Saturday, 16 February 2019

Whom do ye think you be?

Who said a good PhD didn't land you a dream job? Certainly not Joshua Katz, in 2013 a graduate student at NCSU (North Carolina State University) who made some lovely English dialect maps for the USA. You say pop and I say soda and I'll fight you for it because you're wrong. He now works for the NYT and has put out a crowd-sourcing information gathering tool, especially for those who learned their English in the WEA. You really should do the test - it's really fascinating for a mongrel like me with i) a Scottish granny, born in Limerick who lived all her adult life in Dover ii) a father born in London in 1917 and raised in Dunmore East, Co Waterford iii) a list of domiciles longer than will fit on a Garda Vetting form. Katz's software, built on 73,000 [and rising] contributors, smoked my Dover connexions quite clearly [see below], despite my habitually using Irishisms like skanger and eejit. I don't use 'lack' for girl-friend [as in the very focussed map [R] despite my father's Waterford credentials.  Yere's me:
It's really as if I hadn't spent the most recent half of my life in Ireland. But then again, language has quite a bit of inertia, it's hard not to use the slang and curses which you learned at school.
By comparison, The Boy was born in Dublin, left a year later and didn't return until he was 14. Despite 7 of those years being spent in Newcastle upon Tyne, his language is distinctly and surprisingly Irish. Living the most recent ten years of his life in England has had no impact whatsoever. Dau.II [and her sister] was born in a draughty farmhouse near Dublin Airport, she grew up on a different farmstead in the rural hinterland of Leinster and left home to live in Cork City Centre just before she turned 18. Despite this she [above L] speaks middle-class southern [England] received pronunciation. It must be because she didn't go to school but spent all her minor years sleeping in an outhouse, except when she was compelled to clean out the chicken-shit or carry buckets of feed to the sheep in a remote field. That, or the binge-watching of boxed-sets of Kenneth Branagh.
I've sent the link (which came to me from Dau.II) to my brother and sister in England. We grew up in the same highly peripatetic household but have lived all our adult lives in different counties /countries of the WEA. I'm really interested to see how similar our sib-dialects are.

