Wednesday, 30 September 2015

It's your gut talking

Back in college, when I was studying genetics before molecular biology had really taken off, we had to do something to fill the curriculum for two years. One of the topics was testing for potential carcinogens in the environment.  We knew that one of the causes of cancer was mutations in the genes which stop cells growing when they are crowded up against each out. Without these genes you had uncontrolled growth of cells, which is a pretty good definition of cancer. The way we tested the mutagenicity of stuff [R. Ames Test] was to spread out a 0.1ml drop of concentrated bacteria on a petri dish that contained insufficient nutrients for them to grow. If they did grow, then you could suppose that a mutation had occurred which allowed them to make whatever was missing from the medium. This might occur spontaneously, and with 10 million bacteria in the drop, one of them changing was not impossible; so you needed to run a controlled experiment a) plating out the bacteria on the nutrient-deficient petri-dish and b) plating out the bacteria and a potential mutagen on the nobbled petri-dish. Count the colonies on each plate and do a statistical test and you knew what was mutating bacterial DNA and so what was likely to mutate human DNA . . . and cause cancer. It was a method dreamed up by Bruce Ames at U.Cal Berkeley.

Actually, the Ames Test had an additional layer of complexity.  It acknowledged that the liver is the metabolic kitchen of the mammalian body.  Loaded with enzymes to cleave this and add that and detoxify the other, the liver will process pretty much any chemical and reduce it to its component parts or at least change it into something different. It could be that some perfectly innocuous additive to Purina Cat Chow was converted into a potent toxin by the cat's liver and it goes blind and dies. So there was a third option in the full Ames test: c) plating out the bacteria and a potential mutagen and an extract of rat liver on the nobbled petri-dish.  One of the most startling events of my undergraduate career was adding a drop of own brand Quinnsworth Lemon-Lime shampoo to the Ames test and two days later seeing a constellation of bacterial colonies scattered across the petri dish. That shampoo was a fluorescent lime-green in colour that shouted mutagen quite loudly - that was why we tested it. That was just great - we were doing real science - nobody had done that experiment before and they probably should have done. My other triumph was working through a bomb-scare to see polytene chromosomes.

This all came rushing back to me because of the Nature Supplement on Liver Cancer which I have been reading like a really gripping novel.  One of the essays in that compendium is an investigation of the role of the intestinal flora in the cause and cure of liver cancer. That might seem a bit of a long shot, until it's pointed out that everything we eat is taken from the gut up the hepatic portal vein direct to the liver. There are 100 trillion bacteria in your gut of maybe 10,000 different species each containing up to 6000 different genes.  That's 60 million potential enzymes for converting harmless substance A into toxic substance B.  There is evidence for this quite out-there hypothesis in that rats which are treated with oral antibiotics are less likely to get liver-cancer than reg'lar rats.

Given that observation, any trained scientist will be down in the guts looking for likely suspects for a mechanistic explanation: which chemical A is being converted to which chemical B that is known to be carcinogenic? The accusing finger is currently pointing at deoxycholic acid DCA a "secondary bile salt" not a million miles, chemically, from cholesterol [see R]. The story is that the liver manufactures bile-salts which are stored in the gall-bladder and secreted into the duodenum to help absorb fats.  Having done that, the fat is unloaded in the liver and the bile salt is recycled through the gall-bladder. We've met a bile-duct before, getting unblocked.  Some of the normal constituents of the intestinome (the gut flora) convert the 'good' bile-acids into DCA which is not only not good, it is positively toxic not only to humans but also to cohorts of other bacteria. It is likely that the DCA-making bacteria benefit from the conversion by creating a bit of lebensraum for themselves by laying a little light holocaust on their neighbours.

That's a story you can tell to Joe Public, untrained in science, as an internally consistent and coherent explanation of what might be actually happening at the interface between the microbiome and the hard-working liver. It's therefore good enough to write a grant application to pull in a $million$ and start investigating how you might be able to put a spanner in the DCA production works.  One idea, for example, would be to genetically engineer some street-cleaning bacteria that hoover up DCA and convert it back to bile-acid. That way you leave the intestinome intact and just tweak it to your bidding.  Broad-spectrum oral antibiotics really do damage to the delicate balance 'down there' and should only be used as a last resort. FMT fecal-microbiota transplant is one way of delivering bacteria to the dark places to do good works.

Tuesday, 29 September 2015


Never refuse a gift, refusal may cause offense. That applies to children, even grown-up children, when their parents press money on them at the end of a visit. Advice - just accept gracefully: the folks won't be here much longer. The only time to regularly refuse gifts is when they are won in a Pub Quiz which is raising money for charity. It would be hard to refuse the gift that arrived in the post today, because it had been sent from America and didn't have a proper return address. I had ordered something bookish from Amazon but this parcel was weighing too light in the hand for that and it took me a while to twig that it was my PRIZE.  For the last several years I've had a sub to AWAD which was started long ago by a graduate student at Case Western Reserve University. Anu Garg started his education under a mango Mangifera indica tree in India and didn't see a library until he went to college. In 1994, the internet was thin on the ground and it was easier to go viral.  There are now >million subscribers who get not only A-Word-A-Day like it says on the tin but also a little essay and the word used in context in a real sentence in a real publication.  For good measure, you get a quote-of-the-day as well. The quote is often from someone whose birthday is being celebrated and I've often used that as a direction to cobble together my 600-words-a-day SHWAD.  At the end of the week you get a bonus Weekly Compendium with Feedback from readers.  These also are occasionally interesting to read.

I lurk, I rarely contribute but a tuthree weeks ago the word was
Fribble: A wasteful or frivolous person or thing.
That had a huge resonance for me because, when we lived as impoverished students in Boston in the 1980s, going to Friendly's was our occasional treat for The Boy. I was inspired to send the following comment:
Wrong wrong almost right.  As anyone from New England will tell you, Fribble is the name used by the restaurant chain Friendly's for their milkshakes. As the standard portion of this calorie-rich beverage is 22oz > 600g the result is a waist-full person. Should be consumed with a "Very Berry Hot Fudge Sundae" to fill the hips as well.
And at the end of the week AWAD published my comment at the top of the feedback as Comment of The Week. I was delighted, not least because I got a couple of e-mails direct from other readers who shared my affection for Fribbles. Several days later, I got an e-mail asking for my postal address because I had won a PRIZE for my witticism.  It was on the kitchen table when I got back from work last night.  Big parcel, much packing, small tin with a bunch of scrabble-like tiles labelled One-Up and a bitty sign saying "This is a lagniappe" [I've corrected the rogue capital L, we're not Germans] which is a Quechua word that has come to American English via Louisiana French meaning a bonus or freebie - the 13th bun in the dozen, the mints next to the cash-register. That's a new word for me, the second in as many days - superjacent.  My father lived all his adult life in England but he would still insist on giving back a luck penny when he received a wodge of cash (for selling the family silver, that sort of thing) - it's a custom much more widely practiced in Ireland but probably less so nowadays as the old ways die out.

Last week I was at it again because Monday's AWAD was Kenning - a conventional poetic phrase used in place of the usual name of a person or thing.  These are very common in Anglo-Saxon, Old English and Icelandic Eddas and featured on The Blob before. As The Blob gets life-encompassingly bigger, it will soon contain everything I can remember - that's falling precipitously so it's a bit of a race. Accordingly it was easy to recycle a fragment to send another comment that was published in the Weekly Compendium this last weekend:
Some kennings are so common in the (nautical and military) language that has come down to us from the likes of Beowulf or The Battle of Maldon that they are clichés. hron rad (whale-road) is the sea; svana fjöll (swan’s mountains) are waves; grand viðar (wood’s bane or wood-crusher) is fire. But what about hjálms fyllr (helmet-filler) for sword - that’s so disturbingly visual that it should be the title of a particularly violent graphic novel.
No prizes though: there are a million other AWADies out there to encourage!

Monday, 28 September 2015

Baling out

I was a boy once.  When I was 8 in 1962, the war was still vivid in the dreams of my parents. My mother's father lost an eye to a glass splinter when his home was bombed but their immediate families survived. In 1962, we played at being fighter planes: running around the field with our arms outstretched making neeeooooowww  and budda-budda-budda sounds. All good fun, good exercise and nobody died.  20 years earlier lots of young people were dying, especially aircrew and especially those in British Bomber Command.  The only military cohort of the 20th century with higher mortality were front-line infantry in some sections of the WWI trenches. In rough terms half of bomber crews failed to survive the war. My mother was 19 when WWII broke out. In the early part of the war she was serving in the ATS at various locations across the South of England. She dated a couple of really nice boys from nearby RAF bases until they failed to return; I guess it made everyone a bit wary of commitment.

