Wednesday, 31 August 2016

Eat yer algae - it's good for you.

At the beginning of the Summer, I was walking the beach with Dau.II and Young Bolivar at Kilfarrassy on the Waterford Coast when we met a mother and daughter from the Home Education Network. Dau.II was entirely recognisable although all grown up. We stopped and chatted about the best beaches along the coast and what to do there.  It seems that while I'm scavenging fish-boxes, buoys and old rope, more civilized, or hungrier, folks are scavenging sea weed and the other family had recently been on seaweed gathering workshop with Marie Power, director [-and-sole-employee?] of The Sea Gardener.  Seems that these seaweed-pushing workshops and talks and events have been going for nearly ten years.

Fast forw to last week when Marie Power re-surfaced in the Home Ed Network [aka, in this instance, chatting to my pal Russ] at the same time as Dau.I was visiting from England. Both my girls are in the catering trade but Dau.I is of the vegetarian persuasion and is currently a Dinner Lady in a primary school outside of Stroud. It's a bit complicated but the Woowah Veggie Café where she used to work got the contract to serve healthy food to the kids instead of p'ison like chips and pizza; and Dau.I got a job in the country. ANNyway, she cares about food and the politics or food and Marie was looking for people who'd be on the same wavelength.  Seaweed isn't meat after all.  It was arranged that they'd meet in a seafront café in Tramore and compare notes.

Apart from some talk and comparing-of-notes, Dau.I came away with an Almond & Orange Bar . . . with seaweed. The seaweed was honestly in smaller type because organic seaweed mix is only 6% of the ingredients by weight. Here's the whole Table of Contents:
  • wholegrains (rolled oats, wholewheat flour, wheatgerm), free range eggs, grapejuice concentrate, milled organic seeds (flax, hemp, sunflower & pumpkin), butter, organic seaweed mix (6%) (sweet kelp, dilsk, sleabhcan), flaked almonds (6%), coconut, raisins, dark chocolate (unsweetened chocolate, sugar, cocoa, butter, soy lecithin, natural vanilla) orange juice, orange oil (2.2%). allergens in bold print.
    That's 20 ! ingredients, more or less, depending on how you count/bundle them.
Dang those bracketted ingredients! Is it even legal? If flax Linum usitatissimum, hemp Cannabis sativa, sunflower Helianthus annuus and pumpkin Cucurbita pepo were treated as separate ingredients, then butter would float to the top. And there is butter again as part of the dark chocolate; if the ingredient list means anything at all, surely they should be bundled together?  And note the Latin name for hemp and ask what is the difference between this product and the hash brownies of the flower-power 1960s.

The seaweeds (all Irish and organic) are
  • sweet kelp Laminaria saccharina is the new kale as we found with Bren Smith and his vertical sea-farm in Long Island Sound.
  • dilsk Palmaria palmata, aka dulse, dillisk, duileasc, red dulse, sea lettuce flakes, or creathnach
  • sleabhcán - it's hard to discover the Latin/Linnean binomer for this is because  "sleabhcán latin" is a googlewhack. Heck, google doesn't even offer an image for sleabhcan. I think it's the same as laver Porphyra umbilicalis perhaps more familiar from the other side of the world as nori which come to the market as green sheets with which you wrap up sushi. The Welsh make bara lafwr = laver-bread with it. More info here including this memorable (and TMI!) quote somewhat resemble the byproduct of a seal’s hayfever upon the rocks. Any algologist is invited to share their expertise in the comments.
But the proof of the pudding almond & orange bar is in the eating and we shared the 45g bar among 6 people to see what they thought. I guess, in the back of many of the tasters minds was Bob's Famous Flapjacks a bar with only 5 ingredients - 6 if you include the optional pinch of cinnamon and costing about €2/kg. The A&O-bar verdict was "sort of like a tea-brack but drier" certainly not over-sweet and with some substance to it: chewy, like.  It's hard to know when you're meant to eat it though: is it a between-meals snack, a robust dessert or something you'd have with a cup of tea? You can buy these bars direct from The Sea Gardener at €10/4 bars. that's about 5c/g or a fabulous €55.50/kg. But the Supervalu in Tramore is selling the bars, as a local product, at €2 a pop, which is only €44/kg.  That's a LOT of health. I hope that enough are sold to keep Sea Kitchen on the road. For me empowerment and education are the real value of Sea Gardener - you can find simple edible food for free on the sea-shore that will diversify your diet and help your children engage with the food that they eat.

Tuesday, 30 August 2016

blue on white

Blue on white are the GAA colours for Waterford. Despite a rather dubious affinity / connexion with the Déise, those colours don't really make my heart beat faster. In another context, blue and white makes my heart rather sink with a sense of dreadful foreboding:

The blue bits in the picture are supraglacial lakes slopping about on the surface of the Langhovde Glacier in Queen Maud Land in Antarctica. Queen Maud Land is a huge [2.7 million] Norwegian dependency taking up a 65 degree slice of the Antarctic Cake. And the Langhovde Glacier is more or less due South of the Mozambique Channel.  The worrying thing about the lakes is that they weren't there last time anyone looked. Even in high Summer, the glacier remained so cold that the Sun couldn't melt enough of the surface for the difference to be seen from above. At the moment the lakes appear to be superficial but it's only a matter of time before the meltwater pools and then starts to exploit any small breaks and discontinuities in the ice to plunge into the depths. Here's what is happening in Greenland in many places during their Summer. Moulins are tunnelling into the ice. Liquid water on top of a glacier is one thing; liquid water under a glacier is a much more worrying situation because it will lubricate the shift of more ice downhill to calve into the open ocean. Greenland shed about 1 trillion tons of ice-water between 2011 and 2014. Antarctica holds 10x more frozen water out of the ocean than does Greenland: enough to raise sea-level by 60m. Our front gate is 230m above present sea level, so we'll be fine but there will be nowhere dry nearby to go shopping. Even ArdKeen the nearest effective hospital, perched "high" above the River Suir in Waterford, would be all totally submerged [see zoomable elevation map].

Monday, 29 August 2016

Trust in the wooden walls

IN 480 BCE, the Great King Xerxes I of Persia invaded Greece to swat the annoying flea which was nibbling at the distant edge of his empire. Xerxes mustered a huge army which was briefly checked by Leonidas and his 300 at Thermopylae and rolled remorselessly on towards Athens. The Athenians sent a delegation to Delphi for advice. The answer came back "Fly to the ends of the earth. All is ruin for fire and headlong god of war shall bring you low."  Harrumph, the Athenians didn't fancy that as a resolution to their problems and pointedly asked the Oracle to try again. The second answer was more enigmatic but held out a smidgeon of hope: "Though all else shall be taken, Zeus, the all seeing, grants that the wooden wall only shall not fail". Themistocles aka The Mouth, argued that they should abandon the city itself [bummer!] and trust in the fleet of triremes in which Athens had invested so heavily over recent years. And it was so: the naval Battle of Salamis was fought later that Summer and the Athenians gave the Persian fleet a decisive drubbing. With command of the sea, the Athenians and their allies were able to permanently outflank the Persians and make the King of Kings go back home.

But that's all history. We too have trusted in wooden walls - specifically western red cedar Thuja plicata planks making the face and structure of our new woodshed. I took measurements and made calculations and asked Jim Davis the sawyer for 130 6x1 = 150x25mm cedar planks each 8ft = 2.4m long. On the same trip to the metropolis of Graiguecullen, I ordered all the other matériel [screws, bolts, nuts, washers, stock timber in various - 6x3, 6x2 4x2, 3x2 - dimensions] from the hardware-store / lumber-yard down the road from Jim's saw-mill. All the stuff from the latter shop was delivered the next day. The cedar took more than two weeks, so we were champing at the bit when the little truck came up the lane. As we unloaded I noticed that some of the planks were longer than others. I mentioned this to Jim and he said airily that they couldn't get so many planks out of the one log, so (of course) they were slightly different lengths. He also mentioned that John, the cutter at the mill, had thrown in some extra lengths gratis - I suppose on a baker's dozen (=13) argument against any real or perceived shortfall in the contract.

