Monday, 23 July 2018

Restless Earth

A few years ago, someone gave me a copy of Richard Fortey's [prev] book “Earth: An Intimate History”. I really enjoyed it, so much so that I can't lay my hand on a copy now - must have 'lent' it to a friend! The book is a learned but not academic investigation of this our restless Earth. Fortey knows his onions, especially the trilobites of the Ordovician period, about which no person on Earth knows more, but ranges far and wide in place and time to tell the ongoing story. The book is peppered with waggish humour which lightens the tone and makes it easier to read. The first chapter is about "The Temple of Serapis" in Pozzuoli, now a suburb of Naples. The print of the Temple [L] served as the frontispiece of volume I of Charles Lyell's 1830 Principles of Geology. That book was one of the very limited library that Charles Darwin crammed into his tiny cabin for his mind-boiling circumnavigation in HMS Beagle. Darwin, then aged 22, was a bit of  a Lyell groupie even before he left England and Lyell's concept of Uniformitarianism became a guiding principle of Darwin's world-view. The idea is that, given sufficient time, processes with which we are familiar today could have caused all the geological changes which shape the landscape and oceans today. Wind and rain; sun-bake and forest-fire; the tides and the flow of rivers; frost-heave and the grind of glaciers; with an occasional earthquake and landslide can give us the Andes and the Grand Canyon; the fjords of Norway and the Kalahari Desert. I developed this idea last year, again supported by the Lyell print.

The Temple of Serapis was key bit of evidence for this hypothesis. You can see the columns of the ruined temple at the water's edge today on dry land as it must have been when it was constructed nearly 2,000 years ago: it's not a Temple of Neptune / Poseidon after all. But close inspection shows that the base of each column is perforated with little holes aka gastrochaenolites which are definitively characteristic of burrowing marine molluscs of the genus Lithophaga [rock-eater]. Unless you believe in Loki the trickster god, the only rational explanation is that the whole temple gently lowered itself into the Mediterranean like Darwin's maiden aunt; wet its whistle for a couple of centuries; and then rose stately but dripping out the sea again. If a section of the Campanian coast could yo-yo up and down 10m between 100 and 1700CE, then the formation of the Andes was conceivable without calling for help from Jupiter, Poseidon or any other supernatural tinkering. You just need a million years instead of a couple of thousand.

The rest of Fortey's book carries forward the history with other stories and evidence, some of the equally improbably by seemingly true. The world is a pretty strange and wonderful place if we look at it, as did Darwin, through the uniformitarian eyes of Charles Lyell.

A couple of years after I finished the book, Fortey came to Dublin (possibly on a book-signing tour paid for by his publisher) and gave a talk at the ?Royal Irish Academy?.  Like for Heaney's Antigone, I more or less ordered everyone in the lab to come along and hear him talk.  I have to say that it was a big disappointment and my street-cred slumped a couple of notches because the talk was so dull. On the page he was so chirpy and alive, informative and witty, magisterial and self-deprecating; in real-time he was wooden and, dare I say it, boring. Maybe he had a massive headache. Heck, maybe I was hung-over. But such different dimensions or multiple intelligences are common enough in the one person. Me, I'm not stupid but I can be slow on the uptake: some things I can only work out if given sufficient time. Yes yes geological time is often required for me to get the message. And as a scientist I was always crap at writing the results up and getting them published; while I never had trouble writing book-reviews or home-ed newsletter articles or 700 words of Blob. Maybe I have a 700 word attention span and get daunted and exhausted at the prospect of writing a 7,000 word scientific paper. And I'm definitely more comfortable communicating here in Blobland than I am face-to-face: there's nobody to answer back, for starters.

Sunday, 22 July 2018

Mind-boggle 22Jul18

The youngest World Cup goalscorer since Pele, Kylian Mbappé gets a big hug from Kolinda Grabar-Kitarović [PrevBlobboSnark]: the coolest and wettest President in Europe: equal first with Emmanuel Macron. Good Sport. The kid? Doesn't know what to do with his hands but he has magic boots: you don't have to watch the whole thing - if you start to feel inadequate, just stop. Then reflect on what Mbappé does with his money - gives it to the dispossessed.

