Tuesday, 16 January 2018

It's not that simple

Do you like figs? Wasps? Well you can't have one without the other. When I was in Grad School in Boston, I was along the corridor from the lab of Tom Kunz, who taught us Mammalogy 504. He and his people worked on bats, not only the insect-eating chaps we're familiar with in Ireland but also the great flying fruit bats of the tropics. These lads are often part of a complex interacting network of mutually dependent species. The bats eat and disperse the fruit [bat gnawing fig L from Tim Laman] all over the jungle by eating the fruit off the tree and flying off somewhere quiet to digest it. In due course the seeds pass through the bat-gut and finish up as a smear on a tree-trunk, whence they sprout as a network of vines to grow up encircling and eventually strangling the tree. The flowers of the fig "tree", in contrast to garden flowers, develop like an ingrowing toe-nail with all the delicate bits on the inside and a tough exterior; it's called a syconium. Think daisy Bellis perennis rather than daffodil Narcissus poeticus because each syconium consists of multiple florets. There is a little pore at one end, through which the pollinating wasp enters. The female wasp is there to lay a clutch of eggs - for her the pollination is incidental - which hatch as larvae, eat some of the fruit and then exit as new flyers. Without the wasp no fruit is set. Without the bat, no dispersal. Don't think for a minute that figs are 'suitable for vegetarians' though: part of the treat is dead wasp bits. Getting your reproductive parts eaten away inside and out is a small price to pay for thus getting your offspring launched in the world. YMMV! And we have barely even mentioned the tree which supports the fig-tree and eventually gives its life for the system.

From our fuzzy-hearted perspective, some of the players enumerated above are nicer than others. These sort of woowah value judgments have given trouble to some god-botherers, including St Chuck: "I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design and beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of Caterpillars, or that a cat should play with mice " (Charles Darwin). Did someone mention Ichneumons? There are at least 25,000 species of these hymenoptera (the bees, ants and wasps), most of which make a living by parasitising the larvae of other insects. But only because those other species will leave fat, juicy, nutritious morsels lying about unclaimed.

The females who lay the eggs which grow into the larvae sought by ichneumons go to some efforts to hide their progeny from predators; and the wasps exercise themselves to see or smell through these attempts at concealment. One of the better studied species is Ichneumon eumerus which is super-fussy about its host: only a larva of a particular blue butterfly Phengaris rebeli [synonym Maculinea rebeli] will do. Over the evolutionary eons, the butterflies got rather pissed off about this decimation of their progeny until one member of the species was born with a peculiar biochemical mutation. Its larvae produced a pheromone which made it smell remarkably like the larvae of Myrmica schencki a species of small ant; the ants thought so aNNyway and were therefore programmed to carry the butterfly larva back home to their nest and care for it - like cuckoos. For a while, the butterflies were safe from the attentions of the Ichneumon, until one of the latter learned how to find the nests of Myrmica schencki and determine if there were any butterfly larvae in there. If so, the gravid female darted into the ant nest and tried to deposit a clutch of eggs on the butterfly larva. Which led to a bit a barney as the ants tried to defend their trophy "offspring".  The wasps which succeeded left more of their own offspring into the next generation. One avenue to success was to develop and use another 'alarm' pheromone which made the ants run around in circles biting each other . . . thus allowing the wasp a window of egg-laying opportunity. These coils of mutual dependency are now impossible to dis-entangle.  Picture [R] of the dramatis personnae the ant is beige-on-grey to the L from the BBC.

Apart from the baroque inter-dependencies, the peculiar thing is the specificity of it all. No other butterfly larva smells quite right to either of the hymenopteran species. It looks probable that the larval pheromones of the butterfly and the ant are subtly different. Nat Geog suggests that teasing out the differences could help develop chemical agents to control the behaviour of insect pests. The butterfly pheromone is good enough to fool the ant, but different enough to encourage the wasp to assail the nest only if a butterfly larva's reek was wafting out the nest hole. You couldn't make it up! Then again, it suggests that our science is just skimming the surface of what we know about the natural world.

