cheep cheep

As the world knows, the Irish Institutes of Technology become like the Marie Celeste or Flannan Isle during Summer.  The teaching staff take their weary bones off to shop in NYC or hang out in their dachas down the country because they've done their 600 hours of class. The technicians have to clock in as usual despite the fact that they have nothing to do but 'prepare for next year'. Yesterday, I made the schlep into work because there was free pizza.  I was a graduate student once, so free food [cheap cheap] is a bit of a trigger.  On the way, I twigged that the free pizza was for the graduate students (of which I own a couple) and far from getting free food I'd probably be expected to pay for some of it. Dang! But by that time I was half way there and committed so I carried on.

I was very glad because the first person I encountered at work was one of our technicians with a paper bag and a harassed look.
"Do you know about chickens?" she asked.
"Tikka marsala, Maryland or wings?" I replied; but this elicited no smile - harassed look y'know.
Turned out that, driving along the motorway - with her kids in the back - techie had seen a flash of yellow on the hard-margin and then another. That looks like a day-old chick, she thought. Which was not so weird because her older boy had spent the previous several weeks asking her if they could start to keep chickens. The car was stopped, the chick (for so it was!) was scooped into the bag, she drove on. Another chick, another stop. Another chick, another stop. One of the little scraps was clearly dead, so that was left for the crows but she had 3 live ones.

When my girls were small, we had hens and periodically a rooster, and every so often one of the birds would go broody and we'd shovel eggs under her for a couple of days and then wait 3 weeks. If possible we'd solicit our tree-hugging neighbours for spare eggs. With surprising synchrony, some of the eggs would hatch and we'd have a handful of cuties to marvel at. This omnium-gatherum source of brrod-stock meant that our hens were strikingly diverse in size and colour.  One day's egg inventory [R] indicates the accumulated genetic diversity. We'd spend some days providing sufficiently small food and watch the chicks following their "mother" around trying to eat what she scratched up. If the girls went rooting through the compost, they'd usually get a handful of small worms which were relished and I often lifted the bark from the woodpile and swept the revealed isopods and insects into a dustpan for chick protein. Of course, anything that had been on a dinner plate was scraped into a bowl for the chicks.

I shared that info.  Because of the free pizza gig, I'd made a slab of flapjacks, so I was also able to share a handful of oat&syrup crumbs and a whole biscuit for crushing. When I left work, the chicks were up and about, eating, and making a racket . . . so the prognosis is good.  The current hypothesis is that a truck, as it sped toward Rosslare harbour loaded with day-old chicks, had shed part of its load through a hole in one of the boxes, . I think, even if the three escapees don't make it, the idea of raising chucks has gained traction in one Co. Kildare home. More positive propaganda.

Bugging the uterus

I grew up as a geneticist and evolutionary biologist,  at the top of my modest game when analysing DNA sequences on a computer. I was safe there, although a disaster in the lab. Then about 15 years ago I got a billet in a comparative immunology lab on the theory that my expertise could bring a needed new dimension to their research.  It was hard for everyone because geneticists go all weak at the knees with B-cells, T-cells and dendritic cells and affect to be unable to understand the difference between CD4 and CD8 and the other proteins which coat the surface of these immune cells. Immunologists, on the other hand, have a model where CD4 and CD8, and the other proteins poking out of the membranes of cells, are just there without ever reflecting that they are there because of the DNA in the cell's nucleus.

I have a long-standing interest in microbiomes: the invisible freight of bacteria on which a lot of our health and happiness depends. The intestinal flora is one such ecosystem which you should cherish with kale and strawberries straight from the field. If you wage war down there with oral antibiotics for an earache, then you can get yourself in serious trouble with Clostridium difficile or worse.

