Thursday 31 December 2015

Out of Africa

At the beginning of March this year, a strong woman died. As I wrote then, she had taught Dau.I and Dau.II a bit of French and a lot of kindness before she came to the end of a long and remarkable life. Her oldest daughter was their grandmother and her journey has been equally 'interesting' in the sense of the Chinese proverb "May you not live in interesting times". She was named Souad, because her father was Lebanese and that is the name of a Maronite saint; and also after Saint Thérèse de Lisieux, because her mother had been educated by French Catholic nuns. Souad was educated in Northern Nigeria, also by Catholic nuns, some of them Irish, on the edge of the Sahara Desert. The Irish nuns told her of a land where the fields were green, the cows ate the lush grass and gave milk in abundance for butter and cheese and some of their relatives contributed a T-bone steak or two. Souad prayed every night to St Patrick to take her to this paradise far to the North. So when a young chap, more or less Irish, more or less called Pat, whom we've met before, came within her orbit she said “I’ll have him” and she did.  So like her daughter, the Girl who invented herself, Souad chose whom she wanted to be and became that person. Most of us don’t have the gumption or energy for that but meekly accept the plateful we’re born to and eat it with the spoon we get – some silver, some wooden. It’s been quite funny recently to hear Pat telling our girls about how he was calling the shots and making the moves on that long-ago-and-far-away courtship.  But that’s part of Woman's story: let the chaps believe they’re in charge – they’re easier managed that way.

Once married, every penny saved was put towards The Farm, an almost mythic entity that they would buy back home in Ireland to raise their family on butter and cheese and cabbage and spuds and the occasional steak. They did buy the farm but the reality wasn't as shiny as the imagining. In spite of their best efforts, Pat and Souad had to endure adversity and penury and have done so with remarkable dignity, absolute honesty and persistent good spirits. Yesterday, I reflected that Tu Youyou lived in 'interesting times' (in China, indeed) but had luck in her placement: with that and hard work she was able to make a difference. Wherever they’ve settled Pat and Souad  have made people happy in their presence. Maybe that's sufficient contribution: the other stuff is, after all, just stuff. I represent the many strays they adopted along the buckety path of their 65 years of marriage. I was a scruffy and unsuitable youth ‘from foreign’ and the wrong religion, who was making off with one of their daughters, yet they took me in, fed me up, taught me manners and indeed taught me how to live.

It’s true that Souad preferred the company of small-small children to grown-ups: I guess because she knew that too many children grow up to be disagreeable adults. It is usual in newspaper obits to count the number of children, gchildren and ggchildren. Souad was rare and remarkable in being able to take her place in a vertical line of five living generations of strong women: her mother, herself, and three subsequent generations shared our planet for 15 years. The three other great-grandchildren are all too young to have remembered her; the most recent being born 5 days before Souad died in her own home, in her own bed on the Saturday before Christmas. Given that we all have to pass through that gate, and that death is rarely either clean or dignified, such an exit is to be hoped for.

Along the way over my last 25 years living here, I’ve had to endure a certain parochial Catholic Little Ireland assessment of my antecedents. Living in Ireland long-and-long before it became a multicultural society as much at home with pizza as bacon-and-cabbage, Souad handled the inevitable “but where do you really come from” with good grace but not backing down a whit: "From Dunmore" she'd say, or Freshford, or Gladstone St, Clonmel, or Kilkee or wherever they were currently living. She said recently that she considered a good horse the most beautiful thing in the world . . . after a nicely tanned young woman. She was that tanned young woman: everyone has remarked on how elegant she was, how well she carried herself.  But you’d be wrong to call her a thoroughbred because she channelled a shockin’ wide number of bloodlines into her elegant, savvy, kind, generous and hard-working self. The full story was far too long to tell to people who weren't really interested in thinking (or eating) new stuff. And that was their loss because nobody could cook a ham like her. The ham opened the door to more exotic fare: mulukhiyah, kibbeh, groundnut stew, mujadara, tsire . . . acquired from the complex skein of cultural threads that entwined her early life: West African, Lebanese, French. The gallimaufry of food that you might meet coming out of her kitchen was a metaphor for her open-handed embrace of The Other in people. She knew what she stood for - a practicing Catholic with a well developed moral compass - but she wasn't quick to judge if your upbringing and values were different from hers. And she cared not a jot where your people were buried. She was notorious in her family for an inability to get their names right.  She called me Brian at least as much as she called me Bob. Now that she's gone I wonder if there wasn't something significant in this?  It wasn't that she was a little vague or forgetful; it was that, in her egalitarian mind, people were people - there was room in her heart for us all.
Subridens per lacrimas

Wednesday 30 December 2015

Project 523

Never 'eard of 'er!  How many times have you heard someone rabbiting on about a famous woman of science and that's your response? Then again, ask most people if they've heard of Professor Aragorn, inventor of mithril silver and half of them will say Never 'eard of 'im! and the others will acknowledge his contribution as they quaff a foaming mug of ale with Tom Bombadill. I was caught with ignorance-pants on my head when Tu Youyou 屠呦呦 [R mentoring a younger woman-in-science - you can tell they are scientists because both are wearing white coats] won the 2015 Nobel Prize for Phys&Med shared with William "Irish" Campbell and Satoshi Ōmura. Never 'eard of 'er indeed. She's foreign, she's female and her research was carried out behind the bamboo curtain, so it's not the kind of copy chewed over by popular science. Well, it's her 85th birthday today, so we may have a look at her achievements.

In the mid-1960s at the height of the Vietnam War, malaria was a serious drain on the Effectives of both sides of the conflict. A soldier can hardly walk, let alone point a gun in the right direction, if he's weaving about with a fever and headache and the shakes. The original useful prophylactic against malaria, as far as Western medicine was concerned, was quinine aka Jesuit's Bark an extract from the bark of Cinchona officinalis a South American tree. A synthetic alternative was developed at Bayer in 1934 and eventually called chloroquin [structure L]. But 30 years later, a lot of malarial strains were resistant to quinine and chloroquin; and the race was on to develop effective alternatives.  The US military threw down the challenge to pharmaceutical companies: the prize being a lucrative government contract.  The besieged, bombed, defoliated and impoverished North Vietnamese didn't have such access to megaPharm and wouldn't have been able to afford the drugs aNNyway. They asked for help from their idealogical mentors North of the border in the People's Republic of China. hmmm not very fertile ground on the face of it, because the PRC was in the turmoil of the Cultural Revolution and intellectuals of all sorts were suspect: publicly humiliated, losing their jobs, shipped out to be a good peasant in the country, or executed. Science itself was suspected for being bad for progress towards a Maoist paradise of happy workers and peasants in identical suits of blue cotton. The Chinese VP Chou En Lai realised that malaria was a scourge not only for N.Viet soldiers trudging through the foreign jungle, but for millions of peasants and soldiers across the border in Southern China where malaria was also endemic.

