Saturday, 30 November 2013

By the Mark Twain

It's his birthday today!  Samuel Clemens was born on St Andrew's Day 1835 in Florida, MO and grew up down the road in Hannibal, Missouri on the Mississippi River.  Four of his 6 siblings died in childhood and his father contracted pneumonia and died with Samuel was 11.  That sort of thing doesn't happen to families nowadays because of antibiotics, which we really under-appreciate.  Samuel had to earn a living for what was left of his family and his mother and worked as a gopher on the local newspaper before spending several years as a riverboat pilot.  Mark Twain as any fule kno is what the leadsman would cry when there was 12 feet (3.75m) of water.  Twain because 12 feet is two fathoms; "a quarter less twain" is 10-and-a-half feet.  More details including how each depth is marked (leather tags, red white and black cloth strips woven in) on the cord at boatsafe.  "By the mark twain" meant that for the moment the boat was safe from grounding, although with the ever-shifting silting and sand-banks, that margin of safety could rapidly shoal to nothing.  "No bottom" was defined as anything greater than "by the mark four" 24 feet, 7.5m.

Twain in Tesla's Lab
Clemens spent about four years in his early 20s as a pilot on the river, two years learning his trade and 2 practicing it until the Civil War put a stop to all civilian traffic on the river, and he always cherished his time there.  His younger brother Henry was not so fortunate as a riverboat pilot, getting killed when the boiler of the steamboat Pennsylvania exploded.  Clemens went Went West Young Man and worked, unsuccessfully, as a miner and, more successfully, as a journalist and writer, in Nevada and California.  Later on he moved East to New York and Connecticut where he was great pals with Nikola Tesla, Thomas Edison and other technologists.  But he's not really famous for his techie inventions (self-adhesive scrapbooks and improved suspenders) but for his writing - understated, ironic and vehemently anti-pretentious.  Reading, say, Moby Dick by his contemporary Herman Melville you know you're in Victorian times; reading Twain you are outside of time or for all time.  And he's so quotable:
  • It ain't what you don't know that gets you into trouble. It's what you know for sure that just ain't so.” which I've quoted before.
  • A lie can make it half way around the world before the truth has time to put its boots on
  • Every generalization is false, including this one. 
All of which are also attributed to a wild array of different people.
  • Pilgrim's Progress, about a man that left his family, it didn't say why. I read considerable in it now and then. The statements was interesting, but tough. Which might well apply to Moby Dick.
  • It ain't those parts of the Bible that I can't understand that bother me, it is the parts that I do understand. 
  • Often, the less there is to justify a traditional custom, the harder it is to get rid of it. 
  • The more I know about people, the better I like my dog.  
  • The difference between truth and fiction is that the latter must always be credible in order to work.
  • Irreverence is the champion of liberty, if not its only defender.  
  • Many a small thing has been made large by the right kind of advertising.
  • It may be called the Master Passion, the hunger for self-approval. 
 You'll find his books in any good library: Europeans try Innocents Abroad; Atheists - good copy on Mormons in Roughing It.

Friday, 29 November 2013

Escherichia

The bog-standard bacterium, it's a pity it's so hard to spell.  It looks forrin dunnitI couldn't possibly look at the word long enough to remember that the first consonant cluster is sch and the last ch.  So it's almost always written E.coli. The reason we call it Escherichia coli is becauase it is named for its discoverer Theodor Escherich whose birthday (29 Nov 1857) falls today. He died of a very interesting stroke: he had a headache, began speaking several different languages on ward-round and succumbed the following 1911 day at the age of 53.  He was much too modest to name the common enteric bacteria of childhood runs after himself and it wasn't until 1958, more that 100 years after his birth, that the unspellababble name really stuck. I mention childhood 'looseness' because in his day he was the Top Gun in paediatric infectious diseases, writing the definitive tome on intestinal diseases of children as well as books on Diphtheria and Tetanus. He studed in Paris under Jean-Martin Charcot eponymous co-discoverer of Charcot-Marie-Tooth syndrome, which I often use as an example in bioinformatics courses because it sounds so exotic and intriguing. La Leche League should raise a glass of milk to Escherich this day because he instigated a high-profile campaign to promote breastfeeding and its benefits for the intestinal flora.

But if I was looking for mere birthday tribs, like 16th June, there's plenty of choice for 29th November: CS "Narnia" Lewis, Christian "Red-shift" Doppler, Jean-Martin Charcot (cue Twilight Zone theme), António "lobotomy" Moniz, Jacques "Président" Chirac.  Of all these Wikipedia has chosen to front-page an unregenerate Nazi SS-Obergruppenführer Artur Phelps possibly because he was at one time Kurt "Bundespräsident" Waldheim's boss. 

And rather than talk about looseness of the bowel when it is infested with some varieties of E. coli, I'll rant on a bit about the looseness of nomenclature when it comes to assigning names to bacteria. The Venn diagram at left is culled from a paper describing the complete genome sequence of a strain of Shigella flexneri, a cause of dysentry.  The numbers represent identifiable protein coding genes that can be identified in three strains of related enteric bacteria.  All of these chaps are Gram-negative gamma-proteobacteria, and one reason we assign them to the same group is that they all have a common core biochemical functionality controlled by about 3000 genes but they all have wildly different extra attributes.  Shigella, for example, has 175 genes which are not so much different from the other two strains, as completely absent from them: these include iron uptake genes and some enterotoxins.  It's not clear why Shigella should be separated into a different genus while the other two strains are lumped into the same species

In the course Fermentation and Food Microbiology (Food& Ferm or F&F) we've spent a chunk of time investigating "Enterics" which are bacteria like Escherichia found in mammal guts and Salmonella typically found in bird guts but also Erwinia carotovora which as the name implies eats carrots.  One of our tasks has been to differentiate these boys from Pseudomonas and Bacillus using tools very familiar to Theodor Escherich 100 years ago.  Core to these tests are the Gram stain, which reveals half the microbiological world as pink and the rest purply-blue; the catalase test which fizzes (or doesn't) and the oxidase test which turns purple-maroon (or doesn't).  These are routine and dead easy to carry out on any bacteria that you can grow on a Petri dish - so that's what we do. You-the-bacteria get to be called Escherichia or Salmonella or Shigella based on the tests that we can carry out rather than on the key attributes (production of enterotoxins; sensitivity to antibiotics; dependence on available iron) that we can't measure easily but which might have serious epidemiological, medical and therapeutic consequences.  It's like looking for your car-keys under the only street light in the dark alley between the night-club and your vehicle.

Thursday, 28 November 2013

Dreidel-dee dreidel-dum

Hanukkah started at midnight just gone and I'm sure that little Jewish children are waking up today all excited.  Not least because Hanukkah has acquired some of the giftie attributes of Christmas, perhaps because the two festivals often fall in the same month.  But the youngsters can also have intoxicating fun spinning dreidels instead of whacking people playing Grand Theft Auto.  Dreidels are little spinning tops with four different Hebrew letters one to each side. 
shin - nun - gimel - hei
The letters are the initials of a phrase נס גדול היה שם  (Hebrew reads right to left like Arabic) Nes Gadol Hayah Poh which being interpreted is "a great miracle happened here". Each player in dreidel spinning games puts some token into the pot and then each takes turns to spin the top and obey the time-honoured conventions attached to each side.
  • nun - do nothing
  • gimel - take everything in the pot
  • hei - take half (rounded up) of the pot
  • shin - put one (or three) tokens in the pot
Simple enough, hours of fun, scope for bitter recriminations and tears - just the sort of game every family wishes to play during the Winter Solstice Festivities. In Western Europe we also used to play Dreidels except that they were called teetotums and often had the letters A D N T instead of Hebrew.  And instead of as in Hebrew an inspirational mnemonic, the letters stood for straight-forward instructions Aufer - take (one); Depone - put (one); Nihil - take none; Totum - take all. Dreidels culture was all explained to me by Larry Reich at about this time 34 years ago. Larry was a) Jewish b) a deft dreidelist c) the only person I've seen leap full-length on frozen ground to retrieve some data (an escaping field vole Microtus pennsylvanicus) d) a man with a prodigious appetite for ice-cream e) about to give up being a field biologist and fulfill his maternal-driven destiny to become a real doctor and not just a PhD.  I was in graduate school and had a desk in the Bob Tamarin Vole Lab.  Part of the rent (kidding!) was that I'd go out and help when they needed to collect data by bleeding their voles.  It was on the way home from one of these expeditions in late 1979 that I first saw Asteroids being played - quite possibly by Larry - in a pizza-shop near Plymouth, MA.  That was yet another (Scrabble, Monopoly, Diplomacy) nail in the coffin of simple gaming pleasures like spinning tops.  With a little help from William Rowan Hamilton, computer graphics have developed from the simple, efficient vector graphics of Asteroids drug-store consoles to displaying rippling muscles and exaggerated body-contours of Lara Croft Tombraider.

