Tuesday 30 June 2020

Setting an example

In my latter years working at The Institute, as deficits of age accumulated, I would start the year in each class by explaining that, if I cut them in the canteen, it wasn't because I was too grand to acknowledge their lowly existence but rather because my eyesight was too poor to recognise them as mine. And I hoped they would have enough empathy to appreciate that it would be kinda freaky if other students were being greeted effusively by a random silverback. That, and an explicit <shows rainbow wrist-band> affirmation that I was down with the gays. There was a subtext here that I wouldn't tolerate anyone getting slagged on my watch for: coming from Wexford; having facial hardware; being super shy; playing, or not playing, sports; let alone for having: a great tan, XX chromosomes, or any sort of BLT identity.

I also felt very strongly that it was okay if I didn't know all the answers. Indeed that it was a better educational experience because I didn't know everything: my ignorance put more pressure on the students to find out for themselves. But I surely wouldn't have had as much confidence in that theory when I was starting out as a graduate student teaching lab sections when I was only a few of years older that the average UG student in class. And if I was a young woman, or a young black woman, or trans, how much harder would it be to be wrong or to not know the answer?  That being said, it's also really important to convey a Joy of Science enthusiasm for the tasks to be covered; even if those tasks were intrinsically not-the-cutting-edge "discoveries" of, say, Hooke's [1676!] Law about strain, stress and springs.

That was all brought into focus for me by a nice little confessional essay in Science The pressure to assimilate about dress, comportment and being your true self by 'Trai Spikes [R about to get all wet in the field], a black student running ecology labs in Oklahoma U. Along the way growing up, he'd bought into Polonius' advice about apparel oft proclaims the man: that you get more respeck if you dress up. You'd better be stonking bri'nt if you turn up for a job interview in a tee-shirt and trainers; while an ironed shirt and pressed trousers will show who's in charge of the Biology 101 labs. But then young Trai was brought to realise that he was being viewed as a sell-out to The Man by his minority students. And he found that being his true self made him happier in his own skin and that allowed his passion for science to radiate around the room and inspire another generation of young scientists. Double Triple Win!

I have a nice little story about looking the part from when I was a post-doc in TCD in the early '90s of the last century. In the Genetics Department we had a weekly seminar series and a small budget to bring in visiting speakers. My boss, who had done his PhD in Edinburgh, decided to invite Howy Jacobs from Glasgow to do us the honour. Coincidentally the department had recently advertised for a New Professor of Genetics. It was a bit late in the century for punk, but Howy appeared with tartan trews and a mohican [still has] . . . which he'd dyed kelly green to mark his visit to Dublin. My Boss, as you do, took the visiting speaker to the Senior Common Room for lunch. As they sat around having coffee in the deep arm chairs afterwards, a couple of tweed-jacket-leather-elbows academics approached. One of them arched an eyebrow to indicate irony and said
"Ah Paul, is this one of the candidates for the Chair in Genetics? Won't you introduce us?"
"No, this is Howard Jacobs, the Lister Professor of Microbiology, at Glasgow, he doesn't need another chair"
<pffffffff> collapse of stout party!

Monday 29 June 2020

Ceci n'est pas un crapaud

Proceratophrys boiei is not a leaf
Science is one way of making sense of the world. Wordsworth had a view on how a crowd, a host of daffodils impacted the human eye to delight the soul. Wordsworth's distillation has improved my awareness and appreciation of the wonders of the ordinary.  One of the making sense tasks of science is classification: it helps to find commonality among the different ways of making a living on this planet. I was reflecting recently on Dry Heath and the extent to which this biome exists outside of text-books. My tentative conclusion is that biomes are real conglomerations of interacting species which can help us predict what will be present in newly investigated landscapes. Any exceptions may be treasured because they will extend our understanding but the exceptional baby shouldn't require us to deny that the biome bathwater is wet.

Cycloramphus lithomimeticus is not a wet stone
Classification can be applied, not only to ecosystems, but also to the species of which they are comprised. In 1975 I concluded that it was not useful to base your classification on a single obvious attribute - we'll put all the flyers [bats, beetles, birds, butterflies] in this bin; all the sedentaries there; whales and sharks in that tank - not least because some birds swim better than they fly; and barnacles, birches and Bob-the-sofas make a very heterogenous group of sitters. Concentration on obvious features for diagnosis and classification has led us up the garden path a good few times and invisible DNA sequences have really helped to resolve who is related to whom.

Scythrophrys sawayae is not dried leaf-litter
Today, I am compelling you-eeeeuw! to look at the extraordinary lengths to which some frogs have gone to avoid being eaten. Unless you believe in a very diligent and slightly unhinged special creator for each of these solutions to the problem of predation, then the rest of us turn to the incremental changes wrought by evolution to explain both the differences and the similarities. You don't have to be a perfect mimic of a stick to survive long enough to get in a bonk or two and leave similar-looking offspring to posterity; you just need to look a little less froggy and more nothing to see here leafy than your neighbour. It's like you should always distress your bike a little and try to lock it near to a really swish expensive looking model belonging to someone else. Frogs need to keep still too, and be lucky, but looking a bit leafy may get their gametes over the line. For me the interesting thing is that these species are as different from each other as can be while still being mustered into Order Anura.
Cycloramphus lithomimeticus is in the family Cycloramphidae
Proceratophrys boiei is in the family Odontophrynidae
Scythrophrys sawayae is in the family Leptodactylidae
Odontophrynidae used to be lumped in with Leptodactylidae until 2006 DNA data suggested that they were a) a clade - a group of species descended from a common ancestor b)  longtime separated from the Leptos. Thus the evolutionary strategy of trying to look like something else has been re-invented multiple times . . . because it works.

Sunday 28 June 2020

True voices

Lock down last week?
  • Latvian woodcraft-folk folk
  • Meanwhile on the streets of Dublin
    • Allie Sherlock and Cuan Durkin can't help falling in love
    • Cuan Durkin & Rosie Byrne do Perfect
    • Allie Sherlock and Cuan Durkin do Perfect
      • It's not technically perfect but they are all so full of heart. ya gotta love them. And could someone feed that boy up ? He's sooo thin and always cold.
  • Land of sand
    • Mícheál Ó Muircheartaigh making a ham sandwich sets a very low bar: what a terrible bread to bracket sound locally sourced and home-cooked simple food. Any of his neighbours [okay I guess they'd have to be older than 60 and female] could knock up a round of brown soda and have it round to Mícheál's within the hour.
    • Meanwhile in Portugal they blame the French for this heart attack between two slices of bread . . . and slathered in gravy. Não é um milhões de passos do poutine.
    • My grannie's kilo-samosa business
    • Nutella in Reactistan
  • Scienciness
  • The Arts: park your prej its hard to see where the irony ends
  • History channel

Saturday 27 June 2020

They all growed up

If you're new to The Blob, you may not even have met Dau.I and Dau.II (with whom I have half my genes in common) let alone twigged that they educated themselves at home and are now out and about in this dark world and wide [source]. They grew up with a cohort of youngsters who were similarly deprived of that school experience. None of them were struck in the back of the head with a spit-ball; none of them had their head flushed down the t'ilet in the boy's jacks; none of them were told they couldn't play soccer with the bigger chaps; none of them had to ask permission to go for a pee; none of them were told they were crap at maths or that girls couldn't become doctors. Although, to be fair, The Beloved had go Socratic on our 6 and 8 y.o. daughters to demonstrate that doctors were not exclusively male: "Now then: Doctor Farrell, whom we saw last month, is she a man?".