On 23rd May 1967, a cadre of 600 scientists, soldiers and others was brought together at a top-secret "Project 523"and given the task of finding an antidote for malaria. Tu Youyou had been trained as a pharmacologist and spent two years of testing thousands of compounds for a) activity against the malaria parasite, as well as b) very limited toxicity and side-effects in humans. She also had a deep academic interest in traditional herbal medicine and after so many dead-ends decided to go back to The Ancients and see what they had to say on the matter.  Like Anglo-Saxon healers discovering an effective cure for eye-infections, the Chinese had a long history of tinctures and extracts from plants to cure disease or ameliorate symptoms.
Tu went back to her books to identify plants that had promising properties and narrowed down the search to Artemisia annua - sweet wormwood - and some of the phenolics [like Artemisinin L] that her team purified from the plant. Her initial researches, and close reading of ancient texts, concluded that the active principal was heat-labile and so required a cold solvent [ether, hexane] extraction of the plant material. It proved singularly effective against malaria in mice and monkeys and so Tu Youyou decided, like Barry Marshall and JBS Haldane before her, to chug some down to see if it killed humans. It didn't kill her, and so a full scale clinical trial was implemented. It's not a great anti-malarial because the side-effects are not-so-good and it's hard to deliver it cheaply to millions of people but it was better than nothing and may have shifted the balance of power in the Vietnam war. It certainly improved the quality of life for Chinese people in regions where malaria still thrives. After her initial success she carried on doing reg'lar science in China invisible to the rest of the world.  Someone at the Lasker Foundation must have been doing their home-work because Lu Youyou was awarded a Lasker Prize in 2011 and people started to perk up and take notice of the achievements of this octogenarian from China. She is an icon for women in science because she exemplifies that, if you are sufficiently bright and creative AND are presented with a 'lucky' project, then you can make a significant break-through. It's not about academic quals: To Youyou is known as Professor Three Noes: No PhD; No Foreign Post-doc; No membership of the elite Chinese Academies. Yet she done good!

Tuesday 29 December 2015


A couple of years ago, when I read A History of the World in 100 Objects by Neil MacGregor, I was amazed at the scholarship and field work that could track a particular neolithic jade axe, found in Canterbury, UK back to the boulder from which it was cleaved: up a mountain in the Apennines 1000km to the South. That's a wonderful mix of Arts and Science.

At the beginning of December, University College London issued a press release about a finding by their chaps. All Universities have their Press and Publicity section now: a pal of mine, Professor in TCD, who is smart enough to stand astride the Arts - Science divide, was prevailed upon to make a little video about his latest paper. The UCL research was more in the line of filling in details rather than opening up a whole new field of historical population genetics, but was interesting nevertheless.  They have found the precise quarry from which the blue-stones of Stonehenge were prised 600 years ago.  We've known for nearly 100 years that these megaliths were not local but came from Preseli in South Wales, the recent study announces that they came from Craig Rhos-y-felin. That's interesting because it upsets a cosy supposition about how the stones were transported to the sea at Milford Haven and then upriver towards England.  That meant that more than half the 400km could be achieved by boat/raft. The location of Craig Rhos-y-felin on the North face of the hills makes this unlikely.  Also intriguing is that the dates established at the quarry are several; hundred years adrift of the dates at Stonehenge, which implies that the blue-stones had an intermediate function in an, as yet undiscovered, location.  That's pretty cool.

The other day, I was given qualified appro to Patrick Roycroft's 648 Billion Sunrises . One of the short chapters in there looks to see if there is gold in them that Irish hills.  It is undoubtedly true that there is gold in Wicklow, Croagh Patrick, the holy mountain in Mayo and also in the Mourne Mountains in Co. Down. As I hope we established back in July, Croagh Patrick is off-limits for gold abstraction because it is worth more for our culture and consciousness as a place of pilgrimage.  The National Museum of Ireland holds some stunning gold artifacts, which have a reputation beyond these shores for the quality of the workmanship given that they were wrought 4000 years ago when even the Greeks were running about their hills in goat-skin trousers. A pal of Roycroft's, Chris Standish from Bristol U, has done a nifty isotope analysis of several gold pieces - torcslunulae and that sort of thing.  He ignored the gold and zeroed in on the lead which usually co-occurs with gold; but lead exists in several isotopic varieties of different molecular weight.  Standish was able to match the Pb-isotope signature of the bronze age artifacts with none of the existing sources of Irish gold. A wider hunt through the WEA and continental Europe has turned up a best match in Cornwall!  Not a perfect match like the blue-stones at Craig Rhos-y-felin but good enough for a first approximation. The consensus is that, while the gold came from foreign, the craftsmen were doing their work in Ireland: they just needed the right, and sufficient, raw materials.

A new source of Irish gold was announced in March 2015 at Clontibret in Co Monaghan. their geologists are claiming 600,000 ounces of gold at 1oz (28g) to the ton, which will turn a nice profit unless the price of gold tanks.

Monday 28 December 2015

648 billion sunrises

One of my students, who is big into geology had been recommended a book 648 billion sunrises: a geological miscellany of Ireland by Patrick Roycroft.  As it happens, I met Roycroft at a memorial service to Mary Mulvihill in the Autumn. He had worked with her Ingenious Tours company that took tourists round Dublin showing them that we have a rich and fascinating scientific heritage even if we only have one scientific Nobel Prize - ETS Walton. Some folk are claiming 2015 Nobellist William C. Campbell as "Irish" because he was born in Derry in 1930 and has been a US Citizen since 1962, but I don't think that's proper. The Ingenious Tours gig is a welcome antidote to the literary heritage that most people bang on about when they think of Ireland: Swift, Wilde, Shaw, Yeats, Joyce, Beckett, Heaney. Q1.  Which four of those seven secured a Nobel Prize for Literature 'for Ireland'.  Q2. Which of them was about as Irish as Chaim Herzog, President of Israel, was Irish?

ANNyway, I bypassed Amazon and went straight to a Galway bookshop that has embraced cloud-shopping with a limited inventory, mostly of Irish interest. They ship post-free within Ireland.  Two copies, one for me + one for student, were winging their way to work within 24 hours. The book is what it says on the tin: a miscellany of stuff which Roycroft (and his editors) thinks is a ) related to Irish geology and b) can be abstracted from his head with a little pressure and a little research. It is accordingly a little like a blog and, like The Blob, could definitely benefit from a ruthless editor.  Not everything that crosses our minds when we muse on a life-time in science is worth going down in print. What seems hilarious at 0200hrs when you're half a bottle down, can seem labored or arch in the cold light of day.  I wrote a piece a couple of years back suggesting suitable underwear for every country in Europe.  It was in the nature of satire on the idea that every US state has a state bird as well as a state flag.

In all seriousness and with a wodge of pretension, Roycroft has decided that each county on the Island of Ireland should have a geological title "Pegmatite County", "Marble County" as well as a county rock, mineral, and fossil. Most of the Irish counties have nicknames already, few having to do with the local rocks. This idea is a useful vehicle for surfing the landscape and picking out some interesting facts about our prehistory and it's impact on modern life.  But some counties are bigger than others and some are much more diverse in geology and fossils and some are both. So the depauperate counties are given rather more attention than they deserve and a lot of interest stuff is left on the spoil heap because that county has something more glittery.  It's a business model that elects the US Senate: where tiny Rhode Island has the same representation as Texas and New York.

The other interesting thing is a history of the formation of Ireland that goes back 1.8 billion years. I knew a bit about this: that the NW of the island and the SE have very different geological origins. And I was also aware that a supercontinent called Pangaea split into Gondwanaland in the South and Laurasia in the North . . . but I've never really nailed when that happened. It shouldn't come as a surprise that this massive continental drift had happened before with similar sized chucks of real estate. What is amazing is that geologists can discover traces of these increasingly ancient events by scoping the landscape with scientific rigour and the imagination and creativity most people associate with poets. You can make geology (and indeed biology) a tedious exercise in stamp collecting or you can put the data together with a lifetime's experience and come up with something truly unexpected and probably true.  We met this with Marie Tharp revealing the Mid Atlantic Ridge by mapping her transects across the ocean floor.

And it was delightful to meet local polymath Rev Samuel Haughton again in his capacity as the TCD Chair of Geology rather than as a dilettante of human hanging. We only get 2 pages on him, however, and an equivalent amount on two collateral relatives who were also Professors in the following century.  That's what I mean by a little light research to fill out a common-place book or a blog.