Now here comes an interesting study of the uterine microbiome which gives a clue about two of the great immunological mysteries of mammalian reproduction.  The first is the miracle of bearing young at all.  Birds get their eggs fertilised and then unload them in a convenient hard-shelled package where they continue their development until hatching.  Mammals otoh hold these ever growing cluster of 'foreign' cells inside.  Immunity is all about recognising the difference between self and non-self.  The embryo may have half its genes in common with its mum but the other half is clearly foreign, yet women tolerate this interior growth for nearly 40 weeks.  If it was a tumour (which is much closer genetically than a fetus), the mother would be f**ked.  Lots of people have theories about how this tolerance is achieved but we're still short of data and evidence to clear up the conundrum.

The other mystery was mostly in my head and hinged on a false premise. If the uterus is effectively sterile and delivery is such a one-way ticket, then how come so many cows get endometritis [inflammation of the uterine lining] immediately after birth.  This is a major cause of bovine infertility and so economic loss to the dairy industry.  I was wrong about the sterile uterus.  Like every other warm wet place about us, bacteria like to set up home there. Endometritis occurs when the balance among the uterine flora changes with the disruption - physical and hormonal - of delivery.

It turns out that the uterine flora is more similar to that in the oral cavity than the wild bunch in the vagina next door.  I've shown that oral, fecal and vaginal bacteria are as different from each other, despite being in the same person, as the ecosystems of the Serengeti and a Rwandan jungle are different despite being on the same continent.  For a long time we couldn't get a handle on the microbial diversity in real ecosystems because swab we might but most bacteria have never been grown on a Petri dish and were effectively uncharacterisable because of this. Non-culturable bacteria are no longer invisible because of next generation sequencing NGS.  This allows researchers to pick up a mess of potage, give it a good whizz in a Moulinex blender and then sequence all the DNA. In particular they tend to pick out all the 16S RNAs which will tell them what sort of bacteria were present in the sample before they were turned into soup.  We have, for example,  the complete sequence of Neisseria meningitidis, which can be grown in the lab. If they pull out similar but not identical 16S RNA they can surmise that Neisseria unknowniditis is present. And the researchers can even get a quantitative estimate of what's present.

The paper gives a really interesting insight into the complexity of microbial interactions.  Several adverse conditions including premature birth depend on (are caused by) the presence of more than one species of microbe: it's the interactions, stupid. But normal full-term pregnancy seems to be mediated by the bacterial flora of the uterus as well. The solution to the mystery of pregnancy may well lie with our beneficial bacteria.

Dia da Independência

With 196 (or 188 or whatever your position is wrt to the legitimacy of South Ossetia, Transnistria and Nagorno-Karabakh, Liberland, Bir Tawil, the Republic of Cork, or the Principality of Sealand) countries and only 365 days in the year, Independence Day ID is celebrated somewhere on our world every alternate day.  Actually, the distribution of IDs is very uneven with a peak in the Summer and a more pronounced peak on the 1st of whatever month. And of course, several countries, including Ireland and the United Kingdom of Noteurope, don't celebrate ID at all at all. Indeed most of the IDs that do exist reflect severance from the UK.  Maybe as the Island Next Door degenerates into a colour-shirt dictatorship, some goon will suggest raising the date of the Brexit Referendum as an excuse for flag-waving and book-burning.  There is good precedent for this sort of dangerous nonsense on the Twelfth of July when Ulster protestants give thanks to their angry god for the outcome of the Bottle of the Boyne [bloboprev].  The family of a good friend of mine, who grew up on a chicken farm in County Derry, would take the opportunity to go on holiday across the borrrder in Co Donegal so they didn't have to hear the chest-beating parades that go down too many streets in Northern Ireland even in the 21stC.

Today it's an ID double whammy. Two tiny nations, Kiribati (1979) and São Tomé and Príncipe (1975) became independent on the 12th July.  Let's park Kiribati so I have copy for next year and reflect a little on the diacritic-laden República Democrática de São Tomé e Príncipe which is located in the armpit of Africa [L above]. The map betrays the geological basis of the islands which are an extension of a volcanic mountain range starting in Cameroon. The Pico de São Tomé is, at 2024m, higher than anything in Ireland for example. They are indeed tiny, only 3 Irish counties have a smaller area than the archipelago and there are fewer people living there than in Metropolitan Cork.