It quickly transpired that I had under-counted the inventory, not least because I'd imagined that the telephone poles would be left exposed, while Young Bolivar assumed that they would be boxed in with this beautiful new cedar cladding, so that was 8 extra planks used. When I set down to measuring and sorting the planks, I discovered that the shortest set were a full 3000mm long rather than the 2400mm asked for. So all the planks had to be trimmed a certain extent.  I'd fondly and incorrectly imagined that everything would come cut to length and we could just whack everything up [hammers and 65mm sunk-head oval nails] as quickly as we'd put on the roof sheeting. I wanted to minimise waste and useless scraps of off-cut, so it was a dilemma about whether to use the 3000mm planks or the 3190mm planks or the 3300mm planks [See L remainders after the structure complete]. This dilemma was compounded by the fact that the shortest planks were gorgeous straight knot-free, unshook lengths of timber that would be better off as a table than as shed-siding.
Then I realised that the spacing between the horizontal studding was such that we could make up the 8ft = 2400mm as 1600mm + 800mm and have the joint braced by a stud. That meant that we could make 3 planks cover 4 spaces [see L for pictures].  We agreed that it would be temping fate, and ingress of water to put such a joint on the outer leaf of the wall but that alternate internal strakes could incorporate a joint. And it was so: insofar as you notice the joint at all at all, it looks fine - might even enhance the authenticity. In any case, we're hoping that the lower part of the all will be most often invisible behind piles of logs from our sustainable forest.
The up-shot is that, having nailed all the cedar up, including an extra 500mm fascia at the top of the open face [see L], we have 27 unused planks including 5 lengths of the super quality stuff for a table and more than 30 off-cuts at least 900mm long which shout 'chair'. We were conflicted about the design of the fascia: should it too be hit and miss like the vertical walls or solid because we have no requirement for air circulation Up There? We compromised with the plank-gap-plank to echo the walls and cut some of the driving rain from the West.  If that lets too much rain in, we'll have to think about stapling some draft-buster plastic woven netting behind the uprights. That's all the timber installed in our new wood shed; it looks and smells gorgeous.

Sunday, 28 August 2016

The vicar who drew

A bit more respect here, please! We treat of the Archvicar of Haccombe. Haccombe is one of the smallest parishes in the Church of England and the incumbent priest has, since 1315, the unique CoE distinction of being an Archvicar answerable only to the Archbishop of Canterbury. Where is Haccombe? Just North of Coffinswell, [see map R] another microscopic benefice both about 3km outside Newton Abbot in SE Devon. In 1921, W. Keble Martin was offered the benefice of the combined parishes of Haccombe [Archpriest] and Coffinswell [Rector] and he lived and worked there for 13 years until he was promoted to the parish of Great Torrington, in N Devon. Great Torrington is, by comparison, huge with a population of more than 5,000 people. Rector has higher status than a mere vicar because the parish supports him, while vicars get money from the diocese. I get the sense that this easy job was a reward for having paid his spiritual taxes in a series of rough urban parishes in the North of England and then serving as a padre [the title given to any man-of-the-cloth in the armed forces] in France during WWI.

Keble Martin was not an idle sort of chap and spent every available hour hunting out ordinary and rare plants and recording their distribution. His interest in plants grew out of a youthful enthusiasm for moths when he wanted to know which plants served as food sources for his favorite lepidoptera. In 1939, he published the definitive Flora of Devon at the age of 62, as the storm clouds of WWII grew heavy with dread. You can pick this book up 2nd hand - to you, madam, a snip at £86! To record what he was looking at, Keble Martin drew each specimen, often digging up a representative plant to bring it home, but being careful to trek the thing back to its original habitat when he'd finished. In The Institute we have a debate about whether students should be required to draw what they see or just snap it with the smart-phones. If you draw, you can picking out the salient [we don't use that word, of course] features which are key to identifying the species, a photo can become just another smudge of green. otoh, a drawing can introduce an unwelcome sliver of subjectivity into the record. Drawing forces you to consider the thing you're looking at. ANNyway, Keble Martin drew and coloured beautifully and he was persuaded to publish The Concise British Flora in Colour in 1965, when he was 88! As it says on the tin [R showing the dust-jacket], this flora illustrates nearly 1500 different species, in a series of gorgeous plates each faced by a page of short paragraphs describing where you can find each represented plant and defining details of what it looks like. The drawings represented 60 years of careful observation. We used the book a few weeks ago to identify a strange plant in our hay-field:
Rinanthus minor L. Hayrattle
Less robust; branches short; leaves crenate; intercalary none; corolla 15 mm.; straight; purple teeth broader than long; lowest bract teeth less deep; Common in pastures on basic soils. Flo. May-June.
Hmmmm. We're probably wrong on that, so; because our soil is the opposite of basic. Maybe we had Rinanthus serotinus Oborny Greater Hayrattle. Better check things out next year when they are in flower again.
The Concise British Flora in Colour was a huge best seller: my father was one of 100,000 people who bought a copy 50 years ago.  That's good because the price is as low as £4 on Amazon. Make a suitable gift for any British teenager you know: get 'em off their devices and out getting their knees wet in the grass.

If you look carefully at the map [top R] you'll notice the Plant World Garden Centre exactly midway between Haccombe and Coffinswell. It's called Plant World because the 4 ac = 1.6 ha. site incorporates a floral map of the World [aerial pic]. The proprietors, Ray and Linda Brown, have made some effort to grow Asian plants in Asia and so forth, which I think is a nice conceit. If you visit, you can buy plants and seeds as well as a ploughman's lunch and a cup of coffee. But I can't find any acknowledgement of the geographic connexion with W. Keble Martin; that is a missed opportunity in my opinion.

Readings off-blob 280816

Last Sunday in August. I'm back to work on 1st September. There may be less time for idle reading - but then again there may not. ANNyway, here's some idle, but not easy, reading.
And IF you're going to wimp out - please don't make me read, it's Sunday, I'm exhausted, I can't multi-task and I need breakfast THEN you're going to have to listen to:

Saturday, 27 August 2016

Topping off

There is a tradition in the building trade to celebrate the installation of the top-most structural timber with a small ceremony called Topping Off or Topping Out. Old timers in many N European regions will tie a small tree to the chimney stack to propitiate the displaced spirits of place. It is common for the householder to buy a crate of beer for the workers to encourage them to finish the rest of the contract. About half the cost of a new build is the water-proof structure. Fitting the shell out with electricity, plumbing, heating; plastering and painting the walls; putting the final bits of floor down; getting the interior ceilings up, plastered and painted takes the other half. Anyone who has suffered through a building project will remember a Snag List as long as your arm: this is the discrepancy between what the builder has signed off on and what the customer thinks s/he can live with: electric sockets slightly skew; a small drip from the toilet cistern; a really terrible bit of skirting board in the second bedroom; a widening gap between the wall and the window-frame.

For our topping out 19 years ago, we invited the wives and girl-friends of all the contractors to a party with their blokes so that the men could show-off their skills. We figured that if we were real nice to the ladies, that would add a push to get the work finished. As well as a sapling on the chimney we installed small gorse bushes Ulex europaeus in both toilets because a) they weren't plumbed in yet [tsk!] b) they were in gorgeous bright yellow flower c) they smell of coconut.

Our timber shed obviously needed a roof after all the vertical and horizontal structure was installed. We were advised by the chippy that a lattice of 2x4s = 50x100mm with bird's-mouth notches attached to the wall plate crossed by 2x3s = 50x75mm would be strong enough to carry 9 sheets of corrugated steel (and a foot of snow = 1 tonne). Needless to say every visitor to the site with a Y chromosome 'helpfully' told us that was far too much timber; that corrugated steel effectively supported itself; and that we had been gypped about the price paid. These same people were also happy to sound off about the orientation of the shed - why not build it facing East? with steel up-rights? with concrete footings? with the roof at the bottom? ANNyway we went with the chippy, whose parting shot was advising us to sandwich a layer of roofing felt between the 2x4s and the 2x3s "unless you prefer to be dripped on from above?". These structural timbers were meant to be on 3ft = 900mm centres but because of an inventory cock-up [oops] they finished up 1100mm apart - and still looked over-engineered to the know-alls. From the last shed we re-roofed 9 years ago, we had a bucket of 75mm roofing nails, and I dearly wanted to use them up toenailing the timbers together. But it was easier and stronger to use the same 5,0x100mm screws which we'd used to attach the horizontal wall timbers to the telephone poles.

