Thursday, 21 March 2019

sleep early and often

The Wexford Science Café meets on the third Tuesday of every month . . . except when it doesn't. It has been lurching running for more than 4 years now and we've covered:
Stephen J Gould’s spandrels; Galena; Thomas Kuhn’s paradigms; Organic soil microbiome; Composting toilets; Water quality; Bacteria in food prep; Urination once again; Toxicity from botox to beer; Air-quality and asthma; Gravity waves; Neuroscience of torture; Greenland ice melt; Cider making; Zombies; Wolbachia and tropical diseases; Radon; Diabetes & Alzheimers; Marketing generic meds; Oroville dam crisis; March for Science; Allometry; Science book-swap; Erwin Schrodinger; Pheromones; Back-garden astronomy. 
All interesting and showing the reach of science and the collective interests of the WSC participants. I am quite religious about turning up even if it means driving nearly a hour from home to get there: It is one of the few social engagements I have outside of work and nuclear family so is important for my mental health.

Last Tuesday we heard that getting a good night's sleep is also vital for your mental health. One of our reg'lar participants in the WSC Happy Family is Mr Pill the Pharmacist, who has recently become a Daaaad and two years into the gig is still laboring under a sleep deficit as the wean frequently neglects to snooze the night through. If he was a Kiwi, he'd have an instructional video. What the child's father has noticed is that he can be unaccountably ratty at work - amazed at the stupidity of his customers; furious when things go wrong; narky with his colleagues. Then he put two and two together to realise that his anger descended when he'd endured a really wretched night.  He also floated a hypothesis, as yet unquantified, that most of the kids who present a script for ADHD medication are no way ADHD: they are just sleep deprived. When a family comes to the doctor's surgery with €60 and a troublesome restless teenager, it is impossible for everyone if they come out with only a suggestion that a good night's sleep is required . . . and why not lock up the youngster's phone before bedtime? They'd rather dose the trouble away . . . and then get really indignant when Young Jimmy scores a few Es at the weekend.

The hook on which our discussions about sleep were hoist was the book by Matthew Walker, British author of Why We Sleep and Prof of Neuroscience at UC Berkeley. It is Walker's contention that sleep hygiene is at the root of many woes: mental and physical health; success at work; success "ín bed"; that car crash; that slice of chocolate cake. The book was a surprise runaway best-seller in 2017, so must have rung a few bells (or jangled a few chains) with the reading public. Which is a rather diminished cohort because book-reading is soooo yesterday and pushed to the back of the closet as everyone embraces screens. I've written about the negative impact of the [blue] light used to make screens work. Dau.II pointed out that device content is designed to be seductive if not  addictive. What are we like? The evidence of the damaging effects of sleep deprivation is piling up while we're swiping just one more tweet long after after midnight.

The sleepy discussion at WSC led on the work of Annie Curtis and her Clock Lab, now at RCSI in Dublin. She is finding that disruptions to another cycle can have serious health consequences. Lots of things go round and round and up and down for us on a daily basis - core body temperature; sleep-wake; the bowels. Curtis has put together large datasets [like half a million middle-aged Brits] showing that other aspects of well-being and equanimity fluctuate on an annual basis. You're more likely to have a fatal heart-attack in the Winter; surrogate cardio markers also tip up as the days get shorter: we get fatter and our blood-pressure goes up significantly, for starters. And another large cohort study showed that clinical depression descends on many women in Winter. The underlying basis of these adverse events is the molecular clock which is ticking in us all: cranking up the immune system at certain times of the year (perhaps because that's when the pathogens are abroad??) with unexpected side-effects in other systems of the body. Those epidemiological studies are paralleled by lab-based studies in which the undulating concentration key molecular immune markers are tracked across time. What's not to love about someone who can use a quote from Wm. Shagsper as the title of one of her papers.
“Sleep that knits up the raveled sleave of care,
The death of each day's life, sore labor's bath,
Balm of hurt minds, great nature's second course,
Chief nourisher in life's feast.”
Night-caps off!
More Women in Science.