The Air Ministry maintained an Operational Research Section ORS which gave office-space for boffins to analyse data and inform policy. 19 y.o. mathematical physicist Freeman Dyson started working there in 1943 and crunched all the data to which he could get access. Remember Abraham Wald using science and insight to decide where planes needed armour? The problem for the ORS was that the hierarchy of Bomber Command refused to listen to much of the evidence presented by their ORS unless it was consonant with what "Bomber" Harris and his cabinet of death already knew to be true.

For example, Dyson calculated the rate of survival of bomber-crews obliged to exit the bus because it had been fatally damaged by enemy action. British aircrew had a 12% successful bale-out rate compared to 50% survival among their opposite numbers in the USAAF.  The rate was worst in Lancaster bombers and Dyson and his OSR room-mate Michael O'Loughlin were convinced that the small size of the Lancaster's escape hatches was the primary reason for the excess mortality. These doorways to salvation were 560mm x 670mm in size and you are urged to draw a rectangle that size on the kitchen table and imagine pitching through it, at night, at 500km/hr, wearing a padded flight-jacket and a parachute. The equivalent exit on the Halifax was 50mm wider and the rate of survival was thereby doubled.
Yet the Lancaster [R] was deemed to be the most successful of the British bombers by defining success as "delivering 608,612 long tons of bombs in 156,000 sorties" rather than as % disruption of German rail-traffic or ball-bearing factories destroyed. Dyson estimates that the amount of damage to the German economy was about half the cost of having built the bombers which were destroyed in the process. More than 7,000 Lancasters were built at a cost in 1940-£s of £50,000; just under half of which were destroyed and only 35 [0.5%] succeeded in carrying out 100 missions. Ryanair would go out of business with that sort of failure rate.  And for what? Mike Bayon reports that 3% of the payload of British Bomber Command was "on target" as defined as "within 5 miles".

The rates of return after a mission were so appalling that everyone, including the flight-crews, noticed.  Bomber command put it about that the crews that died (tsk tsk most unfortunate very sorry) were the absolute beginners. As you gained experience, albeit by being tempered in a furnace, you were less likely to die.  But Dyson crunched the data and showed that it was just a lottery. You were as likely to go west on your 30th mission as on your 3rd.  That message was going to be extremely bad for morale and so it was suppressed. Dyson & Co. took this information [that something unknown was killing even experienced crews] and reports from rear-gunners to conclude the two rear gun-turrets were useless as defensive weapons AND added an enormous aerodynamic drag. Stripping out the gun-turrets would a) reduce the crew from 7 to 5 and reduce deaths by 30% b) allow the planes to travel 80km/h faster and consequently go there and back, and be over the target getting shot at, for a shorter time. This evidence-driven suggestion was also ignored.  The rear-gunner courageously covering his pals was too propaganda too powerful to edit out.

In a similar matter, Dyson carried out some statistical and theoretical studies to determine the likelihood of two bombers colliding while over Germany compared to their chance of being shot down by enemy fighters. With little data and big errors he was able to show that you had to worry a lot more about the fighters than the collisions and so pilots were safer travelling closely together like convoys of ships were concurrently being protected from u-boat attack. The theoretical answer was sufficiently close to the statistical answer to give mutual credence to the two quite independent calculations.

I don't think that Dyson has ever come to terms with the fact that he was unable to present information and data-analysis in such a way that it would make a difference to the chaps his age who were being shot down in flames several nights a week over Germany.
Science of War I, II, III

Sunday, 27 September 2015

A bucket of cold water

Headline in the WaPo via 3quarksdaily
Why some scientists are worried about a surprisingly
cold ‘blob’ in the North Atlantic Ocean
accompanied by this chilling picture of global temperature variation for the first 8 months of 2015:
The dark red squares are those regions of the World which have, Jan-Aug 2015, experienced record hot weather - California has been burning all Summer and has run out of water to douse the flames. The Pacific (the pool in which Californians bathe) has also been hotter than ever before (well, at least since coherent records began in 1880). That will have an effect on El Niño as I wrote back in May.  The climate scientists have taken to calling this Pacific hot-stirring The Blob - with a conscious hat-tip to a really scary 1950s sci-fi horror movie. . . not the actual movie starring Steve[n] McQueen (the 1958 FX were quite ropey) but the idea of the film: "indescribable / indestructible / nothing can stop it".  Because that Blob was on the other side of the World, I was quite blasé, not to say flippant about the whole story.

The dark blue Blob in the North Atlantic shown on the map above is another kettle of fish entirely. It's much closer to home and it will certain-surely impact on Ireland and the Western seaboard of Europe this winter. What?  According to the boffins from the National Oceanic and Atmospheric Administration NOAA the Blue Blob indicates a severe disruption of another acronym: AMOC [Atlantic meridional overturning circulation].  What usually happens used to happen is that cold dense high-salt Arctic water surges down the Davis Strait between Baffin Island and Greenland and plunges to the depths of the ocean. The 'vacuum' is filled by the North Atlantic Drift aka The Gulf Stream which has been simmering away in the sub-tropical shallows of the Gulf of Mexico and the Sargasso Sea and this starts/continues the relentless clockwise stirring of the North Atlantic surface water. Trillions of tons of water washing up against the shores of Europe has enormous beneficial effect on our climate. A little warm water can heat up a helluva lot of superjacent [never had to use that word before!] air.  That's why we have mild damp Winters (and mild damp Summers as well) and no typhoons, hurricanes, blizzards, dust-storms or plagues of locusts.  The climate is so ambient that you don't really need an overcoat in Ireland - a good Aran sweater will answer for most outdoor occasions. What's happening now is that the overall global warmth has melted billions of tons of ice off Greenland and this cold light fresh water hasn't been sinking. The Gulf Stream is going to have a fight to get here at all and when it arrives it will be kitten-weak and no match for a chilly blast from Steppes of Mother Russia.

Be afraid, very afraid . . . and get a lot of baked beans into the bunker.

What shall we call it?

Scientists are big into naming of parts. If everyone agrees on the name then there can be no mistake about what's being studied. With my multinational readership (Привіт Київ, Gruß Wien, Bonjour La France) I try to be religious about including the Linnean binomer of all the organisms I mention.  There is going to be confusion if I mention "chestnut" because it could be Aesculus hippocastanum or Castanea sativa and only one of them is edible. The toxic one is not that poisonous, and apparently the flower has been adopted to represent the city of Kiev [Привіт Київ]. If it's important for species, it's also vital for genes, which have to be named unambiguously; to replicate molecular experiments for starters. We are collectively much worse = inconsistent about naming genes.  But some areas of biology have been particularly well disciplined and short on ego and one of those is the genetics of the fruitfly Drosophila melanogaster and its relatives.  Flybase imposes a necessary and desirable authority and order on what genes are called and how the data about each gene is presented. It's clear that geneticists, since Thomas Hunt Morgan and his students 100 years ago, have had a lot of fun being clever when naming genes.  Actually, what they have effectively been doing, especially in the early days, is naming mutations in genes - all fruit flies look the same until there has been a mutation at one spot in their DNA that changes the looks or behaviour or development of the fly.