Saturday, 21 July 2018


I was boasting the other day about my "prowess" in sports: which amounts to the fact that, in the course of my very expensive education, I was given the chance to try a number of different ways of striking a ball. In 2002, The Boy told me to pack my traps for a weekend on the Isle of Wight with him and his pal Eoin. "Y'have to come paragliding with me and Eoin, Dad, it will be a bonding experience". As an institutionalised kind of bloke, I can obey orders, so I flew to London and we left early early on Saturday to catch the ferry to IoW and onwards to the Paragliding School at Mellow. Saturday morning was fun, we were kitted out with a "canopy" appropriate to our weight, then taken to a sloping field and taught the elements of take-off and landing. To get airborne, you first have to lay out the nylon canopy in such a way that with controlled tugs you can get it to fill with breeze and start to lift. You then turn round and run like Bernoulli buggery downhill hoping that the the canopy will become a aerofoil generating a pressure differential that gives sufficient lift to take flight. It takes a bit of practice but soon enough one minute you'll be pounding downhill and the next your legs will be rotating in the air 2 or 3 metres off the ground and you can glide to the bottom of the hill.

After lunch, everyone was taken to the bottom of the chalk downs by LandRover and the morning lesson was repeated from the top of the downs maybe 30m up a steepish slope. This is where you get the chance to catch a thermal which means that you don't have to trudge up from the bottom at the end of each flight. You can rather get the rising warm air, the on-shore sea-breeze, and the aerofoil of your canopy to deliver you back to your start point for another go. After a couple of mildly amusing glides downhill parallel to the grass, on my third attempt, most of me was suddenly hoiked vertically upwards about 25m leaving my stomach behind. I was airborne but terrified that I'd be swept out to sea:
I have achieved what every budding paraglider aspires to; and I knew I wanted no part of the game. For the rest of the afternoon, I avoided my turn in the air: as a beginner's class only one person was allowed airborne at a time. But eventually, I stood up to the plate to give it another go - we'd paid a chunk of money for the privilege, after all. It all went wrong, a stiff breeze swept in from the sea dragging my canopy backwards, the instructor tried to pull me straight but suddenly one half of the canopy collapsed as the other side took off and my feet were whisked out from under me. The Boy caught it all on film until he dropped the camera diving forward trying to catch me. I finished up in a heap on the ground mumbling heroic things and looking for someone called Hardy to gie us a kiss:
My fore-arm had a huge bruise the size and shape of half a hen's egg and I assumed I'd broken my arm when it was crushed between the chalky soil and my descending rib-cage. I hadn't. But I had an excellent excuse to spend the Sunday session in spectator mode watching The Boy and Eoin and the others cruising about in the air, landing in shrubberies, and having a flyin' time altogether.

When I got back to work in St Vincent's Hospital, I asked one of the junior doctors to check if, rather than my arm, I'd broken some ribs. "Here Conor, crepitate my ribs to see if they're bust; it will be practice for when you're in an A&E rotation." Crepitation was a diagnostic practice back in Nelson's day: if your ribs were broken the doctor could hear the jagged ends creaking against each other when he pressed the place with his thumbs. Young Conor was having none of that, but he did give me a chit for the X-ray department and duly told me that two of my ribs were fractured but I wasn't going to puncture a lung so I'd just have to wait until the damage repaired itself. "Try not to laugh" he suggested.