One of our kinder neighbours is a recently retired roofer [R - at work] who offered us an hour of his golf-time on Saturday to get the first sheet of corrugated steel up "properly - once you have the first sheet up, the rest fall into place".  That first sheet brought home to us that the building is not quite square. If you put the sheet's long-edge against the end of the 2x3 supports and sighted along the short edge, you could see that there would be no overhang at the far end of the building. Accordingly we aligned the short edge and trimmed off the 2x3s so they looked correct. Having screwed in the first sheet, our resident roofer stayed up there and made Young Bolivar and me pass up the next sheets one-by-one while he tacked them in place with hex-head self-tapping roof-screws. Wup wup wup and up they went.  It took about an hour before he deemed the rest of the task to be within our competence and he sailed off to the golf driving-range. Just having the extra pair of hands was useful - those 12ft sheets of corrugated are not so much heavy as awkward and sharp at the corners. Roofer warned us not to leave the sheets partially secured! The next gale would happily peel them off the roof and leave them 2 fields away in a mangled heap. Young Bolivar spent another hour tiptoeing about the roof putting another 100 roof screws in; while I sank back exhausted and called for tea.

Friday, 26 August 2016

pain paracetamol placebo

I'm an aspirin man myself [prev]. If I feel a headache coming on, which happens about once in two years, I pop a single Disprin ("soluble aspirin, the sort doctors prefer") and that will frequently head the headache off before I start weeping. therefore know nothing about chronic pain except what I see, hear and read about. The other sort of supermarket-available analgesic is paracetamol aka acetaminophen marketed as Tylenol (USA) Panadol (RoW) or Calpol (kids who like the added sweetener) And 100 other names in niche markets.  Unlike aspirin, paracetamol has no anti-inflammatory action; indeed its mode of action at all at all is a bit of a mystery. Nevertheless it is on the WHO list of essential medicines for a basic health care war chest.

In September 1982, when I was living in Boston, 7 USA people died after taking Tylenol capsules which had been deliberately adulterated with cyanide. There was a huge nationwide flap and all Tylenol packets in the country were taken off the shelves by MacNeil Consumer Healthcare, a subsidiary of Johnson & Johnson  aka J&J. Within a couple of months, the product was back on the shelves in tamper-proof triple packaging which is much harder for arthritic people to access.  Nevertheless, long-time consumer loyalty saw Tylenol's market share bounce back to almost pre-1982 levels. It wasn't the sort of event that would make folk change from aspirin though. Oh yes, and don't give paracetamol to your cat no matter how much she asks; cats lack the enzyme glucuronyl transferase, which breaks down the drug, and are likely to die from asphyxia because their blood can no longer carry oxygen. It's a bit like collie dogs and their adverse reaction to ivermectin.

Actually, don't bother to give paracetamol to anyone! Because a recent Cochrane analysis on several hundred people shows that it is no better than placebo at reducing subjective lower-back pain. The Cochrane Index are the Go To people for unbiased, authoritative advice about the efficacy and safety of medicines and medical devices. Cochrane has featured before on The Blob. If it's no good for lower-back pain, it is unlikely to be good for arthritis or headache or whatever-is-annoying-yourself. If one of your family secretly replaces the J&Js with M&Ms in the same bottle, you won't notice the difference. Then again, M&Ms are probably more expensive gram for gram than paracetamol, which costs 1c/US per pill in the developing world.

Then again then again, is paracetamol really as safe as it's made out to be? The trouble with legacy meds is that they have been on the market for so long that they have never been through the rigorous approval process required by the FDA for new medicines. They are generally recognised and safe and effective GRASE. Although, as we saw recently with hand-wash, the FDA will sometimes go after a seemingly innocuous omnipresent product.

We know from the essay "How not to commit suicide" by Art Kleiner in Co-evolution Quarterly [bloboprev] that overdosing paracetamol is a particularly grim way to off yourself.  Unlike cats, we have the enzymes used to process paracetamol and one of the break-down products N-acetyl-p-benzoquinoneimine NAPQI destroys the liver. So when you wake up from your suicide attempt, surrounded by your anxious loved ones, feeling like giving life another go, you find that you have sustained fatal liver damage . . . and have about five days left. That's deliberate o/d, and no amount of legislation is going to stop someone with reasonable resolve from acquiring a sufficient dose. Some effort is made to reduce the likelihood of accidental overdose / toxicity: notably by restricting the amount you can buy in one go. In Ireland this is 12 x 500mg in supermarkets and 24 x 500mg in pharmacies; it's slightly higher elsewhere. The recommended maximum dose is 3g/day, so you'll have to go to Lidl every other day for chronic pain relief. 10g/day puts you in the range of a toxic dose (YMMV), so there isn't much wriggle-room. These simple interventions in the free market have significantly lowered hospital admissions for overdose.

That's the blunt trauma end of adverse effects. What about chronic use for chronic pain, how does that stack up? Quoting from the Cochrane Blog previous cited: "paracetamol is associated with increased mortality, cardiovascular adverse events (fatal or non-fatal myocardial infarction, stroke, or fatal coronary heart disease), gastrointestinal adverse events (ulcers and complications such as upper gastrointestinal haemorrhage), and renal impairment".  You should really make the effort get yourself 'informed-consented' about the actual risks of these 'adverse events' compared to several decades sucking up the pain like some stoic philosopher in a toga.

But will someone please bring to market that placebo that works as well as paracetamol and leaves your liver alone? Placebo works! A lot of research has shown this: Injected placebos are better than oral placebos. Huge placebos are better than tiny ones. Red placebos are particular effective. This is one aspect of the righteous onslaught against homeopathy by the likes of Simon Singh and Ben Goldacre. They insist on a standard showing that homeopathy is better than placebo, because that's the gold standard in scientific case-control studies . . . and then don't offer placebo as an acceptable option on medical prescriptions. So the demonstrable positive effect of placebo on health and well-being is effectively driven from the market and multinational megapharm moves in to fill the void.

Thursday, 25 August 2016

Something's wrong here

It's strange how the mind works . . . ahem fails to work properly.  We are going great guns on the wood shed first mentioned when it was little more than 6 poles in the ground, more or less vertical. We have the wall-plate (6x3s = 150mm x 75mm) at the top of the poles and the skirt (6x2 = 150mm x 50mm) at the bottom. These structural members are bolted through the telephone-poles with 12mm threaded bar which is trimmed to size after it has been seated all tight. Between the top and bottom, we put in 3 runs of 2x4 = 50mm x 100mm for horizontal studding.  I'll talk about the roof at another time; but it is also up to provide a conveniently dry workshop for cutting and fixing the remaining timbers.  These are 130+ vertical 6x1s in western red cedar Thuja plicata which felled out of a great estate in Adare Co. Limerick and milled to size by Jim Davis in Graiguecullen across the river from Carlow.  Say what you want about planter scum the Anglo-Irish, (ahem, my people), but they did play a long game when it came to planting trees. I love the idea of using such a tree rather some nameless lengths of pressure-treated generic wood from who-knows-where.

Anyway, we've spent a few days cutting these 6x1s to length - because of the slope on the site we have two different fundamental lengths and the outside leaf of our hit-and-miss
is longer and has a water-shedding external drip point - see diagram [L] of skirting with two sandwiching 6x1s bearing in mind that inside and outside are only partially in the same plane [see above]. Now there is a helluva lot of bounce in a 12ft = 3.6m length of 4x2 if you're trying to hammer a nail in. So we found it convenient to brace the walls with a wedged spar forming a hypoteneuse between the ground and the wall; and/or brace an off-cut between the point of nail-impact and, say, my capacious pectorals.  That provides an additional lump of inertia against the driven nail.  The most useful piece of kit apart from hammer and nails is an old plywood packing crate that you can stand on to get an additional x y or z of extra height.

