Monday 30 November 2015

The three Rs

Doing the washing up on Saturday last, I flipped on the wireless and caught an interview with Christopher Frayling, the Great Insider of the British arts establishment.  He has been head of the Royal College of Art, a Trustee at the V&A, head of the Arts Council, governor of the British Film Institute and so forth.  The last indicates his abiding interest in film and he's written the definitive biography of director Sergio Leone and is a fan of Clint Eastwood. When poor Mrs Windsor was told to give him a knighthood, he crafted the required motto as "Perge, scelus, mihi diem perficias" which is Latin for "Go ahead, punk, make my day [perfect]".  If you're part of the inner circle you can jangle the establishment chain just a little. The excuse for having him on RTE's Culturefile last weekend was his 'new' book On Craftsmanship: towards a new Bauhaus, which was actually published in 2011  . . . and quite poorly reviewed.  But that shouldn't detract from his message which was articulate, radical and valuable.

As reg'lar readers know, we didn't send our girls off to school but let them sit on the sofa or have small-small adventures on our farmlet and learn by doing.  So the Three Rs - reading writing and 'rithmetic - didn't hang over their early years like an oppressive cloud of external expectation. Even lifelong Anglophones are bemused at how R+W+A got to be called the 3 Rs. Frayling pointed out that RRR was one R redundant because reading and writing are the two side of the coin of literacy. Interestingly, the RRR epithet was first applied to different principles: reading, reckoning and wrighting. 200 years ago, educators believed that, while literacy and numeracy were handy attributes, making was equally important.  Whether you were a shipwright, wheelwright, potter or bodger, being familiar with the material world was essential if you were to function properly in society.  The history of technology in my lifetime can be viewed as progressively disempowering users "for their convenience".  My first car, a Citroen Dyane, had a crank-handle that would start the car if the battery was flat; there is nothing in my current computerised-up-the-wazzoo car that I can fix if it goes wrong. In December 1990, I wrote a Christmas-themed screen-saver, in Fortran, for the computer at work, the computer I'm now typing at has an operating system that is a bloatware kludge beyond my ability to tweak. It costs you more to make your own clothes that to buy them oven-ready. Cooking is about adding a single egg to a cake-mix designed by a food engineer.

Later on, Frayling said that 47% of the third level applied art and design departments in Britain had closed in the last few years. This is partly because students want to be millionaires or at least investment bankers rather than plumbers or potters but its also because technical departments, with their workshops instruments and technicians are, expensive. The host institutions are run by accountants who think that filling classes in more 'academic' subjects is 'efficient' or 'cost-effective' or 'serving society'. The only society it serves is one deeply divided and founded on unskilled proles supporting a diminishing number of excessively rich plutocrats.

Sunday 29 November 2015

Sunday singsong 291115


Hellish hot is how The Boy and his mother like their sauce. But they are nothing compared to their [grand]mother, who sprinkles chili pepper on her cornflakes with a knife.
When it comes to measuring the whoomph of chili-peppers Capsicum spp. you could crush some up, filter it and run it through an HPLC to determine the precise quantity of capsaicin - 8-methyl-N-vanillyl-6-nonenamide- [structure above] and then say a particular chilli is this hot in moles per gram.  It's complicated by the fact that there are several derivatives of the base capsaicin called capsaicinoids which vary as to their pungency. But chili-bums [aka ring-burners?] had developed a comparative scale at least 100 years ago which is independent of HPLC technology. In 1912, a pharmacist called Wilbur Scoville extracted the peppery volatiles by steeping a precise weight of pepper in alcohol.  This essence is then serially diluted in a sugar water until half of a panel of expert tasters cannot detect it. This allows a Scoville Heat Unit scale from 0 for regular bell peppers to much more the 1,000,000 SHUs for chilis like the Carolina Reaper, Bhut Jolokia or Naga Viper. That's a measurement of similarity that is fairly well reproducible even if a dimensional analysis [SI Units?] of what you are actually measuring is not possible.

There is a lot of theatricality, not to say machismo, about the consumption of hot peppers as we you can hear with the hilarity off-stage in Good Mythical Morning, [GMM previously]. If that reminds you of Withnail and Matter, I'm with you. That's all mildly interesting . . . not really funny unless you find boxing or cock-fighting [hmmm haven't covered that yet] amusing. What's more interesting is the variability among people as to their capacity to taste/tolerate hot pepper.  We had an experiment in this line on a visit to Dublin's Taj Mahal forty years ago.

Metafilter had an interesting compendium recently about 'snacksandsuch' Nate a young feller with a shockin' nonchalance as he chews down on a Chocolate Bhut Jolokia and records his subjective impressions for science. I'm afraid it just made me think of people who wake up from a paracetamol over-dose feeling alright but already doomed to die. But his actions also have a taste of JBS Haldane ruthlessly experimenting on himself for science. If you read the comments on the metafilter post, you'll see that, for several people, chili-chewing is a young man's business. As you pass 30 your tolerance of them changes: not so much in the appetite but in the processing. There is a suggestion that the intestinal flora loses the ability to digest capsaicin as you get older - that's interesting and should be followed up.  If your intestinome loses and gains biochemical capability as you age, that may have profound effects in pharmacology. It's sad that Nate adds a note to his Chocolate Bhut Jolokia jaunt "This is my last video. This is because people keep saying my videos are fake." that's a loss for science. But then again, if science post-graduate students burst into tears and went home when a referee dissed their papers, then there would be a lot less science. Then again then again that would possibly be a good thing because 45% of scientific papers have contributed nothing to science.  Here's a suggestion that eating chilis burns fat and reduces weight in the obese, young Nate could follow that up and really help his community.

Saturday 28 November 2015

The Islets of Langerhans

Living on an island gives me a small-small excuse to rabbit on about other islands as I have been doing all week. Argumentative SciFi writer Harlan Ellison wrote a rather challenging short story called "Adrift Just Off the Islets of Langerhans: Latitude 38°54'N, Longitude 77°00'13" W".  In which he pushed the imaginative idea that the Islets were a geographical feature. I'll save you a lot of trouble by noting that Washington DC is located at Latitude 38° 54' N, Longitude 77° 00' 13" W.  There is something romantic-sounding about the Islets of Langerhans, which I first met when studying high-school biology as a teenager. My mentor then - Mr Wilkinson - drew attention to this when we were learning about the pancreas, of which the Islets are an important part.
In the same course he also introduced us to the involucre of bracts, which is are the ring of green leaf-like things supporting the coloured part of daisy Bellis perennis and dandelion Taraxacum officinale flowers and other members of the Compositae Asteraceae. Actually he introduced us to the Involucre of Bracts, which/who might have been an obscure Highland prince like Lord of the Isles, Moncreiffe of that Ilk or the Laird of Glenbogle.  You should know that the inflorescence of Asteraceae is not a single flower with stigma, stamens, petals and sepals but a sweep of tiny separate flowers.  In the daisy there are two sorts: the yellow disc-florets in the middle and the peripheral ray-florets with one enormously exaggerated petal pointing outwards.  Have a close look next time you're making daisy-chains with your daughters.

The Islets are tiny blobs, barely visible to the naked eye (0.1mm-ish or about the size of a human egg) that look a little like warts on the edge of small blood-vessels in the pancreas.  Though they be but little, they are numerous and if all 3 million of them could be scraped into a tea-spoon, they would weigh about 2g.  Each one consists of a number of identical looking cells which have very different functions. As far as we can tell, each cell is specialised for producing one hormone but several different hormones are produced in each islet. You can use a technique called immune-histochemistry to attach different coloured markers to these hormones [L] which are all small proteins. That creates a false colour image - the islets are pinky-beige in real life - which is rather informative. Here [L] insulin has a green fluorescent dye attached while glucagon has a reddish tag.  You can see two things: one is that the insulin producing cells far out-number those making glucagon and also that the glucagon cells are located on the periphery of each islet.