The wasp-ant-butterfly system is covered in a long list of natural peculiarities on http://bizarrecreature.blogspot.com/

Monday, 15 January 2018

Blue Screen of Death

If it hasn't happened to you, then you don't use your computer enough. When I started at The Institute, my office-mate said she never switched her desktop off, because it took so long to boot in the morning. You can take this sort of inconvenience on the chin . . . and grizzle about it. I did this for a couple of years.  It was okay, so long as you didn't need to print something in a hurry for a 9 o'clock class.  Then, I mentioned it to our IT guy and he said "Oh you don't have enough RAM, I'll double it for you" - and it was so - about 2 hours later. Often, the solution is to push at an open door: pissin' and moanin' rarely achieves anything, while a polite request might.  Now I can be super virtuous and switch the computer off every night and be confident that she'd boot up sharpish in the morning.

One morning this last week, the first of the teaching term, both the chaps in the office next door came into work to see the Blue Screen of Death awaiting them. I advised them to "Switch it off and switch it on again" but they'd been there before me. I had a busy day but later on saw the IT guy swapping hard-drives and sorting the problems out. He suspected it was a "rogue update from Windows" which made me think the same disaster would happen to me if I tried "Switch it off and switch it on again". The prospect of losing files made me feel queasy and weak at the knees. The worst aspect of it is not knowing which version of a file you're dealing with among the backups: it's almost better if something is gone-gone and you just knuckle down and recreate it. 

One of the last things I did before Christmas was set and mark a computer exam. I could find the damned exams but not the marks. I could also find an e-mail with an anonymised set of marks which I'd used to show the students that some questions had been better answered than others. But that was a long time beyond my two-week event horizon. I exhausted a frustrating hour trying to track the marks down on my Desktop at work and through my December e-mails. Then it dawned on me that I'd marked the exams At Home; on the weekend before Christmas; when I should have been decorating the tree or making more mince-pies [instead of shop-bought].  I hoped so aNNyway, because the laptop was 40km away and not immediately available. The thought of having re-mark the exams filled me with dread. But that evening, it all turned out okay - pheww! - because the marks were indeed on my laptop.

The Blue Screen of Death event next door caused me more anxiety than was strictly appropriate because I knew I hadn't backed-up my work Desktop for weeks and it would be exceedingly wearing to try to sort out a restored hard-drive. Therefore I nipped across town to buy another portable hard-drive to capture the data and files before anyone [like me, for example] tried "Switch it off and switch it on again" and it didn't work.  The last time I bought such a thing from the same electronics megastore - 2+ years ago - a 500GB drive cost me €70. This week a 1,000GB = 1 TB drive cost €70. 1TB is now the bottom of the available range. I could have bought >!bargain!< a 4TB drive for only €130. But I knew that would have been silly because 1TB is wide-open prairies of space. I loaded my precious workfiles onto my new electronic fashion accessory [it's a fetching red to complement my canary yellow button-phone] and 5 years' work filled a mere whisker [see R] of the available storage. I guess it would be different if I took loads of photos. Take my advice: backup early and backup often - you'll sleep better. 

My souvenir 2400 ft magnetic tape from 25 years ago is about the size of a rather fat 12 inch vinyl LP with a physical volume of about 1500 cu.cm; and a data capacity of about 200 MB. 7 cc for each megabyte.  The Terabyte drive takes up about 100 cu.cm. Now you only need 0.0001 cu.cm for each megabyte. That's a 70,000x increase in efficiency! To put it another way, if were still dependent on mag tapes, my terabyte of crap photos, ripped films and viral fail videos would require a space like our substantial woodshed [R] to store it all. If that's what it cost maybe we'd be more ruthless with the editting.

Sunday, 14 January 2018

Well met by tideline

Saturday was a drizzly mizzly dreich sort of a day after a night of persistent rain. We had planned to set off for the Waterford coast but as I drove down our lane I noticed that the drain was worryingly full of debris from the previous rains. Accordingly, I turned round, got into my cruddiest clothes, and spent a dirty sludgy hour shovelling out the drain, so that I could sleep quieter at night: if the drain backs up in a storm, the lane disappears down the hill.  The delay meant we didn't arrive Down the Déise until after dark. But that's okay, I've stolen time for some beach-bliss on the Waterford Coast before. Sunday, low tide was at a civilised 10am and sunrise was at 0830, so I was down on the beach in time to watch the sun boiling out the sea as I walked over the headland to Trá na mBo aka The Secret Beach where I had the honour to swap quotes with Senator O'Sullivan in 2016.  I had the merest twinge of disappointment when I noticed footprints on the palimpsest of the beach but barrelled straight up to the perp and asked what his obsession was - because the was no dog in evidence.