Meeting other parents at the school gates is, for most normal people, the last gasp at extending your social network which, apart from family, is mainly comprised of people you winnowed out of the crowd in school and college. We became founder members of HEN [the Home Education Network] in 1998, and that became our equivalent of the school gate crowd. Not all the parents were equally lovable and some of the kids (I blame the parents) were frankly bat-shit but the shared experience of educating children at home (not to mention rice-cakes, Birkenstocks, and floaty skirts) made us friends for life. We didn't meet up every M-F day in term-time but the shared experience - washing 100 dinner plates together, that time the tent collapsed, the night Bob set off the fire-alarm - made tight bonds.

In their mid-teen years, Lulu the mother of my Dau.I and Dau.II's Bestie, decided that the whole cohort could do with having their horizons broadened. Accordingly she organised a schedule of events, and called it Transition Year, for about 18 consecutive months that took a dozen or more HENnies to Arboretum, Belfast, Cork, Dublin . . . and through Youghal. We would have done the Zoo as well but were offended that the lions were insufficiently vegetarian. I was the other adult in the room for several of these adventures, so got to know those youngsters quite well. Everyone different, every one good, like sourdough bread. Now they're all grown up, have gotten and used the vote, have steered, and got an old man off his sofa, a couple of key social justice referendums through to ,

Back in the day, when we'd all get together, you may be sure that one of these youngsters had done something entirely creditable or manifested some amazing triumph of their talents. It made our little chicks look paltry because all they'd managed in the previous month was make cupcakes and clean out the chicken shed. It wasn't that the other parents were boasting or boosting. It took me a while to turn this on its end: a) if you have a month or more between meets then you're not going to share the boring bits; they will be effectively invisible while the prize-winning or life-saving events will dominate the mind b) the other families were mostly crap at cup-cakes and were amazed that one so young could be so talented with a wooden spoon c) it's not a competition, it just seems that way sometimes. Celebrating the ordinary became the path to contentment.

Monica O'Connor, [prev] another of the Transition Year Mams, has made good a promise to herself to interview that generation of home-educated kids, including her own, and find out what they've done since leaving home. She's got her self a youtube channel and is giving the were-kids the space to tell their stories. Whatever we felt about their achievements as teenagers, the Kids Done Good as 20-somethings [Quiz-time: spot the half-genes-in-common pair]:
But the hell with "success", which is chimerical and ultimately empty; you could not meet a nicer group of people, they give me hope for the future. Akala says don't let no-one kill your imagination.

Friday 26 June 2020

Bloody covid

A couple of weeks ago, my KK correspondent G sent me a story in The Jerusalem Post about ABO blood groups and differential response to Covid-19. I was in the midst of a Covid moratorium so didn't follow it up. I did pause to reflect on why G was scanning the Jerusalem Post: surely if you live in the SunnySouthEast everything you need to know can be met by perusing the Munster Express?

The JPost is referring to a study in NEJM which has taken a blood sample from ~1600 people in the Spanish and Italian epicentres of early Covid-19 meltdown. At some stage in every patient's treatment bloods were taken and while they were routine checking for creatinine, serum albumin and alkaline phosphatase they also had to check ABO blood groups in case anyone needed a transfusion. I've written about ABO blood groups before in the context of priority - paternity - geography - historydisease association.  But my [slightly delayed] response was ooooo data and I scooted off to the NEJM to download Supplementary Appendix 8 which contains the raw counts and %s for ABO in various geographic and medical-severity bins.

The first thing to note is that Spain and Italy are not the same population wrt ABO blood groups and so, strictly speaking, the data from the two agglomerations should not be pooled. This fact was brought up to the top of my 'mind' because one of the tables in Appendix 8 has gathered a bunch of Basque ABO data as a control. Whoa, lads! The Basques are the Martians of Europe, even more so than the Magyars: their language is not proto-Indo-European PIE and their blood groups look like a sore thumb (mostly Rhesus diffs it must be said). As a side-swipe, note the different colours on the map [R] for Lombardy and NE Spain where most of the Covid-sick in the study came from.

I scraped the pooled ABO / Covid-serious cases / Disease free controls from Appendix 8:
Which tells us a) that there are a lot of data here b) that the number of hospitalised cases is about equal in the two countries (although quite uneven in among the several participating hospitals) c) that sick people include more GpA people and fewer GpO people than you'd expect if they were a random selection of the population based on the controls. Because the paper didn't do this, I checked for ABO heterogeneity between total ES controls and total IT controls with a simple Chi.Sq test. The base-line differences are highly significant (Chi.Sq = 27; df 3; p < 0.001) with their being more A alleles in Spain and fewer B. Which is grand because we effectively have two different parallel experiments which both reveal the same skew: you are about 50% more likely to finish up on a ventilator if you are blood group A and a third less likely to do so if you are Group O. This is the odds ratio OR: [explained] (a/c)/(b/d)  = 1.54 for Italy (it's 1.31 for Spain) where
  • a = ++ number of ventilated As = 388
  • b = +- number of unsick As = 451
  • c = -+ number of ventilated (AB+B+O) = 43 + 91 + 313
  • d = -- number of unsick (AB+B+O) = 50 + 163 + 591
You can do similar calcs with O vs ~O / sick vs well. What are you / me / we meant to do with that information? My correspondent G was jubilant that she was Group O. I'm Group A but I'm not really concerned although the odds look stacked against us the (elite) A-team.  There are far more people with Group A who are uninfected, asymptomatic or who have copped a dose and had mild to moderate symptoms because that's the ~80% in the Covid-19 world. The 20% who get real sick and the 1% who die (or have such a crappy experience that death is wished for) are disproportionately A, yes, but they are far more obese, diabetic, have cardio-vascular issues or are over 80 years old. I am none of those.  Ed Cara at Gizmodo has covered the story with extra input from front-liners “It’s a big headline, but scientifically, if one of my colleagues in the emergency room were to call me up and say, ‘Hey, we were about to intubate somebody, but then we noticed their blood group was O. Should we still do it?’ I’d be like, ‘You’re crazy. You’re just absolutely crazy,’” Gehrie said.

And remember that it takes two to tango: before you get a chance of a go on a ventilator, you have to first catch SARS-CoVi2. Me? I rarely go shopping; I wear a mask in LIDL; I wash my hands afterwards; I don't suck face with young wans in discos; etc etc. I don't think G should take fewer risks than me because her red blood cells each carry a really small titanium Captain America shield.