If you're anything like me - expensively but inadequately educated - you have an excuse for never having heard of glucagon but you're reading the wrong blog if 'insulin' is a totally new word to you. In teaching Human Physiology for the last three years, I've learned a lot that I didn't know or about which I was wrong.  The theme in Hum.Phys is homeostasis, maintaining everything - core temperature, acidity, blood-pressure - in equilibrium.  Insulin and glucagon do this for blood-sugar levels: insulin reducing it and glucagon increasing it.  As I tried to explain about haemophilia and Factors VIII and IX, the normal body manages such things with exquisite subtlety 24/7 while pharmaceutical/medical surrogates are bludgeon-crude by comparison. It's like that with insulin therapy for diabetics: they inject far too much in one go and over the next several hours the concentration in the blood trails down to rather too low when the body receives another deluge by needle.

Mais revenons nous a nos îlots: there are two types of diabetes: type I occurring when the pancreas doesn't produce enough insulin; type-II when the pancreas is chuntering along nicely doing its job but the body fails to react appropriately to circulating insulin. It seems likely that type-I diabetes is an autoimmune disease, in which the immune system convinces itself that beta-cells in the Islets of Langerhans are 'foreign' and need to be taken out.  As the beta-cells produce the insulin on which glucose metabolism depends, this is response turns out to be a costly mistake. A lot of auto-immune disease occurs as a consequence of a viral or bacterial infection.  When the pathogenic insults has been beaten up and swept away, the immune cells are still spoiling for a fight and turn on some part of the body with a superficial resemblance to the ex-parrot-parasite. This is the best explanation for Guillain–Barré syndrome's appearance after a bout of the trots from Campylobacter food-poisoning.  It you wake up screaming tonight knowing the identity of the virus that causes type-I diabetes, and you are correct, you can sit back a wait for the Nobel Prize.

Friday 27 November 2015

Isle of Birds, Isle of Norn

Fuglaey [Old norse] Fugløy [Nynorsk] Fughlaigh [Gaelic] are all alternative names for Foula, clearly the same root-word as fowl. Foula is a contender for the remotest permanently inhabited island in the Western European Archipelago. But I think most people would hand this doubtful honour to Fair Isle, a little further South and midway between Orkney and Shetland. For people Foula is down to about the numbers [N=30] living on St Kilda when that remoter outpost was evacuated in the 1930s but it's only 60km from the nearest Tesco in Lerwick [20km by ferry to Walls, 40km by winding and windy road to the metropolis]. Social services and infrastructure have moved on since then and I don't hear any rumours that Foulanders are going to give up anytime soon.  They used to be fisherfolk almost exclusively, but now are more crofters and there are far more sheep and ponies about than people. Contributing at least as much income is the servicing (B&B, guides, deer-stalker hat sales, binocular-hire, clothes-driers) of twitchers because the island is rather rich in bird-life which is hard to come by nearer the centres of population further South.  The island has been designated a Special Protection Area (SPA) for birds, as well as a National Scenic Area and a Site of Special Scientific Interest (SSSI).

Among the highlights are more puffins Fratercula arctica than you can shake a stick at and the world's largest colony of Stercorarius skua, the Great Skua or bonxie. Stercorarius parasiticus the Arctic Skua is also common hereabouts. Apparently the Anglophone word skua comes from Faroese skúvur, one of the very few English borrowings from that direction. Faroese is spoken further North by 65,000 people mostly in the Faeroes but 20,000 making a living in Denmark and elsewhere. That's almost as many people who speak Irish in Ireland. Faroese is descendant from Old Norse which was spoken by Vikings and written in runes when those people burst from the poor-scrabble farms and fjords in Scandinavia and sought a an easier life elsewhere. Old Norse evolved into Faroese but also Icelandic and Norn which last was spoken in the Norse fiefdoms of Orkney and Shetland for at least 500 years. The language started its slow decline just North of Scotland when Scots-speaking lairds were granted holdings and serfs on the islands and eventually these magnates stopped swearing allegiance to Denmark and started sending their dues South to Edinburgh.  As Scots, which I think is a language distinct from English, came to be spoken in Castle and Manse as the language of prestige, so Norn was spoken by fewer and humbler people. The same process swept Gaelic out of mainland Scotland in more or less the same time-frame. By the time scholars perked up to the existence of another language spoken by natives of the United Kingdom, Norn was gorn.  The last attested speaker claimed to by Walter Sutherland of Unst, and he died in 1850. It must not be confused with the somewhat jocular Norn Iron which is a phonetic pastiche of the language/accent spoken in Belfast.

Interestingly, to Norwegians Shetlanders sound like they are speaking Norwegian by their timbre and intonation until you get up close and find they are yakking in Scots with a Norse accent.  It's a bit like Richard Feynman being confused into thinking that two chaps on a plane conversing in Ladino were speaking Portuguese.  The other peculiarity of Foula is that they are still working on the Julian Calendar with Christmas celebrated when the rest of us have moved on to Epiphany / Twelfth Night / Nollaig na mBan. Whatever!: I don't think that makes much difference to anyone else.
I think I feel a Summer holiday coming on: rock-art, puffins, beach-combing Foula should be good for a tuthree days.

Thursday 26 November 2015

Slocum in the Cocos

For some scraps of land barely 5m above the tide-mark at its highest point and only 14 in extent, the Cocos/Keeling Islands [R 12.12°S, 96.90°E] have had rather a lot of history. The archipelago was discovered in 1609 by William Keeling while employed by the East India Company.  It seems likely that Chinese, Malay and Arab sailors had been there, but the islands remained uninhabited until the 19thC. In 1814, a passing merchant called John Clunies-Ross ran up a Union Flag on one of the islands, claiming it for Britain and also for himself as a tropical island retreat. By the time he returned with his family and building materials, Alexander Hare, another eccentric Brit had installed himself there with an extensive harem of exotic women. There was a bit of a rumpus until Victorian moral values (and a couple of handfuls of younger buffer sailors in the Clunies-Ross party) saw off the degenerate fifty-year old Hare, who sailed away into the sunset.  The Clunies-Ross family is still living out there although the territory was annexed by Australia many years ago to bring the governance, human rights, rule of law into the 20thC.  It's not quite a micro-nation because it is not fully independent but it is micro: having a population of about 600 people, some of Malay and some of European descent.

A few years later HMS Beagle dropped anchor in the sound after her voyage round South America and the Galapagos Islands.  Charles Darwin had been cogitating about all the data he'd gathered and rather inadequately documented. He famously labelled all his Galapagos finches as "Galapagos" and the date, so was unable to twig that each island had a different set of birds. Arriving at Cocos/Keeling, he had time to explore a classic coral atoll [above] with barrier-rim islands surrounding a shallow lagoon. The water depth typically plunges to the abyss a short way outside of the circle of dry land.  Darwin knew that coral was the skeletal remains of living creatures and that they depended for the growth on light.  How, he asked, could this massive pile of solid matter have grown from the darkened depths?  One of his first scientific papers on his return was The structure and distribution of coral reefs in which he put forward an explanatory hypothesis.  Darwin suggested that the coral massif had started growing long ago in shallow seas and that, as the sea-level had risen and/or the sea-floor had sunk, the coral growth had been sufficient to keep pace. It required a helluva long time and suggested a certain restlessness in the earth and so was moderately controversial when published.  It has since become accepted as the only reasonable way in which these wonderful rich colourful biological communities had come to develop.  Better go visit them soon because climate change and pollution are doing a fatal number on many of the best examples.  This is another example of Darwin being firstest with the correctest: as he was with earthworms, barnacles, deaf cats, pigeons, plant hormones, animal emotions . . . the list goes on.