Wednesday, 27 November 2013

East meets West

A tuthree days ago, I mentioned in passing that they had dug up a woolly mammoth in sufficiently good condition, after 8000 years frozen in Siberia, to extract readable DNA sequence.  The Beloved's brother sent me a link to a NYT article about another ancient Central Asian excavation.  The burial prehistorical - about 24,000 years ago - but the excavation itself was historical, happening 50 years ago and the material had been sitting in a Petersburg Museum ever since.  This all concerns a much loved little boy about 3 years old who was buried with care and grave-goods all those years ago.  Lots of other skeletons were buried in the area as well as numerous Venus figurines of a type typical of European art of the same vintage.  Which is a little peculiar as the graves were at Mal'ta very close to Lake Baikal and thousands of km further East than the edge of Europe.  That cultural coincidence doesn't seem to have created much stir.

Eske Willerslev from Copenhagen, and colleague of Tom Gilbert the mammoth man, is an expert on the peopling of the Americas and is ever on the hunt for genetic material to try to nail down the hypothesis that the Native North Americans (NNA) really started their travels in Asia.  When Willerslev sequenced the Mal'ta child's DNA he found that it resembled nothing so much as European heritage. This was so surprising that they checked another skeleton from the same area but only 17,000 years buried and found the same tell-tale sequence. But there was a significant 'minority holding' of NNA tucked into the same genome.  This explains an anomalous quirk in the DNA profile of NNAs where some of them have a signature that is clearly European.  Previous researchers, both scientific and woo-wah, had suggested that Europeans crossed the North Atlantic in canoes 30,000 years ago but this hypothesis can now be dismissed for one which is more parsimonious.

Folks really travelled back in the palaeolithic but you don't need to evoke marathon running to account for the distances travelled.  The paleolithic itself lasted a helluva long time and if you have 24,000 years to play with you can go round the world by only moving one mile (1.6km) per year, or about the distance from our kitchen to the living room fire each day.

There is another extraordinary Europe-in-Asia story in the discovery 100 years ago of a group of  Indo-European langauges called Tocharian locked away in what is now China. The super-romantic adventurer and archaeologist Aurel Stein, whose 151st birthday was yesterday, discovered fragments of ancient manuscripts in Xinjiang, a Chinese province having borders with  Russia, Mongolia, Kazakhstan, Kyrgyzstan, Tajikistan, Afghanistan, Pakistan and India. You can't get more Asia Central than that!  Paleolingists could sort of read the script which resembled what they knew from some Buddhist sutras.  But when they transliterated it, the sound was clearly more like Sanskrit and Greek and Irish and English than it was to any of the neighboring Turkic and Asiatic tongues.  These manuscripts were written in around 400 CE.

It is tempting to suggest that the three connexions - linguistic, cultural and genetic - between Ireland and Baikal are driven by the same migration but this would be as gross an error as having Raquel Welch fighting dinosaurs in 1 Million Years BC.  Because, just as Raquel missed the last walking dinosaur by around 64 million years, the first speakers of Proto-Indo-European PIE were striding across Eurasia 5000-8000 years ago, at least 15,000 years after the Mal'ta chap was buried.  But the idea gives us the opportunity to post a poster of Raquel Welch: I think she looks pretty fit, don't you? I'm not surprised her genes survived through the last 30,000 generations.

Tuesday, 26 November 2013

Once our Science was frothy

We've just finished "Water" in the 4th Year Environmental Chemistry course.  It's been a round the houses on everything I could find out and make interesting about the fluid on which all life depends.  Lake Nyos and Lake Baikal; Water treatment for drinking and water treatment of the other end of drinking; groundwater, wellwater, seawater and freshwater.  A few case histories have been brought in to give a memorable picture on which to hang the academic knowledge.  One tale was the death of Lake Erie in the 1960s.  Erie is one of the Great lakes on the border between the USA and Canada. It is in the heart of a well-populated industrial and agricultural zone from Detroit to Cleveland to Buffalo and back through Western Ontario. In the great post-war industrial boom of the 1950s white-goods were churned out of American factories and bought by every home to match a gas-guzzling elaborately-finned automobile.  Washing machines took the drudge out of sudsing over a hot tub every Monday but, with no effort involved, every day became wash day.  Proctor and Gamble and Lever Bros put their chemists to the task of making washes whiter, brighter and oftener. The effectiveness of these amazing new detergents was diminished in hard-water areas because the Calcium and Magnesium ions in the water ate up the detergent before the detergent could eat up the dirt.  So the boffins threw in 'builders' to eat the Ca and Mg.  The most effective builder was phosphate which was so natural it was not harmful to humans and which broke down after use in a simple biodegradable way that everyone understood.

So far so shining.  But all these washing machines were directly or indirectly discharging into Lake Erie (and other lakes and watercourses) which was naturally chronically short of phosphate.  Indeed it was the limiting element for that ecosystem and when a man-made deluge of phosphate hit the water the algae had a field day.  The lake turned green and the herbivorous insects snails and fish grew fat on the weed, then carnivorous insects and fish ate the herbivores and all players were metabolising up to ninety.  That sucked all the oxygen out of the water and over the course of a couple of decades every living thing in the Lake floated belly up. Bacteria worked away on the corpses and when the last smidgeon of oxygen had been depleted by these 'aerobic' microbes then the 'anaerobic' bacteria lived off the rest producing methane, hydrogen sulphide and other noxious substances. In parallel farmers horsed out cheap phosphate fertilisers onto their fields to boost yield and much of this ran off into drains, rills, streams, rivers and Lake Erie.  So far, so phoooeeew

The Canadian and US governments came together, not for the first time, to sort it out with the Gt Lakes Water Quality Agreement 1972 which sunk $8billion into waste-water treatment plants, issued guidelines on fertiliser use and controlled detergent use.  The Lake has recovered some of it's former biodiversity.  In 1993, the US banned all phosphate in detergents, which sent the chemists scrabbling for builders that were less effective, more expensive and with more questionable health effects than trusty phosphate.  Phosphates are, 20 years later, still allowable in the EU, but they are due to be banned next year.

