Monday, 23 May 2022

History intersects genetics


Science is about finding out. It really makes little odds what scientists study: just let 'em at it. Because the hunt for this thing I have found out is rather a poor predictor for this discovery is a manifest good. Attempts by government, patrons or sponsors (who know bugger-all about science) to guide, let alone dictate, how scientists should spend their time generate a rather poor return on investment. I spent my 20s in a quixotic pursuit of those furry bags of genes known as cats. Not to pet or use to catch rats; but rather to document their variation and see what this could tell us about human [and cat] migration patterns. In my defense, I will say that documenting the coat colour of some thousands of cats from both sides, and the middle, of the Atlantic Ocean cost very little money. Much less than I flushed down the lab sink and spattered over my face during my 6 months of doing real science in a molecular biology lab.

My 'expertise' in the genetics of cat coat colour came back to bite me when Dick Ahlstrom and Aoife McLysaght launched a crowd-sourced investigation of genetic variation in cats in 2015. With results. And much more recently, it transpired that our data from the Azores might be relevant to explainthe peopling of that archipelago by . . . vikings. Normal science is when you spend a few decades doing what your PhD thesis supervisor taught you to do: using the same familiar techniques to crack ever smaller nuts. It can be comforting in a religious practice sort of way - decades of the rosary essentially the same as repeated runs of the PCR machine.

I was careless and clumsy in the laboratory, even when I wasn't being a danger to myself and others. So I was better off on the streets clocking up a tally of feline field notes. When it was raining cats and dogs - and therefore no cats would be out on the streets to be clocked - I was happy to ring the changes in the library reading about New England settlement patterns, or the development of the canal network in Britain and Ireland. I recently mentioned an ancient library search which came to no conclusive end about tailless cats in New Brunswick. 

At the very beginning of my career as a researcher I took advantage of the extensive library of Trinity College Dublin to document the existence of mutant genetic variants more than 1,500 years ago - before the Vikings indeed. I discovered that there was a late medieval translation into Englyshe of De Natura Rerum [On the Nature of Things] which was compiled by the saint and scholar Isidore of Seville in about 600 CE. What floated my boat was that Isidore described the colour morphs of cats that were familiar to folks living in Andalusia all those years ago. Some catte is whyte . . . etc. With my knowledge of Mendelian coat colour genetics, I was able to show that certain allelic variants had been around at least that long. I wrote it up as a note for Carnivore Genetics Newsletter C.G.N. and this insight / angle / result has effectively sunk without trace! 

All this backstory about me interfacing Science with The Arts Block is merely softening you up for a right nifty story about using still life paintings of know provenance and age to establish not later than baseline for the appearance / development of known varieties of produce. Ive De Smet, Plant geneticist, and David Vergauwen, art historian, were intrigued by fruit and veg, plainly intended for eating just as soon as the artist had finished his daubs, that appeared in still lives from the early modern period. That's when technique, training and materials had developed to the extent that painters aspired to create photo-realistic images from a reality they could see . . . and smell.


Ive has a sciency set of tools at his disposal, DNA sequencing can reveal biochemical pathways essential for producing flavor compounds [bananas = amyl acetate etc.] and molecular clocks can estimate the time these traits  were acquired by counting the changes in the DNA since the last common ancestor. But the parallel Art project requires someone to stand in front of a given still life and determine whether tomatoes are present and, if so what colour they are. Browsing a catalog on-line just doesn't have enough detail to be diagnostic. Volunteers sought! chekkittout:
#ArtGenetics on Insta or on Twitter.

Sunday, 22 May 2022

Miss Ellen Annie May

It's exactly 50 years since leftie 1930s poet Cecil Day Lewis passed on.  He was born in Ballintubber, Queen's County, not a million miles from my people. But he's buried in Stinsford, Dorset not 10 million microns from Thomas Hardy. His son is still running. Daughter still cookin'.

Poetry? ‘Home is the place where, when you have to go there, they have to take you in.’ Robert Frost.

What else?