As far as we can tell the islands were uninhabited when they were discovered on St Thomas's Day 21 Dec 1471 and St Anthony's Day 17 Jan 1472 by Portuguese explorers. For context, this is 20 years before Columbus sailed the ocean blue in 14 hundred and 92. Volcanic islands look terrible barren when they burst from the sea but the new rock is inherently richer than depleted rocks of, say, much of Australia and South Africa.  Anything with red soils in Geoguessr seems to be located in one of those places. STeP became an early exporter of sugar until its trade was eclipsed by the islands of the West Indies. Under the Portuguese, the islands were subdivided into extensive roças [latifúndios / plantations / estates] owned by capitalists and worked by slaves indentured servants. Indeed the islands were convenient and defensible entrepôts for the slave trade for about 200 years. Now it's all cocoa, which earns 95% of the republic's foreign credit.

Oddly, STeP is bracketted by the islands of Annobón and Bioko [formerly Fernando Pó] which are part of the same volcanic chain and were formerly Portuguese but were ceded to Spain by the Treaty of El Pardo in 1778 which tidied up a lot of disputes and violations of the Treaty of Tordesillas1494. That pope-mediated agreement divided the whole world between Spain and Portugal without troubling to ask France, England or the Netherlands, let alone the people already living there. Annobón and Bioko are now part of Equatorial Guinea, formerly Territorios Españoles del Golfo de Guinea, which had such interesting stamps when I was a kid.

At the moment STeP is reasonably democratic, left-of-centre, and stable. That may all change if they start to exploit off-shore oil-reserves. The corrupting power of oil has managed to turn Nigeria into a deeply divided and unhappy country.  For today at least, let's party on for São Tomé and Príncipe.

More Islands!

Having bottle

Anyone who 'did' British history at school knows about the Indian Mutiny of 1857 where British insensitivity to religious and cultural difference ended in a widespread break-down of discipline and a revolt by the common soldiery. That Mutiny was ruthlessly crushed but it brought to an end the East India Company which had been running the sub-continent as a profit making gravy-train.  The British government took on the business of running that part of the Empire directly rather than sub-contracting it to a bunch of capitalists.

Last Sunday 10th July was the 210th anniversary of an earlier Mutiny brought on by a similar insensitivity and the imposition of European cultural values on the soldiers of The Company.  Just after midnight the sepoys shot dead the British sentries in Vellore 140 km West of Madras [Chennai nowadays] and took control of the fort and slaughtered much of the British garrison as they slept. One British officer escaped and rode 24km to the next garrison at Arcot to raise the alarm. It was not a good time to piffle about and an officer of the 19th Light Dragoons, called Sir Rollo Gillespie, up early for a ride he scrabbled together a relief force in 15 minutes of frenetic activity and galloped back to Vellore to sort things out. Further troops, including some horse-artillery followed as quickly as they could muster their arms.  Gillespie's ride is commemorated in a truly terrible Victorian poem:

Without a word, without a groan, 

Sudden and swift Gillespie turned, 

The blood roared in his ears like fire, 

Like fire the road beneath him burned.  

etc etc

By all accounts, if Gillespie had arrived 5 minutes later, all would have been lost as the few surviving Brits were surrounded and out of ammunition. As it was, the mutiny was nipped in the bud and far greater slaughter, on both sides, was averted. Because of Gillespie's prompt action, hardly anybody has heard of the mutiny of 1806.

Having read about this in the morning I was off to Sunday lunch with Pat the Salt [bloboprev], my aged father-in-law, his daughter and her aunt Margot. The aunt, like her sister Souad [prevoblob] was born and raised in the city of Kano in Northern Nigeria. Nigeria, like India, is a multi-cultural melting pot supporting several different religions and more than 500 different languages. Like India, there were/are periodical pogroms against racial/cultural groups that were/are locally in the minority. One Sunday, when this aunt was about 15, the family left home to go to the races in the next town. Margot felt crook so she stayed behind. While the family were away, the local Hausa men [Muslims] decided to murder any Igbo people [Christians] they could lay hands upon. This was done, in contrast to the dormitory slaughter in Vellore in 1806, with great gusto and much noise. The thing about a close-knit multicultural society is that you know where the other half lives.