The early genes were identified by something rather what-it-says-on-the-tin obvious: 
  • white w (eye colour); 
  • eyeless ey; (my dog's fly's got no nose eyes)
  • Antennapedia Antp (has legs growing out the top of the head).
Then there were flies that seemed to be less responsive or slower to learn than normal.  I'm not sure which came first but a whole group of 'intelligence' genes were named:
  • dunce dnc (a simpleton)
  • cabbage cab (cabbage is British slang for one supposed to be mentally handicapped)
  • turnip tur (by extension from cab)
  • rutabaga rut (also by extension from cab)
There is a developmental gene which is vital for differentiating the top and bottom of the fly embryo. It also functions as an immune recognition receptor to detect pathogens and start an effective response against them. The equivalent genes in mammals have retained the immune function and seem to be differentially expressed in different parts of the embryo. The first gene in the family was called
  • toll Tl (because Christiane Nüsslein-Volhard was so astounded when she saw the first mutant that she cried "Das ist ja toll!")
  • 18-wheeler 18w (a protein with a similar structure but different function; mutants supposed to look like the tarpaulin over a truck)
Other hilarious ha ha ha ha coinages include:
  • ken-and-barbie ken (because mutant flies have no external genitalia)
  • abnormal spindle asp (has trouble with cell division)
  • cleopatra cleo (lethal if asp <above> is also present)
  • tinman tin (no heart)
  • nanos nos (from νᾶνος = dwarf, as in nanometer)
  • smaug smg (suppresses nanos <above>) 
  • lush lush (inordinately attracted to the smell of ethanol)
  • methuselah mth (remarkably long-lived) 
Parallel sources: io9itsOK2bSmart; bitesize; curioustaxonomy.  It's a bit sad really, all of us re-churning essentially the same information.

Saturday, 26 September 2015

European Today of Languages

As decreed by the Council of Europe in 2001, 26th of September is European Day of Languages:  To promote language plurality, intercultural understanding, and lifelong language learning. Some ways of promoting these laudable aims are more effective than others. Forcing official languages on an unwilling people is not always effective.  More people speak Welsh like a native in Wales than speak Irish in our Republic. Nearly 100 years of crappy and pedantic Irish language teaching in schools has failed to inspire a lifelong love (and use) of the language here, except in a small minority. The fatuity of maintaining the primacy of Irish in all official business was brought into focus this last week. A Romanian national, resident in Ireland, had his conviction for drunk-driving quashed because the docket spat out by new breathalyser machines was monolingual in English. His clever-clogs lawyer desired to keep his client on the road until he kills someone, and a High Court judge felt that the Law [requiring bilingualism everywhere official] trumped Justice or common sense. That establishes a legal precedent which should allow a few hundred similar cases to be thrown out. That is a Bad Thing. But if you hear about some quirky aspect of language on The Blob, you might go and find out more. That is a Good Thing.

The Council of Europe reckons that the top three European languages are Русский Russian [150 million speakers]; Deutsch German [95 million] and Türk Turkish [80 million]. WTF?  I didn't know there were that many Turkish Gastarbeiter slaving away in Berlin and Hamburg. Well, there aren't. The Council of Europe is bigger than the EU and includes the whole of Asia Minor [=Turkey] as well as Russia as far as Владивосток Vladivostok and Камчатка Kamchatka.  Much like Israel competing in the Eurovision Song Contest.  Here's a handy Venn diagram [strangemaps via boingboing] with implicit quiz :
There are six red-and-white-only flags: Switzerland, Denmark, Poland, Malta, Georgia and . . . [one more: it's small]

Q1. What is the official language in Andorra?
Q2. What national flag flies over the town hall in The Åland Islands and what is the official language?
Q3.Where do people speak Llanito?
Q4. Is it sensible for a Sinti speaker to go back to the Punjab to find her roots?
Q5. Draw a tree of relationships among the languages spoken in Metropolitan France: Alsatian Basque Breton Catalan French Occitan (we'll spare you having to slot in Tuareg, Vietnamese, Arabic).
Q6. I've given you an earful about the linguistic argy-bargy in Belgium; what is the recognised minority language in the Netherlands and how many speak it?
Q7. What is the third official language in Luxembourg along with French and German; and is it a real language or a dialect?  How long is a piece of string?
Q8. There are less than 2 million people living in Autonomna Pokrajina Vojvodina, an autonomous region of Serbia. How many official languages are there?
Q9. Is Aragonese spoken anywhere in Middle Earth?  It would help because fewer people speak it in the Pyrenean foothils than speak Irish in Ireland.
Q10.  Is Scots a real language or a piece of string?

Try today to greet someone in a language other than your own?

The Craft

When Dau.I and Dau.II were growing without schooling in the depths of rural Ireland, I discovered where it seemed that you could buy any movie ever made then pay some pretend-money off your credit card and a DVD in a box would arrive in the mail-box about 4 days later.  I bought movies for pretty much every birthday and Christmas (several at Christmas) for about 5 years: things I thought should be part of any child's experience of our common culture. That probably means 'films [Diva] and [Dinner] I liked'. I went off and bought a bunch of Shakespeare films directed by Kenneth Branagh. Much ado about Nothing were just gorgeous and Henry V was truly goose-bumping inspiring.  The Boy, who has high A/V standards, laughed at us huddling round a lap-top on a coffee-table to watch films and bought us DVD projector and a white 2m x 2m Ikea roller-blind to act as a movie-screen. We'd sit in a row on the sofa watching classic movies together. Happy nights.

In the early days, when Dau.II was maybe 7, I put on Much Ado. She was confused; "What's happening?", she whispered, "What's he saying?".  We could have paused the film and explained, but we were take-no-prisoners in our dealings with the girls: they had to work to keep up because we weren't going to talk down. Soon the kidder's expostulations died away as her ear tuned into the cadence, her mind interpolated language she'd not yet encountered and Shakepeare's magic worked on another generation. Drama, including the Bard's, is meant to be played not parsed; enjoyed not explained. I wasn't always on the button in my choices.  Driving in the car one day with the girls, I heard Zorba's Theme on the wireless and thought that Michael Cacoyannis' 1964 version of Zorba the Greek must be on the list in the next parcel.  Hmmm, they still twit me about the inappropriateness of thinking that a woman being stoned to death for adultery was appropriate visual input for an eight year old. "What's adultery, daddy?"  ...."I don't know darling, I'm not married".  The Z theme is still pretty good fun.

Sometimes, as well as the movie, the distributor would throw in 'extra features' with out-takes or director's commentary. That's how I discovered that David Lean had booted Julie Christie's hair in Dr Zhivago. In the extra features of A Fish Called Wanda DVD, there was a series of out-takes with an voice-over explanation from John Cleese, the writer and star.  In lots of the cases, the scene had been left on the cutting-room floor because it slowed the pace of the film; hilarious in itself but sacrificed for the whole. It was the best lesson I ever had in how films get made.

The DVD-era is long gone. The laptop died, its replacement didn't have an inbuilt DVD drive. The movie-screen fell off its bearings. Dau.I, then Dau.II left home. I had so little work that there was no $lack for fripperies. Nobody seemed to have the attention span for a 90 minute movie when there were 5 minute clips on youtube. Over the last Summer, over a few idle evenings, I've discovered the comedian Louis C.K. I'd never heard [of] him and yes, I've lived a very sheltered existence. It's also ironic that I was living about 500m from Newton North High School in suburban Boston when the young LCK was there cutting his teeth in stand-up. His stuff is edgy and the opposite of PC but that allows him to expose some of the evils and pretensions of our times. He is an acknowledged master of his craft, so it's interesting to watch Louis C.K. interviewed after a preview of some of his material.

The last question from the floor is sort of incoherent but his answer is true for every good thing I've ever been involved in. What he says is that film works, film takes off, when everybody on the set - the boom-operator, the best-boy, the key-grip and the continuity girl - is giving it socks. Being attentive to your craft, even if it's fetching tea or repairing the leading man's make-up, is important. It's not about the money, it's about doing it right. My girls are not slavies in the catering trade for the big money, but b'god they work - if the bins are brimful or the sink is full of matter then Dau.I or Dau.II will clean up and set right. They can do no other.

Friday, 25 September 2015

Someone's telling porkies

I was digging through a pile of old Natures, still in their mail-wrappers since 2014!  In the 4th December 2014 issue, there's an article and a News&Views on the cultural dishonesty of bankers. It had a certain resonance because I've just written a bit about codes-of-conduct whereby a group of people formally write down what they stand for and what is beyond acceptable limits. The primary research was carried out by a trio from the Dept Economics at the University of Zurich. It's the sort of study that has a good chance of making the cut at the weekly editorial meeting at Nature. As a general science publication, they have to include some copy that is accessible to a wide tranche of their readers - which is a very broad church from Astrophysics to Zoology. A neat little paper which plays on what everyone knows to be true - either to confirm our bias or to counter-intuitively rubbish it - has a chance.

