Monday, 6 December 2021

Virtual evolution

Psychologist William James (*) characterised the world of a newborn child as a “blooming, buzzing confusion,”; we spend the rest of our lives trying to make sense of it all. With the development of language we can explicitly put labels on things out there [Mom; the other feller; the pink dinner, the beige dinner; Mitsy, the cat next door, Cats] but even illiterate animals, like Mitsy, can put things into bins and react appropriately - food = good; sea-water = bad; dogs = proceed with caution. Most folks go through their entire lives (like M. Jourdain in Molière's le bourgeois gentilhomme who is surprised and delighted to have been speaking prose for the last 40 years) doing this with realising they have the skill. Many of us, for example, have been forced into a radical re-think of pronouns in recent years because {M/F, his/hers, ♀♂} is clearly a bit of a BLunT insTrumenT.

I'm a biologist, not a very good one, out in the field, but I think a good bit about taxonomy - the science of classification. I've written about a profound discussion we had sous le pont d'Avignon about how to lump living creatures into appropriate bins. Some schemes work better than others - because they make better sense - they generate more internal consistency; they make the world a bit less random. "Have wings" is kinda useless because it includes wasps, fruit-bats, mansions, buzzards, 747s, football teams, dragons and angels. It's not always obvious either: whales really are streamlined hippos.

I think this is an important concept to get over and when I was teaching "Evolution" and "Genetics" back in the 80s, I used Caminalcules [selection above: from] as a defined dataset to help students think in classificatory terms. These delightful creatures were invented by Joseph Camin the the 1960s. He started by drawing a cartoon animalcule and imagining how it might evolve. Changes were made to a copy of the original drawing and so, iteratively, through several subsequent generations down several different paths.

At some point Camin aka God called a halt to evolution and assembled 29 extant / living species on a single sheet of paper for a student exercise in practical thunk. The task was to use scissors to cut out each of the 29 Caminalcules and put them into bins of similarity. Like mammalian classification, the task is probably recursive: dogs are more like wolves than either is to foxes; leopards is pretty close to those lads; but cows and bats . . . and wombats are further and further away from Fido. I started doing the same in the 1980s: we'd work in pairs initially; pause, compare notes, discuss, adjust and finish up with a solution that pleased everyone in the room. Usually next year's class was in close agreement with their prev peers.

An additional task is trying to infer the ancestors of the 29 leaves at the end of the branches but that was more than my students needed. Having The Answer in the fossil drawings which Camin had made seemed a bit luxurious to me. In the 1990s, I shifted countries and emphasis and started working on DNA and protein sequences and using them to infer evolutionary relationships; and the pattern and process of evolution along the way. In the 90s there was no fossil DNA (and no fossil-fossil missing link whales, for that matter) so a great deal of the effort was inferring ancestral states in the sequence tree.  This century, Dan Bradley and Lara Cassidy at TCD [yes yes and lots of others across the world] have opened up another dusty can of worms by getting to sequence ancient DNA. Now you can ask 23andMe just how Neanderthal your brow-ridge is.

(*) It might be worth noting that William's younger brother was writer Henry "The Turn of the Screw" James.

Sunday, 5 December 2021

Sintaklaas today

Bring on the boterletter

Friday, 3 December 2021

Timber Wars

Joseph Wood Krutch: When a man wantonly destroys one of the works of man we call him Vandal. When he wantonly destroys one of the works of God we call him Sportsman . . . or a logger.

Following on from my education about the interconnectedness of Salmon, I found myself listening to the a 7 part podcast from Oregon Public Broadcasting called Timber Wars or how the spotted owl Strix occidentalis [R ¿looking hunted?] helped save [fragments of] the old growth forest in the Pacific NorthWest. As we saw in my previous, the forest provides food, shelter, gravel and ambient temperature for the very first teeny-tiny stages of this beautiful and tasty fish. And, of course, the forest as a million year developed ecosystem is home to a beboggling variety of insects, molluscs, fungi and and potential antibiotics . . . as well as board-feet of building lumber.