I set the class up with a co-operative assessed assignment, different from the Fluoride Debate that so engaged them a month ago. Everyone was to read the table of contents of one laundry detergent and consult any ancillary documentation on the wuh.  Then come up with some compare and contrast graphs to show the presence of phosphate and the relative cost.  That worked out very nicely and they chose to clag all the data into a poster.  I got this blown up to A0 size and yesterday in the last 10 minutes of class we trooped along to put it up on the wall in the Science corridor.  They found a clear spot opposite the main Biology lab and we stuck it there to 'stick it to the biologists' who are all doing their final year projects in that room.  I was so proud for them!  I sent an all-staff e-mail to tell my colleagues where to look for informed advice on which detergent gives best value (the green bar is the key metric):


Monday, 25 November 2013

Sang froid

Dau.II came home for feeding this last weekend.  (And no, she didn't bring a sack full of laundry for her mother to process: she's been better trained)  Her visit has been good for my rather sad efforts to Get Down With The Hood and relate to my students - she can tell me about the fads that are sweeping through Cork this Fall.  Cork is a little behind, say, Los Angeles in trendiness but is still a good stretch ahead of us here in the Boondocks. I was intrigued to be shown a youtube compilation of a peculiar sub-class of Epic Fails where the drive wheel of a motorbike is held against the rim of a play-ground round-about while teenagers try to hold on.  It wouldn't be an Epic Fail if they didn't fly off, hit their heads off the motor-cycle or carry away the cameraman.  Like all EFs it is both excruciating and guiltily hilarious. A common feature is where the spinning dude looses his hand-grip and promptly flings out over the edge of the carousel to make a couple turns with head and torso horizontal until his feet have to let go.

Hanging out in this way should slow the whole shebang down in the exact reverse of those spinning figure skaters who go faster when they bring their arms into their sides. The record is in excess of 300 rpm or, briefly, 5 revolutions per second.  As you know, I failed my Physics "O" level, so I couldn't explain why this works without help.  It's because the angular momentum (L) is the product of inertia (I) x angular-velocity (w):
L = Iw
where the inertia is mass x square of the radius
I = mr^2
or to meld the two formulae
L =  m * r^2 * w
the mass of the system (m) and the angular momentum (L) must stay constant, so if you decrease the radius by bringing in your arms and the spare (horizontal) leg then w the angular velocity must increase.

"Inertia" made me have another go at trying to find some evidence of soldiers trying to stop a cannon-ball with their feet and having their leg torn off for their pains.  I was sure I'd read such an account, associated in my mind with the Battle of the Alma in the Crimean War.  There's a discussion here, which wasn't there when I last looked, about being foolish with 'spent' cannon-balls.  One of the commentators offered a telling image of a sledge hammer being seen to move rather slowly but you really really wouldn't want it to make contact with your knee. In 2011 Mythbusters fired a traditional cannonball at some water barrels.  It missed and flew off through a residential neighborhood of Dublin CA perforating several walls, flying straight through a house,bouncing off a roof and finally lodging inside a minivan. You don't want to try catching that sort of ball.

Cannon-balls inevitably makes me think of Henry Paget, the Earl of Uxbridge who behaved like a demon-hero at the Battle of Waterloo charging about and the saving the day at a crucial juncture.  As evening fell and the tide of battle was turning against the French, Uxbridge was was sitting on his horse next to the Duke of Wellington when he cried "By gad, sir, I've lost my leg", to which the Duke replied "By gad, sir, so you have".  The sang was never froider than in that generation of British soldiers.  There is a famous tombstone to Paget's leg near Waterloo in Belgium.  He was 47 when this mishap occurred but lived on for another 38 years.  After that you couldn't call Paget tough as old boots but you could say he was tough as old boot.

Paget and Wellesley inevitably make me think of a collateral relative of mine Lt Col T. Scientist.   He died at the head of his regiment - the 94th Foot - this month 200 years ago at the crossing of the Nivelle on the French side of the Pyrenees at the end of the Peninsula War. According to my father, a minor shoot on a branch of horse-riding cannon-fodder from King's County, my middle name is in honour of this chap.  He was 30 when he pegged out: promotion came thick and fast if you were anything like competent and you survived.  William Napier the historian of the War cited him thus:
"In him also were combined mental and bodily powers of no ordinary kind. A graceful symmetry combined with Herculean strength, and a countenance at once frank and majestic, gave the true index of his nature, for his capacity was great and commanding, and his military knowledge extensive both from experience and study. On his mirth and wit, so well known in the army, I will not dwell, save to remark that he used the latter without offence, yet so as to increase his ascendency over those with whom he held intercourse, for though gentle he was valiant, ambitious, and conscious of his fitness for great exploits. He, like Freer, was prescient of, and predicted his own fall, yet with no abatement of courage. When he received the mortal wound, a most painful one, he would not suffer himself to be moved, but remained watching the battle and making observations upon the changes in it until death came. "

That's a long roundabout from a merry-go-round!

Sunday, 24 November 2013

The Origin

24th November should be celebrated with more oommph by bio-atheists.  On this day in 1859 "ON THE ORIGIN OF SPECIES. OR THE PRESERVATION OF FAVOURED RACES IN THE STRUGGLE FOR LIFE" was published by John Murray.  As any fule kno, Charles Darwin's magnum opus sold out on the day of publication.  It was an expected event among the literate middle class, so they had been able to save up their shillings to buy the book when it appeared.  In our mythology the actual publication is quite a quiet event bracketed by the drama of Alfred Russell Wallace's contact from Indonesia in 1858 duplicating Darwin's great idea and the events of the Oxford Debate in 1860.  The OoS is a chunk of a book at 160,000 words or 6500 tweets but that's less than War & Peace and much less than the King James Bible (30,000 tweets). Nevertheless hardly any evolutionists have actually read the book.  If you're a bio-student at any College in The West, ask a sample of your faculty if they have read our bible.  You'll be disappointed.

When I taught my course Evolution: from primeval soup to hominid nuts back in the 1980s, I used to start with the evidence that Darwin accumulated to convince him that evolution by natural selection was the driving force to explain the diversity of life on Earth.  This identified him as a serious polymath for collating evidence from geology and palaeontology; embryology and development; plant and animal breeding; biogeography and ecology.  He wasn't alone in his polymathistics: in 1850 there was so little data and such a sparse literature that a man with an income might well master all biological knowledge in a short life-time of reading. Darwin was 50 when OoS was published.  After Darwin, my Evolution course then looked at the evidence that had accumulated since he died - he was wholly ignorant about Genetics, which began to be understood by biologists in 1901, for starters.

Twenty years ago, shortly after 5pm, the secretary of the TCD Genetics Department transferred an outside line to me as the only adult person left in the building.  It was the local radio station looking to host a debate between an evolutionary biologist and a biblical fundamentalist who was in town to thump his tub and promote his latest book.  They wanted anyone from Genetics to come down to the studio in 90 minutes time to discuss matters with the visitor.  I refused.  I reckoned that Yer Man would have a well-rehearsed patter and an impregnable position and I would be poorly briefed to counter his set-pieces about the vertebrate eye and archaeopteryx. I on the other hand would be given about 90 seconds to outline the evidence accumulated over Darwin's lifetime or what took me a whole term to lay out for my Evolution course. Why, I couldn't even dissect out the recurrent pharangeal nerve in the time allotted! I only feel a smidgeon of guilt about my refusal to engage - I would be doing rationalism no favours to be seen to be trounced by Dr (PhD in Exegesis from Chatanooga Bible College) Fundamental

I urge you all to get a copy of OoS and read it. It's available in numerous editions on Amazon for $0.01 and of course it's long out of copyright so can be had for a download at Project Gutenberg. Among the relentless accumulation of anecdote and data it has some lyrical passages including the much quoted:
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. 
Yes, yes, that single sentence is nearly 3 tweets long so you'll have to gear up your attention span, but you won't be disappointed.

Saturday, 23 November 2013

Tsk tsk wrong elephant

When I were a nipper, elephants were simple.  Prodigiously memorious it is true but simple in their classification.  African elephants Loxodonta africana had larger ears and two "fingers" to the trunk, Indian elephants Elephas maximus had smaller ears and one finger.  Paradoxically E.maximus was smaller than L.africana too. There were numerous other differences for experts but for nine-year-old me that was sufficient. It is the sort of pub-quiz knowledge that I accumulated by the trunk-load in the decade after JFK didn't come home from Dallas.