I was hammering away like a zen master - we're using 65mm sunk-head nails #210/kg - when unbidden the thought came that a perfect fool might start the blunt end of the nail into the wood. Just then Young Bolivar turned round and said "You've put that one in the wrong way, why aren't you wearing your glasses?". Some part of my mind had been flagging the fact that I was going at it arse-ways but without sufficient imperative for my executive brain to pay attention. Shows I can whang a nail in any which way.

It reminded me of more serious consequences for a disconnected brain. More than 10 years ago, a new family appeared on the Irish home education block. This was good because new people, new ideas, new approaches are to be welcomed. As well as being a new face, the Fear an tí was an engineer for one of the multinational computer companies . . . he might be the chap on whom I could foist the website for our home ed disorganisation. He sort of agreed to do this but nothing active happened in taking up the task. Several months later, we met again: his arm was in a brace and he was limping and had a copper-fastened excuse for not getting down to the HTML:

His kids had been learning about aerodynamics and fluid turbulence by flying a kite. The kite had gotten tangled with some over head wires and the children were roaring at each other and throwing sticks ineffectually at their learning tool. Their father, who was trying to work-from-home, went out to quell the disturbance and got engaged in the problem.
What they wanted, he opined, was a really long stick.
The kids rushed off to find that really long bamboo that's behind the garage.
It wasn't near long enough.
What about if we put out the step-ladder and poke with a couple of extra meters of height?
Still short.
Then The Da had a brain-wave: he remembered the telescopic loppers that he'd bought in the innocent belief that he'd get round to pruning tops of the leggy apple-trees.
As lifted his unused aluminium garden toy tool, the better view from the top of the ladder made him look across the fields to a transformer attached to one of the poles further up the line. His engineer's brain wondered whether that was a 10kV transformer or rather a 20kV job.
The next thing his children saw was their father making a meteoric (flames, blue light) descent to earth to lie there smoking. Obviously he survived: with skin grafts and months of physiotherapy his doctors were hopeful that he'd get 40% function back in his dominant hand.

It all goes to show that you can be a rocket scientist - or an IBM engineer - and still be as thick as pig-dribble in a different compartment of your brain. See my near-death-experience in the lab or foolish remarks to, or about, female students. Then again Isaac Newton, who could claim to be the smartest man ever on the planet, cut a new smaller cat-flap in his door when his cat had kittens - or did he??

Wednesday, 24 August 2016

Sporting nonsense

Three years ago, I wrote Ranking University - abolute bloody nonsense: exposing internal inconsistencies and flabby reasoning in the Sunday Times List of Universities. I should have been less critical because The Institute was deemed to be Top and the administration has been crowing about it ever since. But nonsense is still nonsense especially if it agrees with your prejudice. Three decades ago, a fellow graduate student at BU asked rhetorically "When is athletics going to embrace the idea of statistical significance?" As an evolutionary biologist, he couldn't see how, if two runners are a hands-breadth apart after running 200m, one was deemed to be faster than the other and get a gold medal. Wouldn't it be more sensible, and sufficiently accurate, to say that both were extremely fast . . . way faster, for example, than my sofa at terminal velocity. Why, for example, do we arbitrarily take the first bit of anatomy over the line to define winning? Why not the last toe that might favour shorter people. The IBU specifies the first part of the first foot across the line as the defining criterion.

Here's an interesting piece about accuracy in sports, coming via kottke. Tim Burke says This Is Why There Are So Many Ties In Swimming . . . it's because of engineering tolerance in the design of swimming pools. We've just built a shed using telegraph poles as the main vertical members. These beasts are all different diameters, obviously tapered and some are slightly bowed. They are buried in a hole 90cm deep back-filled with 804 gravel aka 2-down. We wanted the 7.5m x 2.5m structure to have parallel sides and be square, but when it came to the, definitely square, corrugated iron roof sheets, we were about 5cm = 2% out of true. Bummer! but not shameful and structurally sound and sufficient. We had to trim the top supporting timbers on a scow, so that they looked correct wrt to the corrugated roof. We'd have lost our jobs and killed people if we'd allowed 2% error designing a skyscraper. The campanile at Pisa is 7% off.

It turns out the specs for Olympic swimming pools require the lanes to be 50m +/- 3cm long. Swimmers correctly reckon that it is therefore silly to measure speeds to thousandths of a second because at champion swimming speed 0.001s = 2.4mm: a distance far smaller than the potential difference in lane lengths. So Olympic swimmers are deemed to have tied if their clocked speed is equal to the nearest 1/100th of a second. Quite right too! Not so for above-ground events which are measured in 1/1000ths. Tim[e] Burke links to another site which investigates the relevance of the speed of sound: an athlete nearer the starting pistol will be off 1/100ths of a second earlier than his more distant rival.

Here's an interesting little essay from fivethirtyeight about the chaps who measure course for the more nebulous events: 50 km 'walk'; or the marathon.  Did you know that these guys add an arbitrary 0.1% to their measured shortest path, to ensure that no athlete in a particular event in, say, Beijing or Tokyo is able to win because they haven't gone the full distance? It strikes me as obsessively obsessive to obsess about the variables that you can measure /control and treat the unmeasurable as invisible. The XIX Olympiad in 1968 was hosted by Mexico City which is well over 2,000m above sea-level, the air density seems to have favored sprinters and the long jump but the oxygen deficit made long-distance racers slower . . . unless they came from Ethiopia or Kenya and were used to running Up There.

You can say that it is a level playing field because the rules are written down and clearly agreed by all the competitors. But it might be more sporting if Gold invited Silver to share the top tier of the podium when they were separated by a shirts-thickness at the line.

Tuesday, 23 August 2016

Bird's mouth

Mastering the bird's-mouth joint is an essential part of the training for roofers and house-framers. Sensible roofs have a pitch so that rain, and worse snow, don't sit on top of the structure but get thrown off before they can accumulate and start to penetrate the space below. Walls have to be vertical because roofs are heavy and it's better if the force of their weight presses straight down rather causing shear-stress. Likewise the wall-plate (the timber at the top of the wall on which the roof sits) should be horizontal so that the load is evenly distributed. The bird's-mouth is the way traditional carpenters cut the rafters (principal roof timbers) so that they sit directly on the wall-plate with maximum contact between the two faces [R showing how much of the contact area on the rafter is allocated to the vertical and horizontal faces.]. The joint is beefed up with a couple of nails whanged in at an angle from opposite edges of the rafter . . . or use screws if you're flush with money and don't trust yourself with a hammer.

On our wood-shed we had a slightly different problem in that we had two (front and back) wall plates, one higher than the other, and the roof is on a 20% slope. So instead of cutting the bird's-mouth in the end of the rafter, two notches have to be cut out of the long edge of the rafter [see schematic L - our roof is considerably shallower so the notch is flatter and less symmetrical] with a good deal of precision. The horizontal cuts have to be exactly as far apart as the wall-plates and the angle of the notch has to such that it sits exactly upon and parallel to the top of  that timber. Furthermore these two angled cuts in the rafter have to go through the wood so that the notch looks the same from each side. This is way beyond what my hand-saw skills are able for. One of the most useful things I learned in university was to point my index finger along the blade of the saw and hold the handle with only three fingers and the thumb. I was told this by a genuine chippy when I was helping to make stage flats behind the scenes at the college dramatic society. I can cut through a small timber at right angles so that the sawn face is all-square but angles are a different, more taxing, matter.

If you're been with The Blob from the beginning, you'll know that I don't consider myself a good pair of hands partly because I lack a certain painstaking logic in following protocols and partly because I'm a bit clumsy. When it comes to Materials, I've had to force myself to make and do things which I don't feel the least bit confident about. Any 11 year old farm-boy can reverse his daddy's 4x4 and trailer round a corner and into the yard without thinking. I have to school my hands and it takes 3 or 4 attempts to achieve the car-parking objective. Back in the day, when photocopiers were simpler, you could make paper-saving back-to-back copies by copying one side and feeding the copy back into the machine upside-down and back-to-front to do the second side. There are only 4 possible permutations here, but it would often take me 5 or 6 attempts to achieve the paper-saving objective.

