Blockage

It's not obvious to all thinking people but it's obvious to me: chewing-gum is not water soluble. Maybe it's not obvious to thoughtless people. If you spit chewing-gum into a urinal, it stays there until somebody else takes it away. It's a galling indictment of the quality of the education that is being taken on board at The Institute, if chewing gum is routinely, regularly found in the urinal basins of the toilets nearest to the Science Faculty office. Weirdly, the company that cleans the toilets seem to be largely chewing-gum blind, so it is up to me to find a rubber glove and de-gob the bowls myself. Simple solution: takes 120 seconds. Lots of people I know seem to think that lard, butter and bacon fat are water-soluble. So they pop a greasy plate and a frying pan in the dishwasher and press the GO button. The dish-washer is the bane of kitchen thrift and mindfulness far more matériel gets used if you know the robot will wash it for you. Washing up is widely seen as a chore/ burden/ task/ horrible/t ime-wasting, but that is only in the mind, for me it's restful and great for warming the hands in a cold house. If you add some detergent and water and heat the stew of claggy pans and unfinished plates up to 80^oC then the fat leaves the plate and goes  . . . somewhere. It goes about halfway along the sewer pipe until it gets cold enough to precipitate out in a clot like a coronary artery plaque. The next weekend's breakfast fat gets deposited in more or less the same place and soon the 100mm diameter foul-water pipe is almost blocked.  If it gets really blocked, the toilets back-up and you have to spend a fortune getting the drains reamed out by Dynarod Drane-Klene Inc. I was visiting a pal o'mino a tuthree years ago and found that the neighbours had rented a mini-digger and were digging up 20m of  foul-water pipe because the drain-rods weren't long enough to get things flowing again. They have been more careful of the fat burden since.

Having a self-contained water supply/treatment system is a) good because we don't have to pay Irish Water for the utility b) not-so-good because I have to clear any blockage. I don't mind getting my hands dirty but if possible I'd rather not spend Saturday up to my elbows in shite.  Sooooo, we clean the fat off the dishes and pans before we plunge them into the sink to wash them.  Newspaper will usually serve or a bit of toilet paper; we long ago stopped buying paper kitchen towel.  If the washing up has been really greasy, I tend to carry the bowl outside and fire the contents into the ditch rather than risk atherosclerosis of the drains.

There are, it seems, stupider things to send down the sewer system than a bit of fat, like a product called a flushable wet-wipe which is flushable but about as soluble as chewing gum. Young scientist Kian Hennessy did a research project on the things a tuthree years ago.  He put a selection of these plastiwipe things in water and shook it daily for many months and found that the wipes still had structural integrity . . . were still capable of snagging on a small protrusion in a pipe and serving as fat catcher. At about the same time, I wrote (somewhat skeptically about the maths) about the West London Fatberg "the size of a double-decker bus" that blocked the main sewer. Sewer-clogging wet-wipe worms [L from Australia] were in the news (and widely on the blogosphere) again recently.  The cost of cleaning this un-shit from the system should be laid at the doors [which are also likely to be designed for dysfunction] of the product engineers who create them - you have to own the consequences of your actions.

Endless Forms Most Beautiful

Part of OneZoom's Laurasiatheria

With that title I could be referring to a loud song by Nightwish the symphonic rock combo from Finland. But I could equally cut out the middle-Finns and go straight to the horse's mouth Charles Darwin: ". . . from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." with which he wrapped up his Origin of Species.  My son the engineer, aka The Boy, pointed me at an amazing Big Science project which aspires to display the Tree of Life.
This is one link that you just have to follow up: nothing I can say captures the half of what you can find out on the site itself. Any ToL is a graphical display which attempts to capture the evolutionary inter-relationships among different species. Things which share a recent common ancestor are adjacent twigs, while more distant relations appear on different branches of the tree. What the OneZoom project achieves is a zoomable display that enables you to see an overview of the 'tetrapods': the lads who climbed out of the water and began to inhabit dry land about 375 million years ago in the Devonian period.  Remember Neil Shubin on The Blob last year with his fossil intermediates between fish and amphibians?

What the tree looks like is a series of splits where one type of animal separated into two or more sub-types and each went on to evolve numerous variations on that overall solution for living. OneZoom's tree makes an explicit claim for the fractal nature of these evolutionary splits and propagations. Whatever scale you consider, the taxa are divided into proliferating branches of related animals So the tree of whales [L] looks like the tree of mammals looks like the tree of life if you squint up and ignore the labels .