It's a bit like my analysis is Statins. They have demonstrable, statistically significant effect on lowering cholesterol and so will prevent heart attacks. But the number needed to treat NNT for statins is more than 100! 100 people have to be taking statins for 1 to not have a coronary infarction. Statins have wild side-effects in some people and will cost you (or the beneficent HSE) a chunk of money. You'd be better off changing your diet, getting off your couch, de-stressing and being more socially engaged. But these take effort, statins just need a small glass of water.
On Covid-19, you can't change your blood group but you'd be spiffin' bonkers to think
I R O, I R OK, I can share spittle with randomers

Thursday 25 June 2020

Sensei sensori

Seven years ago I drove in the dark through storm and flood to watch Jiro Dreams of Sushi - a documentary about Ono Jiro 小野 二郎 [family name first] who had been working in the restaurant trade for - - - 70 years. Here's a short tributary in which the master of the old school meets René Redzepi, the creator of Noma, a restaurant in Copenhagen [Sunday Supplement] that has twice been voted Restaurant of the Universe by the Inner Circle of Foodies. I'm not a foodie like Dau.II is  Foodie but on some level I recognise the parallels between lab-bench and counter-top. One common feature is the value of A Good Pair of Hands that person who can let their hands do the working without constantly thinking about what's going on. AGPoH is also important in drumming. I am the antithesis of AGPoH but I come closest to that state of being when I'm cooking: it's not reproducible but mmmmm is it good.

My Lockdown foodie book has been Hungry by Jeff Gordinier; its subtitle is Eating road-tripping and risking it all with Rene Redzepi the greatest chef in the World.  I'm not sure I would have gotten round to it if the loan period had been three weeks. I'm glad I was given the extra time, because it's an interesting saga about how a grown man with two children and a breaking marriage becomes a total groupie for an Albanian/Danish cook . . . and haemorrhages a lot of money to hang with his guru in Mexico, New York, Sydney, Norway and Denmark.

It's a genre in't it? Eat Pray Love was about a rich white woman who found that money can't buy everything anything that seems worth striving for. That went viral, was made into a film and made the author another fortune. Then there was Bill Buford's Heat [reviewed here as Heat Braise Shanks] where another Inner Circle journalist goes off to find himself in the white heat of someone else's kitchen. I'm ambivalent about these people. They can't keep their marriage on the rails but can career off in wild directions to find their true selves. otoh, why must we expect them to like the hand of cards dealt to them by fate and circumstance? Isn't it better to have an epiphany like Bill Bryson realising that he should have been born in Europe; or Niall Deacon parking sheep-farming to be a stone-mason? This is what you are likely to be presented with at Noma:
Call me conventional, but I think I'll stick to the traditional recipe for spotted dick.

René Redzepi is neat because he is clearly Out There when it come to giving something a Why not? whirl. Forget slavishly following in the footsteps of Escoffier and doing things because it's always been done this way.  Previously unexploited molluscs and crustaceans get air-freighted from Norway to be plated with ant confit and trout swim-bladders. The expense is "exclusive" and so the only way you and me are going to get a sniff is to sign up as a scullion. But bring your ladle, because you'll need to fight off a score of hungry wannabe plongeurs who would gladly fill your toque.  And Gordinier's book? It's okay, when you get past the self-pity and the eye-watering cost of pushing the foodie envelope.

Wednesday 24 June 2020

The game the whole family can play

Georges Cuvier stoutly maintained that from a single bone, he could extrapolate an entire animal. From an entire skeleton you can infer a lot about the ecological niche its owner inhabited. It's a bit of an ask to go directly from the bone to the biome, because two layers of descriptive fuzziness = noise. I've done my bit [over about 30 years] of reading meaning into DNA sequences [recent - previs - elvis] not all of it frivolous.  But there is a whole level on additional "good pair of hands" skills required to generate new sequence data from really old, poorly conserved, fragmented DNA from bones which have been quietly degrading for thousands of years.  It is amazing that it can be done at all, let alone that the data can reveal expansive insights into the life and times of our ancestors.

An eye opening new paper from Lara Cassidy et al. Dan Bradley is shining a light on the DNA of long dead inhabitants of Ireland. It has required mastery of the three key skills 1) meticulously polished, ultra-careful clean-room technique and 2) a whole other set of skills in computational sequence analysis and 3) appropriate choice of multivariate statistics. Since I last wrote about The Effective = 1st author on this paper  [prev] , she has applied for, and accepted, a lectureship in her once-and-future department. It's super nice to launch her "grown-up" career with the front cover of Nature [R]; like, no pressure for future delivery!

There's a lot to unpack in the paper and most of the technical details [at all levels: ancient DNA abstraction; sequencing and assembly of ancient genomes; statistical analysis of the data] will be beyond my pay-grade. It's beyond the Nature pay-wall as well, so inaccessible to Joe Public. You may therefore choose to jump to the accompanying News&Views Exec Summary by Alison Sheridan of Scots Nat Museum.

There are three neat findings.

1) The salacious one which has made the headlines is the fact that one of ancient corpses, buried in the centre of Newgrange, in the centre of Brú na Bóinne was the product of a brother-sister union. This is the only rational explanation for the fact that long tracts of his genome are identical on both copies of his chromosomes aka heterozygosity = 0:
But the singular of data is anecdote and, notwithstanding the later Pharaohs, there is no justification for saying, from this one case, that incest was an essential bonk in dynastic politics of Neolithic Ireland. You could equally well suggest that Down's syndrome [see para below] was running at 1-out-of-50 = 2% of the population in the same era; instead of 0.1% as now.

2) The second finding hinges on a neat analysis to determine the sex of the bone/tooth fragments from which the DNA was obtained. Modern high-throughput DNA sequencing makes a helluva lot of short 'reads' and then uses a big lump of a computer to line up the overlaps into 'contigs' which in turn can be mapped to The Human Genome to reveal their chromosomal location. The raw read-count for the X chromosome can be compared to read-count for the other chromosomes if the X reads are the same density then you have a XX female if X reads are ½ as dense as the rest then it's a boy. I don't know whether the data shouted out or if some bright spark decided to look but one of the ancient dead had 1.5x reads for Chromosome 21whish indicates trisomy 21 aka The Down's. That boy never grew up to adulthood, but nor was he smothered at birth; and he was buried in a place of honour.

3) The third extrapolatory finding is an analysis of the isotopes of nitrogen and carbon to infer whether there was meat in the diet. There are 2 stable isotopes of carbon: C12 makes of 99% of natural samples and C13 contributes the rest. C14, used in carbon dating, decays radioactively and is registered only as 'trace'. But that trace has a half-life of 5,730 years which is neatly in the range to calibrate the age of the samples under investigation. Likewise there are two stable nitrogen isotopes except that the minor species is even less common N14 makes of 99.4%  N15 makes up the rest. I'll have to take it on trust that [relatively] high N15 and low C13 indicates a high protein meat diet. The Dublin consortium are happy to associate this diet with high status, although I bet that there were poachers on the royal estates who ate nothing but beef or salmon like former day Irish wedding guests.

