a monster analysis worthy of Marie Curie discovering radium, Bunsen reduced 40 tonnes of this water to 17g of a pure new element that he named caesium.  The following year, he completed the alkali metal column in the periodic table by isolating rubidium.  That's what it was like in those heady far-off days, you could discover a new element.  It wasn't easy, you had to work hard, you had to have creative solutions to intermediate problems, but new frontiers were on every side.  In 1877, Bunsen and Kirchhoff were awarded the first Davy Medal by the British Royal Society for their work on spectroscopy. Their investigations opened up the world of astronomy by noting that spectral decomposition of the light of stars could be replicated in the flame of a Bunsen burner in a laboratory.  So elements could be identified in places that were far beyond the reach of human hands. Bunsen never became rich, because he had no desire for money or for 'stuff', he refused to patent any of his inventions because that seemed to inhibit the progress of science. Hats off!

Tuesday, 29 March 2016

Very like a camel

Last year, I was sweeping off my hat and showing a leg for Des Higgins and Dan Graur because they had shaken the mammalian phylogenetic tree and shown that whales are really a sub-set of Order Artiodactyla.  That was counter-intuitive because whales definitely don't have cloven hooves like the other artiodactyls: pigs [not kosher], cows, sheep, goats, antelopes [kosher]; camels [apparently not kosher despite walking in two toes and chewing the cud]; hippos [cousins if not siblings of the whales and dolphins]. The lesson from the whale family-history is that we should be careful not to focus exclusively on the obvious: flippers, blow-holes, blubber and give some weight to the structure of the molecules that hold the body together and make it tick. Enough of whales: dey soooo wet.

Today, Camels!  Because I've just learned something about them that was a bit of an eye-opener.  There are more than 200 species of artiodactyls but the Family Camelidae has only 6 members: the two remaining "true" camels Camelus dromedarius one-hump Dromedary and Camelus bactrianus two-hump Bactrian camel.  These are native to a swathe North Africa and SW Asia.  The 300,000 camels running wild in Western Australia are mostly D-camels and both sorts were introduced as beasts-of-burden by the Brits in the mid-19thC. There were a lot more camels in 2009 before a plan to cull them was implemented. Then there is a clatter of South American species:
  • llamas Lama glama the domestic form of the guanaco Lama guanicoe 
  • alpaca Vicugna pacos the domestic form of the vicuña Vicugna vicugna. 
It's probably a bit silly to claim a separate species for the two domesticated varieties although they have been tame for thousands (but not 10s of '000s) of years.

One of the legs on which Darwin and Wallace and their contemporaries stood to build the over-arching explanatory edifice of evolution was biogeography.  The geographical distribution of today's species gives important clues about how they evolved - Wallace Line, for example.  With Camelids divvied up on two distant continents, it's not obvious where they came from. It's hard to imagine them dispersing across the Pacific on a mat of vegetation. Well it turns out that neither South America, Africa or Asia is the answer.  The first appearance of two-digit walkers was in the Eocene 45 mya of North America!  These camel-like creatures grew and diversified and spread out South down the isthmus of Panama and West across the Bering land-bridge and then died out in the continent of their birth. The last camels 'went West' across the sky-bridge to heaven as part of the great North American mega-faunal extinction of 10,000 years ago; probably driven there by relentless hunting of anything bigger than a breadbox by the ancestors of Native North Americans.

What do we know about camels?  They are the ships of the desert, able to walk for days across the shifting sands of the Sahara without water.  Their feet are uniquely adapted to traction on those shifting sands, we now know that the hump is not a water bowser but filled with fat.  But we're told that in metabolising that fat for energy, water is a chemical by-product and this is recycled.  Oh yes, and they spit. About ten years ago Natalia Rybczynski was hunting fossils at the Fyles Leaf Bed in the Canadian High Arctic, like Neil Shubin, except that she was looking for more recent material than the Devonian.  She picked up a rock from the tundra, thinking it was a fossil stick and realised that it was a fragment of a fossil femur.  Over the next several seasons (!) she went to the same spot and collected 30 fragments of the 3-D jigsaw. Collaboration with Mike Buckley at U.Manchester in England used variation in the collagen molecules (you and I have 40+ different collagen genes each making a different protein) to show that this femur probably came from a camel. Traditional palaeontological techniques showed that the camel had lived 3.5 million years ago and was more than 3m tall. Despite the climate being generally warmer, it was still cold up there, then and the handful of bone fragments suggested a complete turn-around about the what and why of camels.

Maybe the broad feet evolved for walking on snow rather than sand?  Perhaps the back-pack of fat was just that, not a surrogate water-store: it supplied the energy necessary to survive through a 6-month long Winter.  Maybe not, you have to wear your skeptics hat when a journalist extrapolates from a little bone to a big neat story that can be tied up with a ribbon and presented as a TED talk.

Monday, 28 March 2016

Love your worms

I think we all agreed, with President Jimmy 'Peanuts' Carter, that Guinea-worms are A Bad Thing. But is it fair to generalise that to all nematode worms are bad?  That's a helluva lot of badness, because there are probably 1 million different species in the phylum Nematoda; only outpaced by Arthropoda with 1.1 million species.  But let's just focus on the nematodes for which humans are host and hostess; are they always to be extirpated by medicine?  I've suggested that this kill-them-all policy is definitely dodgy w.r.t. bacteria.  Your flora might help you side-step liver cancer.  If we continue to ladle out antibiotics for trivial infections, we might go back to depending on our own 'good' bacteria to fight off the Black Hats.

Take Enterobius vermicularis the common pinworm, it is remarkably common, specially among children with infestation rates of, for example, 50% in England and 29% in Denmark.  When I lived in the Netherlands in the late 1970s, they said that the rate was as high as 70%.  The Dutch obsession with Schoonmaken [cleaning] helped the spread in a very direct way.  It was customary for householders to air the bedding every unrainy morning by stripping off the sheets and shaking them into the street.  Children walking to school and burgers heading for the office would progress through a snow-storm of pinworm eggs, some of which would land on lips or get inhaled.  And so the cycle continued.  When I trundled across to Boston for graduate school, I had several thousand Dutch Guilders to pay my fees but I also had several thousand pinworms aboard. My only visit to a doctor in the US was to get a script to deal with them.  This is part of the reason why Dutch toilets often have an 'inspection pan' incorporated into the design. Pinworms are not only nearly ubiqitous but they are 'mostly harmless'.

Hookworm Ancylostoma duodenale, on the other hand, may be mostly beneficial.  That's probably putting it too strong but we have increasing evidence that asthma and allergies are brought under control if you have a hookworm infection.  An epidemiological study in Ethiopia showed that being hookworm-free made you twice as likely to by awkwardly wheezy. Like pinworms, carrying loadsa hookworms is usually asymptomatic. Ten years ago this, potentially woolly, small-sample association between X and Y was put to a more direct scientific test.  A team from Nottingham deliberately infected themselves with hookworm larvae to ensure that nothing dramatically bad happened.  If this reminds you of young Barry Marshall giving himself an ulcer by chugging a mug of Helicobacter pylori, it must be the way I tell it.  The Nottingham group then went on to infect clients at an allergy and hay-fever clinic.  hmmmm: I can find a review by the lead author two years before the Guardian report, but nothing on PubMed afterwards: maybe all the talk about the mechanism didn't yield statistically significant results in a study in the UK. The supposed mechanism is that hookworms, as part of their survival strategy are able to damp down the immune response and that this damping carries over to the asthma etc. Maybe the report from Ethiopia should be rescrutinised to see if it was just a once-off coincidence? [previously irreproducible results] The other hookworm Necator americanus was used by the Notts folk in a 2010  N=32 study for reduction of allergic asthma symptoms: again no significant effect. It worked for one chap, but that's anecdote not data and your mileage may vary.