Verdict: a definite buy for your Uncle who is into Irish Science and Technology.

Sunday 27 December 2015


Norwegians generally have a good press nowadays although people associate them with Vikings and associate Vikings with looting and pillaging things that didn't belong to them.  But, shucks, that's 1000 years ago and neither your ancestors, nor mine, back then would no have had squeaky-clean white gloves by today's standards. It's true I was recently having a bit of a sideways swipe at the Norwegian treatment of children 75 years ago. But again, it's only useful to bring that up if if helps us reflect on the shakiness of our own ethical stance.

It's an anniversary of sorts at this time of year because 24 Dec 1969 was the date of the first discovery of oil under the Norwegian sector of the North Sea.  In the subsequent 40 years, the Norwegian government has prudently used this unexpected windfall to clear the national debt and set in place infrastructure to benefit future generations of Norwegians. In contrast, the British pissed it all away on tax-cuts and a mad spending spree which has all gone up in smoke with containers full of consumer tat (boosting economies at the other end of Asia) and foreign holidays.

This month has seen a crowd-sourced social-media driven give-away from Norway to Finland which is kind of daft and kind of sweet.  As Hitchhiker fans will know, Norway is particularly rich in fjords; it has a helluva lot of mountains too. When Finland was established as an independent republic, they surveyed their borders with Sweden, Norway and Russia.  Obviously they had to liaise with their opposite numbers in those other countries so that everyone knew where to pay their taxes.  We've seen that casual surveying, or too much arm-waving at peace conference tables, or allowing medieval peculiarities of land-holding to endure can cause all sorts of problems: Baarle; Point Roberts; Berlin; Cooch Behar; Palestine; Llivia.  It turns out that at a prominence called Halti, the boundary between Finland and Norway skirts across the shoulder of the mountain peak rather than going to the top.  Nobody is quite sure why it turned out like that. 
But the current Norwegian folk-movement wants to cede 1.5 hectares of sovereign Norwegian territory to Finland as a present to celebrate Finland's centenary as a nation. Finns tend to celebrate 6th December 1917 as the date the country secured independence from proto-Soviet Russia. Although that ignores a bitter and protracted civil war that ran more or less at the same time Ireland was having its own internecine melt-down. ANNyway, if that is the date, the Norwegians have just under 2 years to get their act of the generous hand together. One of the things that stokes the Norwegians is that the transfer of this sliver of tundra will give Finland its highest point above sea-level. They are as short on mountains as Norway is short on lakes.

This will be a tiny symbolic redress for a major loss of territory that Finland suffered after the mess of WWII. In 1920 at the Treaty of Tartu, it was agreed that Finland would have direct access to the Arctic Ocean at Pechenga. The province of Petsamo Petsamon lääni, was ceded back to Russia under duress  in 1944.  That was small potatoes compared to the loss of the heartland of Karelia down in the South at the same time. You may want to listen to the Karelia Suite by Sibelius, in sympathy.

Saturday 26 December 2015

Recovery position

I think we've all survived Christmas.  Our girls, Dau.I and Dau.II, who left home 4.5 and 2.5 years ago and promptly enrolled in the University of Life have been working in the catering trade. They came home for several days over the holiday and owned Christmas dinner.  All I had to do was slave away at the kitchen sink acting the plongeur for a mountain of used delph, saucepans, chopping boards, glassware and cutlery.  "Do you have a dish-washer?", people ask; "Yes, me", I reply. "Don't you realise that dish-washing machines are mega-efficient in their use of water?", they continue; "Piss off", I reply.  It's a policy decision we've taken: washing the dishes by hand makes you aware of their use, helps you reflect on the process of cooking and eating food. It's the opposite of the take-away, throw-away society we might embrace if we lived close enough to an Indian restaurant to make ready-meals convenient.

I missed the starter of spinach-and-adds salad because I was on the phone to my pal P in Boston.  I was on the phone because my service supplier Vodafone offered free national and international calls on Der Tag. I was talking to P because we go back a long way and her father is dying and I thought she could do with a boost. With 4 at the table, we had a meat end and a meat free end: two of us believing that chicken and ham was both traditional and necessary. The lads at the other end of the table had some rather fine aubergine roulades dressed as you might do cannelloni; they were delicious. I'm with Thomas Jefferson on this, a man who ate meat only “as a condiment to the vegetables which constitute my principal diet.”  For me the main point of Sunday/Christmas/Thanksgiving dinner is the roast potatoes; if these are done right then the whole meal falls into place. Yesterday, they were done right. The girls could do this long before they left home, but formal training can give even the most mundane dish a bit of a lift. There was gravy, of course; the traditional Brussels-sprouts were roasted with chestnuts and pancetta; there was a dark red dish of red cabbage and lemon; a taster of cranberry sauce; and final dish of roasted carrots-and-parsnips. All delicious on their own, a feast together.

After a gasp and a gap of an hour and a Kobayashi shake to settle things, we came back for self-assembled 'trifle' of Pandoro slices with autumn berries, custard and cream. Let us be thankful for a fully-functional gall-bladder to process the tsunami of saturated fat. Really looking forward to hang-sangers today: it's like the dinner yesterday was just a prelude.  But first I'll have another go at some dish-washing.

Friday 25 December 2015

Christmas heartwarming

A handful of Christmas links:
now get back to the family: you know you love them . . . unless you want TMI about land-crabs.

Discovered at Christmas

A ship, the Royal Mary, of the East India Company, Captain Wm Mynors, sailed past an island [R] on Christmas Day 1643. They clocked it at 10o30S 105o30E about 500km S of the Sunda Strait between Sumatra and Java. Captain Mynors named the island for the day that was in it and sailed on into the oblivion of history. No European set foot ashore until 45 years later when two sailors from English explorer Wm Dampier's Cygnet landed at Dales on the West coast. Dampier was the chap who rescued Alexander Selkirk in another place and another time.  Christmas Island is not a million miles from the Cocos (Keeling) Islands of which we treated and the two territories have had an intertwined history. They are currently under the administration of Australia as part of the Australian Indian Ocean Territories. 200 years after Dampier's expedition, Captain P Aldrich, RN of HMS Egeria landed the Cambridge naturalist JJ Lister to collect animals, vegetables and minerals. The main finding was rich seams of calcium phosphate Ca2P2O7 which was recognised as a potentially valuable agricultural fertiliser and led the the island being annexed by the British. Extraction was commenced by the Phosphate Mining and Shipping Company using slaves indentured servants from Singapore and Malaysia.  Phosphate has been the cup which keeps on giving and it still contributes about 90% of the export earnings for the island.

If you think that Europe, Lampedusa, Malta and Kos have a collective problem with emigrants, reflect on Christmas Island which now has more refugees than regular citizens; indeed there are about 3x as many refugees as there are designated spaces, so it must be a bit like an Irish A&E department on any Winter's day.  Reflect that the nearest launching place for an attempted Ozmigration is 400+ km distant, which is about 4x further than Africa to Lampedusa.  If everyone knows that a much longer journey is required to reach Western Australia, then only the most desperate will attempt it. In any case, the Australian government have legislated to prevent landfall on the island being treated as equivalent to landfall on the Australian mainland.  The precipitating political crisis goes back to 2001, when the Norwegian container-ship MV Tampa picked up 400+ Afghanis from a leaking shalloop in the middle of the Ocean and attempted to land them at the nearest civilised country - Christmas Island. ABC coverage. They were refused entry. Currently the policy is to ship landed refugees to Nauru in the middle of nowhere rather than taking them all into the bosom of the Australian family.