Bonus. 4) There's an interesting twist in the N&V. Dr Sheridan is a trad-trained archaeologist who is inclined to dismiss the Cassidy/Bradley best-guess DNA evidence that the incommming high-status agriculturalists, who occupied these elaborate tombs, came from Spain. " . . . the authors seem to fall into the trap of assuming that Ireland’s farmers had sailed up from Iberia — an argument for which there is no archaeological evidence. Instead, the archaeology points towards the Morbihan area of Brittany in northwest France . . .". But Sheridan is possibly clinging to the wreckage of what she learned in grad school and out in the field. DNA has the capacity to sweep all those pot-sherds and digs into the dustbin of history. When Des Higgins asserted that DNA said that whales were a rather specialised artiodactyl his hypothesis was greeted with derision but the deriders were wrong.

Finally, as everyone is talking incest, there will be snitty comments about Dr Cassidy, having done her stellar PhD under the supervision of Prof Bradley, has been parachuted into the newly available lectureship in Bradley's department. But as Freud said, "sometimes a cigar is just a cigar"; it's not useful to over-analyse things. Sometimes the very best is right in front of you and there's nothing to be gained by looking over her shoulder to sweep further and fare worse. There is luck involved, of course, but it's only in the timing which has yielded to proactive serendipity; Cassidy, like my mother, has made her own luck.

Tuesday 23 June 2020

Dry heath

It's a biome! Dry heath is an intermediate stage in ecological succession; where well-drained soil is paused in its journey to becoming a real grown-up forest. This adolescence may be extended for decades if someone runs a bunch of sheep across the landscape and they nibble nibble to scarf up any wannabe trees before they become saplings. The Red Hill, for which our townland is named, is 200 ha. in extent and owned in common by ~20 shareholders. The Department of Agriculture and their puppet-masters in Brussels are interested in doing something different and potentially more productive with Ireland's uplands. On their watch, the foolish application of policies and subsidies has seen the wholesale degradation of the habitat by undergrazing; overgrazing, poaching, soil-erosion; monoculture forestry with invasive species; turf-cutting, not turf-cutting; heather burning. Last year we-the-commoners became part of a pilot study to investigate other uses for the hill than running lean-and-hangry, almost feral, yellow-eyed monsters of the species Ovis aries. Pilot studies are too often driven by haven't-a-clue policy-makers; I suppose, in fairness if they had a clue, it wouldn't need a pilot study.

Whatevs, like. The upshot is that we are now well into our second year of drawing down money from The Man and so, maybe, are in a position to see if anything we did last year has had any impact on The Hill and/or the thinking at head office. I used to share a house with two long-haired botanists (and their long-haired cat) and let's say I was glad I never had to sleep on the dander sofa. But they were super-sound interesting blokes despite having been born across the water.  Project Repurpose has hired another exemplar of the Type, as The Ecologist. And last Saturday a couple of us went for a yomp up and round the hill with Tom the Plant to record the presence / absence of key species on the dry heath. So it was qualitative rather than quantitative research.

Dry heath is increasingly rare in Western Europe and nobody wants to see the last few patches of the stuff disappear under shopping-malls or hundreds of hectares of Sitka spruce Picea sitchensis. There are (at least) three sources of concern:
  • Succession, especially if the replacing trees are foreigners like Sitka spruce and Christmas tree Abies procera. A few hawthorn Crataegus monogyna, black-thorn Prunus spinosa, hazel Corylus avellana and willow Salix spp. can be tolerated for shelter and hedging. And native birch Betula pubescens because it is so pretty.
  • Bracken Pteridium aquilinum: unforgiving competitor for light and nutrients during the Summer. Dangerous in July when they produce carcinogenic spores. Full of toxic secondary compounds, so it's a good thing that sheep refuse to eat the stuff.
  • Too much spiny gorse Ulex europaeus which can grow to impenetrable thickets, excluding or entangling sheep and forming a potential fire-hazard. Small quantities tolerated for day-brightening coconutty blossom and as a source of kindling
This [above looking southeast towards the plains of Wexford] is what we found.
  • The three heathers [all you need to know about the blooming heather, go lassie go]
    • Erica cinerea Bell Heather Fraoch Cloigíneach 
    • Erica tetralix Cross-leaved Heath Fraoch Naoscaí 
    • Calluna vulgaris Ling Fraoch Mór 
  • Other shrubberies
    • Ulex gallii Western gorse native to Ireland desirable indicator species
    • Ulex europaeus Whin/Gorse/Furze/Bushes invasive in blow
    • Vaccinium myrtillus blueberry/bilberry Fraochán [prev] 100 years ago the fraocháns was a big money-spinner for cash-poor families in the Blackstairs - read the book.
  • Sedges
    • Trichophorum cespitosum deergrass  Cíb cheanngheal 
    • Eriophorum angustifolium Cottongrass Ceannbhán
    • Schoenus nigricans Black Bog-rush Sifín
  • Forbs
    • Galium saxatile heath bedstraw Luibh na bhfear gonta [wounded man's herb for its supposed antiseptic qualities]
    • Potentilla erecta tormentil Néalfartach 
    • Stellaria holostea stitchwort Tursarraing mhór
    • Hyacinthoides non-scripta bluebell Coinnle corra [prev]
    • Pedicularis sylvatica lousewort Lus an ghiolla
    • Oxalis acetosella wood sorrel Seamsóg [prev]
    • Polygala serpyllifolia heath milkwort Na deirfiúríní
Tom the Plant needed to record at least 10 of a short list of species indicative / diagnostic of dry heath. He was 9 out of 10 within 500m and 40 minutes of opening the mountain gate, so that ticked the boxes. But he confessed to getting a proper education in the Blackstairs project because every commonage was different and everyone was good. And while identifying and preserving "dry heath" habitat had been a significant driver of the funding, "dry heath" was as hard to grasp and tie down as running water. All that book-l'arnin' was grand but the reality on the side of a blustery south-facing hillside in SE Ireland made for a lot of exceptions. Then again, those names put on biomes do have a predictive quality: if you find tormentil hugging the ground near a bunch of heather you'll be able to make money betting to find heath bedstraw within 5m.

Monday 22 June 2020

What's DNA to him?

What makes a family? It's partly about genes-in-common but it's much more about shared experience. After all IF you're going to claim that a gay couple with an adopted kid are not a family because none of them have a recent common ancestor THEN you may leave The Blob now. Even if they don't explicitly recall that time Mam, two sherries down, dropped Christmas turkey on the kitchen floor; they will build up their own version of the family's shared experience. In families, we train each other up to respond in particular and peculiar ways to internal and external events and thereby become a more cohesive unit. Even if those internal events are horribly dark, they shape the participants so that they look and feel more like each other than they do to outsiders.

When our kids were small, I'd set up an age-appropriate Treasure Hunt for Easter Sunday morning. Looking back on some of the clues, I marvel at my concept of age-appropriate because I seem to have had absurdly high expectations for what a 9 and 7 y.o. were able for. Then again, then again; it was usual for them to rattle through the puzzles quick enough to satisfy their chocolate acquisition drives, with only minimal supplementary clues from me. I suppose I was exercising my educational philosophy of pushing them a little bit more than they might have been initially comfortable with. I reckon a large part of it was that continued practice tuned them into my ways of seeing so it became steadily easier to read me like a book.