When I was running the academic journal club in St Vincent's University Hospital 10ish years ago, one of the clinicians presented a really nifty study in this area of medicine.  Instead of using a natural human helminth parasite/commensal as the experimental infective agent, the researchers used horse nematode eggs. This triggered the expected change in the activity of regulatory T-cells and/which reduced the effects of ulcerative colitis [another auto-immune inflammatory condition] but the eggs never reached adulthood because they were in the wrong species.  Nematodes, lice, and other small-small t'ings that hang about the person are often really fussy about where they can reach maturity. I've tried and tried to track down the original reference to that fascinating study but have turned up bupkes. Maybe it wasn't ulcerative colitis; maybe the paper was a preview that never got published?

The Go To source of authoritative medical research is the Cochrane Index.  The experts who review and re-analyse previous studies of  clinically interesting/important findings have hairs on their statistical chests. They consider that using pig whipworm Trichuris suis is ineffective as a cure for any of the bloody stool trio: ulcerative colitis UC, irritable bowel syndrome IBS or Crohn's Disease CD [previously associated with changes in the bacterial flora of the gut].  While we're about it, Cochrane reckons that worm-therapy for allergic rhinitis [that would be hayfever] is a) safe but b) useless.  Where does that leave us? Resolved to keep tricking about with the bacteria in the gut rather than putting hope in the worms.

Sunday, 27 March 2016


In my piece to ranter about poaching of rhino horn, I pointed out that the price is reaching dizzying heights with a diminishing supply and an insatiable demand: somewhere North of $100,000/kg which is a mind-bending $100/g. And for what? Keratin is what. If keratin is keratin, and I believe it is, then The Beloved and I have come in for a windfall if only we can sort out the marketing and shipping to Hanoi to our medical-woowah agent out there.  Of course, our keratin isn't rhino keratin, it's sheep hoof keratin but I'm betting that nobody in The East would notice the difference in a blind tasting.

Since we offed the last of the ram lambs for chops a tuthree weeks ago. we only have ewes and hoggets on the farm and it's a while before we can shear them, so they need a bit of care and attention in the foot department.  Nothing dramatic like last year's amputation but definitely a trim and a bit of doctoring. Sheep are the very divil for limping.  If the grass is wet they get fungus between the claws, if the grass is long they get paper-cuts in the same slot, if the ground is soft the nail grows soft and covers the pad.  Ideally we'd like to run them up and down the road once a week to sand-paper off the excess but our sheep are wild and wonderful and would be awa' off to foreign parts as soon as the shepherd turned his back. The nails are, therefore, clipped with a variety of tools; none wholly satisfactory. If we did them more often we'd get better at the chore and quicker too. In the middle of last week, after 2 weeks without rain, the sheep were bone dry which makes handling them less soppy and depressing but we were promised a spill of rain in the afternoon, so we were under pressure to finish before the deluge. As it turned out it took us an average of 8 minutes for each of 24 sheep.  Some of them the size of horses and some light enough to lift with one hand.  Each had to be turned and sat down and held still for the clip. For the more docile (not necessarily the smallest), it was possible for me to work away on the front feet while TB got down and dirty with the hind legs. Then the most dangerous thing was to take a flying nail clipping in the face. With the yellow-eyed monsters, however, you can get a slashing blow from a hind-leg if you allow your attention to wander.  Kicks are, naturally, more likely if you cut to the quick. We made them all lighter by a few grams, but the spoil flew every which way, so haven't got {$100 * 3g * 24 ewes = a second hand car} to show for our trouble. Then again, nobody lost an eye and neither of us sustained a disabling kick.

Mais revenons nous a nos keratins.  As quick as thought I started to tool up to the protein database and download the keratin sequence from white rhinoceros Ceratotherium simum and the equivalent from the sheep Ovis aries, to find out just how similar or otherwise the two sequences were. Dang! it's more complicated than the fact that rhinos are members of the order Perissodactyla and sheep, like dolphins, are members of the Artiodactyla.  There's a whole family of keratins and keratin-like and keratin-associated molecules to choose from.  Some expressed in nails and hair and horn and others in the 'squamous epithelium' of the skin - when you talk of old sailors having horny hands you are closer to the truth that you think.  Oh Oh Oh, I feel an undergraduate research project coming on "Molecular similarity between sheep and rhinoceros keratins - an economic  solution to poaching in the Kruger National Park"

Saturday, 26 March 2016

Easter w/e 0316


M.I. Man

Having slagged off The Edge at the beginning of the year, I was then grateful when they gave time to hear what going down in Stephen Wolfram's mind. I'm not changing my stance on The Edge which has a tendency to be exclusive and self-regarding but they do attract some remarkably clever people and when clever people get round a table to talk interesting ideas are likely to be generated.  It's part of the creative process, half an idea is better than no idea: it's a hook or a foundation for developing a whole [new] idea. In the same recent week that the Wolfram interview was published John "Edge" Brockman talked to Howard "Multiple Intelligence" Gardner.  In both cases, Brockman has modestly edited out all his questions and contributions to leave a soap-box for his invited guest. As with Wolfram, you have the choice of a video [no noddies, no car-chases, no fluff, no commercials] or a transcript for those who can read beyond 140 characters without getting fractious or falling asleep.

One of the noticeable things about listening to Stephen Wolfram was the frequency with which he claimed to have worked for a long time and with focussed attention on such-a-project; and how after a few years mollocking ideas about and bringing in collaborators and gophers, he moved on to the next best thing. I'm similar in that I have a lot of interests and the attention-span of a gnat; different in never having brought much to a conclusion. I've only, after all, had three good ideas during a life-time in science, and one of those was probably wrong.  It's similar with Howard Gardner whose idea and book about Multiple Intelligences MI was written more than 30 years ago and is still hanging round his neck as the only idea of his which has reached popular culture. Ken Robinson in his inspirational deconstruction of the Western educational system, noted that there should be more to education than reading, riting and rithmetic; music and dance, and getting on with folks, for starters. This was the core of Gardner's MI idea.  He enumerated eight 'intelligences' which could have been better described as skill-sets or talents. Others identified more, or less, of these incommensurate faculties/facilities.  The spectra/range of these attributes are not completely independent are they? Everyone knows, for example, super-talented musicians who are also ace mathematicians.

ANNyway, for Gardner MI is soooo yesterday and he'd rather talk about his latest project LAS21 - Liberal Arts and Science in the 21stC.  This talks to stake-holders in 10 Liberal Arts colleges across the US - from coast to coast including the Midwest; big and small; famous and obscure; expensive and [comparatively] cheap. The stake-holders include students: prospective, actual & graduated; parents; faculty; administrators; trustees, alumni, benefactors; recruiters, employers.  Each college yielding 200+ interviews = a big dataset of news and opinion. Turns out that there are (embarrassing?) 'misalignments' among the stake-holders: all the Presidents affirm that they turn out 'good, well-rounded,  citizens' but such a concept isn't even on the radar of students or parents: they think it's about getting a nice job or a seat on the board from their four years of fees. Other evidence indicates that, although students get through a lot of late-night life-the-universe-and-everything talks; a lot of sex (and fewer condoms); case after case of beer; they don't really finish up smarter or more knowledgeable [they are different attributes!].  I was a lot smarter when I was 12 than I was for the next 10+ years - those hormones take their toll. And my friend Speedo ablated millions of neurons by drinking a bottle a day in college. We really don't encourage original enquiry in students even college-going students - we're too busy giving them bouquets of dead men's flowers: Kepler's Newton's Boyle's Hooke's Laws; π, φ, e, Planck's constant and Avogadro's number; specific gravity, specific heat, speciation both chemical and biological. All this information makes kids feel like dwarves rather than giants. Wolfram makes the point that with big data, so easily accessible over the WWW, anyone can have an idea, a question, that can be answered with a few [dozen] lines of code . . . that has never been addressed before by anyone.  You see this stuff all the time nowadays: showing the fascinating trends by cross-referencing tweets with GPS or Google queries with gender.