The next round-the-world voyager whom we know to have called in upon Cocos/Keeling was Captain Joshua Slocum, who circumnavigated alone in his self-built gaff-rigged sloop the Spray. That kind of thing is widespread nowadays with all sorts of gimmicks added to make the venture 'new': A Short walk in the Hindu Kush, In Ethiopia with a Mule, Brazilian Adventure, Round Ireland with a Fridge: some of these books are better than others.  Slocum was born within the spray line of the Bay of Fundy in Nova Scotia, ran away to sea in his teens, taught himself navigation and command and made a living transporting this and that from here to there in sail; oftentimes he had his wife and kiddies aboard. In his 60s, he left his family ashore and set off for further adventures - hoping to turn his account to account with a publisher upon his return.  The story is marvellous, partly in the sense of being a good read and partly in a sense of a bit of a yarn.  The consensus is that Slocum was not above stretching the truth for the sake of the tale - and why not??

He had a near-death experience while visiting Cocos after being swept out to sea and only making it back to land through a combination of the enterprise and pluck you'd expect of a bluff Canadian Maritime sea-captain.  He took a trip across the lagoon in another scarcely seaworthy boat with a local pilot to secure some giant clam-shells Tridacna gigas as souvenirs or trade-goods. A sudden squall thrashed the sail to ribbons and he found himself drifting out to sea without oars or anchor or water or ship's biscuit.  The only implement was a pole with which he was able, by superhuman exertion, to propel the craft back into the shallows.  He secured his clam-shells the next day - 30 of them replacing 3 tons of ballast.  Yup that's right: 100kg of clam - makes a helluva chowder. Ten years after his return from the epic voyage, he set off from New England to Winter in the Caribbean and was never heard of again.

That's the peace-time highlights of the history of Cocos/Keeling. The boys among you will want to follow the adventures in:
  • WWI: keywords SMS Emden v HMAS Sydney; Ayesha - Cocos to Constantinople.
  • WWII: keywords mutiny, Gratien Fernando, imperialism

Wednesday 25 November 2015


Roger Deakin's book Waterlog is a record of him swimming across England.  He must have been an otter Lutra lutra in a previous life or will be reincarnated as a selkie. He's dead now [Grauniad obit], and that's a loss - he was only my age, but he's left behind a couple of truly magical books: Wildwood: a journey through trees is the other.  Waterlog starts with a plunge in and around the Scilly Isles 50 km West of the toe of Cornwall in SW England. Between swims he asserts that the little archipelago was once a larger contiguous landmass called Ennor that was drowned by sea-level rise after the last ice-age.  As he swims across the sound, he looks into the depths and sees two ancient field boundaries meeting at a right angle as well as a circular sheepfold . . . read on in Google books. How mystic, wonderful is that? Deakin would hardly be surprised if he flung his wet-suit out to sea and " . . . ere he dipt the surface, rose an arm /  Clothed in white samite, mystic, wonderful, / And caught him . . ." because people assert that the Isles of Scilly and/or Ennor are the same as Kingdom of Lyonnesse or Lyonesse that features so much in the Arthurian legends.  It was, for example, home to Tristan the main squeeze of Isolde.
Scilly consists of 55 islands if defined as "land surrounded by water at high-tide and supporting land plants" but only 5 of them are inhabited by people:
Name Pop Area km^2
St Mary's 1700 6.3
Tresco 180 3.0
St.Martin's 140 2.4
St.Agnes 70 1.5
Bryher 90 1.3
Samson Not now 0.4
As you can see from the map St Agnes is linked, at low tide, to Gugh.  Similarly, further North, Gweal is linked to Bryher.  As Gweal means 'place of trees' and it is now a barren rock, this is toponymical evidence for sea-level rise.  A prehistoric farm-steading is located on Nornour, an islet that is now far too small to support any agriculture. Gugh (=hedge-rows) was big enough to support a population of brown or rats Rattus norvegicus until a determined effort a couple of years ago seems to have been successful in exterminating them. The nesting sea-birds, like on  Middle Island, now have a fighting chance although there are still feral cats.  It seems unlikely that anyone is going to be able to shoot these alien varmints, the British, like the whole interweb, being soft in the head about kittens. Because the area is pretty and has good tourist potential - much better than Juan Fernandez for example - there is a lot of data on alien species of plants, fungi and animals and their effect on the native wildlife.  The biological coverage is almost as good as on Sherkin which has its own Marine Station.

There are reasons why a republican wouldn't want to go visit this outpost of Empire because almost the entire freehold is owned by Charles Windsor as part of his fiefdom the Duchy of Cornwall.  This entity has been parlayed into a multimillion £$ business worth £750million and generating profits of about $20million/year.  You can buy a laborer's cottage in fashionable Tetbury, Gloucs, from Himself if you have £250,000 available. If you're my age, and grew up in Britain, you might also have Scilly-baggage from the fact that pipe-smoking Prime Minister Harold Wilson used to go on holiday to the Scilly Isles. His adventures there in the 1960s helped bring Scilly into view as a potential holiday destination for thousands of citizens of his socialist paradise.

Tuesday 24 November 2015

Moose for dinner

No not you, or me, we'll be eating mousse if we're lucky.  It's the wolves Canis lupus Canis lycaon [grrrr another familiar name, like, Alopex, has been dropped] who will be eating moose Alces alces tomorrow, if they can catch one.  It will have to be small or sick or very old or injured because the wolves I'm talking about are not very fit. We're on Isle Royale today because this week I'm island bound and I thought it would be nifty to extend the theme of population cycles of mammals: last week rodents, this week something bigger.  Isle Royale is a large [70 x 15km] island in the middle of Lake Superior, a little closer to Canada than to USA.  At 535, it's bigger than several countries - Andorra, Liechtenstein, Monaco - so you'd think that would be room enough to support a stable population, but it's not.
You can see [same data better graph in colour] that, in contrast to the near clockwork ebb and flow of lemmings and voles every 3-4 year, the population of both species has fluctuated quite wildly since records began in 1959. Indeed, the wolves are down to the last three descendants from a pair who crossed the winter ice in 1949.  All the subsequent wolves have been descended from that female although there was an injection of fresh semen [eeeuuw] in 1997 from a fit young male who crossed the ice that Winter. That wasn't enough, however, to really slow up the inbreeding depression that the wolves have been experiencing after so many generations of incestuous liaisons. The census bumbled along between 20 and 30 in number until that male died in 2006, but since then has been going steadily downwards.  Last reports claim 3 living wolves, so the end of the experiment is in sight.  In 1981, an imbecile brought his pet dog on a camping trip to the National Park, infected the wolves with parvovirus and killed half the population.