Within tetrapods, amphibians peel off from the stem with a distinctive morphology, then mammals, then lizards&snakes, turtles, crocodiles and finally birds.  In the old days we shoved a bunch of these groups into a bin called Reptiles although the only thing they had in common was that they weren't birds, mammals or amphibians.  Each of those groups forms its own Class [a technical term with a particular meaning in taxonomy]. I show [above Right] part of the representation of the Laurasiatheria, which is one of the four great groups of placental mammals. The other 'superorders' are Afrotheria, Xenartha and the rather chewable mouthful Euarchontoglires. It's been easy enough to recognise membership of a particular/peculiar group from their anatomy: bats have wings, whales have flippers, carnivora have big teeth, insectivores have sharp ones.  What was hard for Darwin and his contemporaries was sorting out how these mammalian Orders [another technical term] were grouped.

That only became possible when molecular sequence data came on stream in the 1980s and 1990s. Des Higgins and Dan Graur were early adopters of these molecular tools to show that whales & dolphins were really artiodactyls: with a lot more in common with cows and sheep than they had with, say, seals or manatees.  That was counter-intuitive, not to say controversial, until the whale-people stopped to reflect that hippopotamuses also were artiodactyls.  Just a few days ago I was talking about the taxonomy of rhinoceroses which are not artiodactyls but not a million miles away from that group either.  Seals are also part of Laurasiatheria along with cats, dogs, bears, and other carnivora.  That all sort of hangs together: even-toes ungulates [artiodactyls] mincing about on their toe-nails with odd-toed ungulates [perissodactyls] along with other large running mammals which eat other mammals as a specialisation. No 19thC anatomist would have thrown bats into the same group: they are so peculiar and so different.  But the molecular data is quite emphatic: bats are within Laurasiatheria.  They are also the second most populated mammalian Order after Rodents: 20% of all mammalian species have wings.

Who gives a damn? I mean there's got to be more to biology than the naming of parts and classifying species into bins and those bins into buckets and those buckets into dumpsters. The OneZoom project also embeds data about the species in question, notably their conservation status, but also the wikipedia entry, if any, and a number of other biological databases, so you can get a picture [literally usually] of each species' position in the wide world. What about us? Well I can tell you that we are part of the Euarchontoglires. But as my pal Karsten observed:

Did you see the leaf for humans?

"Conservation status: Least Concern"

Interesting way of putting it...

Indeed!

Guinea worm gone

I got a real good education in Graduate School in Boston. It was partly the formal courses which I sat on "subjects" that we didn't know existed in TCD back in Dublin: a whole semester on 'evolution' with Lynn Margulis, ditto 'mammalogy', ditto 'physiological ecology', ditto 'multivariate statistics'. But I also learned a lot from my fellow students: eating ice-cream & loading a salad bowl, for example. My boss, a man of wide interests, recommended that I read his old Parasitology text-book, which was on the shelves down in the basement where I was living. He was an aficianado of Dracunculus medinensis the Guinea worm.  You can hardly admit to loving this parasitic invader, but you can nevertheless be fascinated by its life cycle and the peculiar methods used to rid patients of the adult worms.  Dracunculus lives part of its life in tiny copepod crustaceans which swim about in tropical fresh water. When they are consumed my mammals, including people, who drink the water, the copepods get dissolved by the stomach acid and the Dracunculus larvae burrow through the wall of the intestine and develop into adults among the wobbly bits over the next 3-4 months. When a female worm meets a male, they love each other very much, the male sinks back exhausted and dies from his exertions, the female begins a slow shoving journey through liver and lights, muscle and fat, until she comes to rest just beneath the skin. Somehow this creature, knows where the legs are and tends to come to rest in the lower legs. But occasionally she gets blind-sided by other low hanging appendages and heads for the hand or <eeeuuuw> the scrotum. Her journey is exquisitely painful to the unwilling host.

Evolution has shaped the female Guinea-worm's behaviour to facilitate the continuation of her life cycle. If the skin above the lurking female gets wet, then she burrows rapidly to the surface and sheds thousands of eggs into the water in the hope that some of them will encounter a copepod. This sensitivity to water can be used to start a cure: wrap the leg in a wet towel then when the end of the worm breaks the skin surface you can seize it and e v e r  s o  s l o w l y draw the whole worm out. As she can grew to 80cm in length, this pulling can take several days.  You wrap your winnings round a twig or pencil to stop the whole thing slithering back into the flesh.  If you pull too hard then the bloody worm breaks and you have a serious case of septicaemia on your blistered legs. I'm sure that there were experts at these delicate extractions in many sub-Saharan villages.