You really should tune in to Howard Gardner, he's been in Harvard and thinking for more than 50 years, so he's been able to bat his ideas off smart and engaged people;  he's got a lot to share and projects in the pipeline.  As he admits, he wants to use his brain but he also wants to make a difference: make the planet a better place for his having walked its shorelines. He's savvy enough to realise that making a difference through learned tomes and peer-review papers is slow going: you've gorra get down with the social media.  I'll be checking out his and his Professional Ethicist blog.

Friday, 25 March 2016


Stephen Wolfram, [Bloboprev] who has good claim to being the smartest man in the room during most of his daily existence, has just been interviewed on The Edge.  He talks for 100 minutes. With transcript! if you're the least bit nerdy or interested in AI, you could do worse than skim the transcript.  If you like your edutainment without few car-chases and a blizzard  of ideas, then do the video. Towards the end of his piece to camera he asks if there is any evidence that there is intelligent life on our pale blue dot as viewed from space.  We all now acknowledge that you can't see the Great Wall of China from the moon, it's too narrow and wiggly.  When NASA sent it's exploratory landers to Mars, they included some tests to see if life-as-we-know-it exists on the red planet.  That was a very narrow definition/imagination of life - as the ability to metabolise glucose - which we would be ashamed of today.

One of the ideas that Wolfram develops in his ramble across the universe is that big data and computer literacy such as is encouraged by CoderDojo has been highly empowering to young people. Their effective coding ability can ask, and answer, questions about our world which would have previously been only addressable by academics with access to a big library and decades of experience and accumulated knowledge.  The image [L] of the distribution of Norse Placenames was generated by the British Museum and it's wonderfully informative - there is Danelaw after 1000 years.  But that sort of insight could be generated by dozens of 13 year old data-minors.  Of course they are more likely to map the density of Justin Bieber tweet-tribs than the history of the Vikings but the point is that original, interesting research is available to people who haven't been to college and don't have The Calculus or Ulysses under their belts. My pal El Asturiano sent me some wonderful mappy links a couple of days ago: a zoomable map of the Roman World from the Austrian Institute of Technology. And Harvard's equivalent.

Wolfram goes from programming to the Turing Test for evidence of Artificial Intelligence to the wider question of the planet. Who better to ask about evidence of purpose or structure or intelligence on the face of our planet but a bunch of astronauts.  They didn't mention the Gt Wall of China, of course but rather a) a curious straight line across the Great Salt Lake in Utah - which is caused by a man-made causeway that separates the two halves of the lake into different microbial communities b) a curiously precise circle around Mt Egmont/Taranaki in NZ which is due to differential grazing either side of the perimeter fence of the national park.  Other examples include straight lines of lights along the trans-Siberia Railway and on boringest 150km road across the Nullarbor Plain in Australia.  I've always thought Nullarbor was an aborigine word but it's straight Latin: Null-Arbor = the treeless.

You don't want to confuse regularity (straight lines, circles) caused by 'intelligent life' with regularity caused by pure physico-chemical effects. This has been a problem in trying to find evidence of early life in rock-strata which are much are well over a billion years old.  Perfectly spherical microscopic objects don't answer but fossilised  'tetrads' [L] in ancient rocks are most likely to have arisen in the course of two cell divisions to make four identically sized cells still stuck together in this characteristic pattern.

Thursday, 24 March 2016

Loscoe 30 years ago

I don't think anyone would put Loscoe forward as the prettiest village in England. When coal measures were discovered nearby, the weaving and farming community saw a huge increase in population as miners and the families moved near to the pit-heads where they worked. The last pit closed in 1970 when it was no longer turning a profit for the owners. In addition to the mining a large oval hole in the ground was excavated to service a brick-making facility, but this business was also closed in 1971.  The convenient hole in the ground was licenced for landfill shortly thereafter, initially for inert waste and hard-core but later for 50 tons/day of domestic waste as well. Domestic waste was/is any old shite that householders don't want anymore.  Disposable diapers, for example, appeared in Britain in 1976 just after The Boy was born and we were able to discard the bucket of steeping cloth nappies.  Chicken carcases, vegetable peelings, unfinished plates, old paint tines, plastic, lawn-mowings: if it would fit in the bin it was destined for landfill.  The onlt way this has changed in the last 40 years is that we have increased the amount and diversity of our trash.

The local council knew there was a problem with gas seepage in the mid 1980s as cracklines appeared on the surface associated with dead grass. They also recorded an increase in soil temperature as a) methanogenic bacteria converted solid/soiled organic matter into methane CH4 and b) methanotrophic bacteria scarfed up the methane and made a living that way. Methanogens are present in the rumen of cows and in the digestive system of mammals in general. They allow young men to set fire to their farts.  Methane is a potent greenhouse gas and it is being driven up by cow belches as more and more land is given over to feedlots for McDonalds; but bovine contributions are in the ha'oenny place compared to termite farts as they digest wood in what remains of tropical rain-forests. Despite the landfill, its smells and flies, the county council allowed more houses to be built around the site in the 1970s.

Late March 1986 saw a depression over the Peak District, the atmospheric pressure dropped precipitously 29 hPa over the night of 23/24th March. This effectively sucked residual methane, and other gases, from the depths of the landfill.  This gas took the line of least resistance migrating through fissures in the rock, old mining adits and any pipes it encountered. 51 Clark Avenue was, unbeknown to its inhabitants, sitting on a pool of methane which the freak weather drew up into the house until it was ignited by the pilot light of the central heating system.  Nobody died but the house was reduced to chips and the people were seriously injured in the explosion. Since then, efforts have been made to vent landfill and on modern sites you often see little chimneys burning with a blue flame. Occasionally, the methane is collected and converted into natural gas for industrial re-use but usually this is deemed to be not economic. In Loscoe's case, the microbes are generating about 50 cu.m of methane per hour but this is mixed with carbon dioxide and other gases, such a mix needs further processing before it is useful so it is flared off into the stratosphere. Despite lots of new legislation, it was 2011 before the first successful prosecution for negligence in gas management at a landfill site.