The outlook for the moose looks short-term rosy, long-term grim. Without predation the moose will go forth and multiply unchecked to increase their current numbers [N=1000] until they run out of food, which will mean a hammering for balsam fir Abies balsamea, which makes up the bulk of current moosey diet. The monster herbivores have already eaten all the more nutritious birch Betula spp. and aspen Populus spp. If the population gets near to its previous 1995 high of 2,500 animals, there will be insufficient food.  Last time, 80% of the moose died after a couple of years of very short commons.  As if death by starvation wasn't sufficiently awful, the warmer Summers will trigger a plague of Winter Ticks Dermacentor albipictus which can almost literally suck the moose dry. 10,000 ticks have been recorded on a single moose in a 'good' year each filling up with 1 ml of blood before dropping off to breed.  You do the math: I reckon that's 10 litres / 2 gallons of blood lost in a season. Even without the moose equivalent of tick-borne Lyme Disease that's a debilitating infestation, and they scratch themselves raw to get rid of the itch.

That's a great simplification of the population dynamics of a relative delimited ecosystem.  We haven't looked as the shrubby or annual vegetation, nor the busy bacterial community in the soil, or the other mammals which include beavers Castor canadensis [prev]; snowshoe hare Lepus americanus; red fox Vulpes vulpes [prev Australia]; red squirrels Tamiasciurus hudsonicus [prev Ireland] or ravens Corvus corax. Did I mention L. americanus?, the records from the Hudson Bay Company's fur trade, show [R] that it was in a stable 9-10 year up/down cycle with its main predator Lynx canadensis. So its not only small rodents that do this.  It's probably significant that the cycle is longer for the larger animals. The key difference between Isle Royale and lynx/hare is that the latter had the whole of the Yukon and Northwest Territories to play in; compared to which Isle Royale is a zoo with the animals psychotically pacing up and down waiting for feeding time. The likelihood that wolves will go extinct on Isle Royale because their numbers are so low that a bad winter, or a bad virus will finish the last few off is a salutary lesson if we aspire to maintain other ecosystems.  You don't have to chop down the last tree on Borneo to destroy many species; you just need to reduce the space to something less than top carnivores need to maintain a sustainable population.

Monday 23 November 2015

Isle au Haut

If I could give you three things,
I would give you these:
Song and laughter and a wooden home
In the shining seas
Isle au Haut Lullaby - Gordon Bok
Isle au Haut is a town off the shore of Maine set on an island of the same name. "Town" in the sense that it is a community with a certain autonomy, not in the sense that it has a barber, cinema, two pubs and feed-store. It must have a post office because it's got its own ZIP code 04645 different from Stonington [04681] which is the Isle au Haut mailboat ferry terminal. This all sounds a lot like Sherkin in West Cork which has a tiny population, two hotel/pubs and no shops.  For groceries you have to cross the water to Baltimore.  Isle au Haut has a sort of village centre along the 'Thoroughfare' between Isle au Haut and Kimball Island about 200m NW.  This is where the mailboat sets down its passengers, who have to leave their autos behind on the mainland.  Well not really the mainland, because Stonington is itself adrift in Penobscot bay on Deer Isle; although since 1939 it has been connected to the real mainland by suspension bridge.  The Thoroughfare is remarkably similar to the Main Tickle on the Change Islands. waaaay North off the coast of Newfoundland.  That's not all they have in common, for the traditional way of life in both communities involved a lot of fishing.
I-au-H doesn't even have many people: 73 at the last census of 2010 which are enumerated as 91.8% White, 1.4% African American, 2.7% Native American, 1.4% Asian.  Things are getting excitingly multi-cultural on Isle au Haut nowadays: in 2000 everyone was 'white', of, in diminish numbers, French, Irish, {English = Dutch = Scotch}, Finnish, Hispanic ancestry.  With such small numbers it gets a little intimate: "1.4% Asian" is some family's Filipino maid. You can see from the chart [L] that the population collapsed through the 19thC but seems to have stabilised since WWII at half-a-gross or a little bit more. Half the island, about 1000 hectares is owned by Uncle Sam in the National Park Service as part of the Arcadia National Park. They seem a little authoritarian about limiting visitor numbers but I guess that makes for a richer experience for those who do get to hang out there.

Why do I know/care about Isle au Haut?  Because it is tribbed in two songs by Gordon Bok, who grew up fishing in and around the Bay of Fundy and found a poetry in him that burst out in a handful of vinyl albums of his own songs and some covers. We discovered him on the folk circuit when we lived in Boston and I really like his lyrical, quietly politicised style.  Isle au Haut Lullaby [see chorus at the top of this Blob] or The Hills of Isle au Haut [sung here by our own Tommy Maken and Liam Clancy] can start you off, the rest of his oeuvre you may find on on the youtube sidebar. Here's Gordon Bok interviewed Studs Terkel [part 1] [part 2] [part 3] at the end of the last century.

Sunday 22 November 2015

Sunday snow 221115

Selkirk y Crusoe

I suppose if I'd been pushed to it, or been in a grudge Pub Quiz, I could have worked out with which country Rapa Nui / Easter Island was affiliated but I was caught on the hop to hear some E-islanders speaking Spanish the other day. If Chile's political reach can extend so far out into the trackless ocean, I assume that everything between Rapa Nui and Valparaiso flies the same flag [R] and it does. I knew [expensive education and all] that Alexander Selkirk was marooned on an island off the West coast of S South America in the 1700s and that his tale was the inspiration for Daniel Defoe's [DD previously] Robinson Crusoe. But I was wildly wrong on the distance details because  the Juan Fernández Archipelago is 670km from the mainland!  Even 'archipelago' is a bit of an ask because, as it says on the tin in eSpanish, Más a Tierra is 180km nearer to the continent than Más Afuera. Today 22 Nov is the 441st anniversary of the discovery 1574 of the island groups by - Juan Fernández - who was sailing South so far from the coast in order to avoid the North-setting Humboldt Current.  This is one of the few examples of a Pacific island first discovered by Europeans.
There are thus two tiny specks of land distant from each other and really remote from anywhere else.
Actually, as you see on ye antient mappe of Más a Tierra [L]  there are three islands if you include (and you should) the truly diminutive Santa Clara to the South-West.  Santa Clara is only in size and has no permanent human inhabitants, probably because rainfall is sparse and dependent on El Niño. There are a great many feral rabbits Oryctolagus cuniculus and goats Capra hircus both introduced by sailors and both doing serious damage to the native flora.

In 1966, the Chilean government came up with a cunning plan to boost tourism in the remote archipelago.  Did they see all the tour boats visiting the Galapagos far farther North, boosting the economy of Equador?  By presidential decree they renamed Más a Tierra as Isla Robinson Crusoe and Más Afuera as Isla Alejendro Selkirk. At just under they are about the same size but 95% of the 900 inhabitants live on Crusoe most of them in the village of San Juan Bautista.  The tourist trap plan has been modestly successful with a few hundred extranjeros visiting each year, many of them to explore the wreck of SMS Dresden which was scuttled just off-shore to avoid sinking or capture by the British in March 1915.  It's really rather outrageous to sweep up both the real and the fictional castaways in the renaming scheme, because Defoe is quite explicit that his hero is shipwrecked off the North coast of South America near the mouth of the Orinoco River.

As a child, I loved The Life and Strange Surprizing Adventures of Robinson Crusoe, Of York, Mariner for much the same reason as I enjoyed The Day of the Triffids: they both serve as a training manual for  post-Apocalyptic survival. Crusoe's ship is wrecked and the life-boat is wrecked and he alone is washed up on a sandy shore. A while later, the storm having abated, he sees that the ship is a short way off-shore on a reef. Over a number of trips to and fro on a raft, he liberates the materiel to survive for an extended period. The ship's carpenter's tools and bags of nails, sail-cloth, a musket or three with power-kegs and shot, rum, hatchets and lengths of rope. Here: read it yourself, it's mighty.  Whenever I can, after a storm has passed through Ireland, I go down to the sea and hope for something more exciting than buoys, of which I now have a great store.  They'll be handy after Armageddon.