Friday, 20 July 2018

How much wood could a woodchuck

. . . chuck, if a woodchuck could chuck wood. Woodchuck = groundhog [day] = Marmota monax but I'm not here talking about mammals except insofar as I've dived down a rabbit-hole about measures of firewood.  I'm there because I'm reading Richard Fortey's memoir about 4 acres of woodland in Oxfordshire entitled The Wood For The Trees; the long view of nature from a small wood. Fortey, a retired geologist, bought the lot partly because he was fascinated by the ancient language associated with woods and wood: bodger; spile, bavin. On p.154 he elucidates:
  • bavin is a bundle of coppiced firewood 3ft 4in long and 24in in circumference
  • billet a bundle of ditto 3ft long and circumference of 10in
    • in = inch 2.5cm; ft = foot = 12 inches = 30.5cm
    • thinking about it, a billet could be a single length of wood you could hold in two hands to defend yourself from a highwayman.
  • bottle enough birch-twigs to make a besom = witch's broom
  • faggot a bundle 3ft long and and 2ft/24in in circumference suitable for bakers' ovens [prev on The Charter of the Forest 1217]
  • fascine a more robust bundle, of uncertain dimensions, used for filling marshy ground for a roadway or incorporating into [military] earthworks.
    • obviously related to fasces [which prev] the Latin for a bundle of sticks and adopted by Mussolini's Fascists.
  • tal(l)wood wood cut a bit long: 4ft
    • you can with advantage read the Assize of Fuel 1553 an Act of King Edward VI to regulate the buying and selling of firewood on pain of forfeiture, and/or a session in the pillory with a faggot or billet bounden to some part of his body etc.
That got me thinking about other measures of firewood, the standards of which are:
  • cord - a stack 4ft x 4ft x 8ft of cut and split logs typically 16 in long [prev]
    • only really used in North America it is about 3.6 cu.m.
    • cord is 4ft4in x 2ft2in x 8ft8in in Forest of Dean on the Welsh Marches which makes their cord ~25% more total volume
    • it's damn-fool silly to say 1 cord = 3.624556416 cu.m. because that final 6 is 6 or about a rice grain of firewood and you lose that much overnight from the insect damage
  • rick - aka a fireplace cord is 1/3 of a cord = a facecord if the logs are 16in long
  • stack - like a cord but 3.5ft x 3.5ft x 12ft or about 15% bigger than a regular cord
  • stere = stère = 1 cu.m.
    • although in France they still use a corde or a moule which vary [from 2.06 to 4.9 stère]  according to the region in which you source your firewood: 
    • the French revolutionaries wanted to have a décistère as well for widows and orphans and people with extremely well insulated homes; this later became known as a solive
  • load - a quantity of unstacked wood typically about 50cu.ft or under half a cord
  • favn - how firewood is sold in Norway a volume = 1 alen x 1 favn x 1 favn = 2.2 steres
    • favn (think our nautical fathom) is 6 fot or 3 alen alen is cognate with Latin ulna a forearm which is about the same as a biblical cubit.
Soliciting how firewood is measured in your home-town in the comments.

Thursday, 19 July 2018

Nosocomial nose? The noes have it!

Joy! Sometimes the headlines write themselves. Regular readers will know that I lurk-a-lot at Metafilter a site which allows a community of interested and interesting people to post once a day about what is floating their boat. Not everything there floats mine, but there is enough overlap that I check in most days in my restless search for Blob-copy. A MeFi post about I recognized your foul stench [It's a Star Wars ref] just cries to be clicked.

I've been interested academically in the evolution of olfactory receptors and am curious about the refusal of my students to use theirs. Pretty much anything that smells in the lab (or the previous inhabitants of a lecture theatre) will have them elaborately fanning their faces and throwing open windows. Young people don't like silage or slurry [or even know the difference]; they don't like Escherichia coli; Bacillus subtilis; Streptomyces or Pseudomonas aeruginosa - none of them or old bones. Limburger? No thanks! In my human physiology course I tell the students that, before they had pee-sticks, doctors used to diagnose diabetes by dipping their finger in a urine sample and tasting it - sweet indicates a problem, because are kidneys are really good at recovering circulating glucose. EEeeuuww, the students shriek. They must be terrible cooks if they are so unwilling to taste, taste, taste.