Wednesday, 20 March 2019

Iditarod goes Idatadog

We spent St Patrick's weekend at home; and, although Mohammed stayed away, 50 years of strong smart women sat down to Sunday dinner up the mountain: The Beloved in the Matriarch's chair, Dau.I and her SO, Dau.II, Dau.II's odd-mother, o-m's daughter. I won't bore you with the ages but the range was 50+ years. The youngest person present is beginning to run and the adult women present were full of cogent advice and encouragement. Someone cited Chris McDougall's Born to Run [bloboprev] because in the elite ultramarathon world, women are at least as good as the men. If you can run 100km, then your chromosome count [and consequent testosterone titre] is no handicap. I can run 100m, uphill if necessary, but I cannot speak at the end of it and I have neither the wind, nor the bottle, to run 1km let alone 100km. otoh, I did walk 700km in 1989 and 800km in 2004, so I have [blistered] skin in the game. Me I'd cite Feet in the Clouds: a tale of fell running and obsession by Richard Askwith as a source of inspiration for young runners.

My preferred charity is the RNLI because a) it does good but b) it allows people to be their very best = heroic. Running also allows people to be their best selves: against self; in competition but also in compassion and kindness. Marathons and a fortiori ultramarathons really sort the sheep from the goats. I've recently become a bit of a sofa-groupie for dog-sled racing like the Iditarod Race which is not a direct commemoration of the famous diphtheria antitoxin delivery to Nome, Alaska in 1925. The race happens every year since 1973 and takes at least 8 days to cover 1500 km through a winter wilderness by a sled and dog-team. This year the third person across the line was Jessie Rover. Susan Butcher won rhe race outright four times in the last century, while Libby Reynolds was first home to Nome in 1985. That was a dreadful weather year and Reynolds took 18 days to cover the course. This year a lot of attention has been on rookie Blair Braverman who finished 36th and six whole days behind the winners. While she was mushing on through the blizzards, her fan-base were raising $000$ of dollars  #uglydogs to support Alaskan schools. Commentary at MeFi.

BB was one of 17 (about a third) female entrants in 2019, including Jessie Royer. It has got to be harder graft to finish 36th after such an extended and calorie sapping journey than in the top three.. Anyway, our youngest visitor over the weekend is mad-about-the-dogs having acquired a puppy  a few weeks ago to walk and clean up after. It occurs to me that if Jamaica can field bobsled teams, both men and women, Ireland can surely furnish an entrant to the Iditarod in about 10 years time.

[You can stop reading right now unless you are fully nerded up]
Scoping out the results of this years gig, I noticed that one of the variables was Dogs In with numbers from N = 6 to N = 13. Hmmmm, I pondered, is the number of  Dogs In correlated with the time taken and/or is there an optimal number of dogs for getting over the line in the quickest time? That required cut&pasting the data from the results page in Excel and plotting Dogs In vs the time in seconds.
[Time in seconds = days*86,400 + hours*3600 + minutes*60 + seconds].
There are about 700,000 seconds in 8 days.
This picture is a special class of scatter-plot called a dot-plot where the range of values for each count of dogs is graphically displayed. This shows [me] that the range of race-times for a particular number of dogs is greater than any difference in the average time among dog-numbers. The display is far more important, and provides better insight into the distribution of the data than any ANOVA [analysis of variance] the standard statistical test for such data. The intuitive feel that here within group variance trumps mean values is actually borne out by the ANOVA. It takes about 1 million seconds or 11 and a half days to run the race regardless of the number of Dogs In. I'm not sure exactly what Dogs In signifies: are substitutions allowed during the race the way soccer players are ordered off the pitch by the coach and replaced by a player less puffed or less limpy?  Regardless of the details, I'll be using these data in Quant.Meths next year at The Institute to show the value of dot-plots.