The other migration for which Christmas Island is famous is that of the red land-crabs Gecarcoidea natalis which are endemic to Christmas Is and Cocos.  These hefty [10cm across] crustaceans live in the rain forest but once a year set off for the beach where they have a lot of crabby sex so that the eggs hatch into a particular high tide. The larvae are swept out to sea where they develop and dodge predators for 3 weeks before returning to the same beach like salmon to their natal river. Natal? Note the crab's specific name natalis: of Christmas. There are millions of the crabs living in damp parts of the forest: their numbers may have shot up in comparatively recent times since the extinction of the local rat Rattus macleari 100 years ago.  The homeostatic control of population numbers depends on complex interactions among species; as we saw with wolves and moose on Isle Royale.; and also wolves, beavers, willows and rivers in Yellowstone. The role of scythes-man of crabs has recently been taken up by Anoplolepis gracilipes the 'yellow crazy ant', an invasive alien which has appeared on the scene in many tropical and subtropical islands. Nobody knows where A. gracilipes hails from so it's impossible to locate a natural predator to keep the micro-monster in check. If your species of interest is bigger than a breadbox and the predator isn't a microbe, you have a chance of saving the situation by human intervention: as we saw with penguins and foxes off the coast of Victoria. You're at nothing with that sort of solution for the ants.

What makes biological science so interesting is how interconnected it all is.  The reduction in numbers of the land-crabs has changed the balance of plant life in the forest because the omnivorous crabs used to eat seeds and seedlings. In contrast, the ants have a commensal relationship with some species of Hemipteran scale insects and their population increase can have a detrimental effect on the growth and development of forest trees. It will all settle down eventually but the settlement may require the extinction of some of the players before a new equilibrium is established. Try not to think of Anoplolepis gracilipes savaging land-crabs to death as you dismember your Christmas turkey.

Thursday 24 December 2015

The No Cross Word crossword

It is traditional in many families that adults assemble in "the place where, when you have to go there, they have to take you in" to consume more alcohol and saturated animal fat than they are used to. The setting opens up the baggage for the best of us and real or imagined slights are exaggerated until cross words are spoken. Words which will be regretted the following morning if the speaker hasn't drunk enough to forget the whole evening.  That is a most unfortunate state of affairs, so I'm providing an antidote to familial meltdown: crossword therapy. There's maybe enough of a puzzle to divert your mind from a flaming row. Uncle Jim may well be a total ass, but the whole family knows it and so there's no point in telling him in front of them. I've had no compunction about recycling the grid which I used this time two years ago
01ac. ---, Gropius, Werfel   01dn. 150t Holocaust place 060714
04ac. aka Chaldean Aramean   02dn. Birthplace 1714 UKing
09ac. Glutton;Morus bassanus 03dn. [Biblical] interpreter
10ac. 10o28N 61o15W island    05dn. A huge block of ice
12ac. Nb named for her       06dn. A yiddischer gossip
13ac. English Арха́нгельск    07dn. λ 430nm
15ac. Devonian outcrop       08dn. Uncancerous lump
16ac. Boudicca's people      11dn. C.cainii or Fr C.sativa
17ac. Wm 021013 Ml 160313    14dn. Cardiac nerve bundle
22ac. Drugged geologist?     18dn. Shandean postscripter 200114
24ac. 86Rn                    19dn. Geastraceae fungi
27ac. One of the Paridae     20dn. Commiphora africana resin
28ac. Snowbird RV            21dn. 1/5 of the Iroquois nations
31ac. Tribromofluoromethane  23dn. Globus [cruciger]
32ac. Flight eg. LHR to SIN  25dn. Inventor of Kevlar 020714
33ac. The original Hun       26dn. Alexander did it in Gordium
1st name Benzene girl  29dn. C2H5-
35ac. Черное море полуостров 30dn. Heraldic tincture

Happy Holidays! Bingle Jells. Answers in 2016.

Wednesday 23 December 2015

Swedish slang

Along with maps, islands, and women-in-science, The Blob is quite interested in language.  I'm kind of crappy at learning new languages because I have a tin ear and a big head. The tin ear means that, although I can carry a tune reasonably well, I can't hear people when they talk foreign. But that selective deafness is quite likely to be the fact that I tend to over think everything and am relentlessly analysing the material rather than just listening, remembering and repeating. Ho hum, fallible me!  I also have a soft spot for obsessives: people who collect match-boxes or twitchers capturing birds with telephoto lenses.

Lars Petrus decided to help people who don't speak Swedish get as much as possible out of the Ikea catalogue.  He's written out all the daft names the company calls their chairs and cutlery-sets, alphabetised them and shown the etymology - insofar as he was able to divine it.  A number of these words are clear to Swedish speakers but opaque to others, even if they have a dictionary, because they are slang.  I've filleted Petrus' list for just these slangy words.
Bagis 1 krona
Blaska newspaper
Brallis pants-thing: pretty girl
Brasa fireplace = crotch
Bräda board = out-do a rival
Bästis bff bestie
Deka deteriorate
Drälla mess around / spill
Flukta to look
Fläng hurry/bustle about = stupid
Griller whim / strange idea = ice-skates
Hampen grass maryjane
Hemlis secret
Hojta shout
Knodd kid
Knoppa sleep
Knös nob / rich person
Kosting cash / money / flukes
Kvarta to sleep
Lack varnish = angry
Mackis sandwich-thingie
Portis doorman / concierge
Prächtig overly wholesome
Pröjs pay
Rajtan tajtan partying
Reko okay
Skubb a run
Slabang slabang!
Snack talk / prattle
Snitsig nifty / snazzy / cool
Snodd lanyard = stolen
Snålis tightwad / miser
Spänn 1 Krona
I'll leave your own curiosity to follow up on which article of household clutter Ikea thinks should be called 'miser'. You'll thank me for getting you down-with-the-cool in the language department if you take advantage of the Ryanair network and go to Stockholm for a weekend clubbing.

Tuesday 22 December 2015

Doubting equinox

As Dava Sobel explained in her book Longitude, determining precise details of the position of the stars above the horizon is [only?] of vital importance for navigation at sea. Nobody on land is going to die if their observation of Rigel or Sirius is faulty by a few degrees or a few minutes. At sea, especially nearing land after an oceanic voyage, particularly in dirty weather, you really need to know where you were on your last clear sighting of a known star. Otherwise you are likely to pile up on a Scillian reef like Sir Cloudsley Shovell and hundreds of his sailors did on 23 October 1707. So for astronomical data you defer to United States Naval Observatory (USNO) and/or United Kingdom Hydrographic Office (UKHO) probably even if you are part of La Francophonie. I had two txt-greets yesterday from tree-hugging pals saying "Happy Solstice".  Which I had to say was wrong wrong almost right because the Solstice isn't always on the 21st December, but swings between the 20th and 22nd and this year it falls at 0448hrs UCT today 22nd December 2015.  In the period 1900-2100 the Winter solstice has fallen 5 times on the 20th; 103 times on the 21st; 91 times on the 22nd and in 1903 edged 20 minutes over into the 23rd.  So dear readers, before you make a faux pas over the equinox this coming March check with the US military.  I can just see your pagan gods face-handing upstairs "Jaysus! They've got it wrong again, if our loyalest supporters are going to get their kit off to dance in midwinter could they not get the date right?".