Friday, 15 February 2019

Street-light biology

There it is [the Mountain River] running under the (locally) famous viaduct of the long defunct railway that went from Bagenalstown to Wexford between 1858 and 1947. For the last 15 years of its existence the railway operated solely for hauling sugar beet from Ballynowhere to the Sugar Factory in Carlow. The town of Borris, which runs up from the river valley, abstracts its drinking water from the Mountain River, fouls it, treats it and discharges the effluent a little further downstream. It is just as well that, like time's arrow, water flows in one direction. The Public Meeting was called, for 1930hrs 13 Feb 2019 in the boutique wee hotel at the top of the town, to encourage dialogue between ordinary people on the ground OPOGs and All Agency Experts AAEs who occasionally parachuted in to make some desultory, irregular, duplicated, uncoordinated measurements of the river before flitting off to the next project.
  • The OPOGs include 
    • anyone [N=800 incl. 80 Polish-originally] who has to drink the water in Borris; 
      • The town's main's water supply installed in the 19thC was replaced in 2017: Causing transitory transit-jams but great reducing the leakage of treated drinking water
    • farmers with bank-side fields [that would include us as owners of The Field Over The River Aughnabrisky] anywhere up the catchment area; 
    • anglers; 
    • hill-walkers; 
    • fly-tippers.
  • The AAEs include
The Public Meeting was for Consultation on the local River Basin Management Plan RBMP [we are not nearly finished on the acronyms!]. They were hopelessly optimistic about the amount of interest in their work: the hotel's ballroom was rented and 50 wedding-reception seats were laid out in an arc; 15 OPOGs turned up only just exceeding the functionaries who had to be there to answer questions and explain what they had been doing with their time, and our money, since the Local Authority Waters Programme LAWP kicked off two years ago. The OPOGs were not exactly hostile but were certainly critical of how their tax-payers money had been, and would be, spent. The LWAB, for example, just for the Sunny SE of Ireland employs seven people to carry out audits of water quality.
  • One of our OPOGs had been asked by ALL the AAEs for permission to walk through his fields to access the river. "Do you share your data with the Fisheries people?" he asked but what he meant was, the fellow from Fisheries was knocking on my door three weeks before you came. In a free and transparent society these data should be put up in the public domain; as well as the intended schedule of sampling so that IFI and EPA could, say, share the petrol costs. The subtext here was that maybe either the EPA effective or the IFI effective could be laid off and we-the-people could save €80K salary+costs+mileage+PRSI a year. That would go a long way to making the Water Treatment Plant in Borris functional.
  • Another farmer worried that the River Barrow was running dry . . . because so many entities were abstracting water. That's a worry because there will be less water to dilute any accidental (or deliberate) discharge. We wouldn't need water treatment if we banned flush toilets.
  • None of the OPOGs at the Wednesday meeting admitted to fly-tipping their trash over a convenient bridge across the Mountain River, but many asserted that it was a regular occurrence under named bridges in their neighbourhood. 
    • If a hoodlum fires a used soda bottle out of the window, I will clean it up during the annual An Taisce Spring clean.
    • If a hoodlum dumps a load of car-batteries or paint-pots into a river someone has to clean it up ASAP (I'm too busy with the bottles). Leaving them there leaching toxins will make a disaster out of a problem. This is not the sort of things that the County Council prioritises: the crud is out of sight from the road and will cost a lot of billable hours to clean up. 
How do assess the quality of river water? The quick-and-dirty way is to jump in the river and do some kick-sampling. This is what LAWPers do: they kick-sample a bucket of aquatic invertebrates out of the river and count the numbers for different key species of creepy-crawlies. If you find caddis-fly (Trichoptera spp.) [example L] and mayfly larvae, (Rhithrogena semicolorata or Ecdyonurus venosus), the water is safe to drink. If they are absent you may not know exactly what's gone wrong with the ecosystem but you know it is poor quality. You could be much more expensive and "scientific": quantify the metals with AAS or FES; measure the nitrates; the Biological Oxygen Demand BOD; TriHaloMethane THM . . . but that would take time, kit and money. otoh, you're not better off by checking for key mammals like otters Lutra lutra: because that species is rare there is not enough granularity in the data. After the talk Ipulled on the lapel of the head LAWPer to suggest that kick-sampling and counting caddis-fly larvae is sooooo 19thC and salary-time-consuming. Why not, I suggested, take a sample of water + river-bottom and run it through a DNA sequencer. It is so cheap to sequence DNA now  and that will give you an estimate, not only of the countable invertebrates but also, of the microbial community . . . and probably the fish species as well from the fish-shit. Concentrating on the countable is a classic example of street-light science: it gives you a handle on what's easily available which may be almost irrelevant to a true measure of biological diversity or water-quality.
It was clear that DNA analysis hasn't arrived in LAWP-land yet - if it ever will. I therefore switched tack and asked what they were doing about [measuring, legislating for, informing the County Council] light-pollution. Here I must confess that I was channelling my pal Rene from St Mullins who, before he left the Netherlands 25+ years ago, was fattened on eels Anguilla anguilla. When he arrived in St Mullins on the River Barrow in the early 1990s, eels were plentiful. When they came back from the Wild Sargasso Sea as hatchlings, some of them turned right and swam up up the Mill Stream in search of a new home. Then the County Council installed a street-light on the narrow road bridge that crosses the stream as it met the Barrow. That was end of eels up the Mill Stream - they travel at night, avoiding light, which exposes them to predators. Same thing happens where the Mountain River goes under Main Street in Borris. Light and Dark are natural! they happen every 24 hours many / most / all animals have adapted to the change. Now, for the trifling convenience of people walking to the pub at night, we have daylight all night with utterly unconsidered consequences for the natural world.