Tuesday, 19 March 2019


The other day, one of my project students was looking more competent than me [red face] in the tools of his/our trade. In too much of a hurry, I thought that Proboscia was essentially the same as Proboscidea. When I slowwwwwed down I twigged that one Proboscia is about 50μm on length while elephants are about about 100,000x longer trunk-to-tail. What a difference a '' makes! The accident tinkled a distant bell that there were pairs of species which really did have the same name but were completely different.

A recent explanation of the rules and regs for the naming of parts in biology is The use and limits of scientific names in biological informatics by David Remsen Zookeys. 2016; (550): 207–223.  It's something that requires a certain amount of precision to prevent misunderstanding. If you want to communicate some measurements blue-tit [the bird in the picture] wings to your colleagues in Hungary then using a universal [dead] language prevents ambiguity: Cyanistes caeruleus is the only thing it could be I would be skeptical about using the Google - Magyar translate to kék cinege. Not a big problem in this example because the bird appears on both the EN and HU versions of wikipedia. But what about something more obscure: the White-bellied rice-rat Oryzomys albiventer isn't in hu.wikipedia.

One of the rules about taxonomy is naming priority. 25 years ago, I had a heart-in-boots moment on that front. We'd just published a sequence analysis paper on Aspergillus nidulans. and I thought I'd check the database to see if there were any new A. nidulans sequences which I could add to our tiny dataset. When I asked, ACNUC (the then cutting edge database interrogation software) came back with No Sequences Found. It was like arriving at the 13th Floor by elevator in an episode of The Twilight Zone. As Aspergillus nidulans is a widely studied standard genetic organism like lab mouse Mus musculus and Drosophila melanogaster, it wasn't just me who was hopping mad disconcerted. The naming people at GenBank had been following priority rules to rename the species as Emericella nidulans. Luckily they were pragmatists rather than pedants and, at the next full release of GenBank three months later, all my Aspergillus sequences were back on line.

The key element of nomenclature is to be unambiguous. If things are different they get different names. Careful analysis [bloboprev] of the biology and biogeography of giraffes Giraffa giraffa made experts believe that there were really 9 different species of long-necks in Africa and they all needed a separate species name. The names of animals are decided / approved by ICZN; a different body to the ICN namers of plants fungi and algae.
Partly from the inertia of the system; partly because the two entities are unambiguous different there are an least half a dozen hemihomonyms: species which have the same official Linnaean monnicker. Here [L] is a nice pair, both Agathis montana: LL is a braconid wasp widely distributed across Eurasia from Korea to UK. LR is a long-lived conifer from New Caledonia in the far east.  It is critically endangered from a perfect storm of bark-beetles delivering fungal disease, feral pigs, and habitat destruction from climate change and logging. That extinction will nicely tidy up the taxonomic conundrum, no? Here are the other hemihomonymous pairs acknowledged by wikipedia:
venomous fish
another fish
That's only the top of the iceberg, however, Алексей Шипунов from Russia has compiled a mighty database of hemihomonyms - including 12 examples where a Genus is triplicated in bacteria, plants and animals:  Catenococcus  Gordonia  Kingella  Lawsonia  Leptonema  Microcyclus  Moorella  Morganella  Rhodococcus  Rothia  Spirulina  Stenocybe.

Because these worthy taxonomy-mavens are aware of illiteracy, dyslexia and Latinophobia among those who need to know the Names of Life, there is another class of wrong-wrong-almost-right called parahomonyms which are at best discouraged if not absolutely verboten.  Thus Astrostemma Benth. 1880 has been rejected in favour of Absolmia Kuntze; because it was too much like Asterostemma Decne. 1838 another genus of plants in the same family. To crowd confusion on ambiguity Asterostemma depressa is a fossil mammal from Argentina.

A couple of years ago I was laying out a very similar problem with the naming of drugs: where errors are more likely to kills people than mistakes

Monday, 18 March 2019


Kosher is a set of dietary laws which Jewish people take with a pinch of salt. Actually rather a lot of salt because cuts of meat are often ladled with the stuff to draw out the last traces of visible blood. I've worried about whether rabbits are kosher - they are not kosher because they chew the poo rather than chew the cud to max out the nutritional value of what they eat. Camels are not kosher on the other side of the definition - they indeed chew the cud but the hoof is not split.  Whaaa'? Looks pretty goddamned split to me [R]. Note to self: do not google "camel toe".