There are two things going on at midwinter that don't match up precisely. It would be a lot more convenient if the Earth rotated on its axis exactly 28x more than the Moon went round the Earth. Actually it would be better still if the ratio was 30x and the Earth's journey round the Sun took exactly 12 of these integer moonths. But Zeus and Loki and Ganesh have arranged it as a mathematical challenge. The solstice is about the obliquity of the axis [N pole to S pole] about which the Earth turns w.r.t. the plane about which the Earth orbits the Sun. This angle is 23.4 degrees and explains [not here though!] why the Tropics of Cancer and Capricorn are 23.4 above and below the Equator. Weirdly and wonderfully the Earth shuffles round on its orbit with the tilt always pointing in the same direction. When the the N pole is pointing as near as it can directly at the Sun, then that's the Solstice. From our Earthbound Northern Hemisphere point of view, the rising Sun creeps closer and closer to a most Southerly point [sun-stand-still prevlier]and then edges back North again.  Stonehenge and Newgrange are aligned to this point on the horizon.

The other thing that is off centre is that Earth's orbit is not precisely circular as required by Plato with his celestial spheres singing their heavenly song. Ptolemy had to fudge the actual data with a raft of secondary circular epicycles to force 'circularly' on the heavens.  Copernicus had a great leap forward when he suggested that planetary and starry prediction would be easier with the Sun at the centre rather than Jerusalem or Alexandria. As Koestler [prevlier] explained in his book Sleepwalkers, there were more epicycles after Copernicus had finished than under the old system, but at least it was a step in the right direction. It took Kepler to twig that planetary orbits were elliptical rather than circular. Earth's orbital eccentricity is about 3% and the perihelion (closest approach) occurs a couple of weeks after the Solstice, as I explained a year ago. The earliest sunset and the latest sunrise and the shortest day are close but not exactly on the same day as the solstice: it's complicated. Obviously, the tilt of the Earth away from the Sun offsets the fact that the Sun is 3% closer but the tilt is much more significant in its effect on our weather. For us in Ireland it has been the most miserable weeping wet December that I can remember.  With my two-week event horizon that's true for every Winter, hmmmm? If the tree-huggers [meeeeee!] would just do their dance today, maybe the weather gods would cut us some slack?

Monday 21 December 2015

Doubting Thomas

A long while back I suggested, in an ironic outburst against Irish bureaucracy, that my middle name might be Thomas. Later I explained that I was given the middle name as a tribute to a collateral relative who died a hero at the head of his regiment in 1813. I've never really associated myself with "Bob", except in the context of writing The Blob, and in a different world might have happily finished up as Tom Scientist.  I'm definitely a scientist, however: I put that down under "Occupation" whenever there isn't room for "Evolutionary Biologist".

Today is the Feast of St Thomas the Apostle, aka Thomas Didymus [the twin] or Doubting Thomas.  The word Thomas, in this context, is derived from the Syriac Toma and Hebrew Teom which mean 'twin' so Didymus is a redundancy, a gloss for folks who aren't fluent in 5 languages. The official patron saints of scientists are Albertus Magnus, Dominic and Isidore of Seville.  I've no idea how Dominic gets the accolade, except insofar as his monastic order the Dominicans became leaders in intellectual activity and the first rumblings of scientific method in the middle ages. Indeed Albertus Magnus (<1200 - 1280) was an early Dominican and he deserves the cognomen Magnus for his comprehensive researches in an ignorant world. We shouldn't slag him for using his intellectual talents for dead-end pursuits like alchemy and astrology. We only know now that these are dead-ends: partly because of Albert and others who tried to make sense of the natural world through observation and experiment. The Franciscan Roger Bacon, Albert's English contemporary was also a giant thinker and explorer of the natural world through experiment. Isidore of Seville was much earlier writer, thinker and encyclopedist, whose Etymologiae aspired to be quecunque fere sciri debentur, "practically everything that it is necessary to know".

For me Thomas has a much better claim to be honoured by scientists because of one of only two things we only know about him: his skepticism at being told about the resurrection of Christ:
But he [Thomas] said to them, “Unless I see the nail marks in his hands and put my finger where the nails were, and put my hand into his side, I will not believe.” A week later his disciples were in the house again, and Thomas was with them. Though the doors were locked, Jesus came and stood among them and said, “Peace be with you!” Then he said to Thomas, “Put your finger here; see my hands. Reach out your hand and put it into my side. Stop doubting and believe.” Thomas said to him, “My Lord and my God!” Then Jesus told him, “Because you have seen me, you have believed; blessed are those who have not seen and yet have believed.” John 20:25-29.  Even though it's his birthday this week, I have to disagree with Jesus on this one: everyone should require "show us yer evidence" before accepting something as true.

The other thing we 'know' about St Thomas is that when the Apostles scattered across the known world to spread The Word, he went East and finished up preaching and converting in Kerala in Southern India.  There are nearly 1 million St Thomas Christians, or Nasranis, according to recent Indian Census data. They seem to embracing an almost Shaker attitude to marriage and procreation and have one of the lowest rates of natural increase in the region.  They should not be confused with Catholic Christians from places like Goa further up the coast. Those lads have a much more recent coming to the faith. The survival of the Nasranis and their attendant quirks of culture surely cannot be enhanced by schizmatic fragmentation into: The Malabar Independent Syrian Church who are barely speaking to the Malabar Orthodox Syrian Church; then there's the Malankara Mar Thoma Syrian Church; St Thomas Evangelical Church; Jacobite Syrian Christian Church; Syro-Malankara Catholic Church which is absolutely not to be confused with the Syro-Malabar Catholic Church or its cousin the Assyrian Church of the East aka the Chaldean Syrian Church. Splitters!

Sunday 20 December 2015

Sunday Science 201215

This Sunday Miscellany Gig - It's getting to be a habit with me. I hope you aren't going to get dependent on me churning other men's flowers.  Anyway here are some updates on Bloboprevs.

Saint Lucia

13th December is/was Saint Lucy's Day, the Festival of Light, celebrated as Lussinatta in Sweden since they were Vikings.  Because of the cock-up in the calendar, 13/Dec coincided with the Solstice, so folk  needed some magic to help the rebirth of the sun and that has involved a lot of candles over the years.  In Sweden the eldest daughter of the house has to dress in a white shift and put on a head-dress with flaming candles before she wakes the rest of the family with coffee and saffron buns.  Sounds like a dodgy idea to me: it's really difficult to get candle-wax out of the sheets for starters. Swedish cultural imperialism, or the desire of neighbouring people's for an excuse to party, has spread the celebration of St Lucia to other Scandinavian countries.  That's all I have to say about the day because I missed it this year.  I'll try to be more with-it in 2016.

For further St Lucy tribs, you may like to listen to Andrea Bocelli singing Santa Lucia Neapolitan style.  You're on your own with that, though, for some baggage-y reason that song really creeps me out.

Having dealt with candles and song [tick, done that] allows us to ship on out to the parliamentary democracy of Saint Lucia in the Caribbean. They are independent now, but still part of the Commonwealth and still have Mrs Windsor as their head of state. But the island was a shuttle-cock between France and England for 400 years from its discovery by Europeans in the 1500s. The first white-folks to have some sort of settlement were a pirate-crew led by François "Jambe-de-bois" le Clerc. Subsequent invasions were seen off by a deadly mix of tropical disease and warlike Caribs.  St Lucia is still part of La Francophonie despite being finally assigned to Britain by the Treaty of Paris in 1814. This results in the peculiar situation that the official language is English but 95% of the people speak French or Patwa, the local French-like creole. It is clearly French but some ancestral Lucian couldn't trill their Rs: agwéyab = pleasant; nom fam gason ti fi [un homme, femme, garçon, fille] = man woman boy girl; Piti hach ka bat gwo bwa = Little axes cut big trees. The legal system is still based on the Quebec Civil Code of 1866.