Margot's family employed an Igbo steward called William and shortly after things kicked off, a mob appeared in the family compound demanding that William be released into their custody. 15 seconds of frenetic activity had Margot standing at the top of the veranda stairs, with her father's shot-gun and a box of cartridges, haranguing the crowd in Hausa and inviting the first of them to start up the steps to get William. The thing about a close-knit multicultural society is that you know who is as good as their word and none of the men believed that Margot wouldn't shoot and so they slunk off. Courage is doing the right thing without over-thinking it: some people have it in their backbone.

Handiwork 100716

For your video entertainment this w/e, we bring you:

• Watch a succession of people working with their hands. 
• incl Simon "mighty torso" Fairlie scything faster than a motor mower.
• More scything, they cry! Girls do it too.
• The last man to use a pole-lathe for a living.
• Have wood but need to light the fire? Kindling! Use the froe, fool!
• Seven fish with one cast!
• The daftest video for a cute song: Paper Kites do Featherstone.

Motes and beams

Or how wilt thou say to thy brother, Let me pull out the mote out of thine eye; and, behold, a beam is in thine own eye? Matt 7:4 (KJV). Part of the wisdom of the Bible is this recommendation to concentrate on the things that matter rather than piffle about with trivial concerns. That's one way of interpreting the quote above, anyway.

The US Food and Drug Adminstration FDA, has been on the rampage after coliforms and is now recommending that nobody should eat raw cookie dough - cue Gordon "Angry" Ramsey: "This dough is RAW". When we were kids, we'd fight each other to lick the bowl after my mother had made a cake. Those eggs were RAW, supposedly full of Salmonella and Campylobacter.  Sure we got sick: styes, boils, coughs, and suppurating sores but never ever got the runs from raw eggs. It was partly plain ignorance: we didn't know we should get ill, so we didn't. That's all taken for granted now, if you gave your kids a bowl of cake mix to finish off, the district nurse would have the cuffs on you before tea-time; or at least before the kids make it to the shitter.

Now according the FDA, even the goddamned flour is full of fecal coliform. This is because flour is RAW; it is made from wheat and a field mouse Apodemus sylvaticus or a goldfinch Carduelis carduelis might have defecated on the grains before harvest. That mouse or finch might have been carrying Shiga toxin producing Escherichia coli.  It is fine if you cook the flour: baking, boiling, frying, broiling will kill coliform bacteria and neutralise residual toxins.  The problem is eating raw dough.

This is all on foot of a multi-state outbreak of E. Coli O121 at the end of June. This sort of epidemiological investigation needs a co-ordinated response from the FDA and the Centre for Disease Control CDC in Atlanta. It required someone to make a connexion between two or more cases of bloody diarrhoea; it must have been something they ate, of course, but which is the key product in 48 hours of previous consumption?  And you know these obese Americans: they consume a lot in 48 hours. So far the tally is 42 sick people, half of whom finished up in hospital, no fatalities yet.  Seems that you don't have to have eaten the raw dough, just handled it . . . and then licked your hands or reamed out your nose. All the cases had used general purpose flour made by General Mills GM in their  Kansas City, Mo. plant in November 2015. They are blaming the field mice; I presume they have eliminated the chance of one of the mill's line operatives getting careless with the handwash. GM voluntarily recalled 10 million pounds of suspected flour made in the same mill in the same time-frame.

Math: flour packs quite heavy 0.77g/cc or 770kg/cu.m. A standard 20ft shipping container (6m x 2.3m x 2.4m) has a capacity of 33cu.m or 26 tonnes of flour (less if including pallets etc.). 10 million lb of flour will require a train 1km long pulling into a siding in Kansas City. That's a lot of recall and they must hope that most of the stuff has been eaten . . . with little adverse effect.