On the fish front, the definition is also two-fold: if the cr'ature has both scales and fins it is good to eat. Weirdly if it has scales then it is assumed to have fins. This excludes eels, sturgeon (and caviar), catfish, sword-fish . . . and of course a whole rattle of not-fish like shrimp, lobster, crab, mussels, scallops, whales and octopus. I think that one of the delights of kosher for Jews is that it encourages pedantic arguments about whether a kosher fish found in the belly of not-kosher fish is kosher - it is.

The Lord wasn't able to give a neat paired attributes {scale&fins | cud&hooves} definition of permitted birds. Instead the Torah lists -in Hebrew, natch  - 24 forbidden birds - none of which had the unambiguous Linnaean Latin binomer. And even if they had a clear label, would an averagely educated Jewish housekeeper recognise Otus scops or שעיר, שעיר מצו or Zwergohreule if it jumped up and bit him? That's rather inclusive: there being 10,000 different species of bird, only 2 dozen of which are suspect. Ambiguity and identity problems were only a challenge to the scholars of the yeshiva: nothing better than poring over an old manuscript to read the opinions of a long-dead scholastic rabbi from Lvov. The Torah is the word of god (equivalent to the Christian Olde Testament) the subsequent notes, criticism, arguments and counter arguments form the Mishnah, Gemara and Talmud.

If the forbidden birds have anything in common, it might be that they are hawks, eagles, owls and other raptors: birds that eat other vertebrates. The scholars of the Mishnah came to agree on three other 'helpful' criteria
  • having an extra toe
  • having a crop [a muscular pocket for grinding seeds etc.before the contents osdelivered to the stomach - some birds swallow small stones to help the grist-mill]
  • having a gizzard that can be peeled
all these characteristics are shared by chickens. You have to suspect that the scholars were stacking the discriminant function so that, whatever got spat out as not kosher, chicken soup and schmalz was allowable.
That diligent scholarship in the medieval ghettos of Lviv [priv] and Warsawa to determine what a good jew can eat without damageto the immortal soul has been recently emulated on Tumblr.  Here is a list of the (alas all too few = 77/800+) Pokemon which are kosher. Like with the Mishnah dealing with real animals, with clear rules most of the decisions are easy. It is the edge-cases which challenge the scholar; the grey areas; the equivocal; the noisy; the things that are not internally consistent w.r.t. to the rules of the kosher game:
  • Stantler: kosher, in my opinion. the split hooves are only visible from some angles and in some sprites. Consult your local Rabbi. 
  • Psyduck and Golduck: perhaps controversial, but i am going directly AGAINST the Kashrut Laws in Pokémon guide by declaring these two kosher. yes, they’re water types, and could be arguably treated like fish, but look at them; they’re ducks 
  • Cherubi and Cherrim are kosher. if you make them into wine, a Rabbi must be present. 
  • Skiddo and Gogoat are doubly kosher, as both legitimate goats with split hooves AND plants.
The names mean nothing to me; the SOs of Dau.I and Dau.II both know how to spell ポケットモンスター though.

Sunday, 17 March 2019

sh sh sh Sherborne

Sax six *** sox sux

Saturday, 16 March 2019

Suspense threshold low

I grew up watching Richard Greene as Robin Hood . . . from behind the sofa. It was far too frighty-me to watch on the telly while sitting normally. My excuse now, is that I was only 6 years old when the BBC stopped making episodes; of which several are available on youtube. That series is the archetype for such harmless nonsense as Men in Tights. But watching the telly from behind the sofa more or less set my clock with a low threshold for vicarious violence and, especially, for suspense. Getting to be an adult is to acquire a certain amount of autonomy - can choose what to watch without consulting siblings.