It's a psychometrical study, such as economic researchers have been doing both before and after Freakonomics was published. They recruited 128 bankers from a multinational financial institution and split the sample into two groups: experimental and control. Each group was asked a series of questions and then put in a closed room and asked to toss a coin 10x and report how many heads came up. To encourage them to be bothered with such a trifling task the researchers incentivised everyone by saying they would be given $20 for every H that came up . . . provided that the total was more than the average score of a [fictional] pilot study. The punters were on a honour system to report the result accurately.  The experimental group's priming/prior questionnaire included questions about their work and work-practice in the banking industry while the control group were asked more neutral questions about TV and soccer.  Here are the results:
If you toss a coin ten times there is a very precise, symmetrical expected distribution based on the binomial theorem: 5H:5T is much more likely than 9H:1T.  This theoretical distribution is shown as blue bars in the histograms above.  The pink bars represent the distribution reported by N=67 controls on the Left and N=61 experimentals on the Right.  Do you think that the pink bars are shifted to the right=money-winning end of the distribution? Well, so do the boys from Zurich and the result is statistically [p=0.033] significant. (4 or 5)/61 of the experimental group report getting 10H:0T and winning $200 from U.Zurich's research fund. By chance alone you'd expect only 1/1024 to get a result so extreme. The neat thing about such studies is that you can't call any individual a liar but you can put money on the fact that someone(s) has been economical with the truth.  You might also wonder whether $200 was a sufficient incentive for a financial whizz kid who could pull that much down in 10 minutes by finagling the market in Thai Bahts.

The study was very widely picked up and reported by the world media: Les banquiers, tricheurs par culture (Le Monde); Banks breeding dishonesty (Sydney Morning Herald); Folk med dette job snyder mere end andre (; Bankers think they have to behave badly (Grauniad).  This reportage will doubtless have pleased the publicity department at U.Zurich and launched young Alain Cohn's career and Nature can be a bit of a whore for news-coverage, so they're happy.  And everyone who likes to put the boot in for bankers, which is pretty much everyone, is happy because their prejudice is confirmed.

But reflect. In science we use 1/20 or p<0.05 as a purely conventional level of statistical significance. If the chance of getting your result by chance is less than 1/20 then you may be on to something. But the corollary is that for every 20 such studies you carry out you can expect one result to be that extreme.  p=0.033 would certainly not be enough to convince your line manager that the company should invest $1 billion in developing a new cure for cancer based on your weeny pilot-study N=61+67 experimental result. If you were Brian Nosek you'd make the graduate student do the whole thing again in a different bank before rushing such a marginal result into print.  Or you could ask my friend Tony, who is a leader in his field because he has a good crap-detector to say v e r y  s l o w l y "extraordinary claims require extraordinary levels of proof". 

Explanatory note for those not brought up in Greater London (the entire readership?): Porkie is from cockney rhyming slang: pork pie = lie.  Similarly tit for tat = hat; so a hat comes a titfer.

Thursday, 24 September 2015

Effective killers: liver cancer

The liver is an extraordinary organ.  It weighs about the same as your brain but is far more alive.  From the time you're old enough to vote, your brain is getting smaller all the time as neurons die off at the rate of 10,000 per day. After the age of, say, 80 so little remains that it rattles about in your head like a pea in a drum.  If you have a fall now what's left is likely to accelerate hard against the inside edge of your skull and kill you quicker than contact sport encephalopathy.

The liver OTOH has remarkable capacity for regeneration and seems to turn over its cells even as it maintains the same overall shape. If you require a liver transplant you're likely to get a stump of donor liver rather than the whole thing because it's easier to insert. From as little as 25% of the mass, a complete liver can be regenerated in a short time. It's the nearest thing we have to a salamander's tail. Being this much programmed to grow is something of a double-edged sword because the liver is also very prone to cancer and, unless your oncologist gets in there very early with the knife and aggressive chemo- and radiation-therapy, your prognosis is not good. The US five-year survival rate after a liver cancer diagnosis is as low as 16.6% while in the UK 80% are dead within a single year.  I'm getting all this from a really readable 16 page supplement in Nature from 4th December 2014. [Sorry, it's pay-walled, ordinary people]

Liver cancer doesn't always follow from other liver disease but it never seems to happen unless there is a pre-existing condition: viral infection by HCV or HBV, alcohol-induced cirrhosis, fatty-liver disease or fungal toxins, like aflatoxin, from the diet. Where you live determines which of these triggers is prevalent. Hepatitis C Virus HCV infects 180 million people across the world but the rate is far higher in Egypt than anywhere else. 350 million have HBV in their livers but it is much more common in East Asia [10%; 120 million Chinese] than The West [0.5%].  Indeed, the UK government has decided it is not cost effective to institute wide-spread vaccination of the citizenry, although an effective vaccine exists and is making a huge dent in the spread of the disease in the third world.

With 800,000 new cases of liver-cancer being diagnosed each year and no sign that the number is diminishing, there is a huge pot of money for BigPharma to play for.  There is only one effective therapy against hepatocellular carcinoma HCC which is approved by the FDA: Sorafenib [Bayer/Onyx] which acts by inhibiting key enzymes called tyrosine kinases. TKs are signalling molecules and there are lots of them which talk to each other to make biochemical things happen.  The two main processes needed by growing tissue, like a carcinoma, are cell division and better blood-supply to deliver fuel to the dividingcoal-face.  Both of these depend on a cascade of TKs which are seemingly inhibited by Sorafenib.  The problem is that we only have 23,000 protein coding genes to play with, so all these signalling molecules have to double-up and triple-up their roles. If inhibiting cell division in the liver is desired, you want to make damned sure you're not inhibiting cell-division in the bone-marrow or you'll have no white-blood-cells to fight the cancer.  That's the sort of thing that gets labelled 'side-effects'.

"effective" should be taken 3 times daily with a pinch of salt because Sorafenib costs $5400/month and will likely win you only 3 months of extra time to put your affairs in order. Remind me not to bother: $5400x3 = $16,000 is tuition, room and board and extra tango lessons for the grand-child's first year in college [in Ireland, I'm not imagining Harvard here]. The Pharmaceutical herd is not far behind Bayer with their me-too drugs Linifanib [AbbVie]; Brivanib [BristolMyers]; Sunitinib [Pfizer] which act in essentially the same way and are unlikely to be any better.  None of them aspires to cure liver cancer, just make money for shareholders over the last few months of the patient's life.  But I guess they have to keep cranking the arm or BigPharma will run out of cash to develop something really interesting that works. In my socialist paradise, I'd stop this unimaginative duplication of effort and make the other companies go straight back to the drawing board (by which I mean the pure science blue-skies laboratories that are no longer funded by government money) and try a completely different tack.  And I'd make everyone come up with less dorkinib and stupinib names for their products!

Wednesday, 23 September 2015

Today: Eric Bogle

It is Eric Bogle's birthday today: born 23 September 1944 into an honest working-folks family in Peebles on the River Tweed in S. Scotland. It was pretty hopeless in Scotland during the 1960s with the toppling collapse of heavy industry and engineering dominoing large parts of the economy into recession, so Bogle upped-stakes and emigrated to Australia in 1969.  He said goodbye to his mother at the railway station (she promised not to cry) knowing that he might never see her again:
On the far side of the world, he made a living at various jobs and wrote songs which came blurfing up from somewhere deep inside his Scottish heart; full of compassion and anger . . . and loss, as with Leaving Nancy. If you're a bloke you might listen to these songs in the car where nobody will see you blubbing; but drive carefully and stop if you can't see clearly.
When we lived in Newcastle in the NE of England (and not so very far from Peebles) we weren't mad folkies but we heard that Eric Bogle was doing a gig in a hotel in Tynemouth about 15km away on the coast. Bogle was definitely a Name in the folk scene, so it was a bit disconcerting to find it happening in in upstairs room for maybe 50 people. It was plain delightful; he told his stories and sang his songs and broke our hearts and made us laugh.  As I say: a great heart, a man sewn up in kindness.
But Bogle is most widely known for his commemorations of the bloody futility of at Gallipoli 1915
At Gallipoli "Johnny Turk" was led with reckless bravery, excellent intelligence and strategic mastery by a young officer called Mustafa Kemal. After the collapse of the Ottoman Empire in the 1920s he became Atatürk, "father of his people".  In 1934 he paid tribute to the WWI fallen of both sides "You, the mothers who sent their sons from faraway countries, wipe away your tears; your sons are now lying in our bosom and are in peace. After having lost their lives on this land they have become our sons as well."  Well even if he didn't, the sentiment was and is in the air and now carved in stone.

