Wednesday, 18 July 2018

Mountain to Mohammed

The Minister (of Education) was down to The Institute yesterday . . . to turn the sod on our new Sports Campus. As a deeply unsporty person, I look a bit askance at the importance given to sport  by Institutes of Learning. As opposed to other (quieter?) off-curriculum possibilities like archaeology, beekeeping, chess, dance, entomology, fishing, gardening, hairdressing, ironing, juggling, knitting, lego, movies . . , When I was in school, a chunk of my very expensive education was to participate in a wide variety of organised sports, but I mostly played it for laughs. As I saw it then, with so much that needed fixing in the World it seemed, well, unproductive to have 22 people and a referee running in random circles for 90 minutes. That's a person week of steam with nothing to show for it. Insofar as recreational physical activity had a necessary place in my life I preferred to go on a solitary run: at least nobody got to lose that match. Later on I recognised that doing things together - singing, drumming, sporting - is part of the healthy human condition and so had merit. I also got to appreciate that, without the structure of a sports fixture, many people, including self, would find it difficult to ever lever themselves off the sofa . . . and that leads to obesity, atherosclerosis and an early death.

Some sports require more infrastructure than others. Cross-country running requires less organised works than a soccer pitch; a squash court is more complex than a hand-ball alley. On The Institute's main Campus, sports facilities consume about a third of the footprint; and car-parking about a fifth. The main neutral green space, which used to have a lovely avenue of cherry trees, has been built over since I came to work here. The most recent building was opened by the same Minister in January of last year. There are ambitions for further expansion. The college has acquired a parcel of land about 1km out along the road out of town to provide additional pitches and running tracks and changing facilities. It might also be a cunning plan to convert more on-campus green-space into laboratories, innovation incubators, vice-presidential office suites, surveillance towers. Some suggest that all the car-parking should be shifted out to the sports-platz, so that everyone gets 2km of walking every day.

The arrival of diggers and dump-trucks to begin works on that site was what the Minister was required to symbolically start. But the minister is a busy man and speeches have to be made before the shovel is handed to The Great Man. It is 1000m between the new site and the nearest microphone. Accordingly the already symbolic bit of work by The Man in a Suit was shifted to a patch of grass just outside the lecture hall so we wouldn't have to shift all the witnesses and photographers to a different location. If you've ever been to a funeral you'll know how the run of events has a hiccup / pause while the departed is shifted from the chapel to the diggings. The problem is that, except for two spits of rain over the weekend, there has been a drought for nearly 4 weeks. That patch of convenient grass is a) beige b) brittle c) set in concrete.  No problem: as well as importing the Minister we'll also import the sod [there is an obvious comparison joke to be made there]. In the picture below, I've highlighted the 4sq.m. of turf  - the little white van which delivered it is just off camera to the right.
The youth in the photo are two of our sporty students Marcus Lawlor and Molly Scott, the latter with her silver medal which she won in a relay at the IAAF World U20 Championships in Finland last week.
The absurdity of the symbolic sod-turning could only with difficulty be taken seriously, and I'm glad to report that the Minister and Molly played it for laughs by shifting from sod-turning to pancake-tossing. All good fun.

Less jollity down the road at the Minister-less new sports complex which is right next door to a brand-new secondary school called Tyndall College. That school is not going to open anytime soon because the multinational that acquired to the contract to build the complex was Carillion which went bust at the beginning of the year. Another company Sammon which was somehow involved in the stew of contractors, out-sourcers, fixers, consultants and entrepreneurs has also gone down the financial toilet. A whole rattle of sub-contractors: electricians, plumbers, plasterers, painters, steel-erectors have put in time and materiél and now, because of the serial bankruptcies, are out of pocket if not also out of business. While the Minister was tossing turves with Molly and Marcus, several of the subbies were down the road taking down the fencing that they installed just a few weeks ago. The Minister stoutly maintains that the dispute, about who owes what to whom, is nothing to do with the Department of Education. But it is: one or more of his functionaries failed to carry out due diligence on the companies that won the government contracts. That's why we pay the Government's Head of Procurement the big bucks: so that the buck stops on his desk . . . no I don't believe that equation will ever apply here either.

Tuesday, 17 July 2018

Cyclosporiasis

You could be forgiven for thinking that cyclosporiasis was a fungal infection acquired on Le Tour de France, but you'd be wrong. It is rather the consequence of being infected by another apicomplexan parasite. Another? Well, those you may know about include:
These are all protozoan parasites, single-celled organisms with a nucleus, but only a bit bigger than typical bacteria. Cyclospora cayetanensis , the cause of cyclosporiasis was unknown until about 30 years ago, when it was characterised by researchers at Universidad Peruana Cayetano Heredia, who were looking for evidence of Cryptosporidium parvum in the barrios of Lima. What they found was a new species [Cyclospora cayetanensis A in panel below] which was similar to but different from Cryptosporidium muris [B] and  Cryptosporidium parvum [C] and so they got to name it after their place of work. They are all almost exactly the same size as a human red blood cell.