Thursday, 14 February 2019

Flangefokker

In case you wanted more Zoo Breeding [yest] here is a funny-ironic story about sex among endangered species comes from Basel Zoo's Orangutans [Pongo abelii]. The total population of this species is down more than 50% in the last 100 years. There has been huge habitat destruction [for palm-oil plantations and Japanese hardwood furniture] in Borneo and Sumatra and poaching - not to mention the market for captive apes for zoos - but there are still more than 60,000 out in the wild.  Conservation efforts have been complicated by the fact that there are three species of Orangutans each with sufficient genetical, behavioural and cultural identity to justify saving all three. Pongo abelii on Sumatra Pongo pygmaeus on Borneo and another far rarer variant Pongo tapanuliensis living in a separate part of N. Sumatra. Deciding on what is a species and what is a mere variant or sub-species is not a black & white problem. The ultimate test should be whether a male and a female from two groups can produce fertile offspring. But that's a long haul - maybe 30 years for Pongo - and there is some urgency in the matter: in 30 years all the wild orangutans may be dead.  So conservation biologists tend to take a tissue sample (saliva or blood easiest, turd is enough IF you can get access) and sequence [some portion of] the DNA. The % identity acts as a surrogate marker for actual co-fertility.

If we believe that each species is a unique assemblage of traits (genes, behaviours, microbial hitch-hikers) then we can freeze dry some sperm and egg and send them off to a long-term storage facility like they have on Svalbard. OR (and this is the usual preference of active zoo-keepers) we can try to establish sustainable populations of captive born-and-bred individuals for re-introduction into the wild . . . after Armageddon reduces the number of people to more sustainable levels. That unique assemblage of traits is more than a single ape can carry, so the plan is to retain as much genetic diversity in what is available in the zoos and circuses of the world. That means a structured breeding program to mobilise semen from as many healthy males as possible. Nobody in the ape-breeding business believes that a super-fit wonder-male should be identified to 'improve' the species although that is the basic protocol in breeding cattle and other domestic animals. That shows a commendable humility about knowing what is best for wild animals. Diversity is certainly good for the future.

Which brings us back to Basel. With a rather Calvinist outlook on morality among their captive primates, the Zoo has separated their orangutans into 3 family enclosures, each with a [Ma+Pa+offspring] demographic. When Padma the most recent female cub was born, the management took saliva samples from all nine members of their herd stock and sent them off for paternity testing. Ooops! Budi, the younger male who was cohabiting with Maja, Padma's mother, was not the Dad. It seems that, despite a chain-link fence separating them, Maja had got it off with Vendel [R] the Patriarch next door. Clearly the old lady knew whom she fancied. There is speculation that Vendel's attractiveness lies in his 'flanges' - the horizontal dewlaps that surround his face and emphasise the size of his head. Budi may have a six-pack, but a well-turned flange - which only develop in some males with maturity - makes the ladies swoon . . . or at least present their bottom.

Zoos talk large and strong, especially at Christmas when the WWF is drumming for money, about their value as an ark for animals whose habitat in the Third World has been destroyed by people and corporations. But Zoos are also in it as a business - however much subsidised by local and national governments. What brings 'Gate' more than anything else is a new-born addition to the inventory - especially from a cute species - great apes, pandas, bears . . . other large carnivores at a pinch. If they were really interested in the welfare of their breeding stock they wouldn't put the animals out as a raree show for the public where the animals can be assaulted with coins, inappropriate food, and a deafening hubbub of cries and whistles.

Great apes, being clever enough to spot an opportunity to escape from Stalag MenschenAffen XIX, used a storm-broken branch to leave their enclosure in Belfast Zoo last weekend [video footage]. Being seriously institutionalised they didn't much like the open space and small edible children of The Outside and were easily persuaded to return to ad lib bananas Inside.