About 10 years ago one Saturday [+/- 2yr - can't remember, who cares] I found myself in the doctor's surgery waiting for my first MOT [general medical check-up] since leaving school.  Being a man, I hadn't made the appointment myself.  Being biddable I hadn't refused to go when The Beloved fixed a time outside of the working week. It being then considered best-practice, my GP donned a rubber glove and palpated my prostate; as well as dipping a Multitest strip in a urine sample [10 for the price of one: Leukocytes; Nitrite; Urobilinogen; Protein; pH; Blood; Specific Gravity; Ketone; Bilirubin; Glucose all at a glance.]; taking my blood pressure and a couple of vials of the fresh stuff for subsequent analysis and passing his hands lightly over my body looking for lumps.  When the cholesterol measure came back he looked at me very stern and said I was to eat fewer rashers and eggs.
"What rashers and eggs? This morning's fry was the first since Easter"
"Well steaks then, give those up"
"It was a long way from steak I was r'ared"
"Cheese then, stop the cheese"
"Okay, I do eat cheese, so I'll cut that down if you advise it although it will make me miserable and frightening to the children"
"And the full fat milk!"
"When I drink milk, I drink milk, I'm not going to pay money for chalk-water"
We compromised on half-fat milk . . . for about 3 weeks [hmmm, not to biddable, not so compliant],

Years later, I was back in the surgery for another check-up. I'd found a polyp [like Ronald Reagan] up my nose  and thought I may as well get a full MOT if I was going to ante-up €60 for a visit.  This time prostate palpation and a test for prostate-specific antigen PSA was optional because the medical community had reluctantly acknowledged that there was no evidence that either test reliably identified prostate cancer. The false positives were subjected yo needless anxiety and/or surgery, the false negatives metastasised and died aNNyway. He was also much more piano about cholesterol being driven by dietary intake and hectoring me about cheese and eggs. My cholesterol  was still as high as it had been several years earlier, so I was offered a course of statins to help reduce the bad LDL cholesterol.  As that course was going to last the rest of my life and cost money for a statistically small [but significant] benefit, I declined. In fairness, he wasn't pushing them too hard, although he himself was on them, having had a heart 'incident'.

What strikes me most forcibly about this volte-face is not the fact that fashions change in medicine as in haute couture; it's the certainty with which everyone rows in behind the current best practice. The road to truth is littered with ideas that subsequently prove to be wrong. So it's better to push your agenda and sincerely-held beliefs with a note of humility or even skepticism.  Statins are known to reduce the concentration of low-density-lipoprotein cholesterol rather more effectively than the plant stanol esters in, say, Benecol. They are biggest $$$-earner for Megapharm Inc. A desire for cartoon simplicity has taken on the idea that if LDL-cholesterol is bad, then high-density-lipoprotein HDL cholesterol must be good. Indeed a whole industry has built up to find out exactly how HDL will prevent you from a) getting atherosclerosis, b) coronary artery occlusion; c) heart attack d) early death.

Dozens of scientific papers have investigated the niceties of the mechanisms of plaque removal, widening of the arteries and other details of HDL's beneficial effects. The latest study shows that, regardless of all this work, HDL-C is more strongly associated with heart attacks and death than the opposite!  We should treat this finding with due skepticism because the lads with the high-level of circulating HDL-C had it  because they all had a rare mutation in the gene SCARB1 for the HDL-receptor. Hazy [or more likely certain] as we are about mechanistic connexions among HDL, fatty-plaques, atherosclerosis it seems possible that having a nobbled receptor is what causes the heart attacks rather than the HDL concentration per se. Watch this space; more studies, some contradictory, are coming down the track.  Heart disease is big business and Mega-pharma needs basic science to find leads for new drugs that it can sell at fantastic prices to medical insurance companies. And the food engineers are coat-tailing on this magic carpet to El Dorado. Some marketing dork had the contemptible idea of pushing rolled porridge oats as 'the fat-free breakfast' a few years ago.

Wednesday, 23 March 2016


Shortly after we moved into our farm in the mountains, my parents came to stay for a week. It wasn't perfect timing because we had committed to taking the girls off site for two days in the middle of their visit. But it wasn't wholly inconvenient either because we had an orphan lamb that was close to weaning and a dozen sheep to look at a couple of times a day. My father, not the most practical chap on the planet volunteered to feed Flossie the lamb while we were away and we set off with reasonable confidence. When we returned the following evening he was clearly relieved, so we were momentarily anxious:
"How's Flossie?"
"Flossie is fine, but where's the bloody light-switch for the kitchen?"

Woot! The position of the light-switch had been a bit of a problem when we gutted out the old farmhouse and reconfigured the rooms in consultation with architect and builder. The entry to the kitchen from the hallway was constrained by a massive central chimney-breast [L in diagram] and the 500mm thick granite rubble-in-courses outside wall [R in diagram].  We wanted to get as much light into the kitchen as possible so a) put glass in the top half of the door b) asked for a good big window next to the door.  If the door was to open against the outside wall as seemed obvious, then the switch would have to sit at the top of the dwarf-wall under the window and next to the door. At mid-thigh on and adult man, it was a convenient height for the girls who were then but little and we quickly got used to it. My poor parents, not stupid by any means, hadn't been able to crack the logic and had been cooking their dinner early before the sun went down and the kitchen was plunged into darkness - luckily it was Summer.

Where to put switches is a design thing, which is dealt with at some length by Don Norman's book Design of Everyday Things [prev], which I've just finished. Why, he asks, are the on/off switches of computers on the back of the machine?  The book was written in the 1980s, but designers seemed reluctant to put the the button front-and centre.  I can remember a generation of machines where the switch was a whole arm-length away on the side of the box. Remember IBM Selectric typewriter? Its on/off switch was underneath the machine, you had to feel for it! Who thought that was a good idea? Norman's design sense insisted on the electricians coming back to his new lab in San Diego to put the light switches a) near the door and b) so that they mapped the position of the lights in the room.

I was tribbing the design features of my Toyota Yaris the other day, partly because I been driving for a long time and car-design has improved immensely over that period. Hats off to the engineer who decided to have a split back seat in hatchbacks: so you can carry three passengers and a chest of drawers. There was a time in the 1980s when you could only achieve reverse gear on some cars [Opel!] by lifting a flange at the top of the gear lever with your first two fingers.  I first met this 'feature' in a rental car driving 500km from Newcastle upon Tyne to London in 1984. We left the motorway halfway down and pulled into a field gateway for a picnic lunch . . . I couldn't reverse out of the field!  We had to push the car back on the road and stop at a Vauxhall/Opel dealership in North London to learn the reverse engineering trick.  Norman's point about the gears would be that the solution to the reverse-gear problem was arbitrary and poorly indicated and therefore opaque to novices.  Good design for life makes it harder to do the wrong thing and obvious what is the correct action.  Don't blame yourself if you can't make the faucets or the hand-driers work in public rest-rooms. The fault, dear Brutus, lies not in ourselves but in the idiot engineer who won a prize for designing a tap that looks well and works wonk.

Tuesday, 22 March 2016

plant stanol esters

Q. What's the difference between a vitamin and a hormone? 
A. You can't make a vitamin.
At The Institute we've just started on the penultimate 'system' in Human Physiology.  The endocrine system is interesting because it acts in complement to the nervous system to maintain all the homeostatic balances that human physiology requires.  Indeed several hormones double as neurotransmitters - adrenalin for starters. It is also a bit of an eye-opener to ordinary folk that there is more to hormones than puberty and the menstrual cycle: renin controls blood pressure; without melanocyte stimulating hormone MSH, you wouldn't tan on the beach at Tramore. Nobody gets a tan on Tramore beach, they're lucky if it doesn't rain. Another remarkable feature of the chemistry of hormones is how little separates testosterone from estrogens. Add a hydroxyl radical here and lop off a methyl group there and suddenly you're sprouting an unexpected beard or breasts.

The sex-hormones are steroids, but so is cortisol/ hydrocortisone and so is the core of a) cholesterol and b) plant stanol esters.  The core is the characteristic 4-ring structure [L]; both the plant molecule and the animal equivalent have the enzymes to process this key building block.  For the last several years we've been barracked and barraged by advertisements for plant stanol esters as the latest cure-all.  Never having seen it written down I had heard it as stannol and wondered what part tin [Sn stannum L] might play in controlling arterial blockage.  I'll leave to a later, longer post a deconstruction of the truth about good and bad cholesterol and accept that plant stannol esters are a handy additive to managing your blood-pressure.
What I'm ranting about today is Benecol a Finnish petrochemical by-product food which claims "proven to lower cholesterol".