Young Bolivar is a bit different: happy to saw and drill and screw and weld, especially if it involves something noisy like a circular saw or a strimmer. Nevertheless, he made a mistake on one of the cuts on his first rafter [R, we didn't throw the timber away but turned it upside down and had another go at getting the two cuts correct]. Purists will tsk tsk note that the shorter cut, which should be at right angles with the diagonal is actually at right angles to the edge of the rafter. You can just see the head of a 100mm screw awash with the vertical face of the rafter.

The rafters in our wood-shed were meant to be 4x2s = 100mm x 50mm on 3ft = 900mm centres and because our poles were 24 ft apart, I added 9 4x2s to the inventory.  I had duh! neglected to allow for the roof's weather-protective over-hang which meant that the roof was at least 3ft longer than the floor below. So the spacing was nearer to 1100mm than 900mm. But we stuck with 9 rafters because the odd number meant that we had one rafter in the centre sitting on top of the middle poles  and that meant that the roof was symmetrical; which turned out to be A Good Thing. To Be Continued . . .

Monday, 22 August 2016

Up the Déise!

The Déisi, no relation to Bellis perennis, were a Celtic tribe who inhabited what is now County Waterford between 1600 and 1200 years ago. Each county in Ireland has a defining nickname which serves to differentiate them from the short-necked louts who inhabit neighbouring counties. Rivalries, which previously might have been expressed in cattle-rieving and pillage, are now exposed with rather more violence on the hurling field. When the Waterford team turns out in blue and white shirts to moider the opposition, their couch-bound supporters cry "Up the Déise". I'm here today to sing the praises of the Waterford Coast, so the title could be "Along the Déise!".  We live halfway up our mountain, a generous hour from the port of Rosslare Harbour. In the Summer, ferry-boats disgorge hundreds of foreign tourists looking for the authentic Ireland of the Welcomes Brochures. After a punitive 22 hours on the ferry from Cherbourg, Catarina and Lazslo spend another 4-5 hours hammering along our crappy roads to The West in search of salmon, fiddles, round-towers and slaggin'. An hour's journey, over really crappy roads, would get them to the bottom of our lane where they would have access to 3500 ha. of unspoiled upland essentially the same as the hills of West Cork and Kerry.
If you're a woman, in the sense of the Irish proverb "Man to the hills, woman to the shore" then you can ignore the Blackstairs "Mountains" (hills really in the global scheme of things) and carry on along the N25 towards Cork and The West. But between Waterford City and Dungarvan you'll be by-passing one of Ireland's hidden treasures - the Waterford Coast [viewed above] : an infinitely interesting mix of geology, geography, history and silence. Sandy beaches interspersed with rocky coves, little glacial valleys and rugged cliffs, and always on your left The Sea in all her moods. Views of successive headlands, sea-stacks and promontory forts going grey with the distance; each one a source of mystery and wonder. You can see the rain stalking in from The West but know, in a Irish Summer, that the inevitable downpour won't last all day. A bit like Sherkin, but not so far to drive.

I've been reading By Cliff and Shore: walking the Waterford Coast by Michael Fewer, an account of his resolve to walk from the bridge over the Blackwater at Youghal, Co Cork to the bridge over the Suir in Waterford City. Copies are possible but hard to find. This account was published in 1992 and is primarily of interest to those who know, or want to know more about, the 200km between those rivers. It is consciously written in the style of Robert Lloyd Praeger's The Way That I Went (1937) which rambles over the whole island in an era before motor cars and 18-wheeler container lorries made walking on roads a sort of hell. Fewer's walks (he completed the trek in sections over nearly two years, with a variety of companions) took place 50 years after Praeger's and 25 years before the present time. I suppose it's of some interest to the largely anonymous people he met along the way, or their descendants: the farms and bars and B&Bs are identifiably described. There's something quite poignant in the knowledge that the young wans he encountered are now firmly - or more likely flabbily - middle-aged and the old farmers are probably dead.

Like all such commonplace travel books, the people met are given a back-drop of history as and when it seems to have any interest. A lot of shipwrecks feature for example; and well as sieges and slaughters from Cromwellian and Civil War times. Like Praeger, Ireland's most famous natural historian and rambler, Fewer knows his birds and hedgerow plants and it's nice to see that the thrift / sea pink Armeria maritima is still abundant (and wonderful!) along the road between Bunmahon and Annestown. Thrift is notable for its tolerance of copper in the soil, so you'd expect it to get an edge against the competition along The Copper Coast. The account serves as a snapshot of what things were like a generation ago. Fewer and his wife walk past Clonea Castle just months before it was demolished as unsafe, for example, so you can't see that any more. Perhaps more interesting is the evidence that the coast here is being continually eroded, the little winkly cliff-top paths disappear over a sharp edge in numerous places and, if you followed them today, more would have been lost. And a lot of more inland walk ways are reported as being impenetrably over-grown. That shows that there is no footfall in such places: everyone goes by car now.

But a good copy editor would have sacrificed a couple of pages of TMI about the particulars of the time and place. Nobody needs to know that two nice people once had tea and corned-dog sandwiches at Gortnadiha or had a spiffing cup of thermos coffee in Ballinagoul. It's more useful to clock where they got pints, you never know when you might need a pub.  All in all it makes retracing the walk along Coast of the Déise seem possible, and even desirable . . . navigating along a coast, as I found in my Portuguese Walk in 1989, is so easy that you don't need GPS, but a machete might be handy.

Sunday, 21 August 2016

Extra extra read all about it 200816

  • Here's an interesting long-form from the New Yorker with embedded cartoons about face-recognition among London policemen. Seems, as with so much human ability, it's on a spectrum from those with prosopagnosia who can't recognise their own face or anyone else's to these super-recognising cops who remember every perp they've ever nicked. Ethical, psychological and evidential issues abound. Not least in the fact that there is one CCTV camera in London for every 8 inhabitants!
  • The benefits of reading to/with your kids. Better that parking them in front of the telly or even putting them in a corner swiping at a device "And when you cannot tap the picture of the horse and watch it gallop across the page, you learn that your brain can make the horse move as fast as you want it to" Similar arguments are made for radio /wireless being better for the imagination than visual forms of entertainment.
  • Running on from the above:
    Two monks were arguing about a flag. One said: "The flag is moving."
    The other said: "The wind is moving."
    The sixth patriarch happened to be passing by. He told them: "Not the wind, not the flag; mind is moving."
    Ah so. Mumon comments: basically saying that none of them know what they are talking about because they are talking rather than being in the moment. Ah ah ah so.
  • Further to The Blob on Dengue. Here's an interesting link about predicting a dengue outbreak by checking for blips in dengue symptoms on a medical telephone hotline. Computer geeks meet medicos and deliver.
  • Today is the 30th anniversary of the Lake Nyos limnic carbon dioxide eruption that killed 1700 Cameroonians in 1986.

wood shed II

If things hadn't been so busy on the science and geography front this August, I would have blobbed on along the domestic front where Young Bolivar and I have been building a wood-shed out of wood. A couple of weeks ago I was acting all parsimonious when Bolivar cut the builder's line !! rather than untying it. But he's really redeemed himself on the off-cuts.  The design has been to sink six telephone poles into a rectangular grid to form a [ shape: open along one long side. Because the whole site is on a 10% slope and because the closed side is 50cm below the open side to pitch the roof, every pole is a different length. It was hard enough to get our eccentric local pole-supplier to deliver aNNy poles, so it was going to be a bridge far too far to ask him to cut them all to different lengths. So I asked for six 14ft = 4.25m telephone poles and they finally arrived, when I was briefly off site, about 8 months !! after I'd ordered them. 4 of them arrived cut (roughly) to size and the other two had just been fecked in on top of the pile on the bed of his truck. These two were more than 30ft = 9m long and The Beloved and Bolivar were subjected to the poor mouth about whether we'd give him €10 extra for each off-cut as he made a huge meal about cutting one of them. To stop his gab and get him off site so that life could continue, he was paid off immediately. The off-cut was nearly 2.4m long so it will serve as a gate-post in due course. We juggled and sorted the 5 cut-to-length spars and put the longest one at front-and-bottom and the shortest catty-corner opposite.