It's probably the same as an organism isolated from stool samples in Papua New Guinea in 1979. Since its discovery in the tropics, it has been responsible for numerous epidemics in the United States. Including one which made the New York Times 7th Jul 18 because 200 people across the upper midwest had gotten sick after eating Fresh Del Monte Produce vegetable trays containing broccoli, cauliflower, celery sticks, carrots and dill dip. That's what the CDC is saying anyway.

They may be wrong yet, because Cyclospora takes so long to hatch out of its spore and start to go forth and multiply in your gut that a week or more will have gone by before you have symptoms. [Let's hear it for symptoms: Watery diarrhoea; Loss of appetite+weight loss; Cramping; Bloating; Gas; Nausea; Fatigue] What the epidemiologists at the CDC have to do is find something that 200+ random people across 4 states have eaten-in-common the weekend before last. Someone else has to do a [watery] stool analysis to make sure everyone has the same bug. Of the 36 outbreaks of cyclosporiasis this century, CDC were only able to identify a culprit in 16 and of those only 8 were unqualified by 'suspected' or 'likely'.

And Del Monte are having to scratch their heads about which of the ingredients in their fashion-accessory plastic-trayed health-snack to blame: the cauliflower from Arizona? the celery sticks from Belize? Because they have to send their quality-control hard-men down the supply chain to find the source and close it off. Del Monte don't want to annoy their clean and loyal producers of perfect broccoli florets if the slack-bobs two states over, who julienne the carrots, are to blame. It's a globalisation head-ache for producers and consumers alike.

It's ironic that this infection catches people who feel virtuous because they obey Micheal Pollan's dietary instructions [prev and prevlier]  "Eat Food. Mostly Plants. Not Too Much". Well what do you expect if you buy your Mostly Plants in a clam-shell tray filled with stuff from who-knows-where?

Monday, 16 July 2018

More worms are needed!

Early last Sunday morning, I was responding to an e-mail and needed a reference to The Blob to save me re-writing one of my well-worn anecdotes. As a by-product to that search I came across a Trib to The Boy, who helped me declutter about 50kg of scientific papers when he was 'resting' between jobs 12 years ago. My offspring have told me quite clearly that they will pour rancid milk on my grave if I leave them a mess of papers to go through after I pop my clogs. Because I love the kids, I thought I'd wade through one of my filing-cabinets to see if I could simplify their post-mortem paperwork.  An hour later, I'd culled a xerox-box full [~10kg] of discards: Win!  I also found a paper that I've been hankering after since I started The Blob. Win! Win!

It's like with trying to Google a remembered article at the intersect between Beirut and cooking oil without getting lost in a storm of recipes from Claudia Roden. Well like my recent triumph about eggs and Sarajevo, throwing out the dross has surfaced some evidence for the hygiene hypothesis: that we are beset with allergies, eczema, asthma, lupus, psoriatic arthritis and other autoimmune diseases because we never meet pathogens as kids. The immune system, having been crafted over millions of years to aggressively fight infection, is incapable of sitting on its thumbs if there is nothing left to fight. I remember the paper "Trichuris suis therapy in Crohn's disease." because it was one of the most interesting which was discussed that year at the Journal Club which I coordinated at St. Vincent's Hospital. But I got some key data wrong which meant my google-hunt and pubmed-search lurched quickly off the tracks on which I was running. Crohn's Disease is no fun: Diarrhea, Fever, Fatigue Abdominal cramps, Bloody stools, Mouth sores, Reduced appetite, Weight loss, Anal [not St Martin's] fistula, Inflammation of skin, eyes joints, liver or bile ducts, Delayed growth or sexual development.

Trichuris trichiura is the human whipworm a nematode about 50cm long which inhabits the large intestine of about 1 billion people. Not you and me, because we aren't poor and black and living in the tropics without proper sanitary facilities. The adult whipworms, with their heads embedded in the gut epitheium have their arse end hanging out into the lumen of the gut into which the females shed 5,000 fertilised eggs a day. Some of which get into the food supply or on the shitty fingers of the neighbours. Those dispossessed people in the tropical and sub-tropical Third World are notable, not only for their load of intestinal worms but also for the comparative absence of the Diseases of the West: asthma, IBS, MS, etceterzema. It didn't take long for someone to put these two observations together to suggest a causal relationship between them..