Tuesday, 22 September 2015


The Institute can be exciting if you make the effort.  My Human Physiology class meets of Tuesday lunchtime on the outer reaches of the campus in the stand of the GAA pitch which has a number of classrooms in the back over the t'ilets and changing rooms. They were complaining that their timetable didn't allow for lunch, I countered with the fact that you get two walks in the sunshine to get to class.  On the way back to base, I caught the tail-end of the visit of the local fire-brigade to Campus with two fire-trucks, the County Fire-Safety Officer FSO and a load of kit.  They have a little trailer than opens up at the back to demonstrate various fires and how to put them out. As I approached, there was a saucepan of oil burning away.  One of the fire-fighters dressed up with face-mask and fire-retardant hood approached the pan with a half-cupful of water on the end of a very long stick.  Tip it over and WHOOOMMPH! it's a BLEVE [boiling liquid expanding vapor explosion] as the water sinks to the bottom and vaporises to fling the over-burden of boiling oil up and out. It only lasted a fraction of a second but it would have filled half our modest kitchen . . . and the fire was not extinguished,  So they could give the demo another go round.  Until you've been there, you can't quite believe what happens.

Afterwards, I chatted for a while with the young FSO about whether I'd missed anything else interesting because they had examples of the jaws-of-life for forcing crushed cars apart to abstract the humanity within. They do those car-cutting demonstrations, but not today. I was glad that about 20 students had seen the BLEVE, and others had seen earlier examples during the day: they won't hold the chip-pan under the kitchen tap. I was on about BLEVEs in June with the SloMo guys filming it in its roaring detail.  It's not quite the same without feeling the heat at a distance of 6 m.

Lazy Glute

Last Friday we had an event at The Institute to launch a new MSc in Strength & Conditioning.  I mentioned that there were a couple of engaging speakers but only wrote about one (Billy "The Gloves" Walsh) last Saturday. The other was Avery Faigenbaum from The College of New Jersey, who was over in Dublin to speak at a symposium on childhood obesity and got sprung for a lightning tour down to the midlands between sessions. When I was in Boston in the early 1980s, it was as if the Nobel Prize winners were forming an orderly queue to speak at MIT, Harvard, Brandeis, BU, BC, Tufts, or UMass. Whatever the virtues of The Institute, nobody would claim that it is a hub for international science, so I try to rock up to hear invited speakers - whatever they're speaking about. Well Dr Faigenbaum was worth getting home late for. He was in a hurry because he was running late because of the traffic but I reckon he always seems like that. The words poured from him like a fire-hose and they were passionately articulated; so it was impossible to leave the room an unbeliever. As a sofa-guy, I didn't really understand some of the language but it was directed at 150+ young sports-rehabilitors and strength&conditioners and their eyes were shining.

He started off by identifying a number of systemic woes among today's children and teenagers.  They still run around like made things, if given the slightest opportunity, up to the age of about 10. Dancing like nobody's watching indeed. But then they present themselves on more formal sports fields, start to compare themselves to others, find that they are not in the 95th percentile . . . and give up. The comparing and the competition is culturally induced: it's not enough to be the infrastructure in the team; everyone has to be centre-forward.  Actually, 6, 7, 8 y.os don't get out and run jump skip throw [and all the other muscle-coordination, strength developing things that kids do] because they are fattening up in front of the television being role-modelled by Barney the Obese Dinosaur.  All those action words, straight from proto-indo-european; done by kids since the beginning of time; since before we came down from the trees indeed. Animal Play Behavior (1981) by my pal Robert M Fagen is still available on Amazon.

What you have is exercise deficit disorder EDD. Faigenbaum wants this added to the list of identifiable diseases recognised by doctors who are encouraged to prescribe moderate to vigorous exercise for at least 60 minutes every day. In the US they have an epidemic of attention deficit disorder ADD and doctors prescribe ritalin to make the kids sit down. Wrong way round, folks!  He got a bit technical (lost me for a while) about the current philosophy of sports training for youngsters. Apparently the dogma is that you have to make kids fit through exercise first and then you can start on resistance training or strength training. Faigenbaum's position is that kids today [harrummph] are weak as kittens and couldn't sustain 90 minutes on a soccer field: they need building up. One particular muscle needs to be used more, partly because it's the biggest we have.  Lazy glute syndrome [gluteus maximus, my arse] LGS develops because kids spend 3 hours a day stretched out on the sofa watching Barney and then graduate to playing [as in watching, passively] Lara Croft. They spend another 5 hours a day M-F at school glued to a chair in a ritalin coma. Accordingly they can't bend at the waist properly or flexibly so their posture is like an old beggar under a sack. Bad posture means sports injury later.

If you live within 50 miles of The College of New Jersey, you want to switch off the TV and tell yer Ma to drive you down and enroll you in a supervised weight-training course in the school next door. You will "Have fun. Meet new friends. Learn something new". Among those things will be more regular use of the timeless fundamental movement skills FMS - kick, hop, flick etc. Although that public high school's equipment drew an audible gasp of envy and admiration from the audience, it's not necessary.  If you're in the Third World for sports like Ireland, you can use bicycle inner-tubes for resistance training or even and perhaps especially the child's own body weight [L]. Clearly a bit of qualified supervision is required: at 7 the ulna is a thick as a pencil but as the program continues the muscle mass builds up and you develop a fully integrated and highly effective part of the musculo-skeletal system. 

And I loved the science and the crap-detecting. When Faigenbaum makes his pitch to other professionals there is sucking of teeth and tsking of tsks and The Man presents pictures of 'fractures of the growth plate'.  The long bones of children are not fully ossified: one of my students claimed that a child might have 300 bones rather that "206" and a helluva lot of cartilage.  But they need to be ossified at the tips where they articulate with other bones at a joint.  Behind this bony "epiphysis" is the growth plate.  But if you read the original scientific literature from which these scary x-rays are abstracted-without-context, it turns out that none of them were sustained in normal or even vigorous exercise or during supervised resistance training.  Faigenbaum and his international collaborators are re-writing the literature by forcing their anti-establishment papers through the peer-review editorial process.  He and his once radical ideas are now being cited.  A new normal may be steaming over the horizon.

A final telling anecdote. When Faigenbaum speaks to youth-fitness trainers whose results seem palpably better than average, he asks them how they reconcile 60 minutes of moderate-to-vigorous exercise with 3 hours of television. "What television?" is a frequent answer. No television, no conflict, and no goddamned Barney, so there are mental health benefits as well.

Monday, 21 September 2015

Thin surf and fat wallets

I suppose that people do surf on the East coasts of the Western European Archipelago WEA but the prevailing wind is from the West and that's what throws up the big waves. Serious surfers accordingly go to Doolin in Co Clare or Cornwall and North Devon in the far SW of England. I guess those serious dudes go and live in the West too. I know one case of a fit young chap who had a stonkingly successful PhD in Dublin and then upped-stakes to be a secondary school teacher in Sligo because it was close to Enniscrone and other great surf breaks.

That must be the reason why two monster artificial inland surf-centres are located close to the UK West coast facing the Irish Sea.  I gave a taster a week ago about Surf Snowdonia in Dolgarrog.  It wouldn't be fair if I didn't also give a compl{e|i}imentary puff to The Wave Bristol 200km South. It's actually quite hard to get a picture of how The Wave is going to work although they expect to open in 2016.  They've shifted their site from the Portway between the Bristol Docks and the container port at Avonmouth to a greenfield site in deepest Gloucestershire. They're still trying to promote their venture as green and eco-friendly: their mast-head devotes as much space to organic food and a yoga-bimbo [see R] as it does to hard-chaws sending the spray in wet-suits.  That's partly because their business model is multi-focus (unfocus if you will): the central pool is going to be surrounded by car-parks (natch because it's in the middle of nowhere), a bar, a cafe, a conference centre and "activity, sensory, healing, culinary and herb gardens" [that would be a big pink woo, followed by wah].