Two species was good enough for us all for a couple of hundred years although some maverick taxonomists ("splitters!") maintained that there were two distinct species - forest and savanna - in Africa. Nadin Rohland and others at Harvard have confirmed that the mavericks were correct by aligning the DNA of all the suspects.  Included in their studies were woolly mammoths Mammuthus primigenius which had been frozen in Siberian bogs for thousands of years.  The DNA of these chaps was in sufficiently good condition to be sequenced and compared with the living species. Rohland's most recent paper on the subject shows that, while in Asia Mammuthus and Elephas are sister groups separated by some millions of years, in Africa Loxodonta africana (savanna) and Loxodonta cyclotis (forest) are even more deeply divided.  So they really are good species.

Who cares? Anyone who is concerned about the extinction of species cares.  Extinction is forever.  Once the last passenger pigeon Ectopistes migratorius or the last Tasmanian wolf Thylacinus cynocephalus dies in a zoo, a unique combination of genes adapted to a particular place in the world's ecology is irrecoverably lost.  With finite resources we might choose to keep a small breeding colony of African elephants alive until the number of people on the planet drops below 2 billion and the rest of creation can breathe a sigh of fresh-aired relief.  Rohland's work says emphatically that we'll need two colonies for the big fellows from the dark continent.

Carl von Linné (1707-1778) or Carolus Linnaeus as he was known to his erudite Latinate contemporaries or plain Linnaeus was the father of modern classification.  He cemented the convention that each species (a group of inter-fertile organisms separated from other such groups) should be known by a unique binomer Homo sapiens, Canis familiaris etc.  Closely related species get binned into the same genus (first name) while retaining a unique specific name: Canis aureus - golden jackal; Canis latrans - coyote. An objective taxonomist from Barnard's Star would give us at least two more cousins Homo troglodytes and Homo gorilla, but that's another story. For each and any species, it's handy to designate a single specimen as the Type against which other individuals may be compared.  Linnaeus designated the Type Specimen for Elephas maximus as a unbearably cute fetal elephant in a glass bottle held by the Naturhistoriska riksmuseet in Stockholm.  Maverick taxonomists, indeed anyone who looked closely at the tip of its little trunk, have long wondered at this designation.  Several years ago, they decided to sequence its ancient DNA to see where he came from.  But formaldehyde and alcohol are distinctly un-good for preserving DNA and that plan was a bust.

Last week's Nature carries a report that Tom Gilbert and Enrico Capellini have gone and sequenced the proteins which were derived from that degraded DNA and shown unequivocally that the Stockholm specimen's ancestors hailed from Africa.  That's good news for a lot of projects including conundrums of human evolution like Homo floresiensis a vertically challenged relative (cousin? sister?) of ours discovered in Indonesia ten years ago.  Her DNA has been irretrievably degraded in the tropic heat.

Friday, 22 November 2013

Not Dallas, Titchfield

http://goo.gl/maps/H39Zn
Where were you when . . .
Anyone who is now of voting age will be able to recall where they were on 9/11, and many of them will also recall their location when they heard about Princess Di.  Most of us in Europe woke up to the news about the Princess, and so were probably in the kitchen at home. For me, I honestly can't remember and definitely didn't send flowers to Buck House via Interflora. For 9/11 I was working in St Vincent's Hospital Dublin and was offsite for a couple of hours at the crucial time, so was spared from ever looking at the footage of people falling out of the real Towering Inferno.
You have to be over fifty to recall where you were when you heard about the assassination of JFK (today's the 50th anniverary).  I was a small chap in an English boarding school very close to the pointy tip of the red arrow on the left.  It was well after lights-out and we were all meant to be asleep, but one of my pals must have gone out for a pee and bumped into an adult, because he came back to the dorm and woke us all up to relate the news.  It was arresting but not too shocking to a 9 year old and afaik I was drifting back to Nod in short order, ready to hoover up information the following day.  I was at the start of my very expensive education which has put me in good stead winning table quizzes ever since.
Keywords: Dallas - grassy knoll - book-depository - Zapruder - Lee Harvey Oswald - Jack Ruby - Warren Commission - CIA - Cuber - Conspiracy - Moon-landings - LGM

Fred Sanger - gone

Fred Sanger double Nobel laureate for Chemistry died on 18th November 2013, three days ago.  It staggers me that it didn't make the news with sufficient TaRa that even I, in this news-benighted backwood, heard about it. At 95 he was the same age as James Lovelock, so his death isn't surprising but it's still a shock when when a scientific superstar dies. Neither of these men ever threw shapes like a superstar, and Sanger retired to his modest English garden in 1983. I wrote a trib to Francois Jacob in May when that key figure in molecular biology and genetics passed on.  Jacob and Monod made a key contribution by working out how the on-and-off of genes are controlled.  Sanger was more infrastructural, developing methods for making sense of biological macromolecules by sequencing them.  In a broad-brush-strokes metaphorical sense, bio-sequences are codes determined by the order of their constituent building blocks.  DNA is made up of four bases A T C G and long specifically-ordered strings these bases are translated into proteins which are made up of 20 amino acids.  Sanger's contribution was to work out nifty and then niftier ways for determining the order of the constituents. His second, niftier, way of sequencing DNA was used to sequence the human genome and millions of other sequences from thousands of different organisms all through the 80s 90s, and 00s. It was so useful and so idiot-proof that even I was able to use it to sequence a couple of hundred DNA bases in about 1986.  For this Sanger shared one half of one half of the 1980 Nobel chemistry prize with Wally Gilbert who had invented another clunkier method for achieving the same aim.

Sanger's method for sequencing DNA started the data deluge which we are still trying to keep from drowning in.  But I'd rather cite him for his 1958 Nobel for determining the sequence of the hormone insulin. This was a task requiring dogged biochemistry.  Dogged but also remarkably creative as he invented new tricks for abstracting the information and also reading the literature to hear what novel techniques he might mobilise for his project.  As functional mammalian insulin is only about 50 amino acids in two separate chains this is a finite puzzle but far from trivial.  Sanger's task was to reduce a mammoth combinatorial problem - how are these 50 AAs are ordered? (there are more than 10^30 possible answers) - into a number of smaller problems. The first step was to do a total digestion of the protein chains so that he had a countable heap of amino acids A=10, C=6, D=2 etc. Then he was able to use particular enzymes like trypsin and partial acid hydrolysis to cut the larger sequence into manageable chunks.  With a combination of paper chromatography and running the fragments out along an electric gradient he was able identify characteristic finger-prints for each bit. He also invented a way to tag the last amino acid in a chain with a bright yellow chemical and then breaking the chain into smaller constituent parts so that he could then identify what sort of amino acid that last one was. He did this first with the two natural insulin chains and then with the fragments he had created by chemical and biochemical degradation.  By integrating the position of blobs on filter paper and a catalogue of the conditions under which glycine and phenylalanine and the other amino acids acquired their yellow label, he was able to match and braid the fragments of info-string into two coherent sequences.

It took him and a pair of graduate students 10 years (!) and a lot of hard thinking but he cracked the puzzle. In doing so he showed that proteins are not amorphous lumps of amino acids but that the constituent AAs are added one-a-time in a regular, predictable order.  That's something we all know now but 65 years ago it was much less obvious-to-all-thinking-people. That was in 1952.  The knowledge that proteins exist with characteristic linear sequences laid out the biochemical landscape so that Crick and Watson could follow a philosophical beaten path to determine the similarly linear structure of DNA 10 years later.


Thursday, 21 November 2013

Shoe shop boom

In the Environmental Chemistry course, I've just yesterday wrapped up water, which we've been wading through, or joyfully splashing about in, depending on whether you're a student enrolled or me having been given carte blanche to talk about whatever seems interesting.  In a wrap-up lecture on natural water quality, I mentioned Henry's constant for methane, pointing out that was why it bubbled up from the bottom of stagnant pomds.  I forebore to mention (because I was immersed in the water) that methane is lighten than air and so rapidly disperses over such swampy ponds and bayous.  It's a different matter in mines where methane is known as firedamp and has killed thousands of coal and other miners other the years.  Even as I write, I feel I should write me a lecture on methane for early next year.