Friday, 20 May 2022

Careless

In 1966, a young Ethiopian was studenting in NW England when she fell pregnant. Her son was born in March the following year and shortly thereafter the student had to return to Ethiopia after a death in the family. The baby was left in the care of Wigan social services. The first half of his minority were spent as Norman Greenwood fostered by Mr and Mrs Greenwood, devout and rather doctrinaire Baptists. They couldn't adopt the child because that would require consent from the birth-mother, who was uncontactibly abroad. The Greenwood's believed that they treated young Norman as one of their own children but that wasn't really true. To do that, the parents would have to be a) much kinder than most of us are b) oblivious to the actions, reactions and prejudice of their community. 

The story is related in My Name is Why? by Lemn Sissay, my latest Borrowbox audiobook. Guardian review. Young Norman was a sparky, super-friendly, sporty, outgoing child. Energy and openness that is adorable in a boy can take on a different complexion when that same person <teen alert> starts to think for themselves, challenging the roles which everyone seems to be playing. We don't hear directly from the Greenwoods, but the book intercalates the boy's narrative memories with excerpts from his fat, partially redacted, dossier from Social Services. Wh'evs, rather abruptly, when Norman was 12, the Greenwoods decided they didn't want to play any more and requested-and-required that the fosterling be removed from their home before Christmas.

Norman's life spiralled downhill from there: untimely ripped from the bosom of the only family he'd known, he was shunted through a variety of residential homes in Wigan challenging the status quo. Being minded by people who had their own issues and troubles and who were increasingly poorly resourced as the Thatcher-Tories worked to dismantle the welfare state. It wasn't a great place for a troubled youth but social services stoutly and smugly believed that he was better off with them than in, say, Ethiopia. He, au contraire, was determined to celebrate his Ethiopian heritage . . . with ganja; but also by discarding Norman Greenwood and going by Lemn Sissay, the name which he'd been given by his other before she bunked off.

My name is Lemn Sissay
My name is Lemn Sissay
My name is Lemn Sissay

He spent the last several months of his childhood marking time in the Wood End remand centre; where the most troublesome = troubled youngsters were subjected to institutional bullying, sexual and physical abuse on a daily basis. The thing is that employees of such places are not conscripted from the general population but rather self-selected from among those whose sense of self depends on being alpha cock on the dunghill.

At the age of not quite 18, partly through his own determination and partly because specific people working for social services were prepared to support his attempts to fly solo, Norman was airlifted from Wood End and installed in a council flat to mind himself. At the same age, both Dau.I and Dau.II in turn left home to make their own way in the world. They were able for that because they'd been brought up in a secure, safe and loving home, embedded in a wider community of tolerant, supportive and caring adults. No chance of a council flat for them, though; the aspiration that we should all care for the dispossessed has gone the way of flared trousers. Inevitably, because I've read both books, comparisons can be made between Lemn Sissay's memoir and Mark Hodkinson's hard enough tale of growing up the other side of Manchester, at about the same time.

The boy done good, though! Lemn Sissay was given an MBE in 2010 and appointed Chancellor of Manchester U in 2015. This year, his MBE was doubled up to an OBE. He has become a bit of a celebrity as a writer, television personality and public commentator. A Desert Island Discs personality. But it's not good enough to point at Mr Chancellor Sissay OBE and believe that anyone can pull themselves by their bootstraps. But that's just not true!: escaping from the underbelly of society is the exception. Only exceptional people can achieve success [however defined] from such unlikely beginnings. But they also need the breaks! A little luck; a little mentoring; someone who'll take time, make an effort for someone else. And while we're about it, can we remove broken people from being in a position of power over children? Thanks, that would be a start.

Wednesday, 18 May 2022

Clear as day

Dau.I, the family [photo] archivist, was home over Easter and showed us a 2005-dated photo of our polytunnel covered in [super clear] plastic. That really helped nail down the date: pre-Blob documentary evidence is rare and patchy. The tunnel is therefore almost old enough to vote! But like dogs, polytunnel years are not the same as human years and, like me, the tunnel is feeling its age despite having only 25% of my calendar years. Accordingly, in March we went on a jaunt to Highbank to scope out the cost of replacing the plastic. Polytunnel tech has moved on since 2005 and wooden frames are now considered supremely out of style. We got a blizzard of information about the New Way with polythene fixin's. Although we still agreed that a total re-cladding was required, enough unresolved logistical questions hung in the air that we put the whole project on hold. Eventually I called my tunnel-mentor Rene to have him explain the difference between Richel double clip rails and single Richel clip cladding rails and why the latter might be 3x the cost of the former. A few things became clear: 