Their first vision was much like Snowdonia's: gritty industrial site using the Wavegarden plough-on-tracks technology.  Whatever the technology, it's going to be energy intensive. Shifting tons of water left and right and up requires power from somewhere; probably from the electricity grid. Punters might think of their implicit carbon foot-print as they sip their daiquiri watching the waves from the sensory garden.  They'll have to imagine the white sand and the palm trees. But Wavegarden wasn't right for their image, so they signed up with an American company called Wave Loch which has a system that looks as much like an ocean wave as a skateboard park looks like a mountainside.  Piffling about on 5cm of moving water on top of a pale blue neoprene "wave" looks like a lot of fun but it's a long way from Hawaii.  But it's also got to be efficient: a ton of shifting water goes a long way if it's spread thin.

But that can't be what's going to go down in Bristol because they are talking about generating 6 to 8 waves a minuterather than a continuous flat fire-hose. Their website's explanation "Just like the ocean we use wind (pneumatics) to create our waves. After years of research and testing we found that this was the best way to deliver a vast quantity of almond-eyed barrels" is short on techie detail and long on hip neoprene-speak. Just how do they generate those almond-eyed barrels?  It becomes a little more clear from this scale model demonstration, but not much. I think that the business end of the pool consists of a huge paddle which displaces a bunch of water as it descends vertically. The displaced water has no place to go but along the pool pushing people along with it. In effect it's a controlled tsunami. This is both good and bad when compared to Surf Snowdonia. 1) Surfers are kept separate from the solid moving parts and there are no immovable stanchions or pillars with which to make whack contact but 2) "Surfers will be able to paddle back to the start of the wave and therefore improve their fitness and technique"; the waves only go one way, so just like at sea you can to paddle out again to catch the next ride.  Waves may come every 10 seconds but you're going to miss most of them as you develop your upper-body muscle-mass paddling back to the start.

Is there anything that cannot be monetised and productified?  When I were a nipper, we'd play 'battleships' with no more equipment than 2 sheets of squared paper and 2 pencils. In 1971, MiltonBradley=Hasbro ripped off the idea and packaged a lot of plastic in a big cardboard box. In 1979 they made a version which was needlessly complexified to make deeply unsatisfactory electronic sounds to infuriate any adults in the house: they call pushing three coloured buttons in turn 'programming'.  It's now available as which is free delivers you to advertisers. I am happy to report that pencils and squared paper are still widely available and the surf is up in Co Clare too. harrrumph!

I think the saddest thing about both ventures is that the surfers ethos of freedom, rebelliousness, cut-off jeans, beer, chicks and waves has been monetised by blokes in suits whose product is only available if you have a full-time job to pay for it . . . make that 'whose products" because it's no longer only about the surf its about the designer coffee, the sensory experience, the organic snacks and the holistic rifling of your wallet.

Sunday, 20 September 2015

Sports for all

Sunday Sport II. Fed up with Rugger and boxing? Want to try something less intense that still gets you out in the fresh air and reduces your risk of myopia?
I did another set of sports and pass-times a couple of months ago.

Banned Books Week

That would be today and for the next six days. Banned Book Week was pushed out into the stream of public discourse in 1982 by libertarian + librarian Judith Krug while head of the Freedom to Read Association.  It is important that us intellectuals draw attention periodically to the fact that people are not able to read certain books because certain other people think they are naughty. Naughty is the appropriately schoolmarmish mummy-knows-best word to apply to almost all cases . . . except those where my prejudices are endorsed: then censorship is necessary to uphold the rule of law, the fabric of society and indeed life as we know it.  Mein Kampf, for example, is still banned in Austria.  That seems a bit bolting the cattle-wagon door after the train has left for Birkenau. If it was studied in schools today, it could be exposed as badly written, poorly argued and logically inconsistent and, well, silly. In the modern world, such island bans are fatuous: you could drive from Vienna to Szombethely in Hungary and back in about four hours and bring back a copy of Mein Kampf . . . and a family of Syrians in the same trip.  I had a piece a couple of years ago about a BBW hoax that exposed the knee-jerkiness of our reactions to shibboleths like 'censorship'.

Back in 1973, I came to Ireland equipped for college. I brought a steamer-trunk full of clothes, some pencils, a slide-rule, and a ratty musk-rat Ondatra zibethicus fur coat. I also brought a 25x25x45cm box full of books - mostly cherished Penguin paperbacks. Included in there, because it was funny, because it was set in Trinity College Dublin (where I was bound) and because it was banned in Ireland was J.P. Donleavy's The Ginger Man. I was entirely alone and a long way from home and the TCD accommodation bureau had assigned me digs in Sandymount Irishtown where there was nothing to do in the evenings. One evening, two weeks after term started, I was warm and dry in The Phil, the room assigned to the Dublin University Philosophical Society which I'd been induced to join during Fresher's Week. I was curled up in a corner of a sofa in the far corner of The Phil laughing out loud at The Ginger Man. When I settled in at about 7 o'clock the place was full of other 'philosophers' discoursing about Wittgenstein, chatting to their pals or reading the newspapers which were supplied by the Society.  But as time and chapters wore on, I was chortling more or less to myself, because almost everyone else had drifted off home or to the pub or the library. Eventually there was nobody there except for a strikingly pretty girl who had cast up at the other end of the same sofa. I was far too British to talk to her but she asked me a question and we chatted for a bit before College started to close down for the night and we both went to our respective unhomes.  We met again, and then again, and have been together now for more than forty years. So thanks are due to John Charles McQuaid the Archbishop of Dublin and certain prim others who banned that book. "Two years later her [Edna O'Brien] second novel, The Lonely Girl, was also banned after Archbishop John Charles McQuaid complained personally to Justice Minister Charles Haughey that the book “was particularly bad." It would have been a different road in the yellow wood without their definition of obscenity.

Saturday, 19 September 2015

Scupper me mainbrace, lads

Woot!  It's Talk Like a Pirate Day today, me hearties. I was a bit late last year, in acknowledging this 'armless adventure. For some reason, wannabe pirates find it very difficult to carry a tune possibly because they have drink taken.  The scurvy crew who started the v'yage are now hoping to monetize the idea by publishing books and selling t-shirts and other booty.  Why just last month I was having a bit of pirate fun with Cap'n Pugwash on The Blob.

Last month I was also down in Cheekpoint rifling through their book-exchange, and came away with Poison Island by "Q" in a 1932 Kings Treasuries of Literature edition.  Set in 1813, it's an adventure with a mappe of a Treasure Island, a blind Peninsula War veteran, a washed-up sea-captain, a boy hero, his forthright nanny who is surely going to marry one of the adults and roll-up-your-sleeves Lady of the Manor who can finance a voyage to the Caribbean. The black-hats all conveniently die and the white hats get all the treasure. All good fun indeed and all the better for not having to pay a red cent for it. You OTOH will have to pay £3.00 (and a sackful of doubloons for p&p) for your own copy. There are ITLAPD events in some quite unlikely places. You can get a free fish-tender (something you eat apparently) if cry 'shiver-me-timbers' at Long John Silver's, or a free donut elsewhere if you saw off a leg and have a parrot about your person.  Or you can listen to Cap'n B-flat murder the Righteous Brothers with You got that pirate feeling: so dreadful it's okay.

More importantly, O'Reilly is halving the price on all their R-language [arrrrr, geddit?] programming books until 21st September. R is real useful for graphing and statistical analysis and real difficult to get your head around, so the books might be a good buy.


This year at The Institute, my colleagues have parlayed a set of degrees in Sporty Things into a new MSc in Strength & Conditioning.  The first students are now enrolled and they are ready to rumble.  To launch the venture they asked a couple of Names to come and address all the students and any interested staff.  The auditorium was packed with bright and mostly fit youngsters both staff and students and I was the oldest person there by a country mile.  I teach a couple of sections of Intro Biology to Les Sportifs and I have explained to them that as far as sport was concerned I am welded to my sofa while I reckoned the only contact they had with such furniture was to push one from Cork to Dublin to raise funds for the local Soccer Club.