Wednesday, 1 December 2021

New Faller

 There was a time in my life when I had to spend a regular night in Dublin and was too thrifty to pay for a hotel. It was almost always because that night was bracketted by two long days pushing the frontiers of science at work. In those noughty days, you could get a clean bed and toast for breakfast for about €12 and I made it a bit of a project to spend my money widely to see which hostel offered the best value

I now find that I've gotten to know, and paid, quite a number of tree-surgeons and found that some are more fun than others; some are cheaper in the long run; and one was a nightmare - a bully who did none of the physical work but scraped half the actual money into his pocket. That bloke came with three other people - the tree-monkey upstairs and two fit young chaps to do all the pully-hauly ground work. All I had to do was a) pay b) stay out of the way. That was efficient but also wasteful as a goodly amount of [what I would call] firewood was pushed through the chipper without heating anyone's living room.

Ideally, 1 would like to have a couple of days to process the branches rained down from above and only chip the twigs and ivy that were too small to pass as kindling. But in practice it never works out like that because the groundlings have to clear the brash away from the base of the tree lest it builds into a nightmare log-jam higher than a tall man can reach. It's heavy work and has to be done quickly . . . and I think I may be getting to old for that nonsense.

This Summer, ash die-back Hymenoscyphus fraxineus really began to make its presence felt in at least some of the ash trees Fraxinus excelsior on our farrrm. A few weeks ago, a new kid on the tree-surgeon block sailed over our horizon for having sorted out a dangerous beech tree Fagus sylvatica belonging to some pals from the next county. We gave him a call; he came to scope the problem the next day; gave us a reasonable quote and a date three Saturdays thence. The immediate problem was the two ash trees which loom up behind the house, with heavy branches hanging over our little slated toolshed and the heating-oil tank. Eventually these branches, weakened by die-back, will crash down; probably at night in a desperate storm. Before that the tree will be unsafe to climb and so beyond controlled demolition. So we're moving early while the problem is still soluble with money. Three weeks gave me enough time to rig a temporary shelter over the oil tank [R] - if that gets cracked or upset we may drill a new well. An unintended consequence was it provided another reflective surface to annoy our psychotic window-bashing blackbird.

I was far too busy hauling branches about to take time to photo-document the process, but I did take a snap of Seán high up in a denuded tree [L to compare with the Before picture from July]. Yes, he is walking out along a branch 12m up, suspended by a safety rope attached to a residually higher part of the tree. The dense green to the left of this picture all came down after lunch. None of the falling timber, bar leaves and twigs, fell on the oil-tank shelter or the slated roof. But I'm glad I made the lean-to: an in$uranc€ pay-out is never as much as the disruption and inconvenience of a significant accident occurring. A huge pile of brash - maybe 20 cu.m. in size - was passed through the mulcher: about 70% fired directly into two 1 tonne builders' bags. I spent an hour the following week raking up the rest of the mulch spatter and bagging that too. A garden can never have enough wood-chip. Another unintended consequence is that we can now see the mountain from the yard in front of the house; so that's a win.

I tell ya, sad as I am to have one less tree to hug, felling out those too-close-for-comfort ash has been a load off my mind.

Monday, 29 November 2021


"I wish was as certain if anything
as Tom Macaulay is of everything"
maybe Lord Melbourne

I've been listening to "Don't die in Autumn" by Eric Dempsey, one of Ireland's champion birders and twitchers. As a Dubliner who left school without doing his Leaving Cert, he'd be uncomfortable with "ornithologist". The title is from an injunction on his parents to stay out of harm's way at the time of year when Ireland is, hopefully, storm-spattered by rare vagrants from North America and Southern Europe. Fifteen years after leaving school to work for P&T, he presented his parents with the first copy of his first book The Complete Guide To Ireland's Birds with "There! that's me Leaving Cert!". They were most extraordinary parents for 1960s Ireland: not afraid of The Church . . . or child-thumping teachers; proud to be trade unionists; proud to be working class; interested, interesting, supportive, literate and generous.