That's all by way of scene-setting for the bday card I received last week from Gdau.I, who is 8 going on 800. Never underestimate how much knowledge pre-teen kids are packing away. The classics quiz I sent her back-at-you was in response to one she set her parents and grandparents. The grandfathers scored 3/10 and 2/10 respectively while the parents mustered 0/10 and 1/10. Adult honour was marginally restored when Dau.I the Reader clocked up 7/10. I won the Junior Scripture Prize aged 11 because I read, with care and attention, 6 chapters of the KJV of the bible every week for about 24 months.  The card [L] is clearly a cartoon of the iconic DNA double helix; but Gdau.I had helpfully included a key on the reverse. Adenine - Guanine - Thymine - Cytosine . . . well, kidder, that's life, Jim, but not as we know it. Because although you have been careful to maintain consistency in the pairings, all the life on this planet pairs A with T rather than A with C. But that's okay because it gives more options on what the message encoded in the picture might be.

Q. What's DNA to me?
A. It must be a clue to a puzzle!
Because I refused to accept that an 8 y.o. would stick just random base-pairs in her double helix. As you shd know, DNA is read off in triplets = codons using a particular [almost] Universal Genetic Code, but it's not obvious from picture what is the direction of transcription and translation. So there are 4 different ways in which the DNA bases can read: blue up; blue down; red up; red down. There are also one or two points of ambiguity where the turns of the helical backbones obscure the base-pairs between them. But here's the data transliterated:
It is obvious, with a bit of help from ExPaSy's translate tool which is the information-containing strand and its direction (the others are random noise):
CTaATCGATATcGC. where I have interpolated (c) for the backbone-obscured bases
 L  I  D  I  A
Lidia? It's a message! From one generation to its ancestor!! But what can it mean? there are a number of possibilities:
  1. A command to go forthwith to Kyrgyzstan to find an Asian dwarf spider.
  2. A suggestion that I should squeeze into my Traje des Luces [example R] <eeee but I do love some skin-tight sequins> to fight Un Toro de Lidia.
    • I can't believe she advises such a dangerous escapade in my declining years . . .  unless she hopes to inherit my Traje before I'm quite ready to let it go
  3. It is a heads up that the child has acquired a tat. Not my business but I'm cool with that, so long as it isn't on her forehead. I'm also okay with modest metallic appendages in children - ear-rings etc.

Sunday 21 June 2020

Summer Solstice Sunday

Gdau.I has been mad about Greek Mythology for the last year or two, in the way that other kids of similar age might be mad about dinosaurs . . . or Barbie-dolls. She sent the family out a quiz last week with 10 questions about the ancient greeks and their stories. I did woefully, scraping a bare 2/10 right. Then again, at least 4 of the questions I was pretty certain I'd never known the answer. It was the other four which niggled, because when I was her age, I'd been quite interested / knowledgeable in the field.  One of those edge of consciousness question s was "Who tamed Pegasus [the winged 'orse]?  As I dredged the dark reaches of distant memory the word Bellerophon surfaced but I batted that down with naaah that was Napoleon's horse assuming that the retrieval 'bots were just popping up any old nag. I was wrong on several levels:
  • Bellerophon Βελλεροφόντης was indeed the chap who, the help of a magic bridle, tamed and rode Pegasus
  • Belleraphon was not Napoleon's horse - that was called Marengo
  • But Bellerophon is in the same room of the memory palace because after the disaster at Waterloo, Napoleon acknowledged that the game was up and surrendered to the nearest British warship which was HMS Bellerophon, Captain Maitland [bloboprev on the "Billy Ruffian"].
In the course of my scraping the barrel of my memory, I recalled Bucephalus Βουκεφάλας [begins withh B; is Alexander the Great's horse] and Copenhagen: Wellington's horse at Waterloo. He was up top when Henry Paget lost his leg.  Having washed up in København, it seems meet to hang out there for a bit

Saturday 20 June 2020

Chocolate Fudge Cake

Just a perfick day. My birthday, Wednesday, was, like the electron, a bi-locating affair.  The Beloved and I spent the morning pootling about in the garden - a lot of shovelling compost and transporting water - and then set off for Costa na Déise to start a week of caring for Pat the Salt my venerable F-in-L. After a thanksgiving dinner that couldn't be beat we all set to on a generous tranche of of the pictured cake . . . with a few tart strawberries as counterpoint. But Pat goes to bed early, whatever the state of light beyond the window so I was able to escape for a yomp along the beach at Kilfarrasy.
As I haven't gotten my toes salt-wet since the beginning of March, I was delighted with myself.

On going to bed in daylight; my mother maintained that she never taught her children how to tell the time so that she could hoosh us off to bed when she had had enough.
"But can't we stay out a little longer? Vitamin D is still a-makin'"
"Nope, it's bed o'clock; I'll read you a story"

Friday 19 June 2020

Anybody out there?

A few years ago, I wrote about the Drake Equation, one attempt at guesstimating whether we are all alone in the Universe or if there are intelligent beings out beyond the solar system with whom we could converse. I wouldn't be much of a dialogue because the nearest star is Alpha Centauri and that's 4.2 light years [same as radio-wave years] away. Ask a question like "Have you discovered Thorium?" or "Is DNA at all relevant to your lifestyle?" and, even having sorted out the language of communications, it's going to be 8.4 years before you get an answer back. It is evens probable that there's a planet orbiting one of the suns of the Alpha Centauri system and that the planet is in the Goldiloxian 'habitable zone': not too close and torrid or so far as to be frigid.

I was tooling about The Déise yesterday and caught Newstalk FM with Sean Moncrieff interviewing one of the team from Nottingham who have re-jigged the Drake Equation to come up with their best guess about the likelihood of Intelligent Life "out there". Despite repeating the name of the interviewee, I was unable to recall it 30 minutes later when I'd stopped driving and was able to pick up a pencil. I did, however, remember their number of habitable planets with intelligent life that hadn't yet blown itself to buggery or asset-stripped their home to an uninhabitable cinder. So I googled "Nottingham 36" and found a) Bus #36 serves the Queen's Medical Centre, whither my boss decamped in 1993 leaving me i/c bioinformatics infrastructure Ireland at INCBI b) the authors of the habitable planets paper "The Astrobiological Copernican Weak and Strong Limits for Intelligent Life" were Tom Westby and Christopher Conselice. What a crappy, keep the proles at bay, title for a paper of such galaxial importance. The Copernican Principle is the idea of human non-exceptionalism: just because we are the only speaking, dancing, technologically capable species we know doesn't mean that we are specially created by a [beneficent] god. It's much more likely [regression to the mean etc.] that we are just about average

What Westby & Conselice [and Drake] are trying to do is have a punt at the number Communicating Extra-Terrestrial Intelligent civilizations (CETI) to establish a) whether it's worth looking for them b) whether any of them pose a threat, so we should worry about them. The answer is a clear nada, nix, zonders, furgeddit. Their key problem is trying to extrapolate a distribution of data points from a single case [humans [and dolphins] on Earth]. The media is predictably joyful about the proximity of "36" to Douglas Adams' Hitchhiker's "42" as the answer to the question "life, the universe and everything?".