With that in my mind, I perked up when the wikipedia "on this day" section mentioned the Humberto Vidal Shoe Shop Explosion, which happened on 21 Nov 1996, in the Rio Piedras section of San Juan in Puerto Rico.  Folks in the shoe-store and elsewhere nearby had noticed the smell of gas for a few days before and complained to the San Juan Gas Company, a wholly owned subsidiary of Enron.  That trail of ownership didn't bode well because Enron was notoriously cavalier about all aspects of their business except raking in money for it's senior management and share-holders.

ANNyway, SJGC sent a technician to check for the presence of gas and he, inadequately trained by lax management, switched on his machine when he stood in the cellar of the corner-shop shoe-store.  As the machine was calibrated to detect differences in gas concentration, this action registered as zero.  You're meant to switch it on in known clean air and walk on in to suspect areas.  After the explosion, which killed 3 dozen people and injured scores more, Enron stoutly denied any responsibility, pointing at terrorists or sewer-gas (methane) as the culprits.

The building was blown to sticks propped up in a very unstable and dangerous condition but eventually the forensic investigators went in to determine the cause.  A key bit of evidence was an interior pipe that had clearly been blown upwards.  That indicted propane, heavier than air, which pools in the bottom of confined spaces rather than methane which accumulates from the ceiling down.  The lawyers then moved in and over the next 6 years squeezed $20 million out of the parent company, doubtless hanging on to a large portion of that for their troubles.  The municipality's response was to rip out all the gas pipes!  That doesn't seem particularly sensible or scientific.

Wednesday, 20 November 2013

Walking in the dark

After leaving Galway on Saturday I headed in a more less ESE direction for home, but it was a gorgeous autumn day and I dawdled across the country scabbing cups of tea from friends-and-relations.  Then I somewhat abruptly realised that we had promised to take part in a moonlit walk to boost prostate cancer awareness.  So I zinged home, picked up The Beloved and we headed South for Russianside, Cheekpoint, Co Waterford.  We haven't been to Ros an sídhe together since our squirrel-walk in February.  Something in excess of 30 people from 4 to 74 years old met at Cheekpoint Cross and walked up to the top of the Minaun, the local hilltop, in a communal straggle.  That must be a welcome change from being sacked out in front of the television of a Saturday night.  It's a little adventure for the tots and it cements the community.  The fact that €150+ was raised for the night's designated charity, is just the icing.

Next time I'll go on my own (the view from the top, day or night, has layer upon layer of interest) because I was so busy yakking to Sunny South-Easters that I didn't pay any attention to my surroundings.  In what seemed like an eyeblink we were back in the Cheekpoint Reading Room being regaled with butterfly fairy-cakes, cookies and hot chocolate.  The eponymous Russianside is almost the only person who comments on The Blob, indeed I've been at him to start his own, so I can return the favour.  Hats off! to him and his family for so often making this sort of event happen  . . . and serving up hot chocolate

On most Thursday nights in the Winter the hard-chaws of the local rambling club go up our mountain with head-torches to yomp through the woods and over the heather for a few hours.  There's a lot less earthshine and streetlights up there, so you get to see stars that are completely invisible from The City.  One night I'll go up there with them and see if they take off all their clothes when they reach the dolmen.



Tuesday, 19 November 2013

Walking on water

I left Galway in the fore-noon after the VIBE meeting in NUIG, but not before walking down to the shore of Lough Corrib with my host and his two young sons. They live on the edge of the townland Gort na calaí which is really aptly named because the lake is edged with "callows" flat water meadows that flood in winter. Standing on a little quay at the edge a vast body of water watching the wind shiver the reeds was elementally evocative for me because when I was a chap we used to visit a cousin of my father's who lived on the shore of Lough Derg.  Just like the lads on Saturday, we used to peg rocks into the water to see who could make the biggest perLOOSH.  Unlike the lads, whose parents have a modern (but by no means over-developed) sense of health and safety, 50 years ago we used to get up really early in the morning and row out onto the lake.  The hills of Clare were without colour and silent in the distance and it was far too early for traffic so, without then being able to articulate such a thought, the sense of peace was a protective wall around us. I never read Swallows and Amazons because I lived it every Spring. That series of small-small adventures for unsupervised children begins when they discover a boat while on holiday and ask their mother if it's okay for them to sail out on the lake. Their mother sends a telegram to her husband, who is abroad with the Navy.  He telegrams back with the timeless wisdom "Better drowned than duffers, if not duffers won't drown".  That's more or less what my parents thought about the issues, insofar as they thought about it at all.  The sense of empowerment was easily worth whatever small risk attended such antics.  We never felt we could walk on water, it wasn't that sort of empowerment.  But we were put in a position (we put ourselves in a position) where we had to make decisions informed by the reality around us rather than 'learning' the correct response by being told what the answer was.

If you talk about that sort of thing with people today they will go on about how there weren't as many cars back then and certainly no pedophiles.  But I can assure you that there were no cars out on the lake i 1963 and all the local pedophiles (of which there was the usual number) were at least 1000m away and still asleep.

"Walking down to the lake-shore" with the two young chaps implies that they also were walking, but they weren't.  They hitched a ride in their father's canoe which has a little trolley for getting it the few hundred meters from home to the water. How cool is that? As a buggy it's not very convenient in a shopping mall but down country lane, it's The Thing.  Why would you need a little trolley for the canoe? Because that's how you get to work whenever the wind on the lake permits such traffic.  Now really, how cool is that?  Cool as Diva, that's how cool.

Monday, 18 November 2013

Women in Science Series

XXfinder - I've sorted The Blob's women in science series chronologically by birth:
  1. Mary Fairfax Somerville (1780-1872)
  2. Anna Children Atkins (1799-1871) b 16 Mar
  3. Mary Anning (1799-1847) b 21 May
  4. Florence Nightingale (1820-1910)
  5. Mina Fleming (1857-1911)
  6. Nettie Stevens (1861-1912)
  7. Annie Jump Cannon (1863-1941)
  8. Elizabeth Cochrane Seaman - Nellie Bly (1864-1922)
  9. Aleen Cust (1866-1937) b 7th Feb
  10. Helen Beatrix Potter (1866-1943) b.28/Jul/1866
  11. Maude Delap (1866-1953) b.07/Dec/1866
  12. Grace Chisholm Young (1868-1944) b. 15 Mar
  13. Alice Hamilton (1869-1971) b 27 Feb 101! 
  14. Josephine Tilden (1869-1957) b 24 Mar
  15. Clara Immerwahr (1870-1915)
  16. Maud Menten (1879-1960) 
  17. Elizebeth Smith Friedman (1892-1980)
  18. Constance Tipper (1894-1995)
  19. Priscilla Fairfield Bok (1896-1975) dunno her birthday
  20. Gerty Cori (1896-1957) b. 15 Aug
  21. Barbara McClintock (1902-1992)
  22. Kathleen (Yardley) Lonsdale (1903-1971)
  23. Grace Hopper (1906-1992)
  24. Rachel Carson (1907-1964)
  25. Virginia Apgar (1909-1974)
  26. Mary Leakey (1913-1996)
  27. Frances Oldham Kelsey (1914- 2015) 101! b 24 July
  28. Hedy Lamarr (1914-200) b. 9 Nov
  29. Doris Lessing (1919-2013) her best stuff was science fiction 
  30. Marie Tharp (1920-2006) b. 20 July
  31. Rosalind Franklin (1920-1958) b. 25 July
  32. Janny van Brink (1923-1993) b 23 May
  33. Stephanie Kwolek (1923-2014) b 31 July
  34. Maria Köpcke (1924-1971) b. 15 May
  35. Jane Gibson (1924-2008) b. 05 Oct
  36. Mary Lyon (1925- ) 
  37. Tu Youyou (1930- )
  38. Phoebe Snetsinger (1931-1999)
  39. Margaret Hamilton (1936- )
  40. Lynn Margulis (1938-2011)
  41. Monica Hughes (1940- )
  42. Christiane Nüsslein-Volhard (1942- )
  43. Jocelyn Bell Burnell (1943- )
  44. Penny Chisholm (1947 - )
  45. Françoise Barré-Sinoussi (1947- )
  46. Temple Grandin (1949- )
  47. Juliane Diller née Köpcke (1954- )
  48. Alison Gopnik (1955- )
  49. Cliona O'Farrelly (1956- )
  50. Mary Mulvihill (1960-2015)
  51. Niamh nic Daéid (1968?- )
  52. Sara Seager (1971- )
  53. Simone George (1974- )
  54. Danica McKeller (1975- )
  55. Mayim Bialik (1975- )
  56. Aoife McLysaght (1976- )
  57. Nora Khaldi (1978 - )
  58. Jane Ni Dhulchaointigh (1980- )
  59. Emily Graslie (1990?- )
  60. AlaynaWestcom (1991- )
  61. Michaela Brchnelova (1995- )
 Happy to receive suggestions about who to do next, preferably among the living. The dead don't care.