  • in 2005 the cost of the plastic sheeting €240 was the most expensive part of the inventory; (4 x 2)s, (2 x 1)s and screws being cheap as chips
  • in 2022 the plastic was a small amount €420 compared to all the steel engineering infrastructure
  • I've lost my mojo for bodging things up from scraps and off-cuts

Being a highly suggestible sort of bloke, it was easy enough for Rene to convince me that a good clean was the way forward and it would be a shame to dump out all that plastic for landfill. And, more importantly, with care and attention, there might be / should be years of life left in the ould tunnel. R and his pal C came up on Wednesday [midweek! when - I R retire - I didn't have to be at work offsite] with a vanload of hosepipe, brushes and power-washers and started to clean years of gunk from the top of the tunnel.  

I haven't been totally remiss from cleaning what I can reach with a 3.6m long-handled brush. It's a lot like the nun's instructions for bathing in a shift "first you wash up as far as possible, then you wash down as far as possible; then you wash possible". As our tunnel is 13m over the hoops, I've never been able to wash possible on my own. One time many years ago, The Boy and I tied ropes to the 4 corners of a very old foam-rubber-stuffed floor cushion, waited for a good wet day and did push-me-pull-you back and forth along the length of the tunnel. It was really difficult to clean the high-points over the hoops because the cushion would slide inexorably down into the inter-hoop troughs. You can see the contrast [above L] when C got his head higher than the tunnel top and applied a proper industrial window-cleaner's brush with skill and vim: L.L. after his attention to detail; L.R. awaiting his ministrations. 

And here is C himself advising me that the plastic will soon be clean enough to see, not only the hill on the far side of the valley, but the pixel sheep that dot its flanks. And it was so. More light brings out the best in the look-and-feel of the tunnel. But it must also be acknowledged that The Beloved and Dau.II (who was visiting) really cleared the decks inside, so that the boys could have a clean sweep at the task. Imagine how red would be our faces if C tripped over a lawn chair or a bag of potting compost while staring fixedly upwards as he pounded his brush against the interior dust-layer.  The prognosis seems to be that we are good for another year . . . and another. Until we have a dramatic event like Darwinday 2014 which tore the plastic from its moorings.  As a manifestation of good faith in old plastic, one reason for washing the stuff, while it is still spread out and taut, is that it will defo get reused / recycled if we decide to go with new.

Having clear as glass plastic is a mixed blessing. Wood pigeons Columba palumbus are hardly the smartest beasts on two wings. Yesterday I disturbed one in the tunnel and it flew up in a flap - WHUMPHing in to the plastic . . . repeatedly until I seized it with both hands and showed it the door. Not unlike our testosteropsychotic window thumping blackbird; maybe it's something in the water hereabouts? One reason that we might have a random pigeon lost in tunnel is that it is The Year of the Pigeon. Our trees, which usually support a couple of pair, are hosting a couple of dozen pair in 2022. Who knows why?


Monday, 16 May 2022

Fall of Icarus

 I've been paragliding, I even caught a thermal and almost lost my lunch. Then I had a bad take-off, landed hard and [it subsequently transpired], broke two ribs. It's 20 years ago, and I have no intention of having another go to get airborne.

Toby Ferris has been paragliding too. His Short Life in a Strange World Birth to Death in 42 Panels is my current audiobook. The conceit is that,
because he is 42;
because his father was recently dead at 84 [2 x 42];
because Pieter Bruegel the Elder's entire oeuvre is 42 attributed works
because Toby has two young sons himself
. . . he feels compelled to open the doors of perception, stand in front of each publicly accessible Elder Bruegel and reflect on life, death, the Universe and everything. No postcard, or arty book need apply - it must be a several years road-trip to be there. More Bruegel-inspired writing.