Young Eric was interested in wildlife, particularly birds, from an early age but he was able to build up his "tick list" of species seen during the Post Office Workers strike of Feb-Jun 1979, when the young chap was turning 18. After a bit of picketing in the morning, all the strikers had the day off, and Eric hitched lifts further and further afield from The Bull Island slobs and the Tolka River in Dublin. It's a strange community - birders - intensely competitive but also generous with information and mentoring. Nowadays rare finds are announced on Twitter . . . down to the very field or hedgerow or dune where t'bugger is lurking. In the 1980s, domestic phones were rare as hen's teeth and news would arrive from Cape Clear by letter [except during the post-strike, of course].

In 1990, Dempsey set up a premium rate phone line Birds of Ireland News Service or BINS - a clever play on binoculars - the birder's essential tool. News was collated of any interesting observations from all over the country and updated at 2130 hours every night . . . for 20 years. That nightly report was sorted "by rarity", so that real obsessives could drop the phone after "the emu seen last week in Cork is now behind the schoolhouse in Ballycotton . . ." and set off into the night in the hope of catching a glimpse before sunrise the next day. Like everyone who reads content on the internet today and complains about paywalls, in the 90s, there were plenty of begrudgers who complained that information used to be free before BINS came along. Free maybe, but neither time-sensitive nor reliable.

Dempsey is clear evidence in favour of Universal Basic Income, so he could spend all waking hours pursuing his passion, building his skills and sharing his knowledge rather than shifting the burden of supporting him onto an employer who was heedlessly short-changed with a rota of sick-days, leave-days, personal development days, "training days" in a remote location. I don't think he ever ran out of grandparents that he had to bury because, in Ireland, funeral attendance is expected for aunts, cousins, old teachers, employer's collateral relatives, and anyone from the GAA team at the home-place.

After several decades of mitching off  work to go a-twitching, Dempsey reckoned he could go free-lance and make a living sharing his expertise by writing books, giving lectures and guiding enthusiasts less knowledgeable than himself. In one telling incident, he brought a group of 20 absolute beginners to Cape Clear to see what they could see. It turned out that a Baltimore Oriole Icterus galbula [L] was "showing" in a garden on the island. But a score of well-known twitchers refused to let the tyros see this rare vagrant . . . and even cold-shouldered Eric when he returned alone. It's hard to view this as anything less than begrudgery and passive aggressive indignation at . . . something? That was his Road to Damascus: he abruptly stopped competitive twitching and started to celebrate the ordinary: bullfinch in the grass; choughs on the cliffs; dunlins on the beach.

I was in the yard the other day and heard a raucous cackle from our little woodland. I wish I could, from the sound alone, recognise the species. I wish I was better at sorting out hawks, buzzards and falcons in flight. I delight in the colours of bullfinch and kingfisher. But I'm not going to turn my life upside down to sort out the LBJs [little brown jobs] of which Ireland has a confusingly large number. I'll leave that to Dempsey and my friend Des. Here's a task for you:

identify the species which feature above as thumbnails above
Over the years, several readers have complained about the quality of the bloblistrations: it being true that I do try to save bandwidth electrons. But don't use that as an excuse to disengage from the task. Dempsey and Des could recognise each of them at 100m, half obscured by shrubbery, with the last photons of eventide.

Sunday, 28 November 2021

Bunyan Bday 1628


Saturday, 27 November 2021

Arwen Incommming

You may remember my piece-to-camera in September about the naming of 2021-22's storms: Arwen; Barra; Corrie; Dudley; Eunice; Franklin; Gladys; . . . It will be hard to take seriously a boy called Sue a storm named Dudley; but Storm Arwen is on us since yesterday:

For us, the circle marks the spot and 37km/h is pretty mild on the scale of storms. We are protected to a certain extend by a looming Mt Leinster to our immediate North. But the Northern coast is taking a pounding and an unfortunate driver in Antrim has been killed by a falling tree. While over on the bigger island, it is gusting 150km/h; trees are down; railways are blocked in Scotland; and sleety snow is adding to everyone's misery. Meanwhile, much further South Gdau.I reports snow in [the] Bath. Winter has begun.