Doris Lessing - pricker of pricks

Doris Lessing struck out last night after a long innings having been born in 1919.  Along with a lot of women of her generation, Lessing was a favorite author of The Beloved.  I didn't devour the whole opus by any means but I read the first two of books in her Canopus in Argos series, as well as a couple of others.  When the first CinA book Shikasta came out she attracted several disapproving reviews from the Pundits of Literatureland.  They had her comfortably binned in leftist-feminist-lit, where she had been a luminary because she wrote so well that she was easy to read. She was also so open in her exposure of her own struggles for identity and a true life under her own terms that she elicited admiration, empathy and probably a little uneasiness in her readers.  Much later when she was asked which of her books should be saved from the fire, she claimed that CinA was her most significant work.  The response of The Critics was all too similar to celebrity wine-tasters who can identify, describe and critique the difference between Chateau Mouton Richfocker and LIDL Old Red Biddy when they have the bottles in front of them but are shown up as mere boozers when put to a blind tasting without the labels.

As a feminist and lefty Lessing deplored the cult of celebrity and the fact that unknown (women) writers, no matter how brilliant, were going to have a hard time getting their work out in the public domain because of the patriarchal complacency that pervaded English-language publishing. In 1982, to expose the hollow men she wrote a compelling new novel called The Good Neighbour and submitted it to her own publisher under the name Jane Somers.  He turned it down so her agent hawked it round a number of other publishers until Philippa Harrison at Michael Joseph said ''I read it and loved it, and rang him [the agent] up and said it reminded me of Doris Lessing. It has a lot in it that's consistent with Doris's ''Golden Notebook.''.  This is not anywhere near as bad as Robert Pirsig having ZAMM rejected by ten dozen publishers before becoming a best-selling cult classic; but it's not a great record for the publishing industry either. The facts of the matter were summed up recently by data culled from Amazon: "Diary of a Good Neighbor" by Jane Somers (sales rank 2,434,345) and "The Diaries of Jane Somers" by Doris Lessing (sales rank 23,323.).

Does it remind you of the review process in scientific publishing?  The referees are anonymous but the authors are not.  If you get a manuscript to review from the Top Gun in your field and you're really busy that week, there must be an awful temptation to give it a once over, jot down a few comments to show that you've done something and give it your imprimatur.  OTOH, if you get a manuscript from Ravishankar Nobodi from Bangalore Technical University, you might find in yourself a tendency to lean the other way.

A couple of months ago John Bohannon of Harvard, Science, Discover etc. published the results of his Lessing-like exposure of scientific publishers.  Being a scientist he would have regarded the trials of Jane Somers as almost an anecdote.  He wrote a little computer programme that generated dozens of more or less similar marginally interesting cure-cancer papers and submitted each one from a fictitious institution to 300 different on-line open-access journals.  He had read enough crap papers in his time that he was able to include such obvious flaws in the data presentation and reasoning of each manuscript that any competent reviewer would reject it.  The papers were, on the contrary, accepted by about 60% of the editors that were able to make a decision informed by peer-review.  But it's a little bit worse than just exposing incompetents.

Open-access was born as an antidote to a business model that existed through most of the 20th century: authors submit their manuscripts to journals which charge a subscription for access to the information.  (Over)-specialisation in science meant that there was a rather limited demand for the "Journal of Narrow Field Studies", so the fixed costs (the editor's limousine, the champagne-fuelled editorial meetings, the printer's set-up) were spread over a short print run.  Accordingly the subscriptions tended to the astronomical, and researchers at smaller under-endowed colleges were unable to access key findings in their field. The Institute where I work for example cannot afford Nature On-line. Open-access publishers aspired to make all the material available for free to everyone.  This policy is clearly only feasible since electrons have replaced paper as the publishing medium.  Even with electronic publishing, however, running a journal costs money and OA raised this by charging authors (or their grant-giving bodies or their institutions) for the privilege of getting their material into 'print'.  Bohannon's clever project has exposed the gross concordance of interest in this idea - everyone benefits if a paper is published, nobody benefits from its rejection.

Doris Lessing had been ill for a long time since suffering a stroke, but I feel sure she would have enjoyed and approved of Bohannon's cunning plan.

Sunday, 17 November 2013

The Great Western Binfo

UUUAGAAUCGACGCAUAC AUCAAC ACCCACGAA UGGGAAUCCACC
Classes were cancelled at The Institute this last Friday for the Annual Open Day when we showcase the place and encourage school-children to do science and see that it could be both fun and interesting to do that science with us.  Several people asked me what I was contributing for Friday and my answer "Going to Galway" raised a few laughs. For me the only thing that is more important than a chance of pushing science at young people and young people at science is to attend the annual meeting of my professional association VIBE - the Virtual Institute of Bioinformatics and Evolution.  The 15th Nov 2013 meeting was held in NUIG.  The world of Irish Bioinformatics and Molecular Evolution has grown from a single lab in the mid 1980s to a very broad church today.  The students of that first lab are now full Professors with students of their own who recursively have students of their own who . . .  The topics covered in Galway on Friday were unimaginably wider, deeper and faster flowing than the sorts of data we were analysing back in the day.

The exponential increase in data and the power of the tools to analyse it is illustrated in the observation that my first 1992 paper in molecular evolution analysed 45 complete genes from one fungal species Aspergillus nidulans. I read every paper ever written about each of those genes. Ten years later, just before coming to do his PhD with us, my first student had completed a Master's degree in Ottawa by analysing 40 complete genomes in a similar way.  That was a ~4000 fold increase in the amount of data processed.  At about the same time as our Aspergillus paper, TCD won a contract to help sequence the very first chunk of a eukaryotic genome - Chromosome III from baker's yeast Saccharomyces cerevisiae.  That contract was costed at 1 ecu/€ per DNA base.  This Friday I was told that the cost of sequencing was now $0.10c per megabase: a 10-million-fold decrease in the cost of generating primary data!

After a gallimaufry of excellent talks through the day, and a rich and varied poster session over lunch where graduate students show-cased their latest work, we heard a key-note talk from John Greally now of Albert Einstein College of Medicine in NYC but a graduate of NUIG.  His Title "A feeling for digital organism" deliberately echoed the title of Barbara McClintock's biography. Greally started with an ex-tempore tribute to the organisers of, and contributors to, the day's events, saying that the breadth of interests, skills and experience in the room was a) extraordinary and b) had enormous potential for synergistic lift.  He wasn't flattering us as planet-brained rocket-scientists but as comparatively ordinary people who were holding a space regularly for interactions and hopefully collaborations among widely separated disciplines. Those remarks were immediately followed by a story about two of the stars in his group: a computer-illiterate "good pair of hands" and a somewhat geeky coding-whizz.  These two started by trading the secrets of their tool boxes: the one learning a bit of eppendorf-flipping and blaming-the-buffer and the other the rudiments of code.  This gave them a common syntax and some appreciation for what the other did.  The subsequent discussions were extraordinarily rich and productive.  Greally described the future sans peur et sans reproche biologist as "pipetting with one hand, programming with the other".