Saturday 21 November 2015

Cross continental contingent catastrophe

I was tribbing the bold Nils Chr Stenseth a tuthree days ago, for his work documenting the end of boom/bust population cycles in rodents. One of the things that encourages diversity in the finches of the Galapagos Islands is fluctuations in rainfall that affect seed abundance; some years the big-beaked finches like Geospiza magnirostris are favored but they yield to other species when their favorite nuts get scarce.

Stenseth's most recent paper has all the marks of his cross disciplinary approach and it's related to the story of Stephen J. O'Brien and bubonic plague survivors about which I wrote recently. Stenseth's team mobilised people from different disciplines and with complementary toolkits to illuminate the factors that caused the influx of rats, fleas and Yersina pestis from the steppes of Central Asia to the stews of Messina, Venice and London.  The stack of interacting species that this requires reminds me of
Great fleas have little fleas upon their backs to bite 'em,
And little fleas have lesser fleas, and so ad infinitum.
From Augustus de Morgan's Budget of Paradoxes
Which should remind Jonathan Swift fans of:  So, naturalists observe, a flea / Has smaller fleas that on him prey;/ And these have smaller still to bite 'em,/ And so proceed ad infinitum./ Thus every poet in his kind/ Is bit by him that comes behind. from Poetry; a Rhapsody. All rodents carry fleas, and some rodents are infected with Yersinia pestis, the bacterium that causes bubonic and pneumonic plague, the black death, which periodically rampaged through Europe killing thousands of people.

The puzzle is where the plague erupted from and where it struck and what propelled the disease West.  What Stenseth and Co. have shown is that, like a butterfly wing-flap, rainfall in Central Asia precipitated a cascade of events that finished up killing thousands of people half a world away. Plague historians had established many years ago that black rats aka ship rats Rattus rattus arrived at European ports (starting with Messina in Sicily in 1347) laden with fleas (normal) which were full of Yersinia pestis (pathological). The rats came ashore and died and the fleas needed an alternative host, so snuggled up in the family bed with people who died in their millions. Things quieted down when the plague bacteria had killed every person and every rat, dog and cat they could get access to. The pest then went to ground in some, possibly rural, reservoir in Europe until it burst out on the rampage again some year later. Those historians were a bit vague about where - Tuscanyshire? Transylvania? Tramore? - this reservoir was or what was the mammalian host species . . .
. . . because it didn't exist!

Stenseth's team have gone transcontinental gathering all sorts of data.  Just like he revealed an unlikely cause for population cycles in rodents, they have now revealed probable cause for the migration of Yersina to Europe in irregular cycles from 1347 and over the next 400 years.  The key precipitating event is rise in rainfall, as tracked by generous tree-rings, followed by a steep fall in the same parameter. That has the ring of truth: the productivity of the central Asia steppe is limited by water availability and a dump of rain will not only drive forward tree growth but a lot of plants which will bloom and set seed while resources are rich. In Central Asia, down Kazakhstan way, gerbils Rhombomys opimus thrive in damp warm conditions and consequently have a lot more babies. When the good times stop rolling, their fleas concentrate on the remaining gerbils and, if they are infected with Yersinia, these flea-bags help spread the pathogen outwards from the initial focus.  As the last gerbils >!coff-coff!< and die, the fleas jump ship to other mammalian hosts including domestic animals and camels.  It takes several years but travelling down the silk route from go-down to caravanserai, the fleas and their deadly hitch-hikers eventually reach a Black Sea and the trudge West turns to a sprint.

Stenseth & Co. identified original European plague-introductions by scanning the historical literature to find a plague outbreak that has had no local (<500km) plague for the previous couple of years.  That reduces the number of plaguey data-points considerably but gets a better signal-to-noise ratio.  Cross-referencing these plague start-points with the Asia tree-ring data [and having a background in time-series analysis] the scientists have found [L] many cases where the plague start is preceded by a bad-follows-good pattern in the Asian tree-ring data . . . 15 years before. This is just bonzer because it forces us all to think outside the box and because it is published in PNAS, one of the great general science journals-of-record, it will be read by astrophysicsists and nanotechnologists and inspire them to talk to people from other disciplines in the Senior Common Room. It is not impossible to criticise the paper but that doesn't detract from its value as a thought-provoking discussion document.
  1. By excluding all the cases where there has been a nearby plague out-break, they exclude all cases where a local European reservoir might have been maintained since the last out-break. So the traditional explanation of where Yersinia goes on vacation between its killing sprees may still hold water . . . but there is another, previously invisible, factor in the debate now.  Ignoring the European reservoirs is a sort of ascertainment bias  I - II - III: must do Stenseth's paper at Journal Club.
  2. Because they are happy-in-data, they tracked down six climate proxies but only found one (long-living junipers in the Karakorum mountains) which had the significant association with plague in Europe. That's a multiple testing issue. If my students had said "The other climate proxies yielded no significant results at a threshold of P < 0.05, or in the case of the Northeast Qinghai climate proxy, borderline significant results for two threshold combinations. It is possible that these nonsignificant climate proxies . . ." I would have chewed them out: not significant is NOT SIGNIFICANT end of story. As it was I just had to chew my beard.
It's grimly topical because far-distant events are causing the dispossessed to head for Europe in frightening numbers. The current response is to fire-fight at the receiving end with razor-wire and concentration camps refugee centres. A long-term solution requires consideration of the primary causes of the migratory impulse.

Friday 20 November 2015

Universal Children's Day

<ahem!> that would be today . . . in Ireland; although I doubt if I could find 3 people in 100 at The Institute today who are aware of the fact. For the countries where the majority of my readers come from this week, Ireland is the only place which is obeying the United Nations' diktat about when we should celebrate the existence, and vindicate the rights, of children: United States (various); Ireland (today); China (01 Jun); United Kingdom (15 May); France (Epiphany 06 Jan); Germany (Der Westen: Weltkinderdag 20 Sep; Der Osten 01 Jun); Ukraine (День захисту дітей 01 Jun); Malaysia (07 Nov); Russia (01 Jun); Netherlands (Sinterklaas? 05 Dec).  You'll note that the communists and former communists go for 1st of June, so we definitely can't pick that for Universal Children's Day: all our kids will insist on wearing red neckerchiefs and singing the Internationale. [Billy Bragg background].  20 November celebrates the adoption by the UN of the Declaration of the Rights of the Child in 1959. The declaration built on an earlier World Child Welfare Charter (1924) and was extended and updated in the 1989 Convention on the Rights of the Child CROC. The full text in English.

That's great, who could object to the rights of children? The 1924 document had a handful of aspirational assertions, CROC is a mammoth charter with 41 Articles for the children and another 13 full of legalistic weasel-words to allow any signatory country to do whatever it feels like. Why, it's longer than the agreement you sign to sign up to Friendface or PayPal. It is useful therefore to put on your critical thinking hat before saying you agree.  For example, we in the home education movement were concerned when the Irish government started to cite CROC in the run up to the 'Children's Referendum' in 2012.  If CROC Article 28.1 States Parties recognize the right of the child to education . . . was to be adopted, who was to vindicate the rights of our children to an education?  Probably a Minister of Education, advised by the apparatchiks аппара́тчики of his department - none of whom had experienced home education or knew how to spell it.