The four corners allowed us to establish the horizontal line, so that regardless of the rough ground the 6x3 wall plate at the top of the structure was level. It is scarcely credible when you see the "floor" hanging 75cm above the ground at the downhill end [R see the red ticks on a downhill and an uphill pole]. When we finally got round to cutting the long pole to size, we found that we were left with an extra 14ft pole in the off-cut for the extra €10 [win!!]. As the original contract was €110 for 6 = €18+ each, this was double win. We braced each pole with stout pegs in the ground and a hypotenuse made out of any available sufficiently long lumber screwed at each end. The poles all taper because they are milled from the living tree, so we agreed to make the outside edge vertical. But two of the poles had a noticeable bow and we'd had to fudge that. Bear in mind that we were, at the same time, ensuring that the base of each pole was still forming part of a rectangle . . . the diagonals have to be equal, folks . . . but the diagonal has to be taken from the inside edge which, because of the taper, is not vertical.  It's not as easy as building with Lego.

I thought we then had a tedious and teetering leveling job on the top of two ladders to ensure that the wall plate was level but Bolivar was smart enough and confident enough of his measurements to take the level at a convenient 'floor' and measure the vertical heights from this.  Next, we cut 5cm notches at the top of the poles with hand-saw and chisel, drilled a half-inch = 12mm hole through the 6x3 = 150x75mm wall-plate and the pole. We had a 13cm spade-bit for the drill but we needed to borrow an extender because the total depth was about twice the length of the bit. In a workshop with a drill-press you could do this by drilling precisely from each side to meet in the middle but not at the top of a ladder with one hand for your work and one hand for yourself. We had bought a lot of half-inch threaded steel bar, robust washers and nuts [L for a finished joint between two horizontals and a vertical]. For safety, we tied off the standing end of each horizontal beam while working on the other. The wall-plate on the back wall is 50cm below that in front.  The wall-plate on the short edges is horizontal with the lower side so another notch has to be cut in the front poles 50cm below the front wall-plate.
This is 'obvious to all thinking people' but we saved a bit on the 45o braces installed between vertical poles and horizontal wall-plate to stop the whole thing shearing into a pile of sticks if you lean a ladder against it. 6 poles needed 2 braces, one on each side and I thought 4ft = 1200mm would be big enough and a convenient divisor for the 4800mm stock length of 6x2s [see top imagining in diagram above]. But that would require 8 cuts and leave a lot of triangular off-cuts. No sane person would do that with 45o angles, they'd rather employ the lower idea and make 5 this-way-that-way cuts. But IF that person is thinking on their feet, and they make the braces slightly less than 1200mm but still robust enough for function, THEN you can get 5 braces out of each timber and have an off-cut long enough to be useful. With all the savings on the 6x2 front we were able to install an extra braced 6x2 horizontal between the two central poles that hadn't been on the original inventory. Win!! and now we have a nice strong central timber for when we butcher a hawg.

The base of the wall is braced by a skirt of 6x2s = 150x50mm which we stepped down in the middle [see L] to go a small way towards accommodating the fall of the land and make it easier to bolt each structural member to the middle pole. You might think this a bit daft because the poles are braced, indeed hopefully immovable, by the ground but they are robust because they will later serve as the bottom of the wall. Between the wall-plate and the skirt, we had been advised that 4x2s would be sufficiently strong to take nails supporting the vertical planks of the wall. Three runs of these 4x2s at 60cm centres were reckoned to be enough. Rather than bolting these to the poles they were fixed with massive 100mm screws, two at each end. These timbers were lumber-yard stock 4.8m = 16ft long and 'pressure-treated'. As our consultant chippy moaned, pressure-treating is pretty much nonsense because in the rush to get stuff from Swedish forest to Irish hardware yard, you can't tie up capital letting the timber dry out for months. So the pressure vessel is trying to squeeze the anti-fungal preservative liquid into a timber that is already full of liquid so it doesn't penetrate very far. Some of the timbers were noticeably heavier than others.

Although the shed is meant to be 8ft by 24ft to take advantage of the standard 8ft = 2.4m and 16ft = 4.8m dimensions used in the timber world, our shed, like Topsy, had grown a tad because the telephone poles were fatter than our original 2x2 surveyors stakes a year ago. So I needed and ordered 12 lengths of 4x2, three for each between-poles section. Like an eejit, I neglected to order a few extra on the free-delivery truck. But I'd been told that, if I travelled further than the nearest creamery and was prepared to pay a small premium, I could get better quality, more reliable timber from Declan Byrne in Graigcullen, just across the River Barrow from The Institute - 40km from home. Young Bolivar redeemed himself with cutting the builders line by scarfing together two off-cuts of 2x4 to make a single strut a little longer than 8ft [R above for diagram of a scarf joint].

So we had 2 full-length 4x2s left on the ground when we'd installed all the horizontals - win!!. You wouldn't want to have too many of these joints in your structure but you can tolerate a couple if the length isn't too great and these weaker timbers are braced by unbroken timbers on either side. Because we were learning our trade on the hoof as we went along, we found we were measuring, cutting and installing as few as 25 timbers in a working day. But at the end of each day's work we could see progress towards the final structure. Bizarrely, while the unadorned vertical poles looked impossibly tall, especially those at the bottom of the hill; when the horizontals went up then the building [it was now recognisably a building], looked kind of squat: see [L]. We're getting ahead of ourselves with this piucture because the roof-timbers are shown and I haven't told you how we fared on that part of the project. But I think you've had enough excitement for today.

Saturday, 20 August 2016

River blindness - a big challenge

The Beloved's grand-mother lived out the last 10 of her 104 years in the same darkness as Milton (When I consider how my light is spent / E're half my days, in this dark world and wide, etc.) and thereby helped our girls to realise at an early age that there were people who needed their help. Too many young people today live for 25 years or more continually on the take: it does not make them richer or better people. Despite living most of her life in tropical West Africa, the cause of her blindness was not Onchocerca volvulus, which infests upwards of 130 million people in sub-Saharan Africa. The disease is commonly known as river blindness [horrible pictures: you have been warned] because it is spread by Simulium spp. flies which prefer to breed in faster flowing streams. This contrasts with puddle-breeding yellow fever- zika- and dengue- & malaria-carrying mosquitoes like Aedes [prev and prevlier and prevlievier] and Anopheles [prev and prevlier]. At some stage the family got on the mailing list for charities giving it to river blindness, so we've been presented with lots of pictures of poor, sick, and unproductive black people [R above blind man being led by child who isn't yet blind herself].

You can treat onchocerciasis by interrupting the life-cycle in the larval stage with an anthelminthic drug called Ivermectin, which was developed 35 years ago by Merck. It was isolated from the bacterium Streptomyces avermitilis: it is chemically too complicated [see L] to imagine it having been deliberately constructed by chemists: where would you start?? That's why tapping into the delivery pipeline of evolution has been so productive and why it is worth investing in the discovery of weirder and wonderfuller killers. Satoshi Ōmura and William Campbell >!huzzah, born in Donegal, wears a green jersey!< co-discoverers of the avermectin chemical family, shared half the 2015 Nobel Prize in Physiology and Medicine. The other half went to Tu Youyou for her work in malaria.