W&C are much better informed than Drake on one aspect of the necessary conditions for intelligent life. Since the early 1900s, astrobiologists have been looking hard for planets orbiting around stars and now have 4,000-and-rising to choose from; with the discoveries doubling about every two years. The first was evidenced in 1994. And space-hero Sara Seagar has been designing nifty tech to help find more.

Anyway, that 36 comes with error bars: with all their assumptions and extrapolations or best-guesses, there could be as few as four [4!] CETIs in our galaxy or more than 200. But those are, if you pause your rubbish! button for a moment, really confident bounds on the limits of their calculations: only 2 orders of magnitude. As you have been told [I am careful not to use as you know because the numbers involved are waaaaay bigger than a breadbox and effectively incomprehensible] the galaxy has a great many stars but they are spread really thin: loads of space between them. Another view on the W&C numbers is that the average distance between CETI planets is ~17,000 light years. Even if we detect a signal, it will be such old news that we won't be able to respond appropriately. And if we're planning on sending out a signal telling our story, it seems unlikely that there will be anybody intelligent around to process the response.  All good fun, though, or at least "Mostly Harmless"

Thursday 18 June 2020


The best lack all compassion, while the worst 
 Are full of passionate bitchery.
WB Not-Yeats
The day after the Bon Appétit systemic racism story broke I was physically in The Institute zoomin' [and zonin' out] on an interminable meeting. Because I was multi-tasking on company time, I was able to field a txt and an e-mail requesting a meeting from an ex-Student; let's call him Vishnu because that's not his name. I looked at the day's schedule and replied that I'd meet him at the Bridge across the River at 1300 precisely. I couldn't buy him cake and coffee like the last time he needed some bracing; but we could and did go for a walk in the drizzle up the river to watch the swans thrashing about. In February V had been in the dumps because he couldn't get a positive response from his many job-applications. Actually, in most cases he didn't get any response let alone a positive one.

That would be par for the course. A few years ago, I canvassed my final year project students to see who had sorted out their 12 week work-placement. In the InstTech sector, this work-experience is a post-requisite for graduating. That year it turned out to be a completely black & white issue: all the Old Irish kids were sorted but none of the New Irish had found a billet. You just knew that part of the problem is that a CV from Amanda O'Keeffe was more like to get a reading than one from Adefolahan Olajumoke. There wasn't much I could do for V, because I don't have a nephew who runs a paint-factory, neither do I have favours to call in from biotech companies. But I did feed him up a little, and not just with cake.

But by the beginning of March he'd gotten a job as a Pharmacy Technician PT in one of the South Dublin suburbs. That's a step down because, in Tamil Nadu, V is a fully qualified Pharmacist with several years experience in the trade. But €15/hr is bankable money [and more than he'd be getting for a more prestigious job back home] and he could make a case that by starting at the bottom, he was getting experience in the sector in this country. I was delighted for him, because by opting to get work in the not-quite-front-line at the start of the pandemic, he'd be accumulating bonus points towards any future application for residency here in Ireland. It was a bummer that the work was a long way from home and would involve a long daily commute; but mostly it was going forward.

Shortly after he started he'd gotten 'flu-like-symptoms and his line manager had required him to a) self-isolate for 2 weeks b) get a bed nearer to work that didn't involve so much public transport. Well he did both of those and was sitting pretty getting experience and a [barely] living wage. He even managed to get a ♀al of his a half-time job in the same pharmacy. But as soon as he came back from  unpaid sick-leave, he was bullied into signing a contract for a years employment at 32-40 hours / week. Ever since he's been working on exactly 32 hrs/wk and having to keep up his share of the rent with his mates in Carlow as well as paying for his digs in South Dublin. And he's feeling shunned by his work-mates who chatter away about fripperies and TV and make no effort to include him in this phatic exchange. It's heart-breaking to see this confident, qualified, kind and fundamentally happy young man tuning into his depressive side.

But his compassion was all directed at his friend from TamilNadu. Let's call her Hattie? She is really getting the bum's rush. There is high staff turn-over in the shop [and no wonder?] so she is getting some seniority but if there's a shitty bit of cleaning to do, or a super tedious task in inventory, guess who draws the short straw??  Like a lot a businesses, the pharmacy is trying to go on-line and the owner lined up all the staff outside the shop for a group photo; guess which invisible employee got to take the photo??
Oh, but you who philosophize disgrace and criticize all fears 
Bury the rag deep in your face For now’s the time for your tears

It doesn't have to be like that! Before I went to Graduate school in Boston, I went to the Netherlands to work-and-save for my first semester's fees. By great good fortune, acknowledging that we make our own luck, I landed a laboring job in the fish department of  Blijdorp zoo in Rotterdam.  Although I was a foreigner with a rudimentary knowledge of the local language and so couldn't understand a fraction of the coffee-break gossip, m'n makkers made me a fully paid up member of the team.  And I mean fully paid up! If there was over-time to be had (and there was) then I got my share of it. If there was a bucket of coinage mixed with shitty water when they cleaned out the crocodile pit (and there was) then I got all of it.  The idea that I'd be left out of the group photo or the birthday beers was just unthinkable.

Wednesday 17 June 2020

Lón sa Longfort

I grow old ... I grow old ...
I shall wear the bottoms of my trousers rolled.
TS Misogenistiot
Since 0010hrs this morning, I've been eligible for free travel on public transport. This was an absurdly populist measure enbudgetted by Charlie Haughey, the sketchy and absurdly populist Minister of Finance in 1967. Quoting: "While our social welfare services are being continuously improved, there is considerable scope for voluntary effort in providing old people not just with the basic necessities of life but also with some comfort and companionship." I'm not knocking it because keeping Elders up-and-at-'em will ultimately stop them us being a bed-blocking larger burden on state services. And there is a huge grey vote. +13% of the electorate are over 66, and on their rights and privs we are likely to vote en bloc.  It really doesn't look good if a lot of silverbacks protest outside the Dáil until dispersed with pepper-spray and baton charges.

But what about meeeeee? It's move over Manhattan Transfer and Route 66 and go Busáras Transfer and out along the N4. Since September last year, I've been exercising articulating-from-sofa the idea that as soon as I am able, I'll be travelling about the country checking out the lunch-counters of places with train-stations or bus-stops. Believe me, every drizzly market town in the country has one or the other. Dublin sits like Shelob in the centre of all public transport infrastructure with her web radiating out from the capital, so to get anywhere unlocal by bus, you have to go through the central bus station.

Actually, me being me, I shall probably be too mean to purchase Lunch in Longford so will rather be checking out the park-benches and sharing my 'umble cheese-and-chard sandwich with the pigeons. But I might be tempted to a hot cup of tea at Torc Café, The Wooden Spoon, or the Gallery. But that will be enough, because I have to cover Brunch in Baltinglass, Coffee in Cork [scabbing off Dau.II and hoping for macaroons] and Dinner in Dublin with Dau.I.  And like my late much loved MiL, I shall probably start nattering to the unfortunate randomers who are near enough on the train to cough at.