If a camel looks like a horse designed by a committee [quote] then CROC looks like a document that has accreted all sorts of superfluous detail because the drafting committee were worn down by the insistence of special interest groups. " . . . the advantages of breastfeeding, hygiene and environmental sanitation and the prevention of accidents."  Breastfeeding? that's a good thing, but to specify it in the convention without also specifying the maintenance of a healthy intestinal flora ???
Article 28.1.(c) is the only place where water is mentioned: To combat disease and malnutrition, including within the framework of primary health care, through, inter alia, the application of readily available technology and through the provision of adequate nutritious foods and clean drinking-water, taking into consideration the dangers and risks of environmental pollution; that's good, it deals with, say, Arsenic in the ground-water of Bangladesh but doesn't mention de-mineralisation by reverse-osmosis in Jordan.

Today, make sure you vindicate the rights of your children to help with the washing-up, cleaning the bathroom and making their own lunch.  And while they're at it they can make Dad's lunch as well. Thanks.

Following footprints

Nobody would claim that The Institute is at the centre of things.  So when we get a visiting speaker, I do my level best to turn up and also encourage any students who are under my wing within earshot to come along too. What the visitor has to say is surely going to be more interesting than the same-old-same-old drone from the likes of me. Partly that's because the visitors are not a random selection of the community; they are people who have a reputation for being articulate. They also get to be invited by someone on the staff who thinks their material is relevant and interesting to one or more of our student cohorts. We've had
This week we had a talk from Niamh nic Daéid, newly appointed Professor of Forensic Science at the Centre for Anatomy & Human Identification [CAHID] in U Dundee. She came from a 20 year posting in U Strathclyde where she became the first woman in that venerable institution's history to be awarded a personal professorship. She wanted to be an archaeologist when she left school but didn't get good enough grades, so went to read chemistry, maths and physics at an Institute like ours. Her grades may have been unstellar but her determination was mighty and she went on to get a PhD from the Royal College of Surgeons . . . and later a BA in Psychology from Open University! Hat's Off!! We are exposed to a raft of forensic scientists on the TV, in which strikingly symmetrical young women sort through the crime scene with unbelievably sophisticated instruments and wrap up the case within an hour including 12 minutes for ad-breaks. We know that it's not really like that but that sort of nonsense gets a great press, and persuades the gullible to sign up for 'forensics' courses at college. The other side of the forensic coin less so.  Who now remembers Dr Frank Skuse, whose " . . . conclusion was wrong, and demonstrably wrong, judged even by the state of forensic science in 1974" but whose tendentious interpretation of a Greiss test helped convict the Birmingham Six?  Who but The Blob remembers Lucia de Berk and Sally Clark being convicted of murder on the basis of dodgy statistical analysis?

Like any profession there will be a range of abilities between Dr Skuse and the perfect competence of TV fiction.  Prof nic Daéid pointed out that, in her profession it matters . . . rather more than if, say, your HR department cannot get contracts out on time and then sends them to the wrong people. Sending the wrong people to a lifetime is gaol is clearly a more serious issue. One of the skills you need as a top-gun forensic scientist is the ability to explain your findings and their scientific basis to ordinary people, and the pace and presentation of 'our' talk was right on the button: accessible to a raw 1st Year and informative to a professional biologist. FSs can be experts not only in blood-splatter, DNA identification and the chemistry of illicit drugs but also in the chemistry of combustible materials. This last is interesting because identifying how/where a fire started could be the basis for a criminal conviction but seeing how the fire spread is more about building regulations, health&Safety and public good.

Good FSs continue the traditions of Sherlock Holmes in having a technical expertise in written materials. But 70% of their work in this field is puzzling out what was written on the sheet of paper above the one which has been retained as evidence.  That doesn't require any sophisticated instruments, nor does matching a footprint in two different locations, but both can be useful in cracking a case.  At the techie end of the tool-box, there are 8 different protocols for making methamphetamine, each of which will leave a characteristic trace among the impurities that come down with the drug. To those in the trade, this chemical signature is almost as a good as a finger-print for identifying the lab where the drug was made.  How do they know this?  They make serial batches of the drug using each protocol and then run the results through analytical instruments and keep pictures of the output as 'standards'. Using similar standards, you can determine whether a fire was caused by unleaded petrol or kerosene or LPG which will tell a lot about whether arson is likely. That's criminal, but nic Daéid's people carried out research to show that 100% of boys and 80% of girls failed to wake up when a fire-alarm went off in their bedroom! That's a vital piece of data to inform public policy, parental behaviour and fire-alarm manufacture.

But perhaps the most worrying aspect of forensic chemistry is not identifying known substances - MDMA, gasoline, cocaine, haemoglobin, semen - at crime scenes but the ballooning number of chemicals which are new to the experience of the scientists involved.  If there are no standards and no standard protocols it is really difficult to stand up in court and stand over your findings. 350 new psycho-active substances NSPs have come on the market in the last few years and people in clubs and pubs are putting them in their mouths or up their noses without knowing how they act, where they are made or what they are cut with. That's a worry on many levels.
You can hear Niamh nic Daéid talking about similar material in a BBC interview. And she tweets. I particularly like her frequent use of the CEM Joad phrasing "It all depends on what you mean by . . .": until we know what we're talking about, there is very little real science going down.

Thursday 19 November 2015

Cycling rodents

Yesterday I was focussing a blobby eye on evidence for a 26 my periodicity in global mass extinctions.  We can't blame coal-fired power-stations or teak furniture for those events.  Some of the most interesting aspects of biology focus on ups and downs and today we're looking at cycles that are 10 million times more zippy than the wobbles of Nemesis.
When I was in graduate school in Boston I was given a desk in the Tamarin vole-lab, where I learned a lot that wasn't directly relevant to my thesis; like how to eat ice-cream with a spatula. The existence of the vole Microtus pennsylvanicus lab was predicated on the fact that they went through regular boom&bust population cycles of about 3 years.  My office mates used to take blood and other data from these small mammals to see if they could get a genetic handle on the peculiar phenomenon of huge fluctuations in population density.  At the same time on the other side of the pond, Nils Stenseth, a very smart population ecologist was doing similar work on the Norwegian Lemming Lemmus lemmus which showed similar bizarre see-saws in numbers from zero to tons per hectare to zero again on a 3-4 year cycle. No, they don't fling themselves off Norwegian cliffs in a vain attempt to go watch Rangers play soccer at Ibrox Park, Glasgow. Stenseth had studied theoretical evolutionary biology under John Maynard Smith and had a track record for a) interesting ideas and b) an all-embracing view of systems which was not too much fettered by the reductionist norms of scientific practice: he thunk BIG.  Here, as a grand old man of Norwegian science, he is talking about best practice for a rational future in science and politics. Biology is complex, let's not make things so simple that they become simple-minded.

Well it turns out that Norwegian lemmings have stopped cycling in the 30+ years since I was at all up to date with that literature. Apparently its mainly because of the wrong sort of snow.  Stenseth and his team corralled a huge amount of disparate data, not only on weather and climate, but also predator densities and food availability and other parameters and then dumped the whole mess into a computer to sort through looking for patterns that preceded or were coincident with the lemming cycles. Dense population seemed to follow after Winters with the right sort of light, cold, dusty snow under which the lemmings could run about shagging each other senseless and bringing a litter of baby lemmings into the world three weeks later.  No snow or a sludgey Gulf Stream snow and any active lemmings get scooped up by foxes, both Arctic Alopex Vulpes lagopus and Red Vulpes vulpes and eaten. T'buggers have changed the name of the Arctic fox from Alopex: is nothing sacred stable in biological nomenclature? That's a major change, presumably climate-change driven, that affects the distribution of all the other plants and animals in the ecosystem.  Most obviously among the predators and their prey. That's evolution happening before our eyes. It's wonderful and rare to have that happen in a single human lifetime. Although evolution can be seen to happen in a single mm of the fossil record, that's still hundreds or thousands of years of gene frequency change.