The first speaker at the S&C launch was Billy Walsh, who was in the news three weeks ago because he was about to resign from being the Head Boxing Coach of the Irish High Performance HP programme since before the Beijing Olympics.  When I was young enough to actually do athletics and afterwards when my residual interest in running and jumping was fanned by watching the Olympics on TV every four years, the Olympics was 'amateur'. The amateurs from the Eastern Bloc were streets ahead of their rivals from Western Europe because they were only nominally in the army or PT instructors - the state made sure that they could devote many hours every week training and practicing. The Western amateurs had to leave training for the weekend or an occasional weekday evening while holding down a proper job in a factory or driving a milk-float.  Sometime between then and now, everyone realised that winning is a) important b) unlikely, unless c) you put in hours and days and weeks and years of relentless weights and runs and lifts.  The Irish Government allocated a tranche of my tax-payers money to provide modest HP stipends to fit and coordinated young people so that they can do training as a day-job.  The way these HP fellowships were allocated by the Sports Council among sports and among competitors within sports seemed to be, shall we say, a bit random.  There is big money to be made from sport but only very occasionally by the Harry Potter practitioners of each sport.  American University Football & Basketball coaches are, for example, paid more than the College President while the lumpy, agile and fresh-faced jocks get nothing at all.  I've talked about contact sports encephalopathy before and new study has found 87/81 autopsies revealing concussive damage to ex-athlete's brains.

Billy Walsh [L, R] was the man who took all the likely candidates off to boxer's boot camp before the Beijing and London Olympics and put them through their paces and told them that he believed in them and that they should believe in themselves. And the kids came through; winning 3 medals in 2008 Beijing and 4 medals four years later in London. As he pointed out yesterday, since the foundation of the state, Irish athletes have won a total of 28 medals in all categories including John Treacy and  Ronnie Delany, whom we've met before. 25% of those medals had been won under his tutelage in 5 years. That's a striking achievement by any measure. In answer to a question from the floor, he said that Katie Taylor is the most extraordinary boxer he's ever had dealings with. This young woman can always find it in herself to do better. Whatever challenge she faces and overcomes, she is always ready to turn round and try harder against herself and her own exacting standards rather than against the girls whom she pummels into losing.

I was itching to ask the elephant-in-the-room question about how he reconciled concussion and contact sport encephalopathy CSE with a duty of care to the athletes in his dojo, but thought it would be bad manners to be controversial on such a big day for my sporty colleagues. I was glad, therefore, when one of the students asked what Walsh felt about the removal of protective head-gear from amateur boxers a couple of years ago. Well, Walsh was amazed that such a diktat had been issued by the International Boxing Association (AIBA) and frankly unable to comprehend their motives. On his watch over boxing in Ireland he knew of 2 concussions in ten years when head protection was required and 10 concussions in just over 2 years since bare-headed boxing was agreed. Larger samples indicate that concussion is paradoxically less likely in helmeted bouts that unprotected ones. hmmm, I dunno; I think the TV networks will have had something to say about how the spectacle is improved if the viewers can see the blows land directly between the eyes ad-breaks.  I've used Katie Taylor's unexpected success as a vehicle for denouncing boxing as a sport with all to much in common with the circus of Caligula 2000 years ago.  Do you notice an uncanny similarity between Billy Walsh [L above, R] and Ernie Schaaf [L above, L] who went into a coma from injuries sustained in the ring in 1933 and never recovered?  Such a nice happy-looking boy that Ernie - he was only 24 when he died. There are surely less bloody barbaric ways to shine in international athletics - Katie Taylor has played soccer for Ireland for example.

Friday, 18 September 2015

Shut up and belt up

A few years ago there was a chilling TV ad put out by the Irish Road Safety Authority RSA in which an image of a car-full of happy young people is voice-overed with "in 40 seconds young Sean is going to kill his girl-friend" . . . because he'd forgotten his seat-belt and in 50ms will nut his g-f to death from behind. When I was a nipper we'd all pile into the back of the family station-wagon on long journeys in a hugger-mugger of blankets, books, pencils and gumboots. Everything, including three small children, was loose and unrestrained and it was all travelling along some wretched road at 100km/h. Luckily my father hadn't yet taken to falling asleep at the wheel - that came later with the type-II diabetes. In the mid-to-late 60s, seat-belts started to get talked about as a new invention and most opinion was that they were a bore and a chore and probably pointless. Everyone knew someone who had been thrown from a moving car into some bushes just before the vehicle plunged over a cliff to burst into flames on impact.

If one man deserves the credit for the fact that everyone I know wears a seat-belt all the time while in a moving car, it is John P. Stapp, whom we met yest travelling as fast a jet-plane along a railway track in the interests of research. As well as being a medical doctor, Stapp was a full colonel in the USAF and his team was finding out what needed to be done to minimise the death and injury sustained in a plane-crash. Stapp was also moonlighting with experiments putting cars through their final spectacular paces into brick walls. The USAF bean-counters and bureaucrats tried to put a stop to these unmilitary activities until Stapp pointed out that more pilots died in auto-wrecks than plane-crashes. Seat-belts and their mandatory use have been the main force in reducing relative road-deaths to 1/3 of their levels in the 1940s. That's still 43,000 deaths (and 1.9 million road accidents that cause physical injury) every year in the US. President Johnson mandated seat-belts in the USA in 1966.  To put an image in your head, 43,000 coffins is a football-field covered so you can't see the grass and stacked 10 deep.

Colonel Stapp convened the first workshop on car safety and engineering in 1955, that developed into an annual Stapp Car Crash Conference which is a forum for discussion about how to kill fewer people with cars. In 1955, Stapp invited a variety of stake-holders to Holloman Air Base near Alamogordo, NM: doctors, auto manufacturers, academics, the military, traffic analysts and safety consultants.  Over the years, they have changed the interior and exterior of cars so that they are more effective at "packaging people" for safe-delivery. Not just seat-belts and the details of their design and anchorage: rear 'parcel' shelves are no longer available to serve as head-height missile-launchers; hard/soft plastic lines the interiors of modern cars; bumpers have been totally redesigned and crumple zones are now an integral part of car design.  When I had my little tip two years ago, I left the road, mounted the ditch and stove in the off-side front corner of the Yaris but the air-bags didn't blow because the controlled structural failure had absorbed much of the deceleration energy.

The car industry was extremely unwilling to embrace seat-belts to begin with. They felt that having them hanging in every car would imply that cars were not safe and cause a tumble in sales.  It is the same argument that refuses to have explicit codes-of-conduct: the existence of protective measures alerts people to danger and organisations would rather that possibility never enters anyone's mind. But putting your head in the sand never averted danger made it harder to escape it when it arrived. If you want to minimise the chance of your being part of next year's 43,000 cohort of the dead, you can shut up with your anecdote of Gt Uncle Jim escaping from his tractor when he drove if off the pier in Ballyhack and belt-up

Thursday, 17 September 2015

Blow yer eyeballs out

Did I mention that term has started at The Institute? After a week of meetings and setting things set up I am now in the maelstrom of 18 contact hours per week.  That means that I'm spending about 90 minutes a day in the car driving to, and then from, work. That means that I get to listen to the wireless more than I do if I'm sat on the sofa at home. A few days ago, Sean "Newstalk-FM" Moncrieff was interviewing aviation writer Craig Ryan about his latest book Sonic Wind: The Story of John Paul Stapp and How a Renegade Doctor Became the Fastest Man on Earth. Reviewed.  It was surprised that I'd never heard of the chap, but I've definitely seen his deformation pictures [R] as he made yet another run on the rocket-sled at Wright Field (aka Wright-Patterson Air Force Base) outside of Dayton, Ohio. Although he qualified as a doctor, he joined the USAF in the closing stages of WWII, and found himself, the late 40s and early 50s, running a series of trials to see just how much deceleration a human being can endure.  They were also investigating what arrangement of straps and padding and seat-orientation would best preserve human vital organs when subjected to 30x the force of gravity.  There is only so much you can glean from strapping a 70kg sack of hominy grits in a pilot's ejector seat and sending it down a track at 500km/hr. They tried to give some chimpanzees the ride of their life but eventually settled on fit male human volunteers to stress test themselves and their protective gear.  They were better able to tell where it hurt.