Wednesday, 13 February 2019

Tyger tyger

In 1977, I knew as much about inbreeding in captive tigers Panthera tigris as anyone on the planet. That was because I got access to data and the tools to analyse it and presented the results in a reasonably coherent report. The data was all the Dam-Sire-Cub triplets from Dublin Zoo since they started one of the early and very successful captive breeding projects. The tools were TCD's mainframe computer and some software written by a graduate student in Agricultural Genetics called Garry Mahon. Garry's programme, which was designed for horses and pedigree cattle, could work on any data where each individual had a unique ID and its parents were recorded. It generated a family tree and flagged cases where the same ancestor appeared in more than one branch. With a complete dataset it was a doddle to run several potential matings through the mill and decide which was least likely to  have offspring with a pair of deleterious [bad] recessive genes. I keyed all the data onto punched cards in the required format and Garry (who had much higher status than me) took the stack of cards to the computer centre and loaded them in to be number-crunched.
I was on a roll. In the Genetics Department library I found a copy of The Evolution of Man and Society by C.D Darlington; and in that book was a family tree of the Habsburgs. I keyed in that data as well and wrote a report showing that the inbreeding coefficient was inversely correlated with the number of legitimate offspring each Habsburg had. Golly-me, there were several instances where a papal dispensation was obtained to allow uncles to marry their nieces. Vice is nice; but incest is best - the game the whole family can play. These dynastic marriages were all about consolidating wealth and power even if the family developed. The last Uncle-Niece liaison produced Carlos II of Spain [extreme L in the group portrait above; with the extreme underbite which ran through the family] who was slow, short, lame, epileptic, senile "so ugly as to cause fear" and unable to produce an heir. That was possibly because his post-mortem revealed only a single shrivelled testicle. All that extra work at the interface between Arts & Science cut no ice with the examiners when I booted my final exams.

Having made some progress in zoological book-learning in college, I worked in a zoo (Diergaarde Blijdorp, NL) for about half a year in the late 1970s. I was happy-out working there and I finished with enough money to start Graduate School. Everyone was very good to me, even allowing me to choose which male was was to be sperm-donor for a gravid tropical reef-fish.  The problems of inbreeding are still relevant in the captive tiger community and zoos will ship likely males across Europe and across the world to minimise it. Last week one of London Zoo's tiger assets, a female called Melali, was matched with a young male from Denmark called Asim. Shortly after the prospective couple were introduced, Asim threw a strop and attacked Melali who subsequently died of her injuries. That's the downside of these arranged marriages, some unfortunate female is chosen for her dowry, fertility or connexions and she has to bed a ravin' nutter, a senile old drooler or Tio Felipe.

Tuesday, 12 February 2019

Soak the rich

Hey folks, it's Darwinday 2019, Hissonour Charles Darwin, wherever he now be, is 210 years old today. He shook the tree and rewrote the narrative and mixed the metaphors about where we came from. He wasn't the only mover-and-shaker at the time, but he was extraordinarily well connected with the pacifist-industrial complex: his Wedgwood relatives were liberal anti-slavery entrepreneurs. I used to celebrate the day by buying dozens of doughnuts which all disappeared in a bit of a feeding frenzy without anyone reflecting much on Darwin or his manifold contributions to science and society. Nowadays I make a slab of flapjacks for my work-mates at more or less random times through the year when there is less expectation of a reaction. The Irish Humanists are borrowing a lecture theatre this evening from TCD to host Dr Ian Sanders talking about Meteorites and the Birth of the Solar System. It will be a piece of work to see how he works Darwin into his presentation. Darwin had thoughts about the origin of life "if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed", the origin of coral reefs and the origin of species but not so much about meteorites.