Tuesday 16 June 2020

I'm off my food

A tuthree weeks ago, Dau.II aka Cookie from Corcaigh drew my attention to a brilliant inspirational video about fermenting and cooking. I've tuned into the Bon Appétit Test Kitchen before because I bake and you never know what you might learn. But I'm not a groupie. Brad and Sohla make dosas does what it says on the tin, but with a bowlful of élan, expertise and experimentation all stirred together with a  sense of fun. Each player had a part, but it was clear who knew what was going on and who was learning [as in R]; so Sohla & Brad would be a better billing on the stars go first paradigm in the billboard industry. In science, there is a different convention: the Gaffer / PI / Money goes last-author, the effective/student goes first. In my Food Fermentation module next year, I'll make the students watch Sohla and Brad to force some reflection on allowable error / inaccuracy; if you can master that you have profound "Barbara McClintock" [her 118th birthday today!] understanding rather than reliably follow the protocol understanding.

I am very sorry to report, via Metafilter, that the cake batter really hit the fan >!fffrrrrpppp!< in the Bon Appétit Test Kitchen last week. The co-founder Adam Rapoport was discovered, in the near infinity of embarrassing back-story that is the interweb, to have been at a fancy dress party dressed as a stereotypical Puerto Rican . . . in 2004. This hilarious gag is known as brownface and has exactly the same toxic branding as blackface which has meant that, among much else, much everywhere, Zwart Piet can no longer bring cookies to kiddies at Sintaklaas.  In the five alarm fire that is Black Lives Matter this month, that error of judgement requires that the perp falls on his sword. I say "this month" because We the Patriarchy have sadly, shamefully, been here before and wrung our hands and then got back to normal life; rather than wringing necks and implementing to some permanent changes to our collective own hearts and minds.

Aside: I recently coughed up $5 fro lifetime membership of the Mefi community hoping to give back a little after lurking there for a decade because it is such a great source of copy and commentary.  I had this to say on the BonAp farago: I only came across Sohla a couple of weeks ago in Brad & Sohla make Dosas . She is brilliant; a real are we going to measure or are we going to cook cook. She is what we treasure in science: a good pair of hands - someone whose understanding of what's going on down there (on the lab bench or in the oven) doesn't need continual input or instructions from a recipe / protocol. Respect!

Q. Who cares, when there's a pandemic on, what sketchy prank some white dude did 16 years ago?
A. Nobody, because it's optics. But Sohla al-Waylly, pointed out that, actually, the racism in Bon Appétit is not only one boss-man and the past is a different country. It was au contraire, in Sohla's experience,  systemic and pervasive and directly affecting her sense of self-esteem and take-home pay. What rubbed salt in the wound was that the management had recognised that there was A Problem in BonAp: the overwhelmingly white caste of the leading front-of-camera cooks looked bad. And the response has been to try to make it l👁👁k better without actually undertaking to make it really better. Among other shit, there was a cunning plan that dusky Sohla was given more time in front of camera while still expecting her to do the tasks she'd been hired for  . . . and kept on the same barely scraping salary. She and a raft of other young people were effectively in the intern trap where they'd suck it up: low-or-no pay; casual disrespect;  making the effin' coffee . . . just to be in the same room, with half a knee under the Big Time table. The business model is based on the threat/promise that 100 hungry young kids were out there who'd gladly take your place.

And WHEN Sohla spoke up and put out her almost-there-but-always-the-bridesmaid story [and her career on the line!] THEN everyone in BonAp suddenly woke up and joined the chorus of solidarity and support. Because up until that exposure, the king was fully clothed for all the white folks in the kitchen: they were all so driven by their own eyes-front-and-upwards trajectory of ambition that everyone else, especially those further down the pecking order was invisible. With only a few places in the winner-take-all enclosure, solidarity ceded second place to MeFirst and the American dream. Very few people come out well from this sorry tale, except perhaps Sohla al-Wonderwoman. TwitterFans. And rather than just batter the BonAp pancake; we could with advantage reflect on [every?] other industries with the BBC: where all-white companies are blowing hard about BLM while sadly neglecting to hire any actual black talent.

Monday 15 June 2020

A busted flush

Work at The Institute is winding down for the year. I received an e-mail from out external examiner confirming that my marks for research projects were okay. That e-mail was send at 22:53 on Bank Holiday Monday. In my response, I apologised that The Institute paid him so little for his [after-hours] time. I then set to on the next item on my To Do list: putting in another hour's work mentoring MSc PharmRegs students. I get paid for 10 contact hours to see them through the task of writing their MSc thesis. I've put that amount of time in already and I've not seen a correctable draft or, in one case, any data. Our Extern is not the only kid on the Above-and-Beyond block.

My weaker link on the MSc is a very polite, quiet chap from Andhra Pradesh. That's one state North of Tamil Nadu. He calls me Sir. Deference to age-and-experience is all good but it should not replace ooomph and initiative. Early on in our relationship I made the point that an MSc thesis with some crunched numbers was stronger / more interesting than a descriptive comparison of regulatory practice in different jurisdictions. But, possibly because I know very little about pharmaceutical regulation, my pointers to numerical data came to nothing; or very little. And a couple of days ago I got a plaintive cry for help that his exploration had clunked up against a wall. So I replied:

Well that's what can happen when you are doing research. You have an idea, you think, you formalise your thoughts into a [testable] hypothesis, you start to gather data to test that hypothesis . . . and you find that there are no data OR that it will take you longer to gather the information than the hypothesis seems worth. What next?

You are in a better position now; because your search for information has immersed you in the field. You can /should choose a different direction in which to swim. You can call 911 and get airlifted to a totally different field . . . but we are time-limited. Therefore let us stick to generics. What about doing more discursive / descriptive research on the policy / process by which generics are registered by EMA v FDA [I'd really like to throw Indian pharmacy regulations in here]. OR compare the registration policy / process for branded vs generic. Here you could limit the study to either FDA or EMA [or the Indian equivalent] because we're running out of time.

Your "abortive" take-off into the stratosphere of time-lines should not be dumped in the bin. Write that up, carefully documenting why the task has proved impossible. Negative results are really important because they save the community [including your cousin who comes to do the MSc in 2024] from even starting down the path you explored. A big sign [R] will encourage the next explorers to romp off in another direction.

There is far too little of that in the scientific literature. The scientists are too invested in being right in their hypotheses than rigorous in their analysis. There is a well documented bias in publishing only positive findings and sweeping the damp squibs under the carpet of shame. If we are with Edison in “To have a great idea, have a lot of them” we have to accept that many of the ideas will be rubbish. Cutting our losses is the correct thing to do but it would be polite to flag where you've been.

Sunday 14 June 2020

St Fortunatus Sunday

A few links to the outside world for the last days of lockdown.
Wider propagation of a quiz created for Greek Mythology Expert Gdau.I  More background on this grizzly theme on The Blob 

Saturday 13 June 2020

Imperial Math

I just dug out a copy of Pendlebury's New School Arithmetic [with answers!] 1924. It was first published in 1904 and reprinted 22 times over the next 2 decades. Must have been a desirable commodity. Looks like the planner at the publishers was not really on the ball. It must be cheaper to set up once, or a few times, and then print enough copies to satisfy demand. Then again, 20 years is a generation of new pupils coming through schools and looking to master compound interest, book-keeping, measurements, foreign exchange and graphs. The publisher certainly wouldn't want to plunge the whole warehouse space on this one book. If another book came out in competition with Pendlebury then the publisher would look a bit silly with stacks and stacks of unsellable stock.