The paper which surfaced in my filing 'system' is a nifty advance on the hygiene hypothesis into a testable experiment. No Ethics Board is going to countenance deliberately infecting sick people with a known and debilitating human pathogen. Therefore the team from U Iowa Medical School deliberately infected patients living with the Crohn's Disease [see IBD link above] with 8 x 2400 eggs from Trichuris suis the pig whipworm. It has long been known that whipworms are quite species-specific and T. suis just can't get established in the human gut or vice versa. Part of the reason for that is because the human immune system gives it a damned good alien drubbing and stops the eggs from hatching or, if they hatch, from getting a toe-hold in the wall of the human gut. The immune response is necessarily systemic: anti T. suis agents are released into the blood-stream and find their way to the gut. OR the ongoing immune response to Crohn's is diverted to combat the whipworm eggs and leave the intestinal epithelium alone.

Excited as I was back in 2005 when the paper came out, I'm a bit more skeptical now.
  • It's an open label trial (everyone knows the treatment that is being administered).
  • There are no controls - where, say, half the participants get a teaspoon of baker's yeast instead of the eggs
  • The sample is small - only 29 participants with an initial CDAI (Crohn's Disease Activity Index) greater than 220. Hey, you can calculate your own: +20 for anal fistula, +2 for each extra loose stool. The cut off between 'normal' and Crohn's is CDAI= 150; so >220 is definitely clinical Crohn's
  • It is still being cited in the Wikipedia entry 13 years on
Nevertheless, after 24 weeks of getting a dose o' whipworm every 3 week 23/29 patients reported a significant reduction in their CDAI and 21/23 were effectively cured.  It might be a life-time commitment because the study doesn't claim that the treatment has reset the inflammatory clock but that it a small price to pay for such a dramatic reduction in symptoms. Then again, it could be that, without a reset of the clock, eventually the immune system will get used to the whipworm eggs and return its attention to hacking blood out of the bowel.

Sunday, 15 July 2018

Sheep shedder

We own the 20th part of the hill that gives the townland its name. That holding more than doubles the size of our farrrrm by adding 10 hectares to the 7ha which surround our home. The trouble with the 'commonage' is that it is owned in common and we cannot point to a single bush or rock or rich source of fraughans and claim exclusive rights to it. Two generations ago, the mountain was an essential part of the farming economy. In the Spring after lambing, the sheep would be driven up onto the mountain where they would eat whatever they could find. I gave some more exotic examples of transhumance this time last year. The in-bye fields would have a rest from herbivory and be allowed to grow into hay, which would, if everyone was lucky with the weather, be won as winter fodder. The ram-lambs would be sold to the local butcher after which salt, tea, butter, rashers and a new shovel would be bought on the other side of the street. An idyllic local circular economy: the local cinema would alternate between The Quiet Man and Darby O'Gill and the Little People

Globalisation put paid to all that. The butcher could buy cheaper, better quality lamb from New Zealand. The price of wool collapsed so that it cost as much to shear the sheep as the wool was worth. Teagasc, the government agricultural advisory service has, for the last 30 years, acknowledged that no small or medium-sized farm can survive without an external income. In parallel, the EU has determined that there is social utility in keeping farmers in place in the landscape, and funneled grants of money to off-set the losses of running uneconomic farms in the globalised present. Every 5 years, a new Cunning Plan will emanate from Brussels, with a different name and different rules. The rules often change to remediate the disastrous effects of the unintended consequences of the last set of rules. The latest fund is called GLAS [Green, Low-Carbon, Agri-Environment Scheme] and it looks grand on paper . . . laid out across an agronomist's desk in Dublin. Less so when laid out across real fields and operated by real farmers with real sheep.