The birth of the Solar System is long long ago and we have more immediate things to worry / talk about. Did you hear Rutger Bregman's 'elephant in the room' comments about the "T word" at the World Economic Forum this year? He's an economic historian from Amsterdam and knows a bit about the differential consequences of changing the tax-regime and the dominant economic theories of The West. The World Economic Forum is an invitation only gig where the rich, famous and well-connected get to smooze with each other and compare the lengths of their philanthropic yard-sticks. They want to feel good, so they invite some articulate proles to give everyone a frisson of anxiety before they all return to their yachts and boardrooms and carry on as before. They may, in fairness, be induced to donate a bunch of money to the cause espoused by the cutest invited speaker - possibly Greta Thunberg who has gone a bit viral over her concerns on climate change; and so was a shoo-in to be invited to Davos. Davos is a quite like TED in its exclusivity: tickets for 5 days at TED cost more that ordinary people spend on food for a year.

Rutger Bregman's suggestion that we-the-people should TAX the rich (rather than deferentially waiting for them to dispense charity to people they consider deserving) has gone totes viral in the media where millionaires are a bit thinner on the ground than at Davos or TED. Here's an interview where he swats away the suggestion that high taxes for the rich are bad for economies. I'll leave it there; I don't want to start sounding all shouty.

Monday, 11 February 2019

Monoculture ungood

One of the iconic images of the early 20th century are fields of corn [that would be wheat Triticum aestivum not maize Zea mays] brightly studded with nodding poppies Papaver rhoeas. This lovely weed is sometimes called the corn poppy or the Flanders poppy to differentiate it from the opium ditto Papaver somniferum. And not just poppies:  cornflower Centaurea cyanus; corn marigold Chrysanthemum segetum. The corn chamomile Anthemis arvensis and the corncockle Agrostemma githago once common are now all but extinct in Ireland - done to death by 2,4-dichlorophenoxyacetic acid aka 2,4-D [branded Trimec].

2,4D is a selective 'weed' killer, a product of fundamental research into plant physiology that yielded a crucial insight into the difference between monocots and dicots. These are the two major divisions of flowering plants: monocots have a single leaf in the seed curled up ready for launch; whereas dicots have a pair of seed-leaves (think split-peas or your memory of growing mustard-and-cress on blotting paper as a kid). That's only the naming difference: they have many other aspects of their growth and develop that are not the same. Monocots grow from the base of the leaves pushing the old cells up in front of the still dividing cells at the bottom. That's why we have lawns: trimming off the leading edge with a scythe doesn't affect the meristem (growing point). Dicots otoh grow from the leading edge. As in ourselves, the growth, development and branching pattern of each species of plants is controlled by hormones which are switched on and off at different times and places and >!kaCHING!< you get oak leaves or holly leaves. All the cereal crops - wheat, barley, oats, rye, maize - are monocots; almost all of their competing 'weeds' are dicots. 2,4D acts like a growth hormone called auxin; when sprayed on the leaves of dicots, cells start to divide in peculiar places and the plant twists itself inside-out coping with the blizzard of hormone.  The  sown crop, being a monocot, doesn't respond in this self destructive way and all the water and nutrients in the soil are available to boost yield and profit. I call that clever in the immediate time-scale.

But . . . reducing the plant biodiversity will inevitably impact on the microbial life of the soil: microbes that 'fix' nitrogen, solubilise phosphates, sequester heavy metals, leech their own plant growth promoting PGP factors. Because we know bugger-all about the microbial life of any soil, let alone the particular soil in the Keogh's Springhill Field, it is impossible to quantify the adverse effects of a Kill All Dicots policy. I think I'm convinced that the soils have not been depleted of essential nutrients since the invention of 2,4D and other agri-chemical inputs that tip nature's scales in favour of yield.  But the fact that corn chamomile and corncockle have been heedlessly nixed forever on this island, suggests that other key species in the living web (about which we know so little) are dropping off their ecological niches like leaves in an autumn storm. Lost before we even got properly introduced.

Sunday, 10 February 2019

News nose newts

Noodles of Nything