The first picture for such intense contemplation is Landscape with the Fall of Icarus painted in ?1558? and currently viewable at Musées royaux des Beaux-Arts de Belgique, aka Koninklijke Musea voor Schone Kunsten van België. Icarus himself occupies only a fragment of a Narnia like landscape and in deed only his legs and a drift of feathers appears above the wave - Bruegel has made him a shocking but incidental, distant, event in the broad sweep of late-medieval normality.  The painting whooshes Ferris back to his paragliding days when a more experienced, divil-may-care member of his group foolishly larks about while aloft swinging wildly beneath his canopy . . . until he spills all the air from his vital support and plummets to earth; landing with a reverberating thump, on his back, in the gorse. Fantastically he is not dead or even seriously injured. although he spends many weeks in hospital recovering from the results of his folly.

Actually, The Fall is not nowadays believed to be the work of Bruegel de Oude, but rather a copy of a Bruegel original; indeed maybe not even that. But details or attribution should never stand in the way of a great story of real life imitating art. Indeed, the existence of many copies of many certain-sure Bruegel have been valuable in abstracting meaning and de-layering the palimpsest of a work of art. There are, for example, no innocents in the original of the Massacre of the Innocents, all the slaughtered children have been over-painted as sheep, or parcels, or geese. But the full monstrosity of the tale is in your face [and heart] in many of the numerous extant copies. Many of these copies were generated by the atelier of Pieter Breughel the Younger, a man with more acumen at cashing in on his father's legacy than actually applying paint to panel.

Short Life in a Strange World [excerpt] is a find, in that I chose it, because available within a month, after scrolling scrolling scrolling through the finite catalogue of audiobooks available on Borrowbox. It works fine in the ear: I've had it along for the ride walking the hill, washing the dishes, doing the messages and is not too much of a loss that I can't see the the picture described in such obsessive insightful detail. You may get a little TMI about the issues & peculiarities of the Ferris family but maybe that will encourage you to look at the dysfunctions of your own tribe. For a man born just about 500 years ago, Bruegel's reflections on hatching, matching and dispatching haven't become a whit less relevant.

Friday, 13 May 2022

Minié killié

I've mentioned evidence to suggest that conscripts are reluctant point a gun at The Other side and pull the trigger. It is based on analysis by Dave Grossman of unfired, loaded rifles picked up after the slaughter at Gettsburg. It gives a certain hope for the world that individuals will have agency for good deeds even when The Man is trying to dehumanize both parties - killer and killee: “a bayonet is a weapon with a worker at both endsas John MacLean has it.

I am currently on a spellbound [L: list words >4 letters including the middle letter] jag. It takes longer than worldle. I think the original idea for spellbound was launched as Spelling Bee by the NYT but I heard about it as a MetaFilter project. It is a teeny bit frustrating that perfectly good words - achene, tarn, filo - are rejected by the game editors but I'm not going to threaten to eat their first-born about undaunted. The other day I had a spellbound punt with MINIE having a vague idea that it was some sort rifle. tbh, I can't remember whether this was allowable to the wordlist editor or not, but it hooshed me off down a rabbit-hole . . .

Claude-Etienne Minié (13 Feb 1804 – 14 Dec 1879) was a french army officer who solved an intractable battlefield problem: how to fire bullets quickly and accurately at the enemy. It had been discovered earlier in the 19thC that accuracy could be enhanced by imparting a spin to the ball as it left the barrel; and that this could be achieved by 'rifling' the inside of the barrel with helical grooves. Furthermore, it was cclear that a tight fit between ball and barrel would impart more whoomph to the bullet. Breech-loading was in the future, so gunpowder charge and bullet had to be forced down the cylindrical orifice with an, appropriately named ram-rod.  The ram rod became another piece of kit which could be lost, bent out of shape or inadvertently fired at the enemy in a fog of terror.

Minié's insight was to replace a roughly spherical ball with a slightly smaller cylinder which could be dropped, rather than tamped, down the barrel. The front-end of the Minié ball was streamlined but the back-end was hollow. When the powder ignited, the ridged skirt of this pocket splayed out to engage with the rifling and capture the full impelling force. The Minié ball combined more shots an hour with accuracy and a devastating 1oz = 30g crump when it made contact with the target.

Hundreds of thousands of soldiers were killed by Minié balls, first in the Crimean War where Minié rifles were available to the British/French allies but not to their Russian opponents. The damage was considerably greater in the American Civil War where the Springfield Armory in Massachusetts turned out more than 1 million Springfield 1861 Minié rifles. The Confederates relied on then British for Enfield Pattern 1853 rifle-musket.