He went on to suggest a way to paddle up the biological data-deluge by citing his earlier paper on Astrogenomics.  When astronomers started to collect data digitally rather than by looking at distant objects with eyes or silver-nitrate cameras clapped to telescopes, they quickly found that they could generate galaxies of data in a single night.  Why not, he suggested, learn from the approaches, protocols, wrong-turnings and triumphs of the astronomers and perhaps use some of their tools and ideas on bio-data. He also urged us scientists to visit with Artists to help up our game in presenting data in visually appealing and so more readily understandable ways. After more in the same inspirational vein, I felt that even I could/should shift off my metaphorical sofa and start shoving some big science uphill especially if I was shoulder to shoulder with folks who each brought different tools and ways of seeing to the task.

At the end of that talk we were drained and inspired and looking forward to some liquid refreshment but there was one last item on the agenda - where to hold next year's meeting. After trying to remember who had been the least recent host, someone suggested we foist the task on the group that hadn't made it to this year's meeting.  After some further joshin' and slaggin' the silence began to be uncomfortable and everyone was looking resolutely at their feet, so I said "Dang it, I'll do next year". That suggestion was approved nem. con. and we all went to the bar.

Follow me down to The Institute which as everyone in the County now knows is

Saturday, 16 November 2013

Of course it hurts

Surely you're Joking Mr Feynman is full of telling anecdotes about how creative people tick and how science works. But it's also about work-life balance and how insight comes when you're relaxed. When Richard Feynman was at Princeton, his friend and rival Paul Olum showed him a trick for snapping a spring-loaded tape measure back into its housing.  Having seen him do this, competitive Dick spent the next two weeks trying to replicate the trick, but each time the tape over-shot and whipped back on his hand. When his hand was totally raw, he met his rival in the corridor and asked how Olum was able to manage the tape without getting hurt.
"Who says it doesn't hurt? It hurts me too!"

I have no intention of or qualifications for analysing why work trumps home in today's professional environment but I do have a few comments. Anne-Marie Slaughter wrote a piece for The Atlantic last year that went viral on Friendface. It is about how successful professional women have to behave like multi-tasking super-heroines: 'I told her how difficult I was finding it to be away from my son when he clearly needed me. Then I said, “When this is over, I’m going to write an op-ed titled ‘Women Can’t Have It All.’” She was horrified. “You can’t write that,” she said. “You, of all people.” What she meant was that such a statement, coming from a high-profile career woman—a role model—would be a terrible signal to younger generations of women.'

For Ada Lovelace Day I wrote about another successful professional woman, a scientist, who seems to have it all: Director, Mentor, Mother, Professor, Teacher, Volunteer. So she's clearly a role model for younger women.  If they could only replicate whatever it was she did then it would be possible to fulfill their scientific and their reproductive destiny.  But I suspect that, knowing the story of a successful role model, the young women internalise "it's been possible for her" as "it's been easy for her".  But if they were to ask the mentor, she is much more likely to say "Of course it hurts". Even if it hasn't been painful, you'd better believe that the stately apparently effortless swan has feet churning like buggery underwater.  Indeed a major part of mentoring students on any long-haul relationship like a PhD is to provide support and to help find a way forward when the younger person suffers their first major set-back; and often their second and third crisis: of conscience, of confidence, of data or of dating.  The fact that a 'successful' life has been a brutal hard slog against the odds of having been born the wrong sex, into the wrong postal district, or of the wrong colour is not necessarily a source of regret.  But it won't have been easy.

What to do?

Last month there was an essay in the NYT "Why Are There Still So Few Women in Science" by Eileen Pollack who was one of the first two female graduates in physics from Yale in 1978.  If you want to weep tears of frustration at the crap this woman had to put up with a whole generation after Mad Men type sexism had been locked firmly in the closet, then read the whole sorry story. Things we can all do for each other, which were conspicuously absent in Pollack's young academic life:
  • be generous with your time, your data, your ideas and your expertise
  • tell people that they have done well when they have done well
  • ask your colleagues how they are doing and listen to the answer
I'm not saying that watching 25 hours of day-time television is entirely a Good Thing, but it was something I could do with Dau.II. The fellow Luca Man who won Masterchef USA Season Four kept giving his rivals a stick of butter or a handful of flour when the rules of the contest allowed him to just say no.  Do you want to craft your first paper in Nature by not sharing a stick of data with someone who could use it?

Friday, 15 November 2013

Running your heart out

Running your heart out sounds bad, like a heart attack while trying to catch a bus.  On the wireless the other day, they were saying that medical advice after a heart-attack was bed-rest for at least two weeks.  Until some scientists looked at the data and realised that old guys who bucked medical authority and immediately went at it again - they survived better than their peers tucked under the covers. We aren't designed to lie down.

Then I read a nice essay  about a runner, Mike Cassidy, in this year's NYC Marathon feeling so crap at mile 10 that he was about to jack it in. Not wanting to disappoint his family he gritted his teeth and trudged on. Eventually he caught up with Meb Keflezighi, Olympic silver-medalist, who had sustained some leg-damage, who was clearly hurting, and who was a long way from any medals.  But instead of cruising past, ("I left the silver-medallist all standing") Mike hung back with a word of encouragement and they trotted and then ran on together, eventually finishing the race hand-in-hand.  Somehow, the two of them together were better at running than either was alone.  It reminded me of the Tarahumara who run for joy in and around and up and down the desolate and remote canyons in NW Mexico where they have lived for the last 400 years.

Inevitably, I found myself checking out Chris McDougall who brought the Tarahumara to wider attention by writing a book about his brief encounter with them and his return to organise an ultra-marathon among them with some other Norteamericanos. It is a great book and Hollywood is inevitably making a film. There's a much higher profile story similar to the Mike 'n' Meb's which happened three years ago, again in the NYC marathon.  Paula Radcliffe, world champ and clear favorite to win for a third consecutive year, twinged a hamstring about 4 miles out.  Instead of leaving her for dust, Derartu Tulu from Ethiopia hung back to see if a bit of encouragement ("She ran alongside me and was like, come on, come on. We can do it, we can do it,") would help Radcliffe over the hump. It couldn't but not for want of trying. Despite, or quite possibly because of, this compassion, Tulu then hared off, outstripped the the leaders and won the race. She was 37 years old at the time. I don't tell it as well as Chris McDougall at TED.Ed.  And if you want a fatter version of his Tarahumara tale, he's talked at Google.

McDougall has a theory that human beings are honed by evolution as attrition hunters. 2 million years ago a peculiar bipedal primate developed the ability to run down anything that moved. Louis Leakey, mentor of Jane Goodall, was the father of hominid fossil finding in East Africa.  He used to amaze reporters by setting off and running down small antelopes and catching them with his bare hands.  The only other animal that hunts with such dogged persistence is the African hunting dog Lycaon pictus. L.pictus rarely hunts alone, the pack has a far higher success rate (80-90%) than the king of the jungle Panthera leo.  McDougall's (untestable, so utterly unscientific) hypothesis is that our 'watermelon-head' brains could only develop and were only sustainable given the presence of ad lib protein.  That protein was only obtainable if groups of our ancestors behaved like hunting-dogs. Man-hunts, like dog hunts might last 2-3 hours and finish up 40km from their starting point.  So everyone has to run: lactating mothers and growing children who needed the protein most; the old guys who had been on many hunts before and know how the hunted behave; and everyone in between.  In successful tribes everyone runs faster and more importantly further and maybe natural selection gets the fastest young people more shags.  But they all need to run together, so egging each other on is an integral part of the process. Maybe everything that matters - speech, opposable thumbs, empathy, blogging-for-science - follows from this.