Those of you who listen to the advertisements during Irish farming programmes on the wireless will get a tinkle of recognition at the name, because Ivermectin is effective against various parasitic worms, mites and ticks of livestock. In 1992, Merck undertook to donate as many Ivermectin doses as it took to rid Latin America of river blindness and this has been markedly successful. 600,000 cases at the start of the program have been reduced to a mere 24,000 according to a recent survey. 600,000 doses can probably be taken out of petty cash for a multinational pharmaceutical company like Merck: wholesale cost of a treatment course in the third world is 12c/US (and $30 in US, so I guess this is subsidising the good will from Merck). But it requires a different war chest in Africa - Nigeria alone has 30 million cases: 50x more than the whole of South America. Nevertheless in conjunction with the Carter Center [bloboprev], which is moving on to other Neglected Tropical Diseases NDTs having given the Guinea-worm Dracunculus medinensis a drubbing, they are making headway in Uganda and other tropical African countries. Usually the ivermectin program runs in parallel with a much more environmentally destructive, because less precisely targetted, attack on the flies. The government in Uganda just got fed up with Onchocerca's drain on the economy: in areas where river blindness has been eliminated, the production of tea, coffee and bananas has bounced back; and school attendance has started to recover as well. Bonus benefits are that other nematode diseases like lymphatic filariasis aka elephantiasis are also susceptible to ivermectin.

But here's the rub.  In tropical Africa, you might carry more than one loathsome and debilitating disease. River blindness and malaria; dengue fever and sleeping sickness, for example. That usually means that you just double the number of pills the unfortunate sufferers have to take. But IF you have both Onchocerca volvulus AND Loa loa, the eye-worm AND you take ivermectin THEN you are likely to suffer a violent and often fatal inflammatory response. Nobody seems to know the details of the mechanism, but it means that, before you start a community-wide ivermectin drive in areas where Simulium flies are endemic, you need to check who has already contracted Loa loa lest you have a case of the treatment was successful but the patient died. Loa loa doesn't exist (yet) in the New World which is another reason why the river blindness program has been so successful in Latin America. Another oddity is that collie dogs have a mutation in the multi-drug resistance gene MDR1 which puts them open to ivermectin poisoning: not all drugs suit all cases - that's why the FDA is so scrupulous in requiring testing testing testing before new products can be marketed.

Now hear this. Onchocerca volvulus, like many nematodes, harbours endosymbiotic bacteria of the genus Wolbachia, a group that we've met before [vs Zika; vs Dengue] as part of an elegant precisely targetted solution to other tropical diseases. The presence of Wolbachia is seemingly essential for the correct development of the Onchocerca larvae. It is not impossible to imagine an antibiotic which selectively kills Wolbachia and thus causes the propagation of Onchocerca to fizzle and die.  Maybe the protocol that isolated Eleftheria terrae and teixobactin is a place to start? Or talk to Satoshi Ōmura, he seems to know what to do to. There's a final year undergraduate research project in here somewhere!

Friday, 19 August 2016

Down with Dengue

As I showed in a phylogenetic tree in February 2016, Zika virus is closely related to a handful of other human pathogens including West Nile Virus, Yellow Fever Virus and Dengue Fever Virus. Dengue is a tropical disease, we're safe in Dublin, Denver and Dnipropetrovsk Дніпропетровськ. The vector only flies within the Winter 10oC isotherm and not even in all regions within those lines:
Dengue has always been with us, transmitted, like Zika by Aedes aegypti the Asian tiger mosquito. It has been on the increase since WWII for reasons that are not entirely clear but may have to do with the flight to city barrios and A. aegypti's preference for urban environments. Like other mosquitoes they lay eggs on water but Aedes is happy with a puddle, a used tire or a bucket forgotten under a veranda.

Anyway Dengue is now 30x more common than it was 50 years ago. There is no cure and no vaccination available but with palliative care and hydration therapy mortality is reduced to close to zero - 0.2%. But the number of work-days lost and general misery continues to increase. The obvious place to disrupt the viral transmission is by nobbling the vector and we've seen an example of that using Wolbachia spp. bacteria to control the fertility of males to reduce the incidence of Zika. Same vector, different disease; same technique, different mechanism. Scott O'Neill from Monash U in Australia noticed years ago that Wolbachia infection of Drosophila prevented the flies from transmitting any RNA virus. For such a tiny genome, Wolbachia has a peculiarly useful tool-kit! O'Neill has spent the last two decades trying for identify a strain of Wolbachia that will carry out the same trick in Aedes. The double-smart angle has been to get the bacteria to go forth and multiply in wild mosquito populations, so that, once kick-started, no further interventions are required. The Zika/Wolbachia story and down with screwworm drive, by contrast, required continual inputs which were profitable for the program participants / suppliers as well has benefitting the end 'consumers'.

The Monash team have had some success in filed trials. Check out the Eliminate Dengue site for details. I particularly like this approach because it aspires to being a precision intervention against a particular aspect of normal Aedes function. By keeping virus-disabled mosquitoes in place, they maintain the ecological balance. Killing the mosquitoes or preventing them from breeding [same thing really] could potentially void a niche in the ecosystem that will be filled by who-knows-what nameless eyeball-eating tropical monster.

Thursday, 18 August 2016

Line Islands, Pacific

The Line Islands are a string of atolls and reefs that cross the equator - hence the Line Islands.  They extend in the NW to SE direction on the other side of the world from here in Ireland. The Northern two islands, Palmyra and Kingman reef swear allegiance to the Flag of the United States of America, as does the outlying Jarvis island.  The swearing allegiance bit is all highly metaphorical because Kingman and Jarvis are uninhabited and Palmyra Atoll supports a rolling complement of scientists and bird-watchers from 4 to 25 in number. The other islands are all part of the micro-nation of Kiribati which also incorporates part of what was the Gilbert and Ellis Islands 100 years ago. The people all live in Teraina, Tabuaeran and Kiritimati; formerly known as Washington, Fanning and Christmas Islands, further south are the uninhabited Malden, Starbuck, Caroline, Vostok and Flint. Filippo reef charted on some atlases East of Malden and Starbuck may well be a phantom island because it isn't picked up by any of the Earth-watching satellites and numerous ships have sailed straight over it. The Line Islands feature down the rightside of the map [L with Malden Island identified as a lollipop]

Malden Is. is, in many ways, the most interesting / intriguing of the islands because when it was 'discovered' on 30 July 1825 by Captain Byron in HMS Blonde, it was named for the navigating officer Lt Charles Malden who a) first sighted it and b) went ashore for a brief exploration.  That doesn't really have the ring of truth because the first man ashore was probably a humble rating with wet trousers holding the boat steady against the surf and the first chap to see it was probably up the mast, which a deck officer like Malden hadn't visited since he was a beardless midshipman. You have to be quite high up because, although the island is about 8km across [see map R] it is as flat as a soup-bowl with a rim of dunes not more than 10m high and much of the depressed interior is taken up by a lagoon which makes up about a third of the area inside the high-water mark.

Malden and his search party, and subsequent European visitors, were amazed to find evidence of previous habitation in the form temple-flats [L all in a heap now, more structured in times past], called marae or ahu in other parts of the Pacific as well as humbler domestic dwellings. All of these structures were in ruins but the sites showed that a group of engineers had lived on the island for a substantial time in the distant past. Perhaps the dwellers on Malden were not as sophisticated as those on Eiao or Easter Island, but they clearly had a complex social structure and economy.  The wells which appear to be contemporaneous with the above ground structures are now either dry or contaminated with sea-water. Maybe there was a more substantive fresh-water lens under the surface and its failure led to the demise of the community. Is it too wild to speculate that the people sucked the lens dry and so screwed their descendants? That would be a potent metaphor for what we are collectively doing to the whole planet.