I use the past tense advisedly, because at more or less the same time I was reading about Guinea-worms in Boston, retiring President Jimmy Carter was thinking about what he was going to do for the rest of his life. His existential solution was to endow the Carter Centre on some derelict urban blight in Atlanta, Georgia. This institution was established with the brief "to advance human rights and alleviate human suffering".  Grand for a mission statement but What to do next in detail?

• First build a complex of offices and auditoria, a library and museum, all set in lovely parkland, 
• Then appoint a Board of Trustees packed with the great and the good and capable of networking their way to solutions.
• Have the Board appoint Effectives to do committee work and decide how the substantial, but not infinite, endowment can be most effectively leveraged.
• Launch some specific projects: preferably those that will yield tangible results within the life time of the soon to be ex-President.
• It's also important to have projects that can be written up in a headline + 600 words by the Washington Post.

And it was so. Tuberculosis, Malaria, HIV/AIDS were left to other groups [Gates Foundation for example] with far deeper pockets. Along with election watching, the abolition of the death penalty and conflict resolution, the Carter Centre decided that they would take on the dreaded Guinea-worm which at the time in the mid 1980s infected 3.5 million people, mainly in sub-Saharan Africa. The map shows countries in which the worm was endemic in 1985, the hatched countries are those that still had worms 20 years later.  Now I read in Nature 10th Feb 2016, that Dracunculus has almost gone the way of all smallpox.  A combination of Carter Centre monogrammed winding-pencil distribution [kidding!]; water filters, education and political barracking has reduced the disease Dracunuliasis to a mere 22 cases in four countries for calendar year 2015: an astonishingly effective 100,000-fold reduction.  At one point, President Carter bluffed his opposite number in Ghana that with his clout he could persuade science to start calling Dracunculus the Ghana-worm.  “There isn’t a Guinea worm left in Ghana now, Carter told journalists with a grin . . . "  The remaining four benighted nations - Chad, Ethiopia, Mali, and South Sudan - are beset with civil wars that not even Carter's mediators can stop.  Civil war rides with pestilence and makes it really difficult for health-care workers to get where they are needed.

Obstetrics and ovicology

Ob & gyn is a speciality in medicine which until very recently was, like all medicine and most other things, dominated by men.  We still have a Master of the Rotunda [maternity hospital] Fergal Malone replaced Sam Coulter-Smith about this time last year.  We are not yet ready for a woman in that job?? Obstetrics has an interesting etymology coming from obstetrix [Latin] a midwife; which in turn comes from ob+stare to stand across from or opposite to . . .  across from what?  I'm guessing across from the orifice-of-delivery.  Having been an assistant catcher in two home-births, I know something about this.  Gynaecology also has in interesting etymological history; the first syllable comes Greek γυναι ultimately from proto-indo-european PIE gwen = woman from which we also derive queen. The science-speak for sheep is Ovis aries, ovis [Latin] is also from the PIE root owi = sheep, from which we get ewe via Olde English eowu meaning a female sheep. The word sheep is a bit of an orphan, shared by Dutch schaap and modern German Schaf but not by other Germanic [Swedish får, Danish faar] languages, etymology beyond skæpan in West German is unknown.

Last night I was just settling down to a night of aimless youtube when my farming neighbour called asking if we had a sack-needle about the house.  We are currently painting the hall, so everything has been shifted from its usual place and you can hardly see the floor for piles of books. After a bit of shouting and hunting I located the sewing box and set off across the river in the rain with the largest available needle. Fortunately, my pocket also had couple of meters of fine white cotton string which had been sealing a 25kg feed-sack up until I was feeding the sheep earlier in the evening.  As I suspected, my neighbour and his Polish friend had a prolapsed uterus on their hands; or rather threatening to spill out onto the straw of the ewe's bedding. The two feeble spotlights in the barn made it light enough to see by, but not light enough to thread a needle, but these new-fangled mobile phones have a reading light.  With no backup, this was not the time to drop the implement and have us all looking for a needle in a haystack.