Yes, yes, all very interesting about the economics of early 20thC publishing, but worrabout the 'Rithmetic?  You'd think that arithmetic would be the same as it ever was, since the Egyptians used a 3-4-5 triangle to to make their pyramids square but the past is a different country in ways that transcend the fact that pocket calculators only came on the scene in about 1975. Consider the gratituous difficulty of adding in units which are related by different multipliers. In sensible = decimal = "metric" addition "carries" numbers when they exceed ten. In summing weights, as in the top pictured  example:
  • 16 oz = 1 lb [ounces ~ 30 g; pound ~ 450 g)
  • 14 lb = 1 st [stone]
  • 2 st = 1 qr [quarter]
  • 4 qr = 1 cwt [hundredweight which thus weighs 112 lb)
  • 20 cwt = 1 [long] ton [which thus weighs 2240 lb or as close a dammit to 1 tonne = 1,000 kg] 
Everything is chunked differently! When we bought potatoes in Moore Street market in the 1970s, it was typically as a quarter stone = 3.5 lb = 1.5 kg. Now nobody buys loose potatoes, let alone in such bonkers quantities. I've been here before where you can get help to sort out the second illustrative sum, which involves lengths. Exec.Summ: 12 in ; 3 ft; 22 yd; 10 ch; 8 fur; mile; 1760 yd = 1 mile. And don't get me started on the parallel wonkiverse of Troy weights.

That's not the only difference in a 100 year old arithmetic book. The interests and obsessions are quite different too. In the Problems at the end of the book, Pendlebury tries to relate the theory to practice in real life.
  • 83. A besieged garrison have sufficient provisions to last them for 23 weeks at the rate of 18 oz per man per diem; but receiving a reinforcement of 40% on their original number, this allowance is reduced to 15 oz per diem. How many days will they be able to hold out?
  • 99. A ship 600 miles from shore springs a leak which admits 6 tons of water in 20 minutes. 60 tons of water would suffice to sink her but pumps can throw out 70 tons in 4 hours. Find her average rate of sailing that she may reach shore just as she begins to sink
  • 157. The proprietor of a boarding school having already 30 pupils, finds that an addition of 5 increases his gross yearly expenditure by £300, but diminishes the average cost per head by £1. What did his annual expense originally amount to?
  • 194. A rectangular fold is to be made of hurdles 6 ft long, to contain at least 1,000 sheep allowing 8sq.ft per sheep. Find the number of hurdles  needed for the cases where one side of the fold consists of 10, 11, . . . 20 hurdles. Draw a graph shewing the relation between the total number of hurdles and the number on one side. Hence find the smallest number that will suffice.
Lots more where they came from.

Friday 12 June 2020

hahahahaha incommmming

My late lamented compañero Pepe Malpica was rightly proud that his last publication was accepted in the first issue of PLOS One. Pepe was good copy and great fun because he'd often have a different way of viewing the world. PLOS One was, and is, exciting because of its business model: "papers are not to be excluded on the basis of lack of perceived importance or adherence to a scientific field". Submissions are indeed peer-reviewed but only to check the methods section; context, relevance and scientific significance are excluded from the reviewers brief. Good thing too, because a couple of peers bring their own baggage and [limited, because not infinite] experience to the table and you would not want them (or me, or you) to be the sole arbiters of what gets out into the public domain. You have to allow mavericks like Pepe to break out of the box and frame scientific questions differently. Otherwise it's just a mighty - and mighty expensive - echo-chamber.

In that sense, PLOS One can be a little like the IgNobel Awards whose watch-word is "first they make you laugh, then they make you think". Of course, for most people, most papers, most of the time are just zzzzzzzzzzzzz. And that's one of the most wonderful aspects of the electronic world we live in: nobody needs to take the whole journal to read the one paper a month that is of interest. That saves a lot of dusty paper.  "zzzzzzzzzzz" is on message because now we're looking at Hahahahaha, Duuuuude, Yeeessss!: A two-parameter characterization of stretchable words and the dynamics of mistypings and misspellings a recent paper in PLOS One. Because PLOS is the Public Library of Science y'all can read the whole thing without having to mortgage your firstborn for the subscription price. If you can read the whole thing without the Furrowed Brow of Bafflement then you're a brighter star than me. But the paper is useful because it focuses [my] attention on repeated elements.
  1. Romanian soccer commentator Ille Dobre has the longest recorded single breath call of goooaaalll! When the pubs re-open be sure to impress your pals with that fact with or without a hat-tip to The Blob. And for the love of god without an attempt to emulate this feat - that way apoplexy beckons.If you need help being a bloke-in-a-pub, then Moss has you covered with Bluffball.
  2. One of the advantages of having a thick-as-pig-dribble phone like my so so retro  Nokia 3310  is that each letter takes ~2 keystrokes on average, so it damps the temptation to writing incommmming rather than merely incommming. The other huge benefit is that its sad-sack text-only processor acts as a really effective emoticon filter - text me your 👱😜👿🙈 nonsense and it comes in as □□□□. Often this is the sole content of the incommming txt. But emojis, as well as being fashion accessories, are phatic comms [metaphorical hugs and mutual de-lousing] rather than data-comms [actual information].
  3. Back in the day when it was either quill pens or typewriters [remember them?], you had a choice of upper case CAPITALS or lower case, all fixed width fonts so i occupied the same space as w. You will have noticed that The Blob is quite pedantic about putting species names Orycteropus afer in italics. Because that is how it is done. But in typewriter days no italics so, by convention, underlining was used to represent italics. I have seen folks trying to use another form of emphasis by backspacing and retyping the relevant word a tuthree times to make it bold. We haven't got there yet but there's great scope for incorporating colour into manuscripts to add meta-meaning to the text. 
    • Kelly green "#4CBB17" will do for Irish references
    • Orange "#FFA500" for marmalade excursions or fried fish
    • Dull red "#990000" for fury
    • Cambridge "#3d85c6" vs Oxford"#002147" if you're British
    • There's a war on about what best represents the Democrats this "#3333FF" or that " #00A6EF" 
    • and Republicans are divided been electric #DE0100 or plain #E9141D red
    • But then again maybe this train has left the station with Emojis
  4. Apart from being longer and consuming more electrons on the server, is there any downside to having hahaha or hahahaha? Nope! But there is a definite downside to having CAGCAGCAGCAG rather than CAGCAGCAG in your genome. This CAG-repeat is a stutter in one of our standard genes, called huntintin or HTT.  CAG codes for the amino acid Glutamine and you and I probably have a different length of this repeated motif in that gene: the normal range being from 6 to 35 copies. Some families have accumulated a much longer CAGn tract. The longer the repeated unit, the earlier and the more severe will be the onset of Huntington's Disease. HD is what killed Woody Guthrie. I can see I'll have to write longer and deeper about these trinucleotide repeat disorders of which HD is but one.
Actually (revenons nous a nos moooooutons), you might skip all the math and jargon in that PLOS One paper the conclusions are discursive and interesting.