Someone has decided that Pat the Salt, my 90 y.o father-in-law, needs to have his good, bad and indifferent cholesterol managed and that Benecol is the vehicle.  He's a man who lived through WWII in the merchant marine and survived rationing in Manchester between 1946 and 1950. A very good case has been made that the great British public was never so healthy as when on the rationed diet. In 1945, adults were limited to 2oz = 50g of butter a week!  I'd get through that in two slices of toast. Neither Pat nor my own parents stinted themselves over butter after rationing finished.  As kids we used to tease my father with his half&half bread&butter.  That's what butter is: butter.  Benecol OTOH is: Water, Rapeseed oil, Olive oil (11%), Plant stanol ester (9%), Palm oil, Buttermilk powder (milk), Salt (0.9%), Emulsifiers (mono- and diglycerides of fatty acids, sunflower lecithins), Flavorings, Acidity regulator (citric acid), Flavorings, Colour (carotenes), Vitamin A, Vitamin D3. YMMV on this depending on when and where you bought your Benecol but not by much. You can calculate how much you're paying for plant stannol esters = 9% of 500g. Benecol retails at a staggering €5.99/500g so you're paying €75/kg if it's only a vehicle for the PSEs!  With the butter you're paying €4.38/kg or 1/17th of the Benecol PSE price.

It outrages me when the largest ingredient in a food product is 'water'.  You can just see  the food engineers doing experiments to see how much water they can lurry into the product and still bring it to market as a solid. rather than as plant stannol ester soup. One of the table-of-contents rules is that you have to list the ingredients in order of size. If the 3 quantified items  Olive oil 11%; PSE 9% and salt 1% are subtracted and palm oil and buttermilk are estimated at 8% together and the tail of micro-ingredients total 1% then water and rapeseed oil make up 70% of the product. Thus the best case [34% water + 36% oil] is that more than one third of Benecol is water; the rest is 'food' at a price of $16/kg: that's about twice the price of beef-steak. Foodie Michael Pollan said "'Eat food. Not too much. Mostly plants". Foodie engineers say "Eat our food products. As much as you can afford. Mostly Water".  PSEs are not part of Mostly plants, they are a teeny-tiny part of the fatty fraction of plants - seeds, nuts, oils are richest.
Here's a thought, especially if you're over 90: eat butter, 
save money, live it up for the time you have left.

Monday, 21 March 2016

Bus Wars

When Pádraig Pearse died on the cross in 1916, he left this world with a vision of a . . . Republic [which] guarantees religious and civil liberty, equal rights and equal opportunities to all its citizens, and declares its resolve to pursue the happiness and prosperity of the whole nation and of all its parts, cherishing all of the children of the nation equally . . . ?socialist paradise?  Cut off in his prime on 3rd of May 1916, he wasn't put to the trouble of implementing his broad brush-stroke vision across the cities and villages of Ireland. The actuality was set by a deeply conservative civil service bureaucracy and a succession of opportunistic populist politicians who would promise you cake every day of the week if only enough people would vote them into a government billet.

Take public transport: an essential infrastructural component of a modern state.  You could throw that open to 'the market' and allow competition to equilibrate services and prices so that everyone is happy.  The providers make a modest profit, the customers receive and adequate service. That would be nice, wouldn't it? The thing about public transport, though, is that it requires large numbers to work sensibly.  If there is only one person in the market for a trip from Ballyhack to Ballinaboola in the morning and returning in the evening, then even a mini-bus is over-egging the pudding. If a handful want to make that journey, the fares may still not be enough to pay the driver, the petrol, taxes and depreciation on the bus.  It may then seem sensible - for social inclusion, for the planet, for efficiency - to provide this 'loss-making' route with a government subsidy.  If things are only to be run 'at a profit' then prices creep up and the indigent are left on the side of the road.  Of course, the indigent are poor but not stupid: they won't stand on the side of the road, they'll stay at home, probably in bed to keep warm.

It's also clearly desirable to have coordination of the transport system.  Some of the passengers from Ballyhack might want to travel on to Wexford and thence to Dublin. Integration of timetables, commonality of fare-structure would make it far easier for customers and also for accounting. Córas Iompair Éireann CIE was formed by the Transport Act of 1944 to integrate the bus and rail network across the Republic.  It was the state transport monopoly and the culmination of a series of acquisitions both compulsory and 'voluntary' of small bus operators. Like many of the Irish state monopolies and semi-state bodies, CIE was negligent, complacent and corrupt. Legislation was enacted to protect the railways which were notoriously loss-making, over-staffed, strongly unionised . . . and slow. Nevertheless, CIE was a good thing because it integrated buses into the transport system although the CIE buses were also expensive, and slow.  Rail served the bigger centres on a network that radiated from Dublin and buses filled in the holes - by visiting every cross-road and hamlet between hubs.  As students in the 70s it sometimes seemed quicker [and cheaper] to walk than to wait for and then take the bus.  Back then everyone who didn't own a car or have a child at foot went about the country hitch-hiking. Since then the epidemic of axe-murderers has put an end to that.

In the 1980s, the transport monopoly started to lose customers as entrepreneurs began to satisfy block demand - for sporting events, shopping binges and getting home to the farm for the weekend. The Feast of the Immaculate Conception [8th December] was the day when droves of country-folk would travel up to Clery's in Dublin for the craic and the Christmas shopping. Operators had to apply for a licence for each of these events and that was an inconvenience and an expense but more and more buses were appearing on the road in liveries other than Bus Eireann. The civil servants who were meant to prosecute these violators of the railway/CIE monopoly were quite likely to be on an unlicenced bus on Friday evening, so were not assiduous in their hunt for prosecutions.  The fines were infrequent and set off against a profitable bottom line and 'civil service buses' could be found on quiet side-roads all over the city centre; particularly on Friday evening. Dublin- Carlow- Bagnelstown- Borris- New Ross- Duncannon could be picked up under the railway viaduct on Prince's Street South for example.  I used to catch that bus, which was much cheaper than taking the car or train to Dublin, until Big Sean the driver fell off a ladder one weekend and broke his ankle. Nobody could be found to replace Sean for the wages he thought were fair and that was the end of the Duncannon Flyer. In the late 1990s buses were more widely deregulated and Bus Eireann had to fight its corner in the marketplace.  The idea that BE was in business to service the needs and desires of the travelling public was entirely alien to the board of management - they were trying to maximise return on their investment. When JJ Kavanagh started to run an express service Dublin- Carlow- Waterford- Tramore, then BE altered their schedule to run at more or less exactly the same times as JJK in the hope of draining their customers and killing the competition.  But they were also forced to drop their prices which was good for us.

The BE return fare from Dublin-Waterford (160km) is €19.50.  The fare from Cork-Waterford  (125km), essential for Dau.II to get home to the farm for the haying season, was €30! There is no railway between Cork and Waterford.  The journey between the 2nd largest and 5th largest conurbations in the country took an official 2hr20m because it dipped in to every town and village on, and slightly off, the route.  That's a speed of 50km/h which equals the urban speed limit: hardly express.