The MeFi post is more or less about a commercial product called Liquid Ass which 'smells like butt-crack' and has a ready market among fart frat boys even at $13/bottle. Ho ho "I sprayed a small stream of it in my buddy's office and it ruined his entire day!" etc. But there is a minority demand for the product among those who are training nurses, first-responders and battlefield triage medics. Best get the disgust [prev] under control in class before you have to deal with it at the coal-face. As so often on MeFi, the comments are often as rich as the original post. I now know far more than I need  about fisting, for example. And a list from Slarty Bartfast of various hospital smells that knock Liquid Ass into the ha'penny place: yeasty body odour; bloody stool; necrosis and gangrene. And others that are less unpleasant: electrocautery [bloboprev]; amniotic fluid, strep throat

But, given my previous short list of the smell of different species of bacteria; and my ongoing interest in the well-known potentially deadly nosocomial [hospital-acquired] pathogen Clostridium difficile, I was delighted to find the comment by ericales "I've found C. diff to have a very recognizable odor." Yes, yes, but what is that smell? I googled and found lots of nurses certain that they were 100% precise and 100% accurate and no need for the path lab in detecting a C.diff infection by the whiff: moldy like stale bread...tinged with a little skunk; outhouse during 3 months of 110+ degree temperature days; rotten chicken meat smell, (like when you smell that chicken and go..."no way..can't make this tonight!) mixed with baby diaper sweet smell, mixed with old blood smell [which in turn smells like I have nickels in my mouth]; road kill on a 100 degree day mixed with silent but deadly flatus.

But it just ain't true, because when you put normal nurses, even the confident ones, in a proper scientifically controlled double-blind experiment, it turns out that they are piss-poor in matching the smell to real C.diff samples. But you might have know that already from the lack of agreement about what C.diff actually smells like.

Wednesday, 18 July 2018

Mountain to Mohammed

The Minister (of Education) was down to The Institute yesterday . . . to turn the sod on our new Sports Campus. As a deeply unsporty person, I look a bit askance at the importance given to sport  by Institutes of Learning. As opposed to other (quieter?) off-curriculum possibilities like archaeology, beekeeping, chess, dance, entomology, fishing, gardening, hairdressing, ironing, juggling, knitting, lego, movies . . , When I was in school, a chunk of my very expensive education was to participate in a wide variety of organised sports, but I mostly played it for laughs. As I saw it then, with so much that needed fixing in the World it seemed, well, unproductive to have 22 people and a referee running in random circles for 90 minutes. That's a person week of steam with nothing to show for it. Insofar as recreational physical activity had a necessary place in my life I preferred to go on a solitary run: at least nobody got to lose that match. Later on I recognised that doing things together - singing, drumming, sporting - is part of the healthy human condition and so had merit. I also got to appreciate that, without the structure of a sports fixture, many people, including self, would find it difficult to ever lever themselves off the sofa . . . and that leads to obesity, atherosclerosis and an early death.

Some sports require more infrastructure than others. Cross-country running requires less organised works than a soccer pitch; a squash court is more complex than a hand-ball alley. On The Institute's main Campus, sports facilities consume about a third of the footprint; and car-parking about a fifth. The main neutral green space, which used to have a lovely avenue of cherry trees, has been built over since I came to work here. The most recent building was opened by the same Minister in January of last year. There are ambitions for further expansion. The college has acquired a parcel of land about 1km out along the road out of town to provide additional pitches and running tracks and changing facilities. It might also be a cunning plan to convert more on-campus green-space into laboratories, innovation incubators, vice-presidential office suites, surveillance towers. Some suggest that all the car-parking should be shifted out to the sports-platz, so that everyone gets 2km of walking every day.

The arrival of diggers and dump-trucks to begin works on that site was what the Minister was required to symbolically start. But the minister is a busy man and speeches have to be made before the shovel is handed to The Great Man. It is 1000m between the new site and the nearest microphone. Accordingly the already symbolic bit of work by The Man in a Suit was shifted to a patch of grass just outside the lecture hall so we wouldn't have to shift all the witnesses and photographers to a different location. If you've ever been to a funeral you'll know how the run of events has a hiccup / pause while the departed is shifted from the chapel to the diggings. The problem is that, except for two spits of rain over the weekend, there has been a drought for nearly 4 weeks. That patch of convenient grass is a) beige b) brittle c) set in concrete.  No problem: as well as importing the Minister we'll also import the sod [there is an obvious comparison joke to be made there]. In the picture below, I've highlighted the 4sq.m. of turf  - the little white van which delivered it is just off camera to the right.
The youth in the photo are two of our sporty students Marcus Lawlor and Molly Scott, the latter with her silver medal which she won in a relay at the IAAF World U20 Championships in Finland last week.
The absurdity of the symbolic sod-turning could only with difficulty be taken seriously, and I'm glad to report that the Minister and Molly played it for laughs by shifting from sod-turning to pancake-tossing. All good fun.