Anyway we signed up for GLAS because it seemed that the benefits outweighed the deficits (the training has been a total waste of everybody's time and a lot of tax-dollars). One of the key changes in GLAS is that, if you are claiming commonage as part of your holding, then you now have to use the commonage by agreeing to run a specified number of sheep on the hill for a specified number of months . . . just like folks used to do in the 1940s. The trouble is that, of the 20 farmers who own a share of the common, only 2 of them have been using the hill in this century to graze sheep. At the beginning of April we pushed 8 of our most mountainy sheep through the 'mountain gate' to shift for themselves upstairs. We never saw them together again; partly because we were looking in the wrong place. The day after shearing in June:
acting on the advice and hill-savvy of Paddy the Shears [at work above]. I went round to the Far Side of the hill to see if I could find our sheep between there and the Mountain River. I found one which, spooked by my approach, rapidly disappeared out of frame:
It has been 25 days since we last had rain and the bogs on the hill are all dried up but there is still a lot more green up on the hill than there is, for example, in our yard which looks like the green tide is draining away as you watch:
On Saturday we rose before the sun, had a cup of tea and set out to find our sheep. The early start was required because running unshorn sheep about the landscape in the heat of the day is a cruel and unusual punishment. We were delighted, with the help of binoculars, to find six of our sheep [three foreground sheep shown below, the others are a pixel each in the middle distance]:
That was  a dry run really because we had asked to borrow our neighbour Martin and his dog to help bring those sheep down to the bone-dry yard for shearing and a few scoops of sheep-muesli [mmmm good]. On Sunday morning therefore we were again up before sparrow-fart to meet Martin at 0640hrs on the Far Side.

Shedding sheep is a one of the tasks that is required of shepherds and their collies in sheepdog trials. The idea is to separate out two sorts of sheep from a co-mingle flock. How it's done. It was brought home to  me why it is done as our sheep moved across the face of a hill that was already dotted with sheep from other places. It fell to me twice to separate our sheep from a bunch of strangers heading in the same direction - mainly because ours were following them . . . like sheep. Don't forget that there are 200ha of hill up there and at least 200 other sheep to get in the way. The rest of the time my task was to follow a path more or less parallel to that chosen by our girls to discourage them from breaking in that direction. You may call me Rrrrrrex <arf!> <arf!>.
E v e n t u a l l y our sheep were encouraged to start moving quietly in a more-or-less SSE direction until they departed back through the Mountain Gate and down the green lane to home [as L]. Martin left us at the second gate because he'd seen two of his sheep in a peculiar place and intended to bring them back to the fold before they edged out of the county. That was a pity because The Beloved had the makings of a massive fry-up in the kitchen and I had to eat Martin's share of the sausage and rashers. The key thing with moving sheep is to keep the pace measured: slow and steady works. Anything else results in everyone getting hot and bothered and making poor decisions. As for the utility or sense of running sheep on an unfenced hill for which neither they nor their shepherds have any 'heft' [defined prev], I have my doubts. I think it's probably true that many canny farmers who have signed up to GLAS for the cheque have no intention of actually leaving €100 worth of asset on the side a mountain which they cannot reach without getting their arse out of their €100K tractor.

Bits Bytes Sunday 150718

Sunday MidJuly

Saturday, 14 July 2018

drone scope boyne henge scape

The Bend in the Boyne Brú na Bóinne is richer in neolithic structure than anywhere else in Europe. It knocks our wee Neolithic Ringstone into the ha'penny place. Newgrange is the cherry of the artifacts partly because it was 'restored' in 1967-1974 from an ould hape to a structure with a dazzling white wall of quartz which may have existed 5,000 years ago in the same place. The currants in the local landscake are the similar but less impressive, less tricked-about mounds at Dowth and Knowth and dozens of rings, lines, pits, holes, ditches, banks which can be picked up if you know where and how to look [source for more detail].  or Maybe Boyne Valley Landscapes Project Phase III Final Report 2010 by Davis, Megarry, Davis, Barton from The Heritage Council INSTAR Program.
That picture is taken with LiDAR [bloboprev] which captures and exaggerates minute variations in the height of the ground: ignoring plant cover which might be taller than the maximum soil-height difference.
You can see every wart and suture in the landscape EVERYTHING . . .you might think. Because you'll agree that, for the whole field nearest to the extreme SW [bottom left] corner [clipped out L], it's a case of nothing to see here, folks. But you would be wrong because there are other ways of seeing the landscape, with different tools, at a different time, with a different mindset. Anthony Murphy is a local man, a sub-editor on the Farrrrmer's Journal, who has been fossicking about the North of Co Meath for nearly 20 years, looking at things sideways and talking to people and reading books . . . and writing them, and taking photographs and running a website all about the interface between human history, myth and the landscape called Mythical Ireland. A couple of years ago he got a drone and started to look at things from above. And then we had a punishing drought and he took out his drone because of the drought-marks being reported in the UK.  He snapped a picture of that same-old same-old field and found a 'new' circular structure where none was documented before:Gobsmacked, he was:“When I saw it first I was like ‘what’s that? What the hell is that?’ It’s something I had never seen before. It is huge.”
I've turned it upside down to make it clear how the new henge - sacred enclosure - fits into the busy landscape. The circles at the right edge of each picture are the same thing. It was suggested on the wireless, not entirely as a joke, that these henges might have been a 2,000 capacity sports ground rather than a place of religious ritual. Then again, sport and religion blend into each other is a rather uncomfortable way. The drought exaggerates any discrepancy in the water-retaining capacity of the soil. The surface of the field after thousands of years of rainfall and windstorm and, especially, ploughing is flat like a billiard table and so LiDAR-opaque. But the 200m wide circle of wooden pillars sunk into holes 4,500 years ago has changed the soil, its microbial community and its porosity forever. More coverage, better pics: RTE; BBCRIATwitter; Indo
Get yer drones out, folks! (before it rains)