Although the primary export [22% of earnings] is bananas, the economy is more centred on offshore banking and tourism; St Lucia is a frequent stop for cruise liners and tourists also fly in for the beaches and the food: cassava and yams; chicken and goat; green figs and saltfish; rice and peas; often with a generous sprinkling of scotch-bonnet chillis. St Lucia is no desert island, but close to being a tropical paradise where its 600 are shared by 180,000 people. The natives seem to be happy. What Barbadian-Canadians think about them. ". . . they very jokey-jokey, they like a lot of bacchanal . . ."

Saturday 19 December 2015

General Beard

I suspect that you are damned ignorant about US Civil War generals, even if you're American  . . . even if you come from Virginia. Accordingly I've cobbled together a quiz and a survey.
1) Which of the following fought for the Confederacy and which for the Union [in which I really asking the question: which side paid more attention to grooming?]
William Mahone; JEB Stuart; Richard Ewell; Ulysses S Grant
Ambrose Burnside; John Hunt Morgan; Joseph E Johnston; Alpheus Williams
Stewart van Vliet; Samuel Sprigs Carroll; J Johnston Pettigrew; Thomas Leonidas Crittenden
2) Which one has the most extravagant facial hair? Gereral Burnside's rolling white wave was so distinctively noticeable as to give English the word 'sideburns'.
  • Mahone, at 1.65m and 45kg was known as Little Billy "He was every inch a soldier, though there were not many inches of him."
  • Stuart was killed at the Battle of Yellow Tavern in May 1864.
  • Ewell was wounded in his wooden leg at Gettysburg
  • Grant went on the become President. 
  • See above for Burnside's sideburns
  • John Hunt Morgan was the uncle of pioneer geneticist Thomas Hunt Morgan [blob previously].
  • This General Johnston is not to be confused with Gen. Albert S. Johnston who fought on the same side.
  • Alpheus Williams fought much of the war on a horse called Plug Ugly 
  • Stewart van Vliet graduated from West Point in the class of 1840 a dozen of his 42 class-mates became Civil War Generals, including Ewell on our list - about half Union and half Confederate.  The Class of 1915 is called the Class the Stars Fell On. 1840 and 1915 tell you that a) it takes 25 years to grow a general and b) there are more generals and more opportunities for promotion if a major conflict arrives 25ish years after you get your commission.
  • Carroll died of pneumonia at the age of sixty: his lungs were shot at Rapidan River in 1862 and never really recovered.
  • Pettigrew was horribly wounded leading his Brigade during Pickett's Charge at Gettysburg and shot and killed a few days later trying to cross the Potomac
  • Crittenden had a brother who was a general on the other side.
There, TMI on the general front. I hope they come up in a Pub Quiz before you forget who had a wooden horse called Potomac.

Friday 18 December 2015

Suffer the children?

Yes they do!  It's a biblical reference ye heathens: Matt 19 v14.  Like Thich Nhat Hanh prefers to do his walking meditation with kids rather than with neurotic adults, so Jesus wanted kids to hear the message rather than being hustled out of the way by officious disciples.  I have a sorry tale to tell today about the commodification of children. It's only 80 years since the Lebensborn programme was launched 12 December 1935 in NSDAP Germany. One of the key legs of their racial purity nonsense was that the master race should be encouraged to have more children, so that eventually only Aryans were left.  In my book it's nonsense because cultural, genetic and linguistic diversity is what we should be aiming for: life is so much more interesting that way. Lebensborn = fount-of-life was initially a social welfare organisation which set up maternity centres and after-care services to support [some approved sorts of ] women, both married and unwed, to raise their children safely in a world at war. I don't think we have a good leg to stand on in complaining about the exclusivity of the programme. Catholics still get better access to education here and richer women certainly get better access to post-delivery maternity care. The current flap in Ireland is that agnostic parents are 'abusing the sacrament' by getting their children baptised to improve their chances of a place in the better local schools. Almost all schools are almost entirely paid for by me-the-tax-payer but Catholic boards of governors act as gatekeepers for pupils.

Later on the ethics of the Lebensborn programme took a plunge downwards when it started to process children, or whatever parentage who looked a good fit for the master-race. Most of the records were destroyed in the maelstrom of 1945, so we can only estimate how many children were forcibly separated from the parents and taken away to be raised as Aryans. Poland and Norway seem to have been more actively trawled because of the higher frequency of the blonde and blue-eyed preferred stereotype. But no part of the conquered territories was immune. In Norway after the war, as in other parts of Europe, those suspected of 'collaboration' with German soldiers were scapegoated and so were their children. It must take a disagreeable amount of priggish self-righteousness, not to say want of intellect, that could mete out punishment on kids for the sins of their parents.

Tsk! Tsk! we say as we judge the doings of folk back in the 1930s and 40s.  But we've very recently had a sorry record of cultural [white, catholic, patriarchal] imperialism in Ireland and have very recently allowed state institutions [Gardai, Social Sevices] to knee-jerk racial stereotyping to seize blond and blue-eyed children who were a poor external match for their parents. The press and their readership had a fit of the self-righteous vapours over those [temporary] kidnappings of children by the Irish state.  But that, if I might make so bold, is a useless, if not positively damaging, response.  We should rather look at ourselves and try to see the unconsidered certainties that blight our day-to-day actions and interactions. We had a good example of that at the end of last week: most commentators who were old enough to have adult children, and so brought up in an earlier era, were of the opinion that a no harm would come to a child who was occasionally given a slap by its loving parents. As Senator Jillian Van Turnhout responded "and no good came of such an action either".

Thursday 17 December 2015

voluminous nonsense

I had a good time Monday and Tuesday of this week teaching a section of the TCD MSc in Immunology.  There were so many students on the MSc, and the material was so new to them that I asked if the management would rise to a Teaching Fellow to help field the questions in the practical sessions.  I wouldn't have asked if I didn't have an Effective in mind: a young graduate of The Institute who did a stonking good final year research project with me and is now building that into a MSc by research in the Comparative Immunlogy group in Trinity. That turned out to be a good idea: by having to explain things, Ilaina the TF got to understand them better herself and also learned a lot of stuff that hadn't been necessary to pick up yet in her nascent post-graduate career. Meanwhile, back at the day job . . .

At The Institute, I teach a weird and wonderful set of subjects, few of which are what I was trained to do.  That's what makes the job so interesting although it was a teeny bit stressful when I started work three years ago: being 2 weeks or even 2 days ahead of the students in mastering the syllabus. I've had two sections of 1st Year QM remedial maths quantitative methods this term and the end of last week was time for their Xmas Exams. I do have standards, but I also want to get them over the line. Many of them have ingrained Math Anxiety and have probably had crap teachers who are at the edge of the competence (a bit like me teaching Environmental Chemistry). Nevertheless they want to do science and I don't want to hold them back with stuff that may well become easier when they use it for things that matter: their own experiments for example. I've long been a fan of Edward MacNeil's Mathsemantics, which book hinges on the observation that even quite handy number-wonks go all to pieces when the problem is embedded in a sentence and/or you have to define your units and/or you have to have an order-of-magnitude clue about what the answer should be.

In a metric world, one of the weirder units of measurement is a bale of 4-inch solids, which consists of 44 (?!) concrete blocks 100mm x 215mm x 450mm.  Why 44?  It's not because the molecular weight of carbon-dioxide is 44? And to point out that I get 44 flapjacks out of a swissroll tin is to suggest that these popular cookies are like door-stops. No, the answer is apparently that, because the density of concrete is about 2.35g/, then 44 blocks weighs about 1 metric ton: it's convenient for loading trucks.