I threaded the needle and then held the light, the Polish friend held the sheep and neighbour sewed up her vulva so that the uterus aka the lamb-bed would stay in, we hope.  This same operation was carried out on one of our post-partum ewes a few years ago with only transitory success.  I hope it works out this time.  Not more than 30 minutes after getting the call, I was back on my cosy sofa looking up the etymology of obstetrics; youtube idleness forgotten.

Bad Day at Blackrock

I could be referencing the classic 1955 Spenser Tracy film in which the one-armed war hero exposes the Black Hats and takes one of them down after being bullied.  But BDaB was also used as the title of a 2008 novel by Kevin Power.  The novel went over, in fictionalised form [must avoid a libel suit], real life events from 8 years earlier when Brian Murphy, an 18 year old student, was involved in a fracas outside a famous Dublin nightclub and finished up dead from a tonk [repeatedly kicked and punched while on the ground didn't help either] on the head that caused cerebral edema.  It was a cause célèbre and great fodder for the papers because the principals in the tawdry and shameful melée were from very comfortable middle class backgrounds, fee-paying schools and played rugger for fun. Power's tale didn't claim to be the Truth but it was widely seen as having the ring of truth. If boxing is a licence to ape Achilles and Hector, then rugby football is sublimated violence of a tribal sort. And both of them are likely to result in someone sustaining CSE contact sport encephalopathy.  Don't get me wrong, it's okay for young men to puff out their chests and have a brawl: they are primates awash with testosterone.  If they are going to do it though, let it be in the cold light of day recorded on camera rather in the dark with lots of sharp and hard objects in the frame and lots of drink on board. Drink? Club Anabel said they were very sorry and wouldn't be offering 3 for the price of 1 cocktails in future, but only because new legislation made the practice illegal.

If your actions result in someone else getting hurt, then you need to own their pain. If you can vote you can hardly claim diminished responsibility. What actually happened was that the witnesses massaging their memories of the events and the families of the accused lawyered up and did everything they could to prevent their boys suffering any inconvenient consequences for their behaviour. Eventually one chap was sentenced to four years for manslaughter and two others were convicted for violent disorder.  Even those sentences were quashed on appeal. Those involved protested when Power's book brought all the events back into focus when raw memories were beginning to scab over.

There's another Bad Day at Blackrock which hasn't been written yet but which I can piece it together from some circumstantial evidence and write a story that has the ring of truth and may make us reflect on a man-eating serpent in the midst of our society.  We were down in Cork visiting Dau.II over the weekend and we had a long invigorating walk along the River Lee where it widens out to become Cork Harbour. We parked at Blackrock Castle [L] which hangs romantically above the channel on a natural promontory.  After the walk in a biting Northerly wind we repaired for an enormous lunch at the Café in the castle courtyard. It was all delicious and the waitron was engaged and well informed. With two daughters in the catering trade we recognise quality . . . big tip.

But here's the thing; on the way up to the castle I leaned out over the wall over the bit of a beach, looking for buoys, and saw a tinplate sign fixed to the sea-wall promoting the Samaritans.  Feeling crap? phone this number, we're here for you, we will listen. [I paraphrase]. It seemed a peculiar place to put a sign where the only person likely to see it is a deckhand (with binoculars) on one of the container ships passing up-river to the port. On the other side of the wall, where every passing car and pedestrian can see it, is a discrete in memoriam sign for a young chap who died at the age of 26 a few years ago.  Surely there is a relationship.  Is that sheltered and secluded bit of scrubby beach, with a view of the river as a metaphor for the wide and impossibly distant world, the place where the young chap decided to end his pain?  Was his pain made worse by an uncaring, competitive peer group that didn't include him in their brawls games?  Or did some bigger blokes take out their own unhappiness on him? Road fatalities seem to be an essential item in the calendar of Irish news reporting and they are going down in a way that must gratify the National Roads Authority, Insurance Companies and of course the devastated families left behind. But there is no real shame in driving like a mad thing, or with drink on board, so that you kill yourself and others.  Suicide is both lonely and shameful and it takes an epidemic of such deaths to make the national news.  If we could 'out' clinical depression and expose it as a treatable problem the way Bressie has been man enough to do, then maybe we can begin to deal with suicide the way we are getting to grips with car-deaths.