Well I'm delighted to report that has just extended their recently established Dublin- Kilkenny- Waterford route from Waterford to Cork. It's great because their fare structure is bog-simple €5 €10 €15 €20 and is the same for twice the one-way as the return fare.  2x €10 Cork- Waterford- Cork is a lot cheaper than €30 and DublinCoach is quicker too.  The rapacious goons in Bus Eireann have woken up and smelled the competition this week dropped their fare to €19.50. Imprecation:  May they be condemned to turn in their company limos and travel to work on one of their buses!

Sunday, 20 March 2016

Sport sunday 200316

How did the most sofa-bound unsporty person in The Blackstairs get to watch rugger refs ruling the mountain-size players?
No respect for those in authority?  Kurosawa's Throne of Blood


In writing about one of the most important take-downs of the way science is conducted in the modern Western world, I mentioned lunchtime seminars. These days, it is fatal to go mad on free food at lunchtime like I was a starving graduate student in my twenties - I just fall into a drooling sleep as soon as the lights go down and the younger people laugh at me.  Lunch has always been low on my list of priorities - I just throw something between two slices of bread and pop that in flour bag or a cheese wrapper. Sometime during the mad-busy daily schedule at The Institute, I'm able to find time to make a cup of tea and eat my scoff; refuelling before the next class or the next stack of lab-books to mark. The other day, I forgot my lunch on the kitchen counter at home and the sky didn't fall, I didn't develop a headache and I didn't come over all weak in the afternoon classes. At least I made/make lunch at home and take it to work and eat it. The Boy wasn't able to get his act together to do this while he was in primary school.

It all reminded me of the lunchtime seminar programme 30+ years ago in my first job at a University in the NE of England. Everyone was explicitly invited to bring their lunch, so that the hour could be multi-tasked to maximum efficiency. Even back then, I brought along a humble looking sandwich in some sort of recycled bag. One of the sideshows was watching the Head of Department opening his lunch box. He was elderly even then and expected his students and the secretary to address him as "Prof": the last person in the country to embrace this affectation with his tweed jacket. Born in the 1930s and buying his suburban home before prices went mad, he had a wife who had no need to work - and was really nice person as well. He couldn't/wouldn't/didn't cook - not even burgers on a barbecue - so his wife did all the food-prep - including Hissonour's packed lunch.

Every day presented him a different, balanced meal in a plastic box.
  1. two slices of white bread containing cheese or ham and occasionally a leaf of lettuce
  2. a piece of fruit - banana or more usually apple, occasionally a satsuma - no kumquats need apply and kiwi fruit hadn't yet been invented
  3. something else
if 'something else' was a tinfoil-wrapped chocolate biscuit then the old chap, quiet unconsciously, let slip a little moan of pleasure.  The vulgar would say something about Mrs Prof bonking the old chap on the night before or after a chocolate-biscuit dessert.  But that thought just beggared belief: who would want to sleep with a chap who wore a tweed jacket?

Saturday, 19 March 2016

Cut once, suffer much

As regular readers of The Blob know, I teach Human Physiology in The Institute. My only qualification for taking on this task is that I have a body and that I have a boundless interest in finding out how it ticks. All sorts of things, which I took for granted four years ago, I now appreciate as marvels of engineering.  We encounter bone when two heads clunk together on the sports field; or in the middle of a Sunday leg-of-lamb; or as part of a fossil dinosaur - all of these bring to mind mineral or rock rather than tissue. But that would be a false conclusion because bone, while solid, is in a constant state of turn-over, energy consumption and metabolism; why else would it be laced with blood capillaries? Embryonic development sees a cartilaginous matrix outlining the skeleton becoming progressively mineralised as calcium phosphate is laid down to give the neo-bone better engineering properties: harder, less bendy, less likely to fracture under stress. The rate and position of this 'ossification' is determined partly by genetics and partly by the environment: the more it is used the stronger it gets, just like muscles. And vice-versa: a year of weightlessness in the Space-station or a long-term spell in a hospital bed will see significant loss of bone density.

One of the most wonderful examples of bone remodelling is in the symphysis pubis [L at the 'bottom'] during labour. Like many systems shaped by evolution, the human skeleton is a kludge: trying to optimise a number of vital attributes even when they are competing against each other. In our case, over the last couple of million years we have a) started to walk upright on two legs so we can see over the long grass and carry things with our hands and b) acquired an enormous head: all the better to write The Blob with.  The pelvis has required significant remodelling to accommodate these two competing interests. For best traction in the long run after a dying antelope, we need the pelvis as a solid ring connecting both femurs and providing solid attachment for muscles. To deliver the outsize head of a full term baby [cartooned L as a fat red oval], we'd like some flexibility 'down there'. Amazingly most women achieve this: when it matters the very rigid cartilaginous connexion between the two pubic bones softens up as the constituent protein collagen is partly replaced by a protein called [what it says on the tin!] elastin. That makes a little more space, a little more give, and a marginally easier birth. It is driven by the same changes in hormonal flux that are dilating the cervix and contracting the uterus. I know two women who, after delivery, were unable to restore the status quo ante and retained the flexi-pelvis for months afterwards: it was, and is, for them on a spectrum between uncomfortable and bloody painful.  But for most women that's the way to achieve the best good enough solution: by a temporary change and then back to 'normal'. Engineering - it's often by the seat of the pants: what works sufficiently well is what we get to use.
What follows is a story of pain and outrage and 
not for the faint of heart; I write through tears.

For at least 3 decades, hundreds of women in Ireland were subjected to a procedure to speed the process of birth. In particular is was seen as a more acceptable alternative to Caesarian section in cases where the pelvis was narrower than 'normal'. In some cases, the Ob&Gyn man explicitly invoked John 16:21 "A woman when she is in travail hath sorrow, because her hour is come: but as soon as she is delivered of the child, she remembereth no more the anguish, for joy that a man is born into the world." In other words, so long as a fit and healthy baby [preferably a boy] was delivered, any amount of pain and indignity was what had been ordained. It became fashionable to do a 'symphysiotomy' [cutting through the symphysis pubis with surgical shears or a special circular saw] in the labour ward. There is no way for the pelvis to return to running&jumping mode after birth if it has been cut in half by a patriarchal goon in surgical scrubs. It was also intrinsically dangerous for the baby whose head was precious close to the cutting blade. Symphysiotomy fell out of fashion sometime in the early 1980s and the 1,500 women who were "Survivors of Symphysiotomy" SoS suffered in silence: too embarrassed to talk about things 'down there'; too meek to get angry; to isolated to seek help.

In 1999, in the course of her PhD research into the relationship between the catholic church and the medical profession in Ireland, Jacqueline Morrissey turned up too many cases of the invasive intervention to be credible as "nothing to see here, move along quietly". The current take on the debacle is that repeated caesarian section was seen as leading to a recommendation of sterilisation which was repugnant to the catholic mores of the time. The far more radical symphysiotomy was believed to permanently open up the birth canal, so that women could continue to have babies ad maiorem dei gloriam.  Dr Morrissey's finding percolated out to the media and hundreds of disabled women realised that they were not alone but had been subjected to a mass experiment in dubious birthing practice without their consent, let alone with informed consent.  There is a suggestion that 'experimental' symphysiotomy was carried out in Ireland to perfect the technique for the Third World where C-sections were not generally safe or available.  An early symphysiotomy could make subsequent births easier and less likely to indicate a[n unavailable] C-section.  Whatever the validity of this position, it wholly down-played the subsequent and continued pain and discomfort of the mother.