Wednesday, 17 August 2016

Elegant against Zika

I'm on a bit of a microbe jag this month and there's more to come. There are two aspects which interest me
  1. the diversity of the invisible microbiome and its interactions with the nearby bigger-than-a-breadbox world. The technology (Next Generation Sequencing NGS) for documenting this has only developed in the last 10 years. Before than we really hadn't a clue because most microbes cannot be grown on a Petri dish, so we could not characterise, name and catalogue them.
  2. precision use of particular microbes to carry out beneficial tasks instead of a blood-bath kill them all approach which takes out a lot of innocent bystanders. Like Eleftheria terrae's novel antibiotic; or Monsanto's plant-growth promoting bacteria trials.
Wolbachia pipientis is a member of the Rickettsiae a subset of the alpha-proteobacteria. We've met Rickettsia before as the agent of typhus on emigrant ships and as the probable ancestor of mitochondria. They have really small genomes, and Wolbachia is no exception: managing quite nicely with only about 800 genes on a chromosome about a third the length of E. coli's. One of the consequences of a small genome is that Wolbachia needs a bit of molly-coddling.  It wouldn't survive for months in a cold pasture like Mycobacterium tuberculosis, for example. Contrariwise, it can only grow and multiply in the the cosy environment inside eukaryotic cells. See [R] a Drosophila embryo filled, like a cake with currants, with Wolbachia false-stained in blue. W. pipientis has a preference for arthropods so you don't need to worry about catching a dose yourself. In particular it seems to zero in on the reproductive organs of flies, beetles and spiders. There it has a variety of bizarro effects on the behaviour and capability of the flies:
  1. selective killing of males
  2. a switch to parthenogenesis (reproduction in the absence of males)
  3. feminisation of males
  4. restrictive incompatability: Wolbachia infected males cannot mate successfully with uninfected females
If you're going to use Wolbachia as an agricultural or medical intervention you want to be double-plus sure you know which of these scenarios will play out with the particular strain of Wolbachia, the particular insect species and the particulars of the environmental conditions that pertain. Get it wrong and you may reap a whirlwind: turning all the males into blood-sucking females for example.. It may work fine in the lab but eventually you have to carry out a field trial and that will have a more complex system of interaction terms than you can begin to model in a laboratory or as a computer simulation.

In the free back-issues of Nature I picked up in Dublin earlier in the month, there was an article which describes a new proposal to control the spread of Zika. Published in May, it was unaware of the cases of Zika more recently reported in Florida. The Center for Disease Control CDC in Atlanta, Georgia cannot help but get more engaged when the threat is only one state line and 500km away. ANNyway, a biotech startup called MosquitoMate is proposing to infect male Asian tiger mosquitoes Aedes aegypti with a strain of Wolbachia pipientis that will ensure their sterility. When these doctored males mate in the wild with incompatible females, the eggs fail to develop properly like in case 4 above. The descendantless males will be in competition with wild-type males so the company or their customers are going to have to release containers-full of the infected males to make a difference in the reproduction of this species of mosquito. Aedes aegypti is not the only vector of Zika virus, so I guess the argument is that any intervention that reduces transmission of the latest virus should be considered. Field trials by the company with a different mosquito species have been claimed to reduce the population of the flies by 70%. The reservoir of 30% mean that the protocol is set to keep on giving value to the shareholders. If the customers (state health boards, the UN, whoever) don't keep on throwing out doctored flies, everyone is back to the status quo ante except for being several million dollars poorer. It won't be like fatal hammer given to screwworm in Libya in 1990.

MosquitoMate  makes me think of Fianna Fail's slogan in the 2002 General Election:

Tuesday, 16 August 2016

Screwworm screwed

I was a less-than-stellar student in the Genetic Department in TCD in the 1970s. Even as a youth, I had a tendency to flit about from one thing to another and pursue the wrong things with inappropriate energy.  When I should have been knuckling down to studying what was actually on the TCD curriculum, I was off in the library of The Other University [UCD] finding out about inclusive fitness and other material relevant to the then emergent field of Sociobiology. I allowed myself to believe that if I knew quantitative and population genetics really well, I could ignore whole chunks from the rest of the examinable syllabus. I was really interested in Q&PG because it seemed core to understanding evolution but also because it was taught by an outstanding teacher, Paddy Cunningham, who wasn't really on the faculty but had a day-time job in An Foras Talúntais where he eventually finished up as Deputy Director of Research. AFT was established by the Irish Government in 1958 "to review, facilitate, encourage, assist, co-ordinate, promote and undertake agricultural research.". AFT was more or less rebranded as Teagasc in 1988, much to the delight of Irish printers who got large contracts for new letterhead and signage.

Round about the time we came back to Ireland in 1990, Cunningham embarked on a bigger administrative challenge by shipping out to Rome as Director of Animal Production and Health at the Food and Agricultural Organisation (FAO), one of many UN quangos. If no sinecure it was surely a nice billet if you were up to the task: Rome is a cradle of Western civilisation, after all, and the food can be very good. The somewhat ploddy work of FAO's animal health unit was subjected to a very rude awakening almost as soon as Cunningham hung up his hat in his new office.

A consignment of cattle from South America, probably Montevideo, had been shipped to North Africa carrying an infestation of New World screwworm aka blowfly aka Cochliomyia hominivorax [etymology: the snail-shell fly that eats people] The flies were spreading through the African sheep and goat herds from the original focus. Blowfly adults are metallic greeny-blue 2-winged flies about 1cm long. The females mate once and lay 100-400 eggs [cartoon R] in the fur of mammals, especially near wounds, flea-bites or scratches, but also in the nose, vulva or anus if that's the only available opening. Half a day later the eggs hatch into spiney larvae (the screwworms) which plunge into the living flesh and start eating. This feels particularly irritating to the host who scratches at the boil-like larva-filled lesion until it's a bloody mess. The damage looks particularly inviting to other blowflies who lay their eggs nearby: catastrophically extending the wound. About a week after starting to feed the bloated larva drops to the ground, pupates in a quiet spot and hatches out metamorphosed into an adult. The length of the pupal stage is dependent on temperature but it can be as little as 7 days when the cycle starts all over again. The open wounds often overwhelm the animal's innate immune system and get infected with a wide variety of opportunistic bacteria which add the foul smells of necrosis to the already repellent sores.

The people at the FAO were concerned because the New World screwworm is a lot more aggressive, destructive and costly than its Old World counterparts. Two out of two-dozen sheep were fly-struck when we got them sheared, late, this last July. The maggots were icky but it was not a horrible suppurating sore. As you know, they have livestock in America, where C. hominivorax is endemic. But in the 1950s Edward Knipling and Raymond Bushland, working for the USDA, had invented a cunning plan to scupper the lifecycle of the screwworm. It all hinged on the fact the female blowflies mate only once. What if, the two hypothesised, we release enormous numbers of sterile males who will mate with aqll available females who won't then lay viable eggs. Subjecting flies to fairly precise doses of ionising radiation can sterilise the males without inhibiting their desire to mate and ability to fly. This Sterile Insect Technique SIT had been successful in eliminating screwworm from large tracts of prime beef country in North America.

The FAO didn't like the idea of a new disease adding to the hardship of Libyan and Algerian pastoralists, but they were extra twitchy about the possibility that the New World invader would spread to the large livestock in the Serengeti and across sub-Saharan Africa. That would be an ecological disaster of unprecedented magnitude. So they allocated a chunk of money to hit the incipient epidemic really hard while it was still limited in extent. It was similar in concept to the massive investment in Ebola containment which was almost too little too late. The chap tasked to make it happen had just arrived in Rome and he quickly found a telephone booth in which to change.

They decided that SIT had the best chance of success and, rather than starting from scratch locally, FAO contracted with a factory in Mexico to take all the sterile male C. hominivorax that they could produce over the next 12 months. These would be air-freighted weekly from Mexico to Benghazi via Frankfurt. If the timing was right, and this depended on quite precise temperature control throughout the process, the SIT blow-flies could be dumped out of small airplanes as they systematically criss-crossed the affected area. It was a super-elegant precise weapon, that showed how far we have come from spraying DDT from small planes to control other dipteran flies and killing the natural predators of those same flies at the same time <duh!>. It all worked like clock-work, except when one flight was delayed and all the flies hatched out on the runway in Frankfurt. It required much political nicety as well, as it was only a couple of years since the US had bombed Libya and the US was paying for a good part of the SIT program. Over the next months, FAO ground-workers monitored the incidence of fly strike in the region and informed the airplane distribution system so everyone was on the same page. A stark contrast to the 'control' of tuberculosis in Ireland. The North African campaign cost $100 million to release 1.2 billion doctored flies over at area of 40,000 And was deemed to be "the most effective and successful international animal health program in the history of the United Nations Organization".

Prof Paddy Cunningham was awarded an honorary doctorate by UCD, his Alma Mater, in 2009, but I don't think the plain people of Ireland really appreciate the giant in their midst.