It turned out that, like Keiran Russell cited above and George O'Mahony, whom I met at Benvoy strand a tuthree years ago, the chap on Trá na mBo was another photographer, who had driven 150km from Wicklow to capture the light with his camera. He was determined to escape from the shackles of his business as a graphic designer and get in some work-life balance. That meant leaving home, wife and kiddies in the small hours in a blanket of fog and heading South for beaches and headlands which he'd never seen before. To say he was delighted with himself would be this year's understatement. He couldn't stop gabbing about the light, its reflections, the wet pebbles and the wisps of cloud. I was only trying to establish that, by scarfing up some buoys and rope, I wasn't queering his pitch. And indeed, I did discover an unliftable tangled hank of monofilament fish-net with floaty-rope at the top and lead-shot rope at the foot but I couldn't salvage much.

Round the corner in the car-park at Bunmahon Strand, I saw another young chap earnestly scanning the sea, shading his eyes from the still brutal-bright low-slung sun. He also had come a long way that morning - 80km from Enniscorthy; and also left a wife back home in the bed. He was there for the waves and was only mildly disappointed that there was a fresh on-shore wind. Surfers prefer the wind to act against the incommming waves. "But hey, I've got a real thick wet-suit, I'm just going to get out there before the sun goes in" . . . and so I left him to it.

I've noted before that in contrast to Seamus Heaney's Irish proverb "Man to the hills, woman to the shore", men have  a dangerous fascination with water. But my third recent tideline encounter was with a woman, only a bit younger than me, whom I met scanning the sands of Annestown beach with a metal detector. I'm a youtube 'expert' in that hobby so I suggested that all she'd find would be bottle tops and ring-pulls. I was right! She too was delighted to be on the beach escaping from the day-to-day. She was also delighted with her new toy which she had received form he husband for Christmas in fulfillment of a long unrequited desire. I suggested that the desire might be on her husband's side: while she was away with the sea-breeze combing her hair, he could be undisturbed at home watching the darts.  I was almost right there too . . . "It's soccer, actually" she corrected me.

Sunday Misc 140118

The Appalachian Trail AT and the Pacific Crest Trail PCT are two very long-distance trails that go up and down in wild places. It's hard and requires grit and some courage to walk a long section of either. At certain places where roads cross the trail, local people offer lifts to the nearest town, leave caches of water or cool-boxes full of carbohydrates, coke and beer.
Another sort of trail - bikepacking:
Another sort of being alone on a journey Isles of Shoals in Winter
Another sort of obsessiveness: marbles, magnets and music . . . all together now.
Statistics of inequality. Top 1% vs Bot 50% in EU vs US = shockin’

Saturday, 13 January 2018


The photo has been circulating in the Irony sections of the Irish agri-blogosphere. It shows a wonderful wide-open landscape typical of the West of Ireland. The hedge in the fore-ground, an essential element in sustaining bio-diversity, has been flailed to stumps  . . . and replaced by government sponsored wooden bird-boxes. Presumably on the assumption that birds should accommodated in high-rise apartments like the poor of London.

My heart is in the right place, but I am continually being wrong-footed in my greenness.  When I was kid, we had fly-spray in the cupboard under the sink and I used to hunt flying insects round the house going pffft pffft: ignorantly destroying the ozone layer [which wasn't A Thing yet in 1963] with the CFCs in the propellant, not to mention filling the house with a dilute haze of nerve-gas. To be fair, I was also wicked deadly with a fly-swatter, leaving little splots all over the walls and ceilings for somebody else to clean up. 'Organic' hadn't been invented then, largely because the local farmers were very light on the p'isons. But when I grew up and left home, I started to care about organic: we got a copy of John Seymour's Self-Sufficiency, for starters. I harvested a bunch of dandelion Taraxacum officinale roots in one of the scabby back-gardens that we were renting and made organic dandelion 'coffee' from the chunked and dried roots - it was okay but an acquired taste and I didn't stop drinking tea.