Stapp was as eager as any young bucko to give himself to science and was the 44 y.o. crash-test dummy for dozens of experiments including the one where they turbo-charged the rocket-sled to send it down the track at almost the speed of sound.  On that run, in December 1954, Stapp travelled at 632 mph [>1000km/h] getting from 0 to 600 in about 6 seconds and decelerating to a standstill in just over 1 second. When they unstrapped him from his harness he was able to walk a few steps although he was unable to see. His eyeballs had been deformed so badly by this unnatural stress that they filled with blood: they eventually recovered their function.  That's an interesting observation because the eyes are the only part of the body that cannot be effectively harnessed; they appear to be the limiting step.  All of these tests helped the USAF develop seat-belts that spread the load of deceleration over several robust (muscled, padded) surfaces and yet were consonant with their pilots having sufficient freedom of movement so that they could fly the bus. So hats off to The Fastest Man on Earth, who helped work it all out while sustaining only minor injuries - broken ribs and wrists mainly.

In the process of stress-testing the equipment until it almost but not quite failed, the engineers came up with Murphy's Law "If anything can go wrong, it will". And yes according to one elderly informant there was a real Lt. Murphy. But these same engineers put each other through a catechism of the imagination before each change in protocol: they brought all their experience and all the tales they'd heard and all their book-learning together to see where something might fail; and then introduced a fix against that eventuality.  John Stapp and the other volunteers depended on the smart boys to not finish up as hamburger. And more USAF and other pilots survived frightening crashes than happened before the scientific research.

Wednesday, 16 September 2015

Sci Caf Wex Sep

Since February this year, we've been meeting on the 3rd Tuesday of every month in The Sky and the Ground, South Main Street Wexford to talk about science. It's partly to generate some parity of esteem for Science in a town which is dominated by the Arts.  The Wexford Opera Festival has been running for two generations bringing "difficult" sung music to the fore. The attitude of the organisers is that a rousing chorus from Aida or a perfectly eye-moistening duet from Puccini, let alone a jolly bit of Gilbo and Sulli, can be had any fine day on the classical music station on the wireless.  But obscure opera from Central Europe?  Not so much.  Menotti is about as accessible as the Wexford Opera gets. There may be a reason why Lortzing's Der Wildschütz and the knobblier bits of Mozart have been left on the cutting room floor of history.
Last night it was my turn again at the Science Cafe. The venture is along way from going viral and we rarely get more that two handfuls of people to turn up.  So the turn of the usual suspects comes round all too often.  I thought it would be easiest if I cobbled something together about the microbes which are important to food. As always, when you start doing research, even in an area where you think you know something, you turn up some really interesting specimens from under the stones of the interweb. I divided my findings into two long lists.

Bad Boys: the bacteria and fungi that do a number on what we want to eat.  Making it unpalatable / repulsive or downright dangerous. I've written about Campylobacter before. but the fact that this bug is present in all chicken and causes 3x more deaths and lost work-days than, say, Salmonella was news to some of last night's congregation. Everyone knows about Salmonella and E. coli although only a few can spell Escherichia, but Campylobacter is the micro-elephant in the food industry room. As I say my list was a lot longer than Campy and I'll be mining it from now till Christmas.

As an antidote to my woeful tales of talking to the porcelain telephone, I took one example from an even longer list of food Good Girls. To make it real, I made a small batch of sourdough and punched out a baker's dozen of small sourdough buns so that our scientists could have a nibble with their pints. I also brought in an aliquot of the starter which had caused these mini-breads to rise. It was a great batch, even if I say so myself, the insides pocked with large ragged-sized holes like the ciabatta you might buy from an artisan bakery. Good sourdough has to be made a little sloppy if you want it big-bubbly. Like really fine emmental, it is bubbly because it is filled with carbon-dioxide. The CO2 comes from the activity of a community of bacteria (mostly Lactbacillus spp.) and fungi (mostly Saccharomyces spp.) which prop each other up in a multi-species mutual support group.  All the baker needs to do is given them more flour every 1-5 days.  I was told last night that I was mad to keep my starter in a plastic dish - the plastic leaches stuff into the stew than makes the bugs feel a little crook. I'll shift them into a glass jar soonest and see if they go from being good to being glorious.

Tuesday, 15 September 2015

Seaweed for all

Minnesota is about as far from the ocean as you can get in North America - the nearest saltwater is 1500km NE in Hudson's Bay. In a Soviet style centrally managed economy the U of Minn wouldn't be seen as a sensible place to devote a scientific life to the study of sea-weed. But the principle of academic freedom allows for all sorts of logistically daft research.  Egyptologists work from the British Museum in London (3500km SE); while fossil-fish expert Neil Shubin lives in Chicago but carries out field-work in the Canadian Arctic (4000km N).

Josephine Tilden was born in in 1869 in the corn-belt of Iowa but her folks moved to Minneapolis when she was a child and that's where she went to school.  She got her BSc from U. Minnesota in 1895 and stayed around to obtain a Master's degree whose results were published in her first paper On Some Algal Stalactites in Yellowstone Park. In 1897, her Alma Mater took her on as an instructor to teach the students about Algae to round out their botanical education. She was the first woman on the academic pay-roll of the University.  The following year she was off to the clatter of islands that fill the Strait of San Juan de Fuca between the USA and Canada and between the massive Vancouver Island and the mainland.  We've been there before at Tommy Thompson's marine station on McConnell Island. Tilden had worked out that a very low tide was due in the area in early August and was determined to sample algae which are not normally accessible. It was all very derring-do in a classic late Victorian way. Tilden was paddled to her proposed field-site in an open canoe accompanied by her redoubtable mother as chaperon. The rare-in-Minnesota seaweed which she pulled if the ocean floor and pressed into her collecting books formed the start of a massive collection of algae from all all over the wet world.

Thomas Baird, the chap who paddled the canoe, was also the owner of the foreshore on that remote stretch of Vancouver Island. He was so impressed by the doughty dedication of his companions that he offered to sell Tilden enough property for a cabin to serve as a research station to shelter her and her students when she came back in subsequent Summers to carry of further research. As we saw on Sherkin, longitudinal studies of the fore-shore are really important to establish the base-lines of natural variation in abundance and diversity. A single sample is barely scientific.  From 1901-1906, faculty from U.Minn brought students to this remote spot: presumably by train, ferry and open boat.  And not only to collect sea-weed: the geology, botany and zoology of the area were also ripe for research. The Minnesota Seaside Station [R from], run by Tilden and her boss Conway MacMillan, Professor of Botany, served to educate a couple of dozen students in each of those years. The area is now called Botanical Beach and is famous for its tidal rock-pools and foreshore, it looks busy.

MacMillan and Tilden were so caught up in the value of the place for scientific research and teaching that they petitioned the University to take the Station under its financial and official wing . . . and were refused.  The University only saw an administrative nightmare: how to audit and maintain a property that was 2000km distant and in a foreign country. MacMillan was angry enough to resign in protest. Tilden was not so easily put off and stayed on in the University, undertaking some enormous trips across the Pacific and round the world collecting Algae to get a more complete and comprehensive picture of the distribution of the several species. She was a bit obsessed by algae but was also able to see them as part of the web of life and was vocal, and far ahead of her time, in her concerns about the effects of over-fishing and oil-spills on the whole marine ecosystem.  In 1924, she took a party of 15 to a conference on pan-Pacific conservation in Hawaii, and then expected the University to pay their travel expenses. It was only $15,000, she said, a snip compared to the $750,000 raised for the college football stadium.  She must have been a royal [as in Princess] pain for the poor people working in the finance department.  A few years later she set off on a round the world collecting trip with a group of loyal students, who are asked to chip in $1000 each towards expenses. It was successful if 50+ steamer-trunks full of specimens shipped home to Minneapolis is success.  Her new Head of Department had to deal with a flurry of bills for shipping and incidental expenses as his maverick instructor romped round the world with her train of students all getting wet to the knees twice a day as they looted the fore-shore for material. In 1937 she was asked to retire and there was a war over who owned, and should have access to, 'her' specimens which had been paid for by the University.  It's a classic early IP tussle.

She retired to Florida and lived in straitened circumstances for another 20 years before bequeathing 'her' collection to a friend and fellow oceanobsessor from San Francisco. The specimens eventually returned to UMinn where they sit gathering dust today.  It's all in the essay The Algae of Acrimony, which is such a neat title you have to read it.  Science needs people who are so certain they are right that they forge ahead beyond the current frontiers; but equally science needs people to rein these pioneers in, lest they disappear off the rails into whoowhar-land. Someone - that's most of us in science, indeed - has to plod along carefully picking up the pieces and filling in the gaps and someone has to pay for it all.
Now N=45 Women in Science on The Blob.