Friday, 13 July 2018

St Wendy of Dementia

I've now finished Wendy Mitchell and Anna Wharton's book about the walking demented Somebody I Used to Know. I wrote an interim report ten days ago.  There are 55,000 people living with dementia in Ireland; that's about 14/1000 of the adult population. If you don't know someone with dementia, then you're deliberately looking the other way. As a public service, and as an aide-memoire for me lest I forget, I here-and-now capture some ideas, mostly culled from Mitchell's book, but also from her youtube presence, which will make living with dementia easier for everyone.
♫You might, waggishly, choose to have Iris Dement singing along in the background♫
  • Finding the lights. Shortly after we bought, serviced and moved into our farrrm, my parents came to stay for a few days. In the middle of their visit, we had to go overnight to a funeral and took the girls with us. My Dad volunteered to feed Flossy the orphan lamb and the chickens if we made up sufficient Lamlac formula for the 24 hours and showed him where the layer's pellets were kept. When we came back, he reported that the kitchen lights didn't work. Or rather, he confessed that he hadn't been able to find the light-switch, in any of the obvious places where a light-switch should be. Certainly not at knee-level [see R]where we had been constrained to put it by the door-side window and the solid stone wall. [I've polished up this tale before] Wendy also had trouble finding the lights in the new place - muscle-memory and habituation had taken care of that in her old home. Indeed light-switches are, by default, white in colour so they don't intrude on the decor.  Her solution was to paint a coloured border round each switch to remind her that lights existed.
  • Returning home. A couple of years after he retired my old and undemented Head of Department drove into town for a bit of light shopping. Returning home, he opened the front door, and was disconcerted to find that the hall table was missing and somebody had changed the carpets . . . until he twigged that he'd driven to his home of 30 years from which he and his wife had down-sized on his retirement. Wendy also, I suggest foolishly, thought she'd move to a new house in the country when she retired due to her dementia. A couple of times she tried to open the front door of her neighbour's gaff when she returned on auto-pilot from a day in town. Her solution was to bracket her door with a couple of distinctive tiles featuring forget-me-nots Myosotis spp. 
  • Finding the clothes. Wendy's younger daughter came to visit twice in a week shortly after the move and noted that her Mum was wearing the same clobber both times. She didn't smell or anything, she just looked atypically ward-robe challenged. And that was the problem: Wendy had 'lost' her new fitted ward-robes designed to be neutral w.r.t. the decor and so invisible. She solved that, and the related problem about the contents of her kitchen cupboards, by taking photos of the interior and printing them A4-size on the outside of each door.
  • Finding the jacks. For the demented, the doors are all closed; if they are seen at all, it is likely to promote anxiety about what is on The Other Side. Wendy could have put a show-it-inside photograph on the outside of the downstairs toilet. But that would be a bit in-your-face for visitors; so she made a big T sign and put that on the door instead. She removed both doors in her kitchen to ease her mind and minimise anxiety-inducing decision making: "Which door?" and "Is that a door?" and "Are there dragons beyond that door?" were all nulled with a few turns of her screw-driver.
As I say above, the standard advice is to move to your final destination before you lose your marbles. A lot of these tricks would be unnecessary if longer familiarity had embedded the location of switches, cupboards and rooms. Here's a bit more cogent advice on interpersonal relationships between the demented and their carers.
  • Don't argue with your demented. You don't have to be right; and disagreement is more like to promote anxiety, distress and difficult behaviour. Trying to establish your own innocence is going to wrong-foot your demented and crank up the anger and anxiety.
  • There is no future in catching your demented in a lie. It is their truth.
  • Don't bother using your powers of logic and reason with your demented. They are demented! You might just as well speak to them in Latin.
It's not easy dealing with the demented but you can make it a whole lot harder on yourself if you play your cards wrong. otoh OTOH if you are totally hands-off with engagement and challenge as these diktats seem to recommend, then you may precipitate the persistent vacant state/stare that is the cliché of dementia. Keeping fit is an important predictor of better life quality; keeping fit is exhausting; someone needs to be the trainer here and probably take some flak. A cross Mammy is better than one with weeping bed-sores.