By the time we moved back to Ireland in 1990, we'd internalised the organic aspiration and set about finding "an old farmhouse with out-buildings and 10 acres" to raise organic veggies. That aspiration took 6 years and 2 more children to fulfill. In the search for Seymour II, we started to buy organic milk and organic greens and joined the Dublin Food Co-op for beans and cheese. Then my sister came to visit and said (I paraphrase) "Yes yes organic is fine and dandy but what about the air-miles?". My smug right-on bubble collapsed with a flabby pffffffffff. Of course, it was stupid to observe the niceties of organic while condoning the air-freighting of baby asparagus from Kenya - a practice which was destroying the ozone layer and converting a lot of aviation fuel into greenhouse gas. I then started to obsessively read the labels on the stuff we bought and you've seen the result throughout The Blob over the last 5 years.

We've been living up the mountain on Seymour II for more than 20 years now and trying to do the right thing. We sought advice from Teagasc, the government agrivisory bund and signed up for a succession of schemes that encouraged us to Do Right. Who wouldn't accept financial help from Brussels to do what you were going to do aNNyway? And it worked! getting the grant impelled me off the sofa to tidy up the hedgerows, cut back the bushes from the field margins and put in some fences which were sheep-proof.

One's cynical suspicions would have been alerted by the frequency with which the schemes changed their names. REPS (rural environmental protection scheme) I II and III were binned and AEOS (Agri-Environment Options Scheme) rose phoenix-like from the ashes of burning brochures and letterhead. In turn AEOS has been replaced by GLAS (Green, Low-Carbon, Agri-Environment Scheme). A cunning desk-johnny in the Dept of Ag has made a backronym of the Irish word for green. We signed up for REPS I because it gave us money for doing what we'd do aNNyway, with our place . . . IF we could find time between raising two children and earning an honest crust off-site. We planted 400m of hedge ten years ago, which is now full of bird-nests. I was encouraged to cut the gorse / whin / furze Ulex europaeus back from invading the fields but leaving it to augment the field boundaries with the scent of coconut. 2016 was the year of the boxes when Young Bolivar [multiprev] made a few dozen wholly artificial nesting boxes to encourage bees, birds and bats to share our space [L - bat-boxes were required to be installed in triplicate facing different points of the compass].

It's mostly a bunch of greenwashing nonsense: making folk like us feel virtuous by rowing in behind the available cash.

Friday, 12 January 2018

Joint Speech

I think this might be profound; I'm not sure because I haven't read the book [200 pages! . . . but free] yet. It's by Fred Cummins a Cognitive Scientist [and more] from UCD [Uther College Dublin]. Although he, like me, is a graduate of TCD where he read "Computer Science, Linguistics & German". On the face of it, that's a rather cross-disciplinary mouthful of a degree . . . a bit like geography.  But it sounds interesting; you could go a long way in a variety of different directions with that under your belt: voice recognition, automated translation, relationships among language groups, lie-detection, unconscious prejudice . . .

In the classic way of science, Cummins paid attention to something that is so common, so universal as to be invisible. He identified something intriguing - that humans are really good at calling cadence.  They are really good at marching too; unless they're a good way along The Spectrum, people naturally fall into step together. It's something to do with psychological resonance but can be real bad for mechanical resonance as when crossing bridges. As a scientist, having had his insight, he checked the literature to see a) if this was common knowledge and/or b) what the giants on whose shoulders we stand had to say. And he found that nobody had been there before; which was neat because it meant he could invent all the technical terms.