Of peripheral interest is the fact that three different brands of flour are being cited / recalled: Gold Medal, Signature Kitchens, Gold Medal Wondra.  If we're blaming the poor field-mice, we must conclude that these brands are essentially the same.  If it was a leaky mill-worker then the contamination could have continued after the production line was switched to a different product. What's with Wondra?  It's not a spelling mistake, it is rather ". . . the flour you’ll want for extra- creamy, lump-free gravies and ultra- flaky and crispy pie crusts. Its lightness also makes it perfect as the dredging flour for fish and poultry".  Regular Gold Medal by implication is lumpy and heavy and is presumably used mainly to cement rock-buns.  But according to GM, This flour is great for nearly everything. And because it doesn’t add color, it’s especially ideal for baking white breads and cakes. 'Nearly everything' ? Great for climate change, acne, refugees, solving cross-words and interplanetary travel?

Do you find this response by GM, FDA, CDC slightly out of proportion?  As Kottke said about the hoo-har The FDA cautions against eating raw cookie dough. (Guns are still a-ok though.)

Tropical sanctuaries

I woke up screaming in the middle of the night after I wrote about Paul Cox and his Seacology non-profit. I'd forgotten a number of relevant references. Cox went off to the third world for his field work as an ethnobotanist, talking to the knowledgeable older blokes about healing plants. A generation previously Carleton Gadjusek had been doing fieldwork as an anthropologist in New Guinea.  In addition to doing the research on the neurodegenerative disease kuru that won him a Nobel Prize, Gadjusek was talking to younger chaps to persuade them into his bed. Most people, including almost all who had dealings with him when he came to Dublin, disapprove of this sort of thing. We have to be cool with homosexual acts between consenting adults nowadays but sexual acts between adults and children are inherently unequal and unfair.  Actually, students in college are technically adults [can vote, join army, do jury service] but sex between them and their teachers is generally disapproved of, for the same inequality of power reasons.

But how are we about pushing your religion? Is that okay? Paul Cox, in addition to making the connexions between a tree and its curative properties [which hasn't gotten him a Nobel . . . yet] was also shilling for the Church of Latter Day Saints. "For two years beginning at age 19, I served as a volunteer missionary to the islands of Samoa. It was a wonderful opportunity for me to explain our faith to any who cared to listen, and to engage in humanitarian efforts." Did he stop explaining his faith when collecting his ethnobotanical data? Does it make the tiniest bit of a difference in Seacology's allocation of funds if the recipients are converts? Is it correct for me to push agnosticism? Should religious organisations be privileged with tax-free status?  Should they be exempt from criticism?

Who else is doing good for the tropics with First World cash? WeForest is. This tree-planting charity was founded by a palomino called Bill Liao, and they insisted that their mission statement Making Earth Cooler is readily understandable by folks who don' spik Ingles ver' good. Name familiar? Bill is the cofounder of CoderDojo [prev, and prevlier] which is empowering kids to drive computers rather than sit in front of them with their gobs open.

Willie Smits gave an impassioned early TED talk about his work creating a sanctuary for orang-utans Pongo pygmaeus in at Samboja Lestari, Kalimantan on the island of Borneo. It is a great example of a TED talk: the Samboja Project saves primates by saving their habitat, and this Good Thing generates all sorts of positive unintended consequences.  These include:

• reversal of local carbon emissions
• through reforestation
• through preventing forest and subterranean fires 
• beneficial changes in rainfall patterns
• increased biodiversity
• ecological complexity
• filtered water
• farmable plots interspersed with the Orang habitat
• fuel ethanol from sugar palms Arenga saccharifera
• 3000 new jobs locally

all articulated in a modest, even humble, way in 20 minutes. 20 minutes is the attention span of the attendees at TED talks. They need $5000 as well for the privilege of hobnobbing with 'Effectives' like Willie Smits and other people who have $5K of disposable income. Smits' presentation was so compelling and so neatly tied up with a ribbon and bow that it generated a standing ovation. Too good to be true?  Too good to be even truthful?? Some people thinks so.