Less jollity down the road at the Minister-less new sports complex which is right next door to a brand-new secondary school called Tyndall College. That school is not going to open anytime soon because the multinational that acquired to the contract to build the complex was Carillion which went bust at the beginning of the year. Another company Sammon which was somehow involved in the stew of contractors, out-sourcers, fixers, consultants and entrepreneurs has also gone down the financial toilet. A whole rattle of sub-contractors: electricians, plumbers, plasterers, painters, steel-erectors have put in time and materiél and now, because of the serial bankruptcies, are out of pocket if not also out of business. While the Minister was tossing turves with Molly and Marcus, several of the subbies were down the road taking down the fencing that they installed just a few weeks ago. The Minister stoutly maintains that the dispute, about who owes what to whom, is nothing to do with the Department of Education. But it is: one or more of his functionaries failed to carry out due diligence on the companies that won the government contracts. That's why we pay the Government's Head of Procurement the big bucks: so that the buck stops on his desk . . . no I don't believe that equation will ever apply here either.

Tuesday, 17 July 2018


You could be forgiven for thinking that cyclosporiasis was a fungal infection acquired on Le Tour de France, but you'd be wrong. It is rather the consequence of being infected by another apicomplexan parasite. Another? Well, those you may know about include:
These are all protozoan parasites, single-celled organisms with a nucleus, but only a bit bigger than typical bacteria. Cyclospora cayetanensis , the cause of cyclosporiasis was unknown until about 30 years ago, when it was characterised by researchers at Universidad Peruana Cayetano Heredia, who were looking for evidence of Cryptosporidium parvum in the barrios of Lima. What they found was a new species [Cyclospora cayetanensis A in panel below] which was similar to but different from Cryptosporidium muris [B] and  Cryptosporidium parvum [C] and so they got to name it after their place of work. They are all almost exactly the same size as a human red blood cell.

It's probably the same as an organism isolated from stool samples in Papua New Guinea in 1979. Since its discovery in the tropics, it has been responsible for numerous epidemics in the United States. Including one which made the New York Times 7th Jul 18 because 200 people across the upper midwest had gotten sick after eating Fresh Del Monte Produce vegetable trays containing broccoli, cauliflower, celery sticks, carrots and dill dip. That's what the CDC is saying anyway.

They may be wrong yet, because Cyclospora takes so long to hatch out of its spore and start to go forth and multiply in your gut that a week or more will have gone by before you have symptoms. [Let's hear it for symptoms: Watery diarrhoea; Loss of appetite+weight loss; Cramping; Bloating; Gas; Nausea; Fatigue] What the epidemiologists at the CDC have to do is find something that 200+ random people across 4 states have eaten-in-common the weekend before last. Someone else has to do a [watery] stool analysis to make sure everyone has the same bug. Of the 36 outbreaks of cyclosporiasis this century, CDC were only able to identify a culprit in 16 and of those only 8 were unqualified by 'suspected' or 'likely'.

And Del Monte are having to scratch their heads about which of the ingredients in their fashion-accessory plastic-trayed health-snack to blame: the cauliflower from Arizona? the celery sticks from Belize? Because they have to send their quality-control hard-men down the supply chain to find the source and close it off. Del Monte don't want to annoy their clean and loyal producers of perfect broccoli florets if the slack-bobs two states over, who julienne the carrots, are to blame. It's a globalisation head-ache for producers and consumers alike.

It's ironic that this infection catches people who feel virtuous because they obey Micheal Pollan's dietary instructions [prev and prevlier]  "Eat Food. Mostly Plants. Not Too Much". Well what do you expect if you buy your Mostly Plants in a clam-shell tray filled with stuff from who-knows-where?