McDougall is also eloquent on the virtue of running on bare, or at least uncushioned, feet, which we had been doing for 1,998,000 years, whereas the foot-deities Nike and Adidas have only been worshiped for 19.98 years.  If you run you should listen to him because it just might stop you buggering your knees with your new pedal fashion accessories. As an encouragement, I'll point out that about ten years ago we set out as a family to walk to the top of Mt Leinster which is a hike of 5km horizontal and 600m vertical. Dau.I was then about ten years old and just after the mountain gate she started to develop a blister.  So she left her boots off on top of a wall and walked to the top and down again in bare feet, jogging part of the way down.

But I think the most compelling observation to relate about the Tarahumara is that after running for 100km when faced with a daunting climb in the path that would cause a normal runner to grit their teeth, their faces are transfigured with joy.  Even the least religious gal on the ultra-running circuit Jenn 'Mookie' Shelton knows this  “I thought if you could run one hundred miles, you’d be in this Zen state. You’d be the fucking Buddha, bringing peace and a smile to the world.  It didn’t work in my case—I’m the same old punk-ass as before—but when I’m out the only thing in life that matters is finishing the run. For once, my brain isn’t going bleh bleh bleh all the time. Everything quiets down, it’s just me and the movement. That’s what I love: just being a barbarian, running through the woods".


Thursday, 14 November 2013

Running in the Dark

In the last 1980s recession, The Beloved and three of her four siblings did upstakes and left Ireland to seek, if not their fortune, at least a life off the dole.  That was typical for families of that generation.  In the early 1990s two of that sibship saw the glimmer of green shoots in the economy and returned to Ireland to shift the ratio from 4/5 abroad to 3/5 home. By contributing to the moribund economy and paying taxes we returnees helped to bring the Celtic Tiger to life - sorry.  Our generation is a bit long in the tooth now to head off to Perth with the current recession-led Irish diaspora.

Since the foundation of Raidió Telefis Éireann RTE, the state broadcaster, they have solemnly rung the Angelus on the wireless every day at noon and 6pm.  In an increasingly secular state, there was pressure a few years ago to ditch this intrusion of the catholic church and its rituals into the, perhaps unwilling and mostly unheeding, ears of protestants, muslims, sikhs and atheists.  I am as much against organised religion as the next chap (I keep a pitch-fork and a flammable pitch-brand handy in one of the sheds), but I was taken by one argument for retaining the Angelus.  This was before skype and smart-phones;  a mother phoned into a chat-show to assert that she and her children (every one of whom had left the country) could listen out for the bells, pause together and quietly reflect on their blessings and good fortune and think of each other.  I don't know how they handled the time difference because one of the children was in Australia and two were in the USA, but such pedantic scientific details didn't hold them back.  It's a bit like Mary Robinson burning a candle in the kitchen window of Aras an Uachtarán.  You wouldn't chide her because the candle's vapour is carcinogenic.

Last night all five siblings were on the street together to participate in the Run in the Dark, two of them in Kilkenny, one in Dublin, one in Singapore and one in Cape Town.   This is a charity fun-run first done in 2010 in response to Mark Pollock's accident.  We all know Mark rather well because he's engaged to the sibs' first cousin.  "Run in the Dark" rather cleverly honours the Our Mark because he has been doing that since his retinas dropped off when he was in his final year in College, plunging his world into a Miltonian blackness. You may hear the story here.

There a rake of things I don't do: I don't do medieval, I don't run except up stairs (trudging up is so tedious) and I don't do windows.  But I do infrastructure.  So last night I was given a Hi-Viz vest and a woolly hat and told off to stand at a round-about on the Kilkenny ring-road to tell the runners to turn and go back towards civilisation rather than trotting off into the countryside to be eaten by ravening farmers.  It is November and it's cold, but it's not Yukon cold and it was only spitting rain in the last few minutes of my shift. They also serve who only stand and wait at the roundabout with a fluorescent arm pointing left.

Since Mark Pollock spilled out of an upstairs window and broke his back, he hasn't been running.  But such is his never-say-never courage that I feel sure we'll see him walking again in the next few years as robotics technology catches up with his determination not to be ground down by adversity. We need heroes and we should endeavour to support organisations that allow people to find the heroic within themselves. To the RNLI, the OU and the Jack&Jill Foundation, I'll add Run In The Dark insofar as it helps to provide the financial lubricatioon that allows an epically heroic man to show us his mettle.

Wednesday, 13 November 2013

Science Week I - The Police

It's Science Week in Ireland and The Institute is contributing and and benefiting a little.  On Friday afternoon a couple of Detective Sergeants came round from the Garda Technical Bureau to talk to the students.  Some of whom are bound to be interested because their degree is Biosciences with Forensics.  We're gradually covering the bases having had the State Pathologist and the Governor of Mountjoy Gaol here before.  Years ago, the department in which I was working had a professorial chair to fill and invited all those on the short-list to give a job-seminar to see a) whether they were capable of presenting to an audience and b) whether their research had anything going for it.  One of the candidates went on (and on and on) for an hour and forty minutes about his stressed mice.  As we staggered out of there with numb buttocks, I said that I fervently hoped we'd hire someone with better editing sense and more consideration of the value of other people's time.  We didn't.

Our two guests went over the limit to the same extent as the Professor and I brought shame upon The Institute by a) falling asleep at minute 70 and b) snoring at minute 75.  Thanks to the quick reactions (prod!--->) of my HoD the snickers were limited to our immediate vicinity. It could have been worse. At about the same time as that earlier job seminar, a prestigious event quatercentenary? 50th anniversary? at my alma mater was celebrated with a day of internationally acclaimed speakers in the biggest auditorium in the University.  After a generously lubricated lunch, the Professor of Genetics fell extravagantly asleep in the second row from the front and, as nobody was sitting near him, he continued to snore through the rest of the talk and everyone pretended that it wasn't happening.  That convinced me that there was no essential difference in the bystander effect between the English and the Irish when in a crowd.

Mais revenons-nous a nos flics.  Apart from going on too long, it was a pretty good perf, especially if you've never seen the analysis of blood-spatter before.  As a fainter, I knew enough to look fixedly at my hands while that section was going on (and on and on) so I didn't cause a real commotion like I did in my chain-saw handling course in 1998.  What I have learned:
  • the number of IEDs (improvised explosive devices - pipe-bombs) has gone from about 3 a year in 1970 to 3 a day now.
  • mitochondrial DNA is insufficiently discriminatory for forensic evidence:  there are only about 100 detectable differences in the DNA sequence, so each variant is shared by 40,000 other people.
  • the erased uniquely identifying 17 digits stamped on a car chassis can be recovered with Fry's reagent because the crystalline structure underlying metal is deformed by the stamping process
  • clandestine buried bodies can sometimes be found with GPR ground-penetrating radar; GRS ground-resistance surveying; and Magnetometry.
  • candles can cause fatal house-fires
  • GSR gunshot-residue is labile and so needs to be analysed within hours of the crime
  • Western ammunition is rich in lead Pb, barium  Ba and antimony Sb with lesser quantities of aluminium Al, zirconium Zr and titanium Ti
  • whereas Eastern-bloc ammo has more mercury Hg, tin Sn, antimony Sb and lighter elements.  Mercury having been banned from ammunition in the West because of its toxicity!
  • that at least one of our students has served in the armed forces because he knew as much about guns as the Gun-garda.
Verdict: worth going to hear and I'm sorry I nodded off.  It won't happen again, officer.