After the scale of the problem surfaced, there was a predictable closing of the ranks by the Health Service and the Institute of Obstetricians and Gynaecologists (IOG). If you couldn't supply paper-work in the form of hospital records [from, say, 1952!] then your claim was either thrown out or subjected to hoop-jumping scrutiny that tended to exclude equivocal cases. The fall-back position was that symphysiotomy was normal best practice at the time. That was rejected by anyone who took the trouble to look at the data from Sweden or the UK or anywhere else but New Guinea or the Congo, where special conditions applied. A redress scheme was reluctantly instituted in which women who had unequivocal proof of the intervention could claim compo. Pay-outs of €50,000, €100,000 or €150,000 were made, mostly at the lower end of the wholly arbitrary scale. You can see why a cash-strapped exchequer would want to limit access to the funds: 1,500 women x €50,000 is €75million! Why, that's [slightly] more than we pay each year to keep our 200 haemophiliacs in working order. The women were also expected to indemnify the government from any subsequent legal action if they 'took the soup' and pocketed to €50k. Such muzzle clauses are repugnant to natural justice but also to the UN Commission for Human Rights. The Redress Scheme stopped entertaining applications at the end of 2014. Earlier this year, they started to wind-up its affairs and announced that it would shred their accumulated symphysiotomy records this weekend unless individual SoS women came to collect their papers in person from Hawkins House in Dublin city-centre.  SoS and others are objecting to this 'extinction shredding is forever' action and are trying to put a stay on its implementation.

The shredding sounds like further evidence of cover-up and obfuscation by The Man . . . until you hear that the Redress Scheme records are copies of the original files held by the HSE. Nevertheless, here is a valuable consolidated record of a sorry story in the history of modern Ireland that would be useful for research and investigation by historians, statisticians, epidemiologists, human-rights activists. Therein lies the rub: who should/will get access to these highly personal and emotive records?  You've got to have some sympathy for The Patriarchy: damned if they gather and store personal data for no clearly defined reason and damned if they destroy personal information lest it be misused by Johnny Whoever down the line.

Wiles lands another goldfish

Even if you'e crap at maths you know there are many, many solutions to this equation: a2 + b2 = c2 It's the Pythagoras, silly! 3,4,5 triangles for anyone who has tried to square off a building etc. The great 17thC French mathematician Pierre de Fermat wondered about when the exponent/index n is greater than 2: an + bn = cn and in 1637ish famously proved to his own satisfaction that there were no such cases. He neglected, however, to tell anyone else his answer to the problem! That conjecture or theorem sat there for the next 400 years in the consciousness of mathematics like grit in an oyster - making the quants develop rich and beautiful ideas while marshalling their evidence towards a solution to the puzzle. About a year ago, I tribbed true Brit Andrew Wiles for finally slotting the last piece into the ragged and extensive jigsaw that had grown out of Fermat's Last Theorem with a proof that satisfied not only himself but also the mathematical community at large.

It didn't make the RTE news because Wiles doesn't come from Athlone, but I'll share with you that Professor Sir Andrew Wiles KBE FRS has landed the 2016 Abel Prize.  The Abel was set up at the turn of this century as an antidote to the fact that Alfred Nobel didn't institute a prize in mathematics. It's worth 6 million kroner [€635,000/$715,000] cash. It is just the latest in the tribs that have rained down on Wiles's head since he used it to crack The conundrum of recent ages.  Before the Abel there were: Whitehead Prize (1988); FRS (1989); Schock Prize (1995); Fermat Prize (1995); Wolf Prize (1995); NAS Award (1996); Royal Medal (1996); Ostrowski Prize (1996); Cole Prize (1997); Wolfskehl Prize (1997); King Faisal Prize {1998); Clay Research Award (1999); KBE (1999); Pythagoras Award (2004); Shaw Prize (2005).  He was too old for the Fields Medal so they gave him, uniquely, a silver plaque instead.  Of course he's been given a shower of honorary degrees too: Warwick, Columbia, Nottingham, Oxford, Cambridge, Columbia and Yale. No better man!  But there are plenty of equally good mathematicians who get nothing but their salary.

Friday, 18 March 2016

Will eat your pet for free

The North Pacific Gyre [prev] is one of humankind's largest, ugliest and most recent creations. Eeee when I were a lad only 50 years ago chemists knew all about PET: it was invented/patented in 1941.  PET = polyethylene terephthalate. It was one of the polymers that launched the tawdry, cheap-and-cheerful Age of Plastic. Plastic brought huge utility to the Third World where it appeared in a rainbow of jugs and basins, buckets and bowls that could store food and fetch water and be easily kept clean. PET is a chemist's dream; they can make the stuff in two different condensation reactions
one expelling methanol and one expelling water from the input monomers. It is a thermoplastic: it liquefies with increased temperature. And temperature changes up and down have crucial effects on the properties of the final polymer.  Rigid, strong, infinitely durable soda bottles and cuddly warm fleece blankets are the same stuff chemically. The difference is in the temperature at which the polymerisation takes place and more importantly the speed with which the product is cooled down.
The PET bottle, formed when the plastic is rapidly cooled to an amorphous clear, rigid solid, was patented by Nicholas Wyeth in 1973. Wyeth was an engineer employed by DuPont and thought up a disposable plastic bottle that would replace glass for Coke Pepsi DrPepper sales.  After rejecting various forms of polypropylene as unable to withstand the pressure of carbonated liquids, he experimented with PET until he had developed a product that has been used in its billions. He retired a few years later so PET bottles was his last hurrah.  Wyeth?  Any relation to Andrew Wyeth the painter? Yes = brother. So I'd rather show a picture of The Brother's most iconic painting Christina's World than a billion Coke bottles.  Their father N.C. Wyeth was also an illustrator and artist not without talent.

The strength of PET is what makes it a) useful and b) indestructible.  The cost of each item is so low that manufacturers and users can afford to throw it away when empty. That's part of the reason why you pay €1 for a bottle of water (that costs 0.1c) and some mystical ingredients and a lot of sugar or aspartame to make it palatable. Whatever, a fraction of the bottles finish up in water-course and get washed out to sea where they bob about forever. If the bottle gets crushed by an idiot shark, the fragments continue to float - another advantage of PET is its low density, light weight and minimal shipping costs. Boyan Slat has floated a mechanical solution to sweeping up the fragments of our wastefulness. If you missed that boat, you can get aboard and contribute to SeaVax on Avaaz.

Another potentially useful player in the clean up process hit the blogosphere earlier in the month. Ideonella sakaiensis is a betaproteobacteria which reverses the condensation reaction that forms PET by using a pair of enzymes to ease apart the so-hard-to-break chemical bonds. We've met 'betas' before in the not-very-nice Neisseria "clap" gonorrhoeae and  Neisseria "head-banger" meningitidisI. sakaiensis was isolated by a team of Japanese microbiologists just outside a plastic recycling facility and made a huge international splash:
Une bactérie mangeuse de plastique!
бактерий, которые бы смогли «поедать» ПЭТ!
una bacteria capaz de comerse un plástico muy común!
Plastik-fressende Bakterien!
I. sakaiensis was the most successful bacteria at breaking down a thin film of PET working at 30oC. That is a regime utterly different from the cold wet salty environment of the North Pacific Gyre but knowing that the capable enzymes exist is a huge first step in scaling up a solution to the plastic dump problem. The problem with mechanical solutions to sweeping-up plastic is that the particles are so small that plankton [on which the entire oceanic ecosystem depends] become by-catch. For a bacterial predator the small size is, if anything, an advantage because it exposes more surface area to attack.  As you do, because you can nowadays, the Japanese team sequenced the genome of their star PET degrader and identified two orphan genes ISF6_4831 and ISF6_0224 which code for the enzymes that do the work. 4831 and 0224 are genomic locations, so the genes are a long way from each other but also apparently a long way from any similar genes in other betaproteobacteria - they appear to have come from nowhere.  Oh oh, I feel an undergraduate research project coming on to see where I. sakaiensis acquired it's ability to exploit a novel food-source.