The key unifying theme of a number of quite different activities, he calls joint speech, "where two-or-more people say the same thing at the same time", With 'say' interpreted broadly: The examples he gives include
You might think that contemplative prayer and angry protest were as different as different could be but they have this in common: the voices of participants tune with each other, often through repetition. If they don't equalise the cadence on the first round, people slow down or speed up and modulate the stresses so that they get it right on the rebound. Typically, you do a decade of the rosary often at a furious gabble: blessedisthefruitofthywombJESUS. I have written about the Joy experienced On Singing Together. What was amazing about being song-schooled by Sian Croose was that a) none of us had any formal training in voice-work b) few of us could read sheet music (of which there was none) but c) with minimal but charismatic teaching we could raise our collective hearts and voices to very heaven. You know you've had a wonderful experience at a pop concert if everyone in the auditorium has sung the chorus together.
As a deeply inhibited person, I refused to participate in "Give me a T; give me a U; give me an I - what's that spell? UNION" because it seems dorky and, well, wrong. If I parked my Self, I/we might develop a better sense of Solidarność, which as we saw in 1989, can topple a regime.

Over Christmas, I was playing face-games with just-2 y.o. Gdau.II. It was fascinating how the child, not yet able to utter a grammatical sentence, was able to accurately imitate whatever scowl, pout, grin, or grimace I 'uttered'. Perhaps as interesting was the fact that a) inhibited me was happily participating and b) imitating her gurning. Now, those responses are simply extraordinary: imagine the neuronal activity required to fire up a particular peculiar combination of motor nerves without having to think about it let alone analyse what's going on. Since a serendipitous discovery at U Parma in the late 1980s, we know about mirror neurons which drive feelings of empathy with what's happening to our neighbours. Last Winter I experienced an almost barf-inducing example of mirror neuronal activity. Because I teach human physiology, I was able to articulate my visceral feelings as conflict between the sympathetic and parasympathetic wings of my autonomic nervous system. Young Gdau.II don't need any of that wordy nonsense to participate . . . and neither did the macaques Macaca mulatta at U.Parma. Because her larynx and its nervous connexions aren't properly developed yet, Gdau.II's parents have taught her (or she has taught them?) a large vocabulary of sign-language. We all suspect that this child is going to have less of a 'terrible twos" time because her levels of inarticulate frustration will be drained by the faucet of signing.

My experience is that [X=large]% of dialogue is entraining the emotions and sense of empathy with whomever we're chatting. Have you noticed how many conversational cues repeat the last phrase of what the other chap said and then build on it? Before they had speech, our ancestors were achieving the same effect but picking nits and skin-flakes out of each other's fur. The actual content of most talk is comparatively small: Did you see the match?  It's cold out there. How was your Christmas? How d'ye do? Nobody really cares what the response is. My generic greeting in the corridors of The Institute is a sort of 'ay-up which many, not having done time in Geordieland, interpret as Hiya [itself a debased how-are-you] and respond Grand, thanks. Frankly Scarlett . . .I'd rather be nibbling some scurf.

15 minute TedX executive summary. I suspect that Fred Cummins might have identified a key element of what it means to be human = primate.
Source: I came across this story on MeFi the other day "Can I get an Amen"

Thursday, 11 January 2018

Microbial fingerprints

Over Christmas, I was given the spare half of a 2for1 sub to the New York Times, this is grrrreat because in my part of the blogosphere, the source is often either the NYT or WaPo the Washington Post. WaPo has closed it's free-access doors recently, so I need one USA source for following things up. Or indeed getting at some original stories that aren't yet being rechurned on the blogosphere. For the last 10 years, I've been really interested in the microbiome - the community of microbes which we tote around with us all the time and largely take for granted.  Then I came across a NYT quiz to see what microbiologists can/could tell about me if they swabbed some of my orifices and characterised the bacteria found there. Can they tell:
  1. my biological sex?
  2. what I had for breakfast?
  3. if I have a pet?
  4. with whom I live?
  5. where I work?
  6. if I get migraines
  7. if I was at a crime scene?
The answers are: 1 Y 2 N 3 Y 4 Y 5 N 6 Y 7 N :era srewsna ehT. Mouse over. The bottom line is your local environment will charge your microbial flora, but it takes time to execute the change-over. Thus your workmates have much less effect than your housemates, with whom you likely share a bathroom, a floor (if you're a shoe-free house it matters), and meals. If you pet the dog, likewise. Even if you don't pet the dog, your human cohabitants probably do. Your diet defo has an effect too but it takes more than one breakfast to register a change.