Rhino - black and white

A tuthree years ago, I reported on a nifty study using DNA molecular evidence to make convincing statements about the inter-relationships among elephants.  The conclusion was that there are two species of African elephant Loxodonta africana and now Loxodonta cyclotis which are as deeply separated from each other as Asian elephants Elephas maximus are from long since dead woolly mammoths Mammuthus primigenius. That was not totally unexpected, because some taxonomists had suggested such a division, but the depth of the divide was quite surprising because the two types look very much alike.  Molecular evidence can lump together as well as split, as we saw with penguin species where a trivial superficial difference between local races led people to designate two different species. But the DNA data showed that only one species should be designated - not least because the two types were inter-fertile.  For me the best story of molecules trumping morphology in determining relationships is Dan Graur and Des Higgins proof that whales were a subset of hippopotamuses.

I clearly have an appetite for this sort of thing and got another valuable earful last Friday when Dr Candace Scott came from St. Lawrence College, Kingston, Ontario to visit The Institute and gave us a talk about her work as a conservation biologist. She has worked with lions Panthera leo and hyaenas Hyaena brunnea, but the love of her scientific life are the rhinoceroses, especially those in Africa. As with two species of elephant that turned out to be three, when I was growing up any fule kno that there were two species of African rhino: black and white. We all knew that white rhinos weren't so colored - 'white' was a corruption of Dutch/Afrikaans wijd/wyd which referred to their shovel-like grazer 's upper lip. Black rhinos had a pokey-pointy upper lip more suitable for browsing foliage higher than the knees. Scott  has used the tools of molecular genetics to identify signature DNA variants which distinguish the African rhinos from each other and from their more distant cousins in Asia. Dramatis personnae:

• White rhinos Ceratotherium simum with subspecies
• NWR Northern White Rhinos C. simum simum critically endangered, probably extinct in the wild; original range where Uganda, DRCongo and [S]Sudan now meet
• SWR Southern White Rhinos C. simum cottoni doing okay down South Africa way
• Black rhinos Diceros bicornis with subspecies
• D. bicornis bicornis 
• D. bicornis michaeli 
• D. bicornis minor 
• Note Wikipedia claims at least 5 extant subspecies.
• Indian rhino Rhinoceros unicornis
• Sumatran rhino Dicerorhinus sumatrensis 
• Javan rhino Rhinoceros sondaicus

Candace Scott, has worked for many years in quite primitive conditions to obtain reproducible data that separates, or doesn't, the various sub-species [MSc thesis]. She is not the first person to attempt this work, but she found that previous studies yielded very noisy results: it was hard to assign an individual rhino to its morphological category (species/subspecies) based on the genetic markers the earlier scientists had developed. On the contrary, her discrimination is commendably crisp and shows [Above] two interesting findings.

1. It is impossible to distinguish D. bicornis bicornis DBB from D. bicornis minor DBMIN which are intercalated in the bottom right corner of the multivariate statistical analysis.  So they should be treated as equivalent and interchangeable. D. bicornis michaeli DBMIC, OTOH, is quite distinct, indeed as distinct as the two Asian good species Rhinoceros sondaicus JR and Dicerorhinus sumatrensis SR.
2. Likewise , the two subspecies of white rhino SWR and NWR should be promoted to separate species, like the elephants before them.

These results haven't been without criticism. Very small sample of NWR, the pundits tsk, but those half dozen rhinos represent half of the remaining adult NWR still out in the bush. One could also question whether picking markers that best discriminate the existing sub-species is desirable. Take humans, if you pick eye and skin colour as your genetic markers then you can quite easily distinguish Norwegians from Nigerians but ABO blood groups or pretty much any other genes or combination of genes will be equally variable within each group and you'd have to conclude that the two types were interchangeable.  Why is this important? Because, with limited resources the WWF, or whatever conservation group has the loot,  has to allocate the money to saving this or that but cannot do both. The genetic data suggests that you can let either DBB or DBMIN go to  extinction-is-forever despite them being 'separate subspecies'. For whatever reason, rhinos don't seem to get much traction among the general public: giant pandas, elephants, killer whales, even wolves are considered more cuddly by potential conservation-patrons.

More women in science.

Sunday in the sun 060316

Cold but sunny in South- East Ireland this morning. Elsewhere?

• I wrote already about the myopia epidemic in July here in video form, is the recommendation to get out in the sun.
• Sun? What about Kenya? in 1983, Ayub Ogada was discovered singing Kothbiro while busking the London Underground.
• Travelling to the Sun?  Better check out the weather: today hot with sunspots, low probability of solar flares.