Wednesday 18 November 2015

26 Million year cycle

In the early 1980s just after Luis and Walter Alvarez had made their extraordinary claims about the events which terminated the dinosaurs, two smart and incredibly hard working biologists came together in collaboration at U Chicago. David Raup [who died this year: obit] and Jack Sepkoski shook up the field of palaeontology by leveraging their skills to analyse a lot of data rather than going out to find more fossils at ever more remote transitions in the geological strata. We need field scientists like Neil Shubin, for sure, without their primary original observations and interpretations there would be no data. But we also need broad-brush people to put the details into their evolutionary context. Looking through the data Raup became convinced that there was a logical disconnect between a) the dogma that every species has been honed and polished by millions of years of evolution to be uniquely well adapted to its ecological niche and b) that same near-perfect specimen being hustled abruptly off the stage of life to the oblivion of extinction.

Raup started talking to his colleague Jack Sepkoski because Jack had the data, all of it, in his head.  If Neil Shubin is the hard chaw of palaeontology with his field work in the remote arctic subsisting on iron rations and working like the devil between incoming storms; then Sepkoski was the hard chair of palaeontology, spending his waking hours in the library reading the literature and taking notes. At least for ancient marine fauna, Sepkoski knew when and where every species lived that has ever been described. He was following one of Claude Shannon's precepts for the creative break-through: know your field. His first major contribution was to sort the bewildering detail of 600 million years of fossils into three great sequential themes - in development, architecture and ecological complexity - that dominated the living world one after the other: the Cambrian Fauna - dominated by trilobites - giving way to the Palaeozoic fauna - rich in brachiopods - which in turn yielded to the 'modern', mollusc-ocentric fauna.  I say 'modern' because their rise to the top started 230 my ago.

Since Jurassic Park we know that the fossil record is divided into convenient lumps which can be found piled up one on top of the other in the same order wherever in the world the layers are exposed. This principle of stratigraphy was one of the evidential corner-stones of Darwin's explanation of the Origin of Species.  The order of play of Periods follows the mnemonic
  • Camels ordinarily sit down carefully perhaps their joints creak too quickly
  • cambrian ordovician silurian devonian carboniferous permian triassic jurassic cretaceous tertiary quaternary
the last two, which are richer because more recent, are further subdivided into Epochs
  • perhaps early oiling might prevent permanent rusting
  • palaeocene eocene oligocene miocene pliocene pleistocene recent
Notes: some geologists, especially US, divide Carboniferous into two chunks Mississippian and Pennsylvanian. Since I was in school, they have split Tertiary into Palaeogene and Neogene.
For a long time, I didn't appreciate is that these geological Periods and Epochs are not just convenient bins for the filing of fossils but that they represent major shifts in the faunal assemblages from what appears in the fossil record before or since. Sepkoski's uber-groupings suggested that some of the transitions were greater than others.  The picture on the Left taken from U. Bristol "after Jack Sepkoski" shows that the Great Dying is not #5 the dinosaur-dumping end-Cretaceous extinction but #3 at the boundary between the Permian and Triassic which created the conditions /cleared space for those same dinosaurs to start their 100my dominance of the terrestrial fauna.
In 1976 Raup calculated that 96% of marine species died [exec summary] in that event 250mya. The calculation hinges on an interesting statistical tool called rarefaction analysis. His overview analyses of species distribution deliberately stepped away from counting species and concentrated on higher taxonomic classifications; documenting whether whole families or orders of animals had gone extinct. All it takes for a species like the Tasmanian Wolf Thylacinus cynocephalus to go extinct is for a gunned up farmer called Wilf Batty to avenge the loss of his chickens. That's a random event, an anecdote, not a pattern or data. Loss of some orders is going to reduce the number of species more than the loss of other orders. Extinction of Order Chiroptera in mammals, for example, would mean the end of 800 separate species while Order Tubulidentata only has a single member - the aardvark Orycteropus afer.

But the most important contribution R&S made to our ways of thinking about the pattern and process of evolution was to push the idea that mass extinctions are random, external, unfair events that had nothing to do with how well adapted those species had been . . . and then assert that the external events were not random. If you take the inverse of the previous graph [L above] and plot % extinctions against time, you can a) identify the peaks which we call mass extinctions and b) note that there seems to a periodicity about the data.  Biological data is noisy: we're not sure of the dates; the fossil record is patchy; most species, because entirely soft-bodied, don't fossilise at all; most terrestrial environments leave no fossils; we have barely even started on the fossil record of South America; while for Africa we've just skimmed the surface looking for hominids. Raup and Sepkoski's 1984 PNAS paper is available in its classical entirety. I like that paper very much, Sepkoski had the data, Raup was happy with time-series analysis, their complementary skills and the to-and-fro of half formed ideas gave the rest of us something to really think about. People were not slow to add the increasing certainty that the Cretaceous-ending event was due to an asteroid collision to the regular return of Halley's Comet to suggest that every 26 million years the Earth was likely to have a close encounter with something large enough to knock your socks off.

One of the more coherent theories to account for the periodicity is Nemesis a companion start to our Sun, which regularly comes close enough to whack some lumps out of the Oort cloud at the further reaches of the Solar System.  Some of these fly towards us and sometimes they miss, so there may be gaps in the 26my cycle. Nemesisologists believe that the most likely candidate is a red dwarf star of which there are 3000 near enough to make a difference. But before we invest a lot of money/time in seeking the cause of the periodic events we need to be really skeptical about whether the periodicity is real or an artifact of time-series analysis which can all too easily find a pattern if there is no prior constraint on the time between peaks. I've been caught by such a wishful thinking trap.

The good news is that the last such event was 11 million years ago, so its not going to impact on the next soccer World Cup.

Tuesday 17 November 2015

Extinction is forever

I think most people who read The Blob will be aware of mass extinctions, when a disproportionate number of species step off the plank into the seas of oblivion. Extinction is forever, and when the last member [or the last member of one sex] of that unique conglomeration of genes and homeostatic systems dies, we'll never see the like again.  Evolution is the result of a long series of accidents and contingent events that would be impossible to reproduce. There are some who claim that the study of evolution is not scientific because of the impossibility of replication.  Whatever . . . it has a great deal more explanatory power than the idea that every sperm is sacred and individually crafted by a deity.  Extinction was happening in a dribbling out fashion even before I was born: the last Quagga Equus quagga quagga went West in 1883 and the Tasmanian Wolf Thylacinus cynocephalus bought the farm in 1936 [or possibly survived, a guerrilla in its own neighbourhood, into the 1960s].  The latter is the bigger loss because there was nothing like the thylacine - the biggest carnivorous marsupial that survived the arrival of man in Australasia. The quagga OTOH is a subspecies of the same clade that holds Chapman's Zebra Equus quagga chapmani and it's conceivable that we could 'recover' the quagga by selective breeding from related, living animals.  A project that seems to me to be a quagga-quixotic time-wasting distraction on the scales of biodiversity.