So I thought, I'd pop a question in tne QM exam, for the boys, like:
Q. What is the volume of 44 (100mm x 215mm x 450mm) concrete blocks in scientific notation and SI units [cu.m]? A. 0.426 cu.m. or 4.26 X 10-1
Only one student got it right, having converted it, correctly, to 0.1m x 0.215m x 0.45m x 44.  Another was wrong wrong-almost-right at 4.257 X 101. The majority of the students plonked for 4.257 * 108. On the assumption that mm are essentially the same as m.  A minority view had 4.257 * 105 as the answer; under the mistaken impression that if
1mm is the 1/1000th part of 1m so
1cu.m is 1000x the size of; when in reality it is 1000 x 1000 x 1000 times bigger.

Whatever about the maths, the thing that distresses me is that 425,000,000 cu.m. is about the volume of the entire domestic housing stock of the Republic of Ireland ! How could you write that down as an answer for the volume of half-a-hundred blocks; which wouldn't even make a garden shed large enough to shelter a lawn-mower.  What to do? Throw the kids out of the classroom!  Stop them doing pages of Victorian sum-copy exercises and make them measure timber and mix concrete and order up enough plywood to make a play-house in the garden. They'll soon get the measurements right if the first version of their play-house hasn't sufficient plywood for the roof. You can't invite your dolls to tea if the sandwiches get all wet from the rain.

Wednesday 16 December 2015

Sexiest Protein Competition

Pubmed is a database of the scientific literature. A key element of science is endeavouring not to unwittingly reinvent the wheel by doing an experiment that someone has already carried out. Replicating another group's experiments by design is another matter and carried out less frequently than might be desirable. So before you launch your research project you should read the scientific papers that have appeared on the subject. This will stop you getting a red face from being seen to copy someone else's work as if your contribution was totally novel. Reading will also fill in the gaps in your knowledge, give you inspiration and food for thought and help you see places where you and your students can usefully make a contribution. But b'gob you cannot read every paper ever written: there are 26.7 million papers indexed in PubMed, with 1.15 million which came out this year.
You had better learn how to use Pubmed effectively so that a) you get to read, or at least scan, all the papers of interest b) you don't have to trudge through lots of irrelevant off-topic material to locate the jewels. Years ago, I wrote a manual called Better PubMed, and I've updated it periodically. At the end it points out some of the hilarious blunders that lurk in this all-compassing database like a number of papers which include both psuedogene AND pseudogene in the same Abstract.  You can't do anything about that but you can find
  • papers published out of Institutions in Waterford: waterford [AD]
  • the couple of papers published by Dr Mouse ignoring the couple of million papers published about The Mouse Mus musculus: mouse [AU]
  • papers published by Dr S Bob: Bob S [AU]
  • papers published in the noughties: 2000:2009 [PDAT]
I've been on about PubMed before insofar as it exposes a pernicious HarryPotterism at the heart of science. Aled Edwards in Canada has made a devastating analysis of this funding-fondling problem.  Scientists don't study what's important, so much as they study what other scientists are working on.  Some areas, some genes, some proteins 'get legs' and sweep all before them, leaving a lot of orphan genes weeping for lack of attention in the corners. How to encourage students on, say, a Masters of Imm course to find out how to use PubMed effectively?  Why, run a competition, of course! offering a small bag of Werther's Original butter candies.  I asked them all to bring to class the name of an immune Protein-of-Interest on which they would be carrying out their molecular evolutionary analyses.

The first step in any research project is to discover what the competition is doing . . . by reading the literature . . . using PubMed to open the door to these data. I suggested that we could look into the hypothesis that some proteins/genes were more "sexy" [as in hot current trendy] than others.
Q. How to measure that?
A. Count the number of publications about Protein "P"; then count the number that have appeared since, say, Jan 2014. Divide the latter by the former  et voila! you have a Sexy Quotient.

Protein PubMed Recent Sexy Qt Protein PubMed Recent Sexy Qt
NLRP3 2173 1024 0.47 CD47 870 157 0.18
IL28B 1249 462 0.37 CTLA4 5647 882 0.16
CD3g 39 12 0.31 ERBB2 22375 2691 0.12
NFKBIA 212 64 0.30 CD56 7874 941 0.12
IL8 2586 712 0.28 p53 78696 9351 0.12
NFKB1 781 195 0.25 iKba 69 8 0.12
MyD88 5031 1239 0.25 CCR5 8208 871 0.11
STAT3 14356 3518 0.25 CD154 7209 584 0.08
TLR4 13752 3345 0.24 EBAG9 164 8 0.05
RAG1 1417 273 0.19 recA 6351 260 0.04
I've sorted the chosen proteins by hotness, and there turns out to be an order of magnitude in the difference between Princess and Cinderella. Why might this make a difference? You can see that some widely cited proteins, like TLR4 and STAT3 are really going off the boil, while NLRP3 and IL28B are on the up-and-up.  If you have a choice, I suggest you are going to pull down more grant money and find it easier to publish in Nature if you devote your time to Sexy Proteins than tired old dowager proteins. 

Tuesday 15 December 2015

Bigger than a bread-box?

This week, Mon/14 and Tues/15, I'm up in Dublin doing a couple of honest days' work teaching for the TCD MSc in Immunology. Because I spent a decade working in a Comparative Immunology lab, I know some of the language and some of the key concepts but I wouldn't call me an Immunologist. You may call me an evolutionary biologist if you want, though, and I've been trying to transmit that angle, that way of thinking, to these smart young immunologists.  It's quite intense, 2 hours theory in the morning, 3 hours on the interweb in the afternoon using an unfamiliar toolkit to answer some immunological questions. I can't expect, in two busy days, to cover all the information I've internalised during two decades immersed in the field of bioinformatics and molecular evolution. But if they learn one or two things that are new-and-interesting, and maybe later use some parts of the manual which I've written for the course, then I feel it will have been worth talking myself hoarse.

As in a lot of my courses/modules I started them off with a pre-quiz so that they would have a bench-mark to compare against the new things they will learn over the next couple of days. In 2013, I asked that class to put in order of size: a molecule, a macromolecule, a cellular organelle, a cell and a tissue. That turned out to be easy for almost all the Msc students - although it's eye-watering hard for my first year students at The Institute. This year, I thought I'd quantify the question, to further emphasis the relative size of the objects immunologists talk about quite casually - mostly various proteins and various cells - as if everyone is intimately familiar with them.  It's my belief that many scientists compartmentalise their knowledge - ecology is out there in the Serengeti; biochemistry is here on the side-table; genetics and evolution have nothing to do with biochemistry; drug actions have nothing to do with the intestinal flora . . . aNNyway, here's the question:
Q. If this room [5m x 7m x 3m]  was a T-cell [a vital part of the immune response to pathogenic attack]; how big would the T-cell receptor TCR [a key protein embedded in the cell membrane of the T-cell] be?

If you know, or can calculate/guesstimate this ratio, you'll know how many copies of the TCR there are likely to be. You'll also be able to hazard a guess about the number of copies there are of CCR5, another T-cell membrane protein that opens the door for HIV to infect and ultimately kill T-cells. The cartoon [L from Nature Immunology so it has some authority] suggests a ratio of about 1:100. My answer based on a larger classroom in The Institute and some assumptions about the size of the cell was
A. a sultana.

My assumptions were a bit off because a T-cell is a bit smaller at ~15μm than an average cell in diameter. A typical protein is about 7nm across.  So in that room with that cell specified, the answer is more likely to be
A. a grain of rice
But I was a bit nearer than the other people in the room who variously offered:
a raisin; a stapler / a computer mouse; the paper-bin [twice]; a chair seat not the whole chair / 50cm / 10% / a chair; 20% / the door [twice] / the [small] white-board; half the diameter; the office next door; no idea [tsk tsk: damn and blast you have to commit!].  That's a lot of variability, and I think we're all exaggerating.