Thursday, 17 March 2016

A song or two for St Patrick's

You'll be fed up with diddle-i-dee-dee music before the day is out. So here are some of my recent discoveries:
And, Irish-Americans, don't be drinking any of that green beer - it's neither authentic, nor healthy.

Wednesday, 16 March 2016

The Mensch of Malden

When the girls Dau.I and Dau.II were little and still living at home, ALDIDL would periodically sell blankets of polyester fleece under the trade-name Merediso.  They were brightly coloured, super-warm and very cheap, so I bought them each a blanket to wrap up in while they were educating themselves sitting on the sofa watching Masterchef.  We have a stack of them now; red blue and brown but I never thought to enquire what they were made of or where they came from.
Well it turns out that fleece was invented in 1979 by a company called Malden Mills of Lawrence, Massachusetts.  They took an existing thermoplastic called polyethylene terephthalate [Above for structure] and extruded it as an ultrafine fibre that could be woven into fabric. The company called it Polartec and marketed it as a synthetic wool: water-repellent, with good TOG value for its weight and capable of taking colourful dyes. It was wildly successful and helped make PET one of the most widely produced polymer/plastics in the world, in megatonnage only exceeded by polyethylene (PE), polypropylene (PP) and polyvinyl chloride (PVC).  Aaron Feuerstein, the 3rd generation CEO of Malden Mills refused to patent the process because he felt it was immoral to profit excessively from such a wonderful invention. For those god-hating readers, I put it to you that religious belief is not without value. Feuerstein was a regular reader of the Torah and took his moral compass direct from the word of god: "You are not permitted to oppress the working man, because he's poor and he's needy . . ."  He continued to make the stuff and make a lot of it, making himself wealthy and his 3,000 employees comfortable  . . . until one night in December 1995 the mill went up in smoke in a huge conflagration that vaporised the building and everything in it.  Feuerstein didn't use this as an opportunity to shift his manufacturing base to Bangladesh and slash his wage-bill.  On the contrary he called an employee meeting and pledged to keep everyone on full pay for 30 days; and then another 30 days, until the factory was rebuilt and back in production. These 'non-productive' wages cost him and the balance sheet at least $25 million. Rebuilding the factory as a going concern cost $300m insurance + $100m borrowings.

An interviewer asked him why he continued to pay the employees when there was no factory, let alone no product.  "Surely the correct business decision for a 70 year old guy is to take the $300 million insurance pay-out and retire?"
Feuerstein replied "What would I do with the money? Eat more??"  I guess you could call him, like Nicholas Winton, a Mensch.

Although most (60%) of the PET polymer produced finishes up in fabrics like Merediso - trade names include Dacron [US], Terylene [UK] & лавсан [USSR] a further 30% is used to make bottles for water and fizzy drinks.  Unless the manufacturing process is rigorously quality-controlled QC, acetaldehyde can be generated as a by-product and this dissolves in the molten plastic when it is blown into the bottle moulds.  No problem in most cases, but the market for bottled water is so enormous now that QC can get a little slack and you may well have noticed a sort of guck taste off cheap bottled water as it approaches its sell-by date - the acetaldehyde is leaching back into the water. This is one reason why fashion-accessory water is often marketed with a Hint of Lime/ Orange/ Guava/ Kumquat to mask the off-taste.  Bottled water is the biggest scam that ever duped the gullible: €1 a bottle when a generous glass of Chateau Tap costs 0.1c. The €1 subsumes the cost of manufacture and disposal of the container and having paid for it, most people have no compunction in firing the empty bottle out of the car-window as it passes over a bridge. Bottle goes bob bob bobbin' along until it reaches the sea where it rubs shoulders with millions of its sort in one or other of the Ocean Gyres.

Tuesday, 15 March 2016

Lá an Fhorógra 2016

On Easter Sunday 24th April 1916, Padraig Pearse walked out into Sackville Street from the newly occupied GPO and read a Proclamation to a small crowd of bemusedonlookers from the provisional government of the Republic of Ireland. "IRISHMEN AND IRISHWOMEN: In the name of God and of the dead generations from which she receives her old tradition of nationhood, Ireland, through us, summons her children to her flag and strikes for her freedom etc. etc.[Full text]" Even now there is a slight intake of breath at the hubris of Pearse and his slightly bonkers revolutionaries claiming to speak for God and the dead generations.  But the leaders would all too shortly be joining the entities for whom they claimed to speak, along with 450 other people, the majority of whom were by-catch of the crossfire - 254 'civilians' were killed and about 10x that number wounded over the next 6 days.

Easter was well late in 1916 and it is rather early in 2016 so there is a dilemma about whether to celebrate the week of 24th April or the week of 28th March.  The dilemma is quickly resolved by doing both - and throw in St Patrick's Day as well - because everyone wants to put on the razz for Pearse and Co. Not me, I'm with Samuel Johnson "[harrrumph] patriotism is the last refuge of a scoundrel".  Not least because it tends to precipitate war so you finish up with "A bayonet is a weapon with a worker at each end".

The number of people who were in the GPO for Easter Week 1916 has grown and grown until there were more revolutionaries inside the building than there were square feet of floor space to hold them - standing shoulder to shoulder indeed.  When the Free State was launched 8 years later, the war having been won, and pensions were on offer for those who had fought for Ireland, there was a real incentive to have been there.

As part of the 1916 Centenary Celebrations, Today 15th March has been designated Proclamation Day and schools and other educational institutions have been incentivised [prizes, project packages] to engage with the idea of nationhood by presenting historical research projects and celebrating the Republic in story, song and dance.  The Institute will be doing its bit for using 1916 to create a vision for 2016 Ireland at 2pm today in the largest lecture hall.  Followed by a reading of The Proclamation outside. I hope that nobody will have the bright idea to dress up some young chap to guy Padraig Pearse [R looking resolutely into the Leftist future] down to a volunteer green great coat and a slouch-hat.  That sort of pantomime is not looking forward to a more equable society in Ireland.  The business manager of The Institute announced the order of events a couple of weeks ago and added, wholly predictably, that classes would carry on as normal during Proclamation Day.

It didn't take long for someone to set down, in a calling-all-cars e-mail, their 1916 credentials and decry the idea that they and their class would be unable to attend because Technical Drawing 106 was scheduled for 2pm Tuesdays this term. Credentials: "My grandfather was interned in Frongoch Camp . . ." - "My grandfather carried dispatches  . . . " - "My grandmother carried dispatches . . .".  After a day of this, another lecturer plaintively asked "Can we all go?"  My (tactfully unsent) response was that you could only go if you claimed a near relative in the GPO.  But as a)  'the dead generations' were now stacked like cordwood in the smoking ruins of the GPO and b) the Irish are 'strong breeders' [except the Protestants!] and c) 3 generations had passed; there was a racing certainty that everyone in the Institute could go.  Of course I was over-egging the pudding, because the best that our German trade union rep could claim was that his ancestors might has supplied the Mausers that filled the Aud before she was scuttled of a beach in Kerry.  The best that my naval ancestors could claim is that they were aboard the Helga directing shells into Liberty Hall from the River Liffey. They weren't, but neither would my family be swimming against the tide of history to admit it.