An event that weighs heavier on those scales is the great Cretaceous extinction of 65 mya which notoriously wiped out the dinosaurs and created the opportunity for the rise of mammals including ourselves in all their wonderful diversity.  We are, of course, and understandably, mammalocentric but there are only 5,000 species of us and we'd all look boringly samey to scientific insects [?10? million species] or nematodes [another million of them] - "all" mammals have seven cervical vertebrae for starters.  We've inferred quite a lot about the Cretaceous extinction from the fossil record and particularly from the strange observation about Iridium made by Luis and Walter Alvarez in 1980.  Luis was a Nobel Prize winning particle physicist and his son Walter was a professional geologist who discovered a thin band of Iridium-rich rock at the geological boundary between Cretaceous and Tertiary rocks.  That was weird because Iridium is heavy, has an affinity for Iron and is rarely found in the Earth's crust. Alvarez and Co [there were other collaborators who tend to get washed out of the story] suggested that the Iridium came from an extraterrestrial source as a massive asteroid collided with the Earth scattering debris from itself and the impact crater far and wide.  Being scientists they could estimate the size of the asteroid and the size of the crater and part of the scepticism with which their hypothesis was jeered received was the fact that no such crater was known to geologists.
In fact, the crater had already been discovered by a couple of petroleum geologists, Antonio Camargo and Glen Penfield, who had difficulty recognising it as a crater partly because only 40% of the crater rim was on dry land in 1978.  In the map [L] of the Northern Yucatán peninsula you can see gravitational anomalies [Red scale] and cenotes, freshwater sink-holes as white dots. It is centred on the seaside town of Chicxulub which now gives its name to the geological formation. The crater is about 180km in diameter and might have been 20km deep when formed. It took a couple of decades to sort out and reconcile all the data: geological, biogeographical, climatological, palaeontological, ecological and biological. The consensus now is that the ejected dust created an earth-wide darkness at noon that might have lasted a decade: that put paid to photosynthesis as the primary source of biological energy on the planet.  The vaporized calcium carbonate rocks shoved up the atmospheric carbon dioxide levels to give an instant greenhouse effect.  There is even a suggestion that the impact was deeper than first thought and that sulphates were mobilised to causes deluges of acid rain.  Poor old dinosaurs with their peculiarities of metabolism were just not able to weather the changes.

In contrast, he little furry creatures, scurrying about between the dinosaur's legs and happy-as-larry in the dark, started to grow and diversify so that in a geological eye-blink all 20ish Orders of mammals were strutting a fretting their hour on the stage: bats, rodents, carnivores, cetartiodactyla, elephants, armadillos and uncletomcobblios.  Why is this event important? Because I am, even at this moment, using electricity to whack out another post on The Blob and so cranking up my carbon footprint for 2015. Shoving up the temperature a couple of degrees centigrade doesn't sound like much to us - sounds pretty good in drizzly Ireland - but may knock out a single over-sensitive species in our complex of inter-locking ecosystems.  Because it is system, that loss will have unpredictable and cascading effects on the members of the ecosystem who remain.

Monday 16 November 2015

Golden navel

There is an old, long and potentially moralistic shaggy-dog story about a boy who was born with a golden screw in his navel. As he grew up he became more self-conscious about this anomaly and wished that he was like everyone else.  After visits to his GP, a dermatologist, a general surgeon, a chiropracter, an aromatherapist [continue list for as long as your audience has the patience], he finished up in a wigwam on a remote island of the Pacific North-West coast with a shaman.  The shaman required him to return at the next full moon, remove all his clothes and lie precisely here on the floor of the tent. As he lay there in the dark, he noticed a moon-beam passing through a hole in the fabric and tracking down his midline.  When the moon beam reached the golden screw it seemed to pause and the screw turned and turned [continue for as long as your audience has the patience] until it fell with a clunk to the floor.  He jumped up, shouting for joy . . . and his arse fell off. Moral: be content with who you are and resist peer-pressure. Ah so!

It's mildly amusing the first time you hear it. At The Institute, we've been doing some Golden Navel work in Year 1 Cell Biology. An ethical cat is among our scientific pigeons because, since the year dot, we've telling students to analyse a drop of their own blood a) to demonstrate osmosis and hypothesis testing b) to view the different sorts of white blood cells and see if they really are 1% of the total (99% being red blood cells) c) to determine ABO and Rhesus blood group status and calculate the gene-frequencies. We may be able to continue, but the bureaucratic burden may make it not worth the effort.  Which is a shame because there is rather more pedogogical benefit in these practicals than some of the others which are boring but safe. OTOH, we could have a very useful session discussing the ethical issues of taking your own blood. We needed something to replace the scheduled blood practicals that wouldn't burden the support technician with a long list of hard-to-source material.

As Cell Biology is for Sporty People, I thought it might be interesting to test reaction times in left and right hands by having a confederate drop a 30cm rule between the thumb and fore-finger and see how far it fell before a pinch stopped its gallop. Scope for prior hypotheses: variation among people; right-hand quicker/slower than left; women quicker than men; short people (with short arms) quicker than bean-poles. Scope for data analysis: consistency of replicates, appropriate statistical tests, sample size sufficiency.  Actually there are ethical problems here too: Q. what do you do when a student is so slow on the uptake that he misses the falling ruler entirely; A. prior statement asserting that slower reaction times are associated with more reflective thinking. Then during the weekend before The Off on these new practicals, I found a youtube video on the Fibonacci series and φ Phi [preφously] the golden ratio. In among all the guff about φ being "most pleasing to the human eye", the harmony of the spheres and the profile of the Parthenon, it is frequently asserted that the height above ground of the toupée and navel is in the golden proportion [L rule applies not only to the Greek God in pale blue speedos, but also to fat-arsed sofa-pilots who could only wear those same speedos as a hat].  So my Cell Biologists tested that ratio in themselves.

But not before I described the cunning plan to Dau.II. She immediately put her finger on the issue of multiple testing [I'd have her on my scientific crap-detecting team in a trice]: the human body is well complicated and you can measure pretty much everything with a tape-measure: hat size, digit length, hand-span, girth.  Then you can compare a long list of measurements with each other: somewhere in that tsunami of numbers, you'll get something close to 1.6 : 1.  The interesting extension of such thoughts is that there are fundamental similarities among members of the same species which allow us to recognise each ‘type’.  Dogs, despite a huge range in size and shape are nevertheless dogs and obviously different from cats.  Likewise, all humans are more similar to each other than any of them are to dogs or cats . . . or chimpanzees, our nearest relatives.  Gibbons, our primate cousins, are literally knuckle-draggers [R. very handy for swinging through the trees] and distinctively different from humans.

Results. Up to a point Lord Copper it is true that the navel/head height ratio is in the Golden ratio.  But there's a disturbing level of variation about the average.  It doesn't look normally [bell-shaped, Gaussian] distributed to me.  There is no significant difference between men and women for this proportional parameter.  Indeed, for our students there is no significant difference in the height between M & F: we have some stocky blokes and tall girls.  In the histogram [R], I've marked where 1.618 falls and acknowledge that it is rather close to the average but there is more than 10% difference between lowest and highest ratio.  By the end of next week, we'll have a sample of more than 100, so some of the random variation may even out.  There may be an issue that these measurements are taken by the students themselves rather than by fully trained Navelmetricians.  One chap reported his height as 1m77, which is within the normal range but claimed his navel was only 66cm above the floor.  I'm about the same height but 66cm is about my mid-thigh; so this fellow must have a prosthetic navel at the end of an elastic ligament . . . or no legs?

So far, so predicable? Well get this: I am 177cm tall, the height to the top of my knee-cap is 56.5cm: the ratio 3.133 which is within 3 parts in 1000 of 3.14159  = π !!! I am tied in a circle with irrational numbers: must mean I am made in the image of the deity.