Why does it matter? Because the scale difference between biochemistry and cell-biology is so enormous that it's impossible to fit in a textbook diagram: if you show a cell at a reasonable size on an A5 page, then the cell's proteins would each be a single pixel wide.  It's like trying make a scale model of the solar system where those attempting the problem say things like "Jupiter is a chestnut, more than a city block from its nearest neighbor in space!" We, all, need to integrate knowledge from across disciplines: specialization is for insects!

Monday 14 December 2015


Ireland took another step away from being a medieval theocracy last week by starting the implementation of new law forbidding anyone, including parents, to hit a child.  It's one of those things for which our adult grandchildren will look at us closely and wonder what kind of people we were in those days when whacking children for real or imagined misdeeds was widely accepted.  One of my earliest solid memories is a conversation at the school gate in the year I turned 8. I rather smugly confessed that I'd been in school for nearly a whole year and hadn't been beaten by any of the teachers. I should have stopped my gob, because in the last two weeks of that school year I was hit with a stick no less than 4 times . . . I was seven, I was struck, with a stick, by an adult, who was in charge of my education.  It was typical of that time and place that boys used to have a session in boxing after lunch one day each week.  Hitting other people was thus institutionalised; but assymetrically: children were not allowed under any circumstances to strike out at an adult - that would be disrespectful.

The weird thing is that if asked baldly "Is it okay to batter/bludgeon/beat a child?" a majority of adults will say "NO!".  Asked if it is okay to smack or slap a naughty child, the unequivocal No! is likely to get a little wobbly. Is it all in the language? Under English Common Law, which we inherited at the foundation of the state in 1922, it was deemed okay for a parent or guardian to use "reasonable and moderate chastisement" to discipline a child in their care.  Indeed this phrase was enshrined in the 1908 Children Act.  But the problem is that one person's reasonable chastisement of an annoying little pillock who won't listen when asked to stop; is someone else's assault on the person and dignity of one much smaller than you. Senator Jillian van Turnhout was interviewed on the wireless that evening.  She claimed that the new legislation was really just tidying up loose ends by repealing the relevant section of the 1908 Act but also by explicitly scotching the common law defense. She also pointed out that there were no sanctions if you were caught giving young Maisie a whack: and that omission was deliberate.  The current change was just to make it easier to prosecute when a gross violation of a child's rights and dignity had been perpetrated.  There is, now, no excuse (Maisie being lippy; The Da being drunk; The Mammy being worn to ribbons by sleep deficit) for striking a child.  That's great in my book because it will make it really difficult to sustain boxing in youth clubs and elsewhere.

One thing about The Law is that's its requirements are, in some sense. what the majority want or believe to be necessary to maintain a happy society. Writing "thou shalt not strike any child" into the statute books brings that idea into everyone's consciousness.  It's like a lot of inconvenient intrusions into our freedom: wearing seat-belts and not consuming alcohol while driving a car; not smoking cigarettes in aeroplanes and pubs; not burning rubbish in suburbia on Saturday morning; picking up dog-shit; paying for clean water.  Once you break the old habit and embrace the new, oftentimes you wonder why you (and we all) put up with the other nonsense for so long.

Our sense of smug satisfaction of occupying the high moral ground in the world (like when we put a charge on disposable plasic bags aor banned smoking in pubs)  lasted until Sunday.  Marian Finucane on her RTE1 chat-show was all over the victory of Irish Cage-Fighter Conor McGregor. Whatever you think about boxing with its rules of not hitting below the belt mixed martial arts competitions run by the UFC Ultimate Fighting Championship are another level of brutality. McGregor finished off his Brazilian opponent José Aldo in 13 seconds with a few extra blows while Aldo lay befuddled on the floor. Because he was Irish, it was considered worthy of widespread media coverage: not only on RTE. Will our diminutive President welcome McGregor back to the country with the same razzmatazz granted to boxer Katie Taylor?  Will nobody learn from Primo Carnera's 1933 victory over Ernie Schaaf which left Schaaf in a coma from which he never woke up?

Sunday 13 December 2015

Sunday sausage 131215

Last Thursday it was the Annual Works Christmas Dinner and I voluntarily went out to dinner, in a restaurant, with colleagues from work. I won't say it's the thing above all that I would rather do in the evening but it was pleasant enough.  Everyone ate too much and when it came time for dessert there were some groans round the table.  I suggested that complainers could make room by doing a Kobayashi shake: a little shimmy of the torso perfected by Takeru Kobayashi the world's most well-known competitive eater. This injection was met with blank stares - my experience of popular culture is clearly different from theirs. Kobayashi has recently been toppled from his hill-of-beans by an up-and-coming young feller from California called Matt Stonie who won this year's Coney Island hot-dog eating contest despite being a slight 54kg 175cm young chap.  He has to be seen to be believed:
That calls for a song or four to lighten the load:


A while back I wrote about the Harry Potter aspects of the moon-landings: everyone over a certain age knows that Neil Armstrong was the first man to walk on the face of the moon. To the nearest whole number nobody among 100 people could name the last man on the moon.  It was Eugene "Gene" Cernan, the commander of the Apollo 17 mission which touched down on 11th December 1972. You can see him here [R] throwing up dust as he does wheelies about the lunar surface in the Lunar Rover. There were many aspects of the mission that exemplified the throw-away society that was, and is, riding our planet to a dusty and depleted desert. It took 50 tons of Saturn V rocket and fuel to deliver 5 tons of material to the moon.  At each stage in the process, bits were discarded so that the moon is now littered with 180 tons of space trash.  It's a bit like the approaches to Mt Everest, or the Camino de Santiago: someone else will pick up my discarded packaging.

The Lunar Rover program was budgetted at $38,000,000, but forced by politicians to have a declared budget of $17,000,000. Cost over-runs led to the final cost of deploying 3 throw-away vehicles to the moon being . . . $38,000,000.  Obviously, they had to be engineered under the constraint of a declared max-weight and still be functional to transport the men and material and bring back lunar rock samples to the landing module. Cernan brushed against the fender of one of the wheels while getting it ready for use . . . and ripped off a chunk of it. The first trip was thus carried out in a fog of moon-dust. Something similar had occurred on the Apollo 16 mission, so a roll of duct-tape was available on-board. They also had some stiffish paper lunar surface maps.  Guided by bodgers and engineers back at mission control, Cernan was able to construct a replacement fender-extension to keep the dust down on the second day's excursion. I like that story very much: using 50c's worth duct-tape and a bit of cardboard to fix a $10m luxury people-and-clutter carrier. Except that the duct tape was probably sold to NASA a Space Duct Tape - a snip at $5,000.  It's like that in science: the glassware you buy in a hardware store is sold with a 10x markup through a medical supply catalogue.  It's like that with weddings: book a table for a Works' Outing and it will cost €X, book it for John and Mary's wedding and the cost is €3X and the quality and menu choice is worse.

Cernan and his "Lunar Module Pilot" Harrison H Schmidt, launched back towards home on the 13th December 1972.  Schmidt, a geologist, was the only scientist to go to the moon and back - the rest were pilots. Apollo XVIII had already been cancelled by the money-people. Nobody has been back for 43 years. In 1994, Cernan became Rád Bieleho dvojkríža a Grand Officer of the Order of the White Double Cross [see R] having been bestowed this honour by the Republic of Slovakia "for the outstanding spread of good reputation of Slovakia abroad" ie because of his Slovak ancestry and out-of-this-world achievements. Slovaks live in Slovenská republika so you can see why the rest of us confuse it with Slovenia Republika Slovenija an entirely different place with a less interesting flag. But that's politics, here we are removing our Dan Dare space-helmets to Gene Cernan - no better man!