I walked out of Straw Dogs in 1974 even though I'd paid money to the UCD Film Society to watch it and I was quite a fan of Dustin Hoffman. It wasn't so much the rural English thuggery and viciousness as the expectation of RET&V in the very near future. I had, for example, sat through Peckinpah's The Wild Bunch despite its balletic bloodiness. The Beloved walked with me, so that was a bit of a mistake-date. Or maybe not, we probably went somewhere else and gazed into each other's eyes and talked about poetry. I'm not stupid, and I can read, so now I'm generally able to avoid getting into under-seat-puddle situations.

At the end of last month, I walked out of Dogman [trailer = summary] which was the Feb 2019 choice at the Blackstairs Film Society. I have a standing request in with the BFS organising committee to have more fluffy films: a gentle rom-com is what I'd call entertainment. Of course, having subtitles is desirable / essential - so a French rom-com from the 1970s would be ideal . . . but it ain't gonna happen. The committee have limited choice through Access Cinema and quite different tastes to mine. Dogman is about a dog-groomer living in a relentlessly bleak Italian sea-side town where affluent tourists have been replaced by graffiti and petty crime. Call me judgemental but dog-groomer is on my list of utterly useless ways to make a living - somewhere between telephone-sanitizer and currency-trader. The film started to go pear-shaped when the fellow's dog refused its kibble and started eating yer man's pasta - from the fork and then from the bowl [R from trailer]. We have been inured to the pornography of violence but most of the audience were audible in their disgust at these antics. The dog-groomer takes up with an enormous psychopathic petty criminal and, shortly after the dog-bowl incident the psychopath tries a bit of mindless violence. More seepiness ensues with barely-clad young women at a night-club . . . and I made my exit as quietly as possible.  No point in laying my values / sensitivities on other people.

If you want a better film about low-lifes you could shed the final N and watch Dogma written and directed by Kevin Smith. I enjoyed that.

Friday, 15 March 2019


Come on, Bob; where's yo bin livin'? Under a stone? With your interest in Braille - Irish Sign Language which is very different from British Sign Language - American Sign Language - Ogham - Morse - Kanji - Unicode . . . surely you should have picked up on Makaton [words and sentence in which above] before this.

I'm in Makatonland because the oldest son of John and Sally Bercow [he's Speaker of the UK House of Commons; she is a celebrity in her own right] was diagnosed [early] with autism. He got an early identification and therefore appropriate intervention partly because he had two articulate, well-connected parents; but also partly because they all lived in Westminster which has allocated some resources to those issues. Without early intervention a youngster who is without language is fritzed for school and social life and work. Makaton came up because Sally B. included it in a list of things she embraced to do the best by her boy. He's doing fine now, thanks, he's in regular school, has tolerant friends, forgiving siblings and hopeful parents. He could have finished up clutching a blanket and rocking himself in a corner of a bleak institution. Autism is generally not high on the list of priorities for governments in allocating social / health resources. Heart transplants, yes; dairy farmer subsidies, yes; auditing educational attainments, yes; ministerial car, yes;; but council houses, nah; mental health, nah; sex education, nah; drink education, nah.

My pal Lulu worked for years in the catering trade and late in life landed a job as a care assistant in the National Rehabilitation Hospital NRH in Dun Laoghaire, Co Dublin. There were young men there who had come off motor-cycles at speed; had been patched up in A&E; and then discharged. Their physical and, especially, neurological deficits could be immeasurably improved by early and intensive intervention. While the damage was fresh it was possible to restore function, or by-pass lesions, or develop sustainable work-arounds. With each passing day, the fluidity decreased, systems hardened into sub-optimal troughs and it became increasingly impossible to achieve any substantial improvement. There is only one NRH in the state containing a finite number of beds but there is a mountain of rehabilitation need. The [terrible] solution is to eke out the resources 'fairly' so that nobody gets the full whack of treatment that will give them the best chance of a fulfilling and productive life after their disaster. Huge waiting time means that any treatment people get is too little, too late.