Monday, 31 August 2015

Pour les autres

Some people seem to be put on the planet to serve humanity. They get up every morning, have breakfast and start the day's work and at the end of most days they've helped someone who was in a less fortunate position. They are the ones who stop the school bully, question authority or normality when they see a manifest injustice or just go out and clear drains because that will clearly help lots of people and nobody else seems to be doing it. I don't know what your experience of facing up to bullies is, it's not something I do and I don't see it happening very often, even among adults . . . even among scientists. And nobody, nowadays, cleans drains for a hobby.

These servants of humanity may have an ordinary or extraordinary life but their unspoken and probably unthinking baseline is looking out for other people. I think that Françoise Barré-Sinoussi is one such. I know nothing about her early years, so I can't say what she was like in school, except that it was in Paris, and that she went on to study in l'université de Paris and thereafter to work in the l'Institut Pasteur whence she obtained her doctorate in 1974.  It's possible that she might have motored along working in France's premier research institute on the study of viruses but she was in the right place at the right time when the Pasteur received a biopsy from a young man dying of AIDS in 1983. Because she had developed appropriate tools on her earlier virus projects, she was able within 15 days to show conclusively that the death of lymphocytes in the mystery sample was associated with the appearance of a virus. It took another 15 weeks to tie up the loose end and publish the paper and 25 years before the Nobel Prize appeared, but the discovery itself was "easy". I covered the HIV story a couple of weeks ago as a battle for prestige, priority and payola between a two big personalities and two world powers - the boy stuff.

A few months later, Barré-Sinoussi was in San Francisco for an academic conference about the new virus. It was an appropriate venue because it seemed at the time as if San Francisco was the epicentre of the epidemic - nobody had started counting the bodies in sub-Saharan Africa. One of the delegates asked if she'd like to meet someone who had the AIDS and she seems to have shrugged in a Gallic way before saying "Sure, why not?" It had a profound impact upon her: as she took the hand of the wasted, cadaverous, dying man in the hospital bed he mouthed "Thank you" in a barely audible croak.  When she asked why she was being thanked he said "Not for me, for the others". He knew he was fucked, but he saw that her scientific breakthrough was a source of hope for a cure. That benediction was almost the anonymous San Franciscan's last act - he died that night.

She spent the next 30+ years tied to and tied up in HIV and AIDS. Her then boss, Luc Montagnier, has moved onto very different things and they no longer collaborate. Significantly and usefully, Barré-Sinoussi has a total view of the HIV/AIDS and her whole life since 1983 has been focused on this one Big problem.  In this sense she is a Hedgehog "πόλλ' οἶδ' ἀλώπηξ, ἀλλ' ἐχῖνος ἓν μέγα" Archilochus; Multa novit vulpes, verum echinus unum magnum Erasmus; A fox knows many things, a hedgehog knows one great thing. Isaiah Berlin.  You can hear her speaking at the 2015 Lindau Conference [Lindau previously with Hans Rosling].

Antiretroviral treatment ART is fine but you have to a) take it regularly relentless forever b) get it to everyone: not just those who are rich.  Some countries do far better at this than others. The uptake of ART in Cambodia, a former French colony with which FB-S has worked for many years, is 80%.  In the USA the rate is a shameful 28% - poor black uninsured Americans with HIV just die. The incidence of HIV infection is higher at 3% in Washington DC than in Dakar, the capital of Senegal. It was one of the staggering successes of medical science, how it took about a dozen years from the formal identification of the syndrome to the launch of a successful therapy. Partly that was because a shed-load of money was thrown at the problem but it was also because of the solidarity between patients, clinicians, and scientists.

But it's much better if you don't get HIV in the first place, so Barré-Sinoussi has been a strong advocate for properly informed sex-education among the young . . . and not only in Senegal and Cambodia.  She finds that youngsters are plug-ignorant about the sources and consequences of HIV. After she got the Nobel Prize in 2008, she acquired the inevitable talking-head celebrity status that accrues to Nobellists and took it to The Pope the following year after the old man had said something demonstrably silly about the relationship between condoms and HIV transmission. Show me the evidence for your assertion, was the admirably scientific sense of her open letter to the Pontiff, which was never answered or acknowledged. She could also have asked about the compassion of his assertion or the economic and social consequences of his assertion and she does ask those questions in other forums.

She is also vocal in questioning the social, medical and economic sense of stigmatising homosexuality in Third World countries like Uganda and Cameroon where she has worked and where homosexual behaviour can result in a jail term.  Before we get too complacent, let's remember that Ireland only decriminalised homosexuality in 1993. Like the vocal Caitlin Moran expressing the anti-value of dismissing the contribution of women, Françoise Barré-Sinoussi has been talking seriously, to those who count, about the self-destructive social consequences of treating drug-users and homosexuals as untermenschen.

Today, the last day of August, Françoise Barré-Sinoussi will step down from her position in the Pasteur under the normal French compulsory retirement scheme. She is content to do so at least partly because a protegée of hers Dr Michaela Muller-Trutwin is going to be given her own lab as the old make way for new. In the Paris of the 1970s it was really hard for a young woman to get a start in science. Young Françoise had to use all her assertiveness and determination to find a lab that would accept her application. Her father and all the father-figures tried to discourage her from pursuing such an unsuitable career for a woman. She showed them! And she showed the world what a difference a woman can make . . . pour les autres. Bonnets bas!

Sunday, 30 August 2015

Like sheep

We were talking at home the other day about The Girl With The Dragon Tattoo the viral detective novel from Sweden. I said I was a little sour graped that a key plot hinge - an old photograph reveals that the baddie had been in town when he said he wasn't - was something I would have incorporated into the novel I never wrote when I was 17 . . .because I hadn't then the stamina I have now to whang stuff down for The Blob. I struggled through TGWTDT and didn't pick up the other two books in the trilogy: the casual misogyny and violence was too much for me - the original Swedish title was Män som hatar kvinnor [Men who hate women] - and I certainly wouldn't have started a book with such a creepy title.

My Old Man died 15 years ago and my sister and I went home the following Spring to sort out his Shed; which was filled with paintings. We sorted them into categories: nautical, landscape, local, foreign and selected a few which had nostalgic or visual appeal.  One of them he had called "A Long Way Home '96" showed a small flock of sheep walking behind their shepherd down a broad-verged lane.  Several years afterwards, The Boy scanned several of his grandfather's works and send e-copy out to the family for interest and 'the record'.
This morning The Boy sent me a link to the B&W photograph below The Da's watercolour. The photographer was James Ravilious and he called it "Irwin Piper taking his sheep for slaughter" which is a little different in sentiment to my father's title; but probably more true to actuality. Ravilious collected an enormous archive of pictures of everyday life in North Devon in the 1980s. I don't think there can be any doubt that my father plagiarised copied was inspired by the photograph, although I haven't the foggiest idea where he would have come across the photograph. When we were young, I think he'd use the painting as an excuse to get out into the fresh air and away from the wrangling mill of children and domestic responsibility.  After he'd retired and his children had left home, his holiday watercolours evolved into a wider variety of genres, media and materials and he started to attend art classes in the local town. Maybe his one of his teachers had presented the photo as a class exercise?

Sherkin folks

Any regular readers who imagined me slaving over the kitchen table to launch early morning posts at the beginning of the week would have been would have been mistaken.  I learned from the tech-savvy Dau.I that you can have the blogspot robots to get up in the morning and do the launching for you while Blob-the-author lies in the bed snoring or goes off-site.  I don't ever do lies-in-the-bed but I do occasionally go off-site; so this feature is going to be handy in future.  As I mentioned yest-yest, I was off on Sherkin [map] for two nights loafing about the island and getting some inside dope on how it ticks. Advice:
  • You shouldn't go uninvited to the Sherkin Marine Station. 
  • You should bring raingear. 
  • It's surprisingly warm in the sea. 
  • Lunch at the hotel might be uninspired and expensive (view from terrace compensates).  
  • The ferry trip is worth the fare even if you didn't step off onto the island.
  • Take the minibus from the dock - all the latest gossip.
On our way to and from the hotel for lunch, we passed the village school which looked impressively well resourced, the original stone building right on the edge of the bay which almost splits the island has been supplemented with two temporary classrooms; there is a tarmac playground and some neatly mown grass and a tree and a painted gate.  On the bus to the ferry on our last day, we asked how many children were enrolled because the total population of the island was rather less than 100 and most of those are artists, musicians, photographers all of a certain beyond-young-children age.  It turns out that the enrollment last year is two (2!) a brother and sister who live near their teacher in Skibereen.  They all catch the ferry-then-minibus every morning, have five hours of schooling and then go home to Skib in the evening.  There is a part time secreatary employed to cope with all the paper work: the tedious-and-difficult morning roll-call, letters to the parent, reading and implementing circulars from the Department of Education. There is a certain ambivalence on the island about this extravagant use of tax-money: if the school is ever struck from the register then it will never get reinstated; and many of the islanders think / believe / hope that children will someday again be raised on the island.  Seems like a better place for home-educators than school-educators but it must be hard to make a normal living and raise a family on the island itself; cripes, it must be hard to make even a weird living on the island.

 If that casts a rather negative light on the circumscribed world of island living, there are advantages.  While we were there, The House suffered a culinary embarrassment: they had promised some unexpected but welcome guests a particular dish that required coconut milk and then found that they were fresh out of it. They phoned the Gala store in Baltimore to ask if they might have any in stock . . . expecting the answer No. But there is a demand for such exotica among the yachties who come for the regatta season and the shop agreed to send over two tins on the next ferry.  Someone on the ferry was happy to deliver to the Sherkin shore two suitably addressed tins wrapped up neatly in brown paper. I like that immensely, it shows a sense of community. It's probably against the rules and lost someone some money but rules are there to serve the people rather than vice versa.

One of our fellow guests was an antique dealer from Oz. I've never met one of them before and could even have got snitty about whether anything in Australia would classify as an antique seeing as the country wasn't settled by Europeans until the day before yesterday. We think of Europe as stuffed with history, antiques and culture as a cake is full of currants. But I would be wrong and there is a distinctively Australian style of mid to late 19thC furniture.  The distinction is mainly in the use of Australian Red Cedar Toona ciliata rather than mahogany but there are more subtle differences visible the discerning and well-trained eye.  The dealer was saying that his trade was not as brisk as it had been in the past and it's only partly because all the antique escritoires and chiffoniers have reached their final destination.  Another significant issue is the Australians are now wider than their forebears. Nobody can believe that a nice side chair with finger-thick legs is going to support their enormous bottom and no couple sleeps in a bed 140cm wide any more, so there is much less demand for old, hand-made furniture.  That's kind of interesting - I'd never have found that out in The Institute; it pays to travel.

Saturday, 29 August 2015

Get yer cameras out

Wikipedia is on a promotion trying to beef up their photo banks. They are running a Wiki Loves Monuments competition across the world with local/national top ten going head to head with each other later in the year. If you're not from Ireland (likely) you'll have to trick about with the URL to get your local page.  The Irish 2014 winners represent a clatter of National Monuments across the whole country.  I guess the judges of the competition are looking a) for photos that will show what the monument looks like but also b) have some artistic merit.

I would have been very surprised to see that one entry in the Irish top ten list is Ballymoon Castle [R by poleary91] almost exactly halfway between home and work for me. I say would have been surprised because until this Summer, I'd never seen it. Indeed until this Summer, I'd never even heard of it and it's a huge pile of history less than 20km from where I live. But in June I was out collecting water samples and took a new route to Bagnelstown and !Shazzam!  In the middle of a grassy meadow was a castle with walls 2.4m thick, and 6m tall.  It has been there for 700 years! The romance of the name and the site is, as ever, enhanced by french Château de Ballymoon and they're also trying to persuade us that it could be Замок Баллімун.

Ireland is as thick with culture as a fruit-cake is full of sultanas. I think we should share images of this rich history and so do wikipedia: the top prize is €200 [and immortal fame] and there are others on a sliding scale.  The deadline for submission is 30 September 2015. Last year's global winner was 1st Place – the Holy Mountains Monastery, Sviatohirsk, Ukraine by Konstantin Brizhnichenko. It's interesting how many of the global winners were low down in the national heats. If you're from foreign, your mileage may vary, but you should still enter.


Last Thursday of August was the 2015 VIBE meeting held in Dublin City U.  Last year The Institute hosted this annual meeting of the Virtual Institute for Bioinformatics and Evolution because the year before in Galway, I had loudly volunteered to make it happen. Hosting a national meeting was one of the criteria that got me promoted from Assistant Lecturer to a higher payscale; indeed I was personally congratulated on the event by our President. The organisers of VIBE 2015 did away with the poster session and substituted it with a section between coffee and lunch of flash-5 talks.  This is a five minute opportunity for a young researcher to lay out their stall of preliminary data for feedback from the community.  I was delighted that one of my final-year students presented the results of her project work supplemented by a 12 week work-placement in my old lab in TCD. She has some interesting findings that give us a hypothesis to test and it's all about marine mammals which are, if not exactly cuddly, at least recognisable by everyone in the room.  Lots of feedback, therefore: almost certainly more than if she'd been required to stand by her poster through all the coffee breaks.  I thought that flash-5 talks were a radical and positive change in the workings of the conference but it turned out that the poster-session was cancelled because a different conference elsewhere on the DCU campus had commandeered all the poster-display boards.

The first full talk of the day was a substantive piece of work by a DCU graduate student who is clearly going to go far - at least as far as Leeds because his boss is brain-draining from the country next month. But I wish someone would tell him about its vs it's because he got it wrong in the title slide of his talk and there are enough apostrophe nazis in the room and they notice these things and it makes them more critical of the work. It shouldn't matter but it does and it's better to learn the rules than annoy potential employers, grant-reviewers and paper-referees.  One of the many things I learned from Bob Tamarin, one of my mentors in graduate school, was that you wear a suit and tie to interviews . . . because it shows that you keen enough on the job to go through with such conventions.

Looking beneath the hood it's easy to find gross spelling errors which show that the authors couldn't be arsed to proof-read their manuscript. If you look for "psuedogene AND pseudogene" on Pubmed or Google Scholar you get hundreds of hits including one from Nature. If nobody on the team has picked up those errors then you should be double-plus skeptical that they've labelled the axes of their graphs correctly.  Years ago, I put together a list of these bloops as an exercise for learning how to use PubMed: lenght, developement, chromotin and chromasome are all wrong contra convention.

I've got a pal in Manchester who wrote The Book on Bioinformatics. It was almost more trouble than it was worth.  She wrote the book easily enough because she had been teaching a course on the subject for a few years and more or less transcribed her notes and illustrations.  The pain came in getting it published by an American company. She was a tiny bit on the unbending side as you probably have to be successful as a women in science: if you don't have some backbone, lesser blokes will gallop through you for a short-cut. It came down, at one point to a termination war: she wrote realise, they corrected to realize and she decorrected the proofs.  As the deadline approached, some idiot did a global-search-and-replace s/ise$/ize$/ and it went off to print; including the phrase "it is no good being wize after the event". If the bard himself couldn't be bothered to spell correctly, how come know-nothing copy editors feel they can do it better than the author?

Friday, 28 August 2015


Sherkin, Inis Earcáin, [the island of the Fair (ie. golden) Head] is one of a clatter of islands striding out from Roaring water Bay in the far SW of Ireland. Baltimore, the ferry-port, is 2 hours of twisty roads West of Cork. If the trend of the islands in the map above looks like a drowned fractal version of the parallel WSW pointing fingers of land that make up the coast SW Ireland [R: they've only bothered to include Clear Island; the Southernmost inhabited part of the Republic.] then there are probably good geological reasons for that.  We had two nights on Sherkin at the beginning of the week as guests of Mike-the-Vet who runs a 'residential & cultural centre' called Sherkin North Shore.  It was the only time we could squeeze into a Summer busy with other commitments; but I'm right glad we made the effort.

The standard version of Bed & Breakfast is designed to give all guests their privacy.  The dining room is usually full of piffling little tables laden with plates and cutlery and condiments where couples talk to each other in whispers while sawing away at rashers and eggs and pretending their fellow guests are not there.  The best B&Bs a) serve yoghurt, muesli and fruit salad b) have a single dining table which requires butter and tea, toast and marmalade to be passed to neighbours.  If the latter situation holds then it turns out that the old chap is a retired embalmer from Chicago while the young couple with matching jumpers are triathletes who won a medal in Skopje in 2005.  In other words, far more interesting than discussing the itinerary for the day's rubber-necking with your partner. Sherkin North Shore is like that, in spades. Because only a certain type of traveller will take a passenger ferry to a sparsely inhabited island and walk 3km to the place they are staying.  That is a tiny exaggeration because there is a minibus supported by the government which will take you anywhere on the island for €2 a head; conveniently this service meets every ferry except at lunchtime.

There isn't a lot to do on Sherkin: no fair-ground rides; no cinemas; no candy-floss; no lettered rock.  just the sea, the fore-shore, a limited network of lanes connecting the extremities of the island and the cliffs, caves and beaches in between. With so little external entertainment you're better off if you are happy in your own skin.  It being the West of Ireland, you should also remain happy if that skin gets wet. Sitting in a chair above the rocks at North Shore, you can see the grey curtains of rain drifting in from the ocean, so you know you have 4.5 minutes to throw your book into the common room and help bring the sheets off the line.  But sure, if the sheets get an extra rinse, you know that the sun will be out again in 30 minutes.  If you pay attention in the evening you'll see seals Phoca vitulina bobbing about among the rocks waiting for mackerel or even an otter Lutra lutra weaving along the rocky shoreline. There's also plenty of bird-life to amuse twitchers.

Sherkin is famous for its Marine Station founded 40 years ago by Matt Murphy and still run by his family. Every Summer since then, they have enlisted volunteer help from the mainland and abroad to survey the life drifting through Roaringwater Bay, the foreshore and its hinterland.  Sherkin has a staggering number [N>500] of plant species recorded at least partly because of the attention given to it by these observant visitors: coming back from the pub in the evening, someone will stop to urinate in the ditch and see another plant not previously recorded. That long term record is the sort of thing Maude Delap was doing in Kerry 100 years ago but is desperately unfashionable now.  If you imagine that Matt Murphy is a a sort of Ed Ricketts from The Log from the Sea of Cortez, you wouldn't be far wrong but he's retired now and a bit fed up with uninformed and uninvited people rocking up to his door and expecting an effusive welcome and a cup of tea. You can get both from Sherkin North Shore about 400m East.  Sherkin is more widely known for the fat tabloid newsletter called Sherkin Comment, produced by the Marine Station on a quarterly basis.  When our girls were growing up we often picked up an issue or three from ENFO in the centre of Dublin.  The Comment is like a blog in print, a gallimaufry of information about science and the natural world.  I couldn't resist picking up a few back-issues from the "free take one" stack at the Islander's Rest Hotel where we went for lunch on Tuesday.

After lunch we walked the 5km to the far end of the island for a closer look at the storied heights of Clear Island. We found a rich stand of peppery water-cress Nasturtium officinale growing in a roadside drain along the way. At the end of a fuchsia-overgrown lane there was a little shingled beach between two headlands pointing West, I was disappointed in my search for buoys but I was happy to sit on a rock looking out to sea and not thinking - sometimes I sets and thinks and sometimes I jest sets - we're all better off to think less and sit in the quiet for as long as we can bear it. As long as you can bear it is how people treat swimming in the seas around Ireland. A friend of mine has just returned from Switzerland where he was swimming in the Upper Rhine just after it spilled out of the warming basin of Lake Constance and before the river is turned into an industrial sewer as it passes Basel: the water temperature was 22oC!  I took a because-it-was-there-and-so-was-I plunge into the sea at the Silver Strand nearer to Sherkin North Shore, it was bracing but a long way from murderous; with practice I could get to enjoy it.

Thursday, 27 August 2015

Things that go whoosh in the night

Last year I was on about Aluminium: how we depend upon it to hold 7-Up and Indian take-aways and 500 people aloft in a wide-body aeroplane.  Aluminium the element is abundant in the lithosphere but aluminium the metal is extremely costly to produce.  The key process is electro-smelting of aluminium oxide Al2O3 which requires megawatts of electricity. That is why aluminium plants are usually situated near a source of hydro-electric power.  More than 100 years ago in 1907, the Aluminium Corporation of Dolgarrog started to output tons of aluminium sheets. This venture depended on damming a tributary of the Conwy River in North Wales and running a pipe [R with adjacent tramway] from the Coedty Reservoir formed behind the dam [290m elevation] to the turbines of the hydro-power plant below [50m elevation].
In the 1920s, the rapacious directors decided to dam Llyn Eigiau a further 100m higher up the valley.  That dam was poorly surveyed, poorly engineered and poorly built with sub-standard materials on superficial foundations. On the night of 2nd November 1925, after a week of torrential rain - 650mm in five days! - the Eigiau dam failed and released a 15m wall of water which over-topped and then destroyed the Coedty embankment below and carried on downhill to wipe out the lower part of the village of Dolgarrog.  The power of 1.5 million tons of water was able to shift 500 ton boulders, so the puny works of man didn't resist for long. The church and a couple of rows of houses were batted aside and at least 16 accounted people were killed. With a fair amount of turn-over in the works work-force nobody can be sure if there weren't itinerant labourers billeted in the village who disappeared without trace. Luckily, it was film night at the village hall, so much of the population was above the plume of destruction and survived.  It was quite similar to the Vajont dam burst 40 years later.  In that case I calculated that it took 25,000 tons of water to kill each of  2000 people.  The Dolgarrog disaster was much smaller both in absolute, but also in relative, terms: it took 100,000 tons each to kill the misfortunate Welsh people. Dams are one of the mightiest engineering feats of which man is capable (beavers Castor canadensis are pretty good too) but they have to be built right and in sensible positions or they are a ticking time-bomb that is difficult to defuse or deconstruct.

Wednesday, 26 August 2015

yesterday's bread today

Following on from yesterday's post about baking we'll have a bit of historical research. As I've been making bread from scratch for the last 30+ years and with sourdough for the last 3, I know a bit about the process and am interested in it. So I was delighted to see some very old news brought back to life concerning very old bread. In 79 CE, a baker in the fishing village of Herculaneum outside Naples put a batch of loaves into his oven.  It never got eaten because the village and the neighboring town of Pompeii were overwhelmed by pyroclastic flow when Vesuvius blew its top. In 1930, during careful archaeological excavations, the bakery was revealed with the loaf [R] still in the oven.  A couple of years ago the British Museum asked celebrity chef Giorgio Locatelli to recreate the bread using the best information that we have as to the recipe.  It looks like the circumferential indentation might have been for a piece of string to facilitate carrying the load home with the other groceries. The BM was interested because in 2013 it held an exhibition of the artifacts from Pompeii, including the carbonized loaf. This is preserved in astonishing detail: the string line and the maker's stamp on the 8 0'clock segment saying "Made by Celer, the slave of Quintus Granius Verus".

Baker's stamps were an important part of the trade in bread in ancient Rome. You needed to know that your loaf was authentico, but large and important families would leave their stamps at the baker, so that they could guarantee that they got what they had paid for.  And there was a whole bureaucracy associated with the manufacture and distribution of free bread to the citizens of Rome.  If you've got spare $$$ you can but ancient baker's seals when they come up for sale.

I was just going to slap this up on the 24th August because that's the date of the 1936th anniversary of the final fatal eruption that buried the Roman streets under meters of rocks, ash and pumice . . . except that it isn't. In the stables at the back of the bakery is a heap of fodder for the donkeys mainly beans and oats but also annual herbs that you wouldn't expect in August. And in another part of the site, a lady's purse has been found with a commemorative coin for late September 79 CE.  Other preserved bodies are found dressed in Winter woollies rather than a light Summer chiton. The fossilised food in the market spoke October rather than August. The known direction of wind from the distribution of fallout is not typical of August and agree with a long term study of weather records from meteorological stations in Rome and Brindisi from later in the year.  All that weight of evidence against a single line in a letter from Pliny the Younger to Tacitus saying that the disaster occurred "a.d. IX kal. sept." [nine days before the 1st of September].  Occam's Razor indicates that the standard date is more likely as a typo for a.d. IX kal. nov. or less likely a.d. IX kal. dec.  and that the eruption happened on the 24th October or 24th November. Pliny's uncle Pliny the Elder, the local admiral, was the most famous casualty of the eruption succumbing to ?fumes?asthma?corpulence?stroke? while on a search and rescue mission that got bogged down in the maelstrom.

Tuesday, 25 August 2015

Coffee and cookies

A tuthree years ago, I went to spend a week with my sister in Slad just outside Stroud in Gloucestershire in the very heart of rural England. This is the hamlet in which poet and traveller Laurie Lee had grown up and from which he Walked Out One Midsummer Morning. Indeed The Sister and her feller now live in one of the cottages the poet inhabited when he returned to this native valley as a grown-up.  It was great to hang out with them. But every day that Summer, I Sneaked Out One Midsummer Morning long before either of them had woken up and padded through the gorgeous waking countryside into the town of Stroud, picking up Dau.I from her digs and continuing on to the Star Anise Café. We were there to work!  The baking shift had arrived and croissants / cookies / rounds of sourdough had to be made and baked and trayed before the rest of the staff, let alone the first customers, arrived. It was hard work but honest work and I learned a lot about ergonomic efficiency. I also got all the gossip about the town. Those croissants wouldn't pass muster in Toulon or Montpellier but they were good enough for the Brits who, like the Portuguese, prefer their cakes robust. All our children have left home at the earliest possible moment to seek their fortune and get an education in the University of Life. The Bachelor's and Master's degree will come in due course.
I was reminded of those happy mornings because Star Anise has just commissioned a photo-shoot of the workings and the workers from which I've clipped three to show the hands of Dau.I making the coffee that keeps the cafe afloat.

Monday, 24 August 2015

Try this for size

Years and years ago, my boss, his daughter and I were on a field trip to The Azores, Cabo Verde and the Portuguese mainland. We hopped about the islands of Cabo Verde by plane because the tickets were absurdly cheap and were too short of time to be cruising about by local ferry. Arriving to the broiling dry heat of Sal, the international terminal, we hung around waiting for the short-hop prop-plane to carry us to Praia, the capital on the island of Santiago 200km to the SW.  We amused ourselves by looking at the local people (the landscape was an uninviting mix of sand, sandstone, salt and salt-bush). One woman dominated the scene - an enormous black woman in  a wide black dress decorated with a discrete scatter of black sequins. We dubbed this redoubtable Cabo Verdean fellow-traveller "Her Vastness" and speculated whether the engineering of the seats of the small plane would be up to the challenge. Imagine our chagrin, and indeed anxiety for our knees, when she sat down into the row of seats in front of us. The seats gave ground with an ominous creaking sound . . . but held. My friend El Asturiano's grandmother was so shaped that her family used to tease that it was quicker to jump over her than go round her. There's a lot of obesity about nowadays and that's a lot of extra weight for flight-planners allocating fuel to optimise the loading of planes. Nobody wants to run out of fuel if there is a slight delay in-flight and the flight-planner has been using a ready-reckoner of passenger weights from the 1950s which says that 100 people weigh 7,000 kg.

Running out of fuel??  That's what happened on 24th August 2001 on Transat Flight 236 [Toronto-Lisboa] in the middle of the Atlantic. Captain Robert Piché, the pilot, demonstrated The Right Stuff when a fuel-line leak drained the last drop of fuel from the engines when he was still 100km from his emergency destination at Lajes Airbase in the Azores. He glided in! taking in a 360 degree turn to shed some height and further slaloming to shed speed and bring the airplane to the runway.  Everyone survived, the most serious injuries occurring in the evacuation. If you can't imagine what it might have been like on board, you can get a flavour from a participant (and check out the comments for other views on the same events). On returning to Toronto Captain Piché said curtly ''I don't consider myself a hero, sir. I could have done without this.'' These pilots: ice-water in their veins. It's in the movies.

The Boy, who through hard graft at Open University made himself an an engineer, is working on the railroad these last several years. In particular his company has had relatively tiny chunks (mere millions!) of the £15 billion which has been allocated to Crossrail - Europe's biggest engineering project driving new railway lines right through London from West to East. I'll do something to bring the propaganda videos to your attention later on this year - it's a HUGE project with some interesting ways-of-thinking. Mais revenons nous a notre fils: for the last year he's been doing a MSc in Railway Systems Engineering and Integration at U.Brum.  Since the book Freakonomics came out, it's been clear that all sorts of human behaviour can be investigated by economists and they can have a ball while doing it. Talking to The Boy, it seems that a similar case can be made for engineers: machinator sum humani nihil a me alienum puto.  

He led a group research project in the Masters investigating how trains can cope better with the obesity epidemic.  Because fat people are going to be using mass transport along with the rest of us. One element of the research was discovering what it is like to be overweight on today's trains. Being engineers they made up an Obese Body Enhancer OBE suit with a 117cm circumference and took turns wearing this on trains. Unaccountably this neoprene uber-jumpsuit [R above taking up a seat-and-a-half] had a Union Flag on the front. They designed a staggered seat arrangement [L] that was reasonably efficient seating everyone within the 95th percentile for girth and also successfully accommodated those beyond this limit. I think that's just great; it's silly and counter-productive to use obviously discriminatory blunt instruments like charging large people for two seats - especially as seat assignment is done at the last minute at the airport.  If we can adjust the engineered world to the reality of the people who are out there, travel will be more efficient and ultimately cheaper and more convenient for all users.

The Boy's solution to the seating problems of the Great Travelling Public made me think of the flap last month about hexagonal seating on airplanes. This is a patent taken out by Zodiac Seats France for a novel arrangement of seats for coach-class passengers in the future. The HD31 design [R with mannequins masquerading as sardines Sardina pilchardus]  inter-digitates forward- and rearward-facing seats to give more shoulder room; to do away with shared arm-rests; and pack more passengers in the tube of 3+3-seat, single-aisle, short-hop aeroplanes. The commentary has been filled with words like cram, horrible, personal space, awkward, and no thanks.  But these are just the negative reactions of people who are terrified of The New. Me, I'd give it a go if presented with a choice; especially if allowed to book the rear-facing seat - famously better to occupy if you desire to survive when the plane hits the deck off piste.

Note added in proof: A paper including the "Thinking Big" project has been accepted for the
Fifth International Rail Human Factors Conference in London next Month

Sunday, 23 August 2015

Captain Pugwash

Weekend: light-relief. Had a peek at yesterday. It's all about poor interactions between what people want to write and how computers read it. It sent me down two parallel rabbit holes: one in my mind/memory and the other clicking out and further out on the interweb. Staying close to nerdihood, in the comments there is a link to a classic xkcd cartoon about Little Bobby Tables.  You don't have to know the code to appreciate the joy of one clever woman whacking a foolish bureaucracy. There are some things that you must not write when dealing with computers. When Speedo was installing software on my enormous national bioinformatics computer in 1994 he decided that he should tidy up by deleting some of old intermediate files.  Thinking he was in one limited part of the system he typed "rm * -R" and then muttered "this is taking rather along time" before realising the computer was recursively [-R] removing [rm] all the files [*] of all the directories because he'd forgotten that a previous command [cd /] had delivered him to the very top of the directory structure.  Oooops, luckily we'd backed the system up as it was the night before.

Some errors at the human-computer interface are annoying but not fatal as I found in 1992 when I was writing a program for public distribution in the narrow world of bioinformatics that existed before the WWW launched in 1994. My code was cleverly menu driven.  On starting, the user would be presented with a numbered list of options and invited "Enter a number between 1 and 7".  That seemed to work fine as I was debugging but not so well when I asked The Lads to stress test it. One of them entered "l" [el] instead of "1" [one] and the program collapsed with a "system stack error".  Easily done, see how similar l1l1l1l they are? I had to write an additional few lines of code dealing with alphabetic input: "That input invalid: enter a NUMBER between 1 and 7". You see similar exasperated comments, often in red and usually in very small print, when you leave the zip code out of a web-form.

Getting computers to process subtle differences which are obvious to any six-year-old is a pervasive modern problem.  Our postman can deliver letters with all sorts of weird and wonderful variations on our address but the robot that will replace him as soon as driverless cars become normal will just blow fuses.  Here is a nice list of fatal assumptions to make when writing software to process personal information. Is Joe Blowe of 121 Mimosa Drive the same as Mr Joseph Blow, 12 Mimaso Drive?  Probably; but how to instruct a computer of the fact? Google guesses the intent of typos really well, Wikipedia just gives up. My promotion prospects depend to a certain extent on the number of the scientific papers I've published.  So it's good that I am cited both for my 1991 paper in Molecular & General Genetics v. 230 p. 288 and my 1991 paper, with the same title, in Molecular & General Genetics v. 23 p. 288. Two hits because some careless person made a typo in his list of references and a couple of culpably careless people cited my paper without having read it: they just read the intermediate paper and copied their [incorrect] reference.  There is a LOT of that lazy-arsed science about.

I've written about the prudishness of Google protecting us from things that Masters Brin and Page think are naughty. Apparently this is known generally as the Scunthorpe problem: where businesses in that town just north of Flixborough were unsearchable by Google because of the 2-5th letters in the name.  In the early 1990s, all the Polytechnics in the country became "Universities" in a fatuous central government policy decision.  Everyone knows which institutes of UK higher learning are real Universities and which are Polys masquerading as such.  It was a jamboree for letterhead printers, publicists and designers, because the institutes could re-brand with the re-name.  I had just left the [real] University of Newcastle upon Tyne across the park from Newcastle Polytechnic. When the latter was up for renaming, the governing body were all for City University of Newcastle upon Tyne: expressing a Bluff Northern, Urban, Can-Do effectiveness. That was scotched when it emerged the most likely domain-name to differentiate it from the existing (for answer see underlined capitals in previous sentence). They settled for Northumbria University which is going from strength to strength but has a dreadful, busy, and hard to crack website.

That led me off to those widely-circulated unintentionally inappropriate domain names including the Florida fishing tackle shop An Italian energy utility is no longer using which was been acquired as a dating jumpstation. These sources of hilarity ante-date the WWW by many decades. Eeee, when I were a nipper in a sailor-suit there was a series of 4 minute short TV cartoons called Captain Pugwash [L. with Cabin Boy and Ship] originally made with cardboard cut-outs about a ship full of pirates and their inconsequential adventures.  Contra the urban legend, there were no such characters as Master Bates, Seaman Staines or Roger the Cabin-boy, the assertion went to court in 1991. However, either I'm deaf or "Find me the ship's dictionary Master Bates" does appear at 25s in the first episode of the 1970s re-run of the series.

Saturday, 22 August 2015

Gaming the dinner

In the early 90s, I was post-docing in TCD in O'Hara's the old Genetics Building.  There were two damn-smart graduate students working in the same group who are now a Professor in Manchester and Project Manager at Oxford.  We all worked all the hours that the gods sent and the lads would often go to the café across the street for their dinner before it closed at 7pm. As the last of the "starving" variety of graduate students, before that animal was replaced by the casual-affluent grad-studs of the Tiger Years, it was important to get value for their limited money. One of these chaps discovered that if you ignored the tum-filling menu-item "Lasagna with chips" and asked for "Lasagna" with a side order of chips you could get the same amount of food, or even a little more and save £1.

Interns are the new graduate student. Youngsters with oomph sign up with Megacorp or a political party or in a professional office to "gain experience" while working for nothing-or-buttons. Some interns aka work-experience personnel are a burden: you have to allocate one of your effectives to train the intern up which seems to take an unconscionable long time. How long can it take to work out how to do back-to-back photocopies??  In other cases, it's a dream: girl turns up with a sunny disposition, is quick on the uptake, does whatever you ask and soon enough is suggesting ways to make the process more efficient. The custom nowadays is that neither sort of intern expects to get paid, so they have to mind their money while they work off-stage hoping for an opening.

Dylan Grosz is/was in intern at with a penchant for burritos. He carried out a controlled experiment to see how he could get the biggest burrito for his bucks in Chipotle Mexican Grill Inc. [L for normal size and shameless plug for the company]. It's the Lasagna . . . with Chips story gamed to the max . . . and duly measured, recorded and compared. If you ask for half chicken & half beef + half pinto & half black beans + half white & half brown rice then you get as much as 86% extra food for the same price.  Well strictly, you only crank it up to 86% extra if you demand all the 'freebies' at the very end of your order: a generous handful of "fajita-veggies" and "grilled corn" is colorful, crunchy, 'free' and good for the bowel.  What happens is that the counter staff can't easily make a half portion so they throw in a short portion of maybe 75% of the standard amount. A fully extra'd burrito amounts to 900g (= 2 lb) of food wrapped up in tin-foil. That's a lot to carry let alone eat, so be sure to take a wheel-barrow when you go for lunch. The joy with which young Dylan reports putting one over on Chipotle w.r.t. the free stuff makes me wonder why he doesn't snag a few ounces of sugar sachets and non-dairy creamer on his way out and add that to the mix.

Back in the 90s, those two graduate students followed the boss to England when he got his own Chair in one of the UK Universities. I stayed behind to set up some bioinformatics infrastructure for the country.  Part of that infrastructure was the mother of all computers which was delivered in a van-load of cardboard boxes.  I was too technophobic to wade in and set up the hardware, the firmware, the software, the databases and the first users, so I asked one of the young chaps, let's call him Speedo, to come back for a month's consultancy and £1,000 to help me put the show on the road to the frontiers of science. I called him Speedo because he was so quick and confident of his own ability. After watching over his shoulder as he carried out some frightening elaborate and brain-melting task, I balled up my fan-knickers and threw out "Jaysus, Speedo, how come you're so clever."  He replied "You think this is clever? You should have seen me before I went to college, I was really smart when I left high-school."  It turned out that in the freedom and lack of oversight of being a student he started a social drinking lifestyle that he soon parlayed into a 'bottle a day".  "Bottle of beer?", I asked. "Bottle of vodka", he replied. While most of us have a million neurons die all through our adult life; Speedo was wasting about 10 million a day for several years. Let that be a lesson to you: sometimes Less is More . . . both for burritos [obesity] and booze [cirrhosis].

Friday, 21 August 2015

Don't do this at home kids

Now I'm not stupid. I had a very expensive education. I've won prizes in pub-quizzes. I've spent a life-time in science. But I shouldn't be left alone in a laboratory because I don't think quickly enough. Many people are a lot more useful to science because they are a good pair of hands even if they don't know as much as me.  I've had my own disaster with radioactive material, so I am especially sensitive to stories of avoidable nuclear accidents. I've told the story of Chernobyl from my point of view 2000km to the West rather than investigating the failures of protocol and management on site that caused the melt-down and blow-up. I was a little more up-close-and-personal in my coverage for the Windscale fire which was brought under control by heroic, experienced and very smart technicians who stayed at their posts. I would have been useless in those hours; the best thing I could of done was either make tea or run like buggery to get out of the way.

You had to have a certain type of smarts to get a post on the Manhattan Project building the first atomic bombs.  It was time critical; every day of delay meant more allied servicemen dying, so only the smartest boys in the room need apply. Harry Daghlian was such a boy.  He grew up in Connecticut and went at an absurdly young age to MIT to read mathematics, switched to physics and was sent to Los Alamos while still working on his PhD in particle physics. He was assigned to a group that was working to determine how to minimise the critical mass of a radioactive 'pile'. Uranium and Plutonium were insanely expensive and each hard-won lump was destined to cause an explosion over distant Japan. It was clearly better to use as little as possible in each bomb-assembly.  How little was enough? That was the The Question.

70 years ago today, 21st August 1945, was just after the unconditional surrender had been agreed (15/08/45) but before the documents had been signed on USS Missouri (02/09/45). Meanwhile back at Los Alamos basic science was still going on.  The Critical Assembly Group was working with a 6.2kg sphere of radioactive Plutonium to see if they could make it "go critical" under controlled conditions.  The experiments that day involved adding tungsten carbide bricks one at a time around the 'hot' sphere and listening to the Geiger counter go fzzzzz.  Each alteration of the pile was recorded and another idea was tried out. Tungsten Carbide acts as a neutron reflector, so that these sub-atomic particles go back into the core to cause more fissions rather than dissipating into the surrounding air.

After dinner that night, Daghlian went back to the lab alone because he'd had an idea and couldn't wait to check it out. He was alone in the room except for a squaddie called Pte Robert J. Hemmerly who was there to stop unauthorized people stealing stuff. Daghlian went to work building up his Lego bricks in a 'let's try this' assembly [L] until it was damned close to going critical. As his hand hovered over the plutonium core and . . . he dropped the brick. Tungsten carbide is really dense (15x heavier than water), so each little brick - about the size of a tin of beans - weighed 5kg. Daghlian was probably wearing cotton gloves, he was well fed, it was near his bedtime, he'd been working all day and the golldarn brick slipped from his grasp.  There was a blue flash and the young researcher sustained a fatal dose of radiation.  He was alert enough to unpack his fatal pile and tell Hemmerly that something bad had happened. Another graduate student was on-site and drove him to hospital. Over the next 25 days, Daghlian's skin peeled off in layers, and he suffered through progressive system shutdown until he fell into a coma and died. Hemmerly was more fortunate, he lived for another 33 years before dying from leukemia. That's why we have SOPs [Standard Operating Procedures] in laboratories, so that it's more difficult for accidents to happen. When I flipped radioactive phosphorus into the corner of my eye I was definitely outside the SOP, and I was alone in the room.

15 years ago, Daghlian's surviving relatives unveiled a plaque in his home town of New London, CT "A brilliant scientist on the Manhattan Project . . . though not in uniform, he died in service to his country".  Whatever about de mortuis nil nisi bonum that statement is really not correct.

Thursday, 20 August 2015

Straighten Up

This last Tuesday was the third of the month and so it was Wexford Science Cafe night!  Until the local films-with-subtitles season starts up again in October, SciCaff is the high-point of my Bobby-Few-Friends month.  This month we were privileged to hear, from, the Senior Executive Scientist Environment Section at Wexford County Council aka the horse's mouth, about the EU Water Framework Directive and how this might affect our lives.  The WFD was a classic piece of European legislation which aimed to define 'water quality' and standardise the tests for it across the countries of the EU; and also to require us all to up our game on this aspect of the environment. If you wanted to summarise the impact of the EU in two words, they might be "equilibrate upwards". Give everyone a level playing field whether they come from the slums of Brindisi or from leafy suburban Bristol; but don't achieve this by setting the standard to the lowest common denominator.

As with all EU legislation, the WFD requested-and-required national governments to enact legislation and implement the law to comply with the standards agreed across the Union.  Some member states are quicker to embrace the necessary change than others, and Ireland had to be dragged through the European courts and fined a large number of teachers, firemen and wheelchairs before they started doing something about the environment. We get complacent about our environment because there are not many of us to pollute it - the population density/ of Belgium is 5x that of Ireland - but everyone agrees that less water is safe to drink, swim in or fish from than was the case when we were young.

As with all good legislation, the WFD tries to cover all the bases and adopt a holistic view of water quality: it's not just about measuring pH, nitrates, BOD, or phenols.  These criteria are all important but the overall score given to particular watercourse is that of the parameter which scores lowest. It is one of the few times when something EUish sets the bar to the lowest measurable parameter. We all undertake, over each of several five year plans, to a) get each water catchment to the next highest classification category and b) to let none slip from a previous high.  That's hard but it looks like an achievable aspiration. One of measured parameters is the 'morphology' of each watercourse.  The morphology of a river is what we were on about with Yellowstone and the impact of introduced wolves a couple of weeks ago.  It has been the relentless desire for mankind to trick about with water: when we were nippers, me and my sibs did it with plastic buckets-and-spades. Rivers are dammed for power and irrigation, rivers are straightened and dredged for navigation, harbour walls are built to encourage scouring for the same purpose.  This is wholly un-natural because all rivers prefer to meander and the meanders encourage more diverse habitat which enhances the ecological complexity, which means that the homeostatic equilibria [of pH, BOD etc.] are maintained with less exaggerated swings. Gravel suitable for spawning salmon is impossible to sustain in an artificial canal created to get ships from the Irish Sea to Manchester asap.

Straightening rivers reminded me of one of the great engineering achievements of the 1600s - the draining of the fens between Cambridge and the sea in the East of England. This was undertaken by a group of "adventurers" led by the 4th Earl of Bedford.  The deal was that the reclaimed land would be divided three ways: a) 1/3 for the corporation to be let out to tenant farmers b) 1/3 for the King and c) 1/3 for the adventurers themselves: that would be nearly 40,000 hectares. What they saw was an enormous soggy pancake-flat plain, more than 1000 in extent.  One of the principal rivers was called, appropriately, Ye Great Ouse. What resulted in 1636, after 6 years with shovels and wheelbarrows, was the 30km dead-straight Bedford River between Earith and Denver. That seemed to work a treat, the river flowed rapidly between its artificial banks, there was much less flooding and the land was drying out so that it could be used for agriculture. In 1649, after the Civil War finished grinding the country to a standstill, Bedford's son the 5th Earl was given a contract to drive a second parallel channel which became known as the New Bedford River aka The Hundred Foot Drain.  It opened up the floodgates for a series of cunning drainage plans with uninspiringly matter-of-fact names: the North Forty Foot Drain; Vermuden's drain [he has lost his central "y" to anglification]; The South Forty Foot Drain. The foot in each case refers to the width [=30cm] of the channel.

Among the unintended consequences was the fact that as the water was sluiced off the region and out to sea, the predominant peat of the Fenland dried out and was exposed to the air.  The acid anaerobic matter which was so good at preserving Tollund Man, was rapidly oxidised and disappeared into the atmosphere in an invisible plume of carbon dioxide.  That reduced the volume of material, which was already half water anyway, so the land on either side of the drains shrank away until the water was far above, dead straight and dead flat.

Dead flat?!? That would be an ideal situation to prove that the Earth is flat.  If, or rather IF, the Earth is round with a supposed circumference of 40,000km, then a flag should be invisible if waved from a boat sufficiently far along the Drain. Through the 19thC, several Flat-Earthers demonstrated to their own satisfaction that they could see the flag no matter how far away the boat went. Famously the issue was put up to challenge as a wager in 1870 by a slightly unstable individual called John Hampden. Our own Alfred Russell Wallace, ally of Charles Darwin, was a trained surveyor and he undertook the challenge and proved conclusively (i.e. to his own and other scientists' satisfaction) that the flag disappeared well before it was 10km distant. There were all sorts of shenanigans, libel-suits, murder-threats and the issue was still being debated, with and without photographic evidence, as much as 35 years later. "The door of a bigoted mind opens outwards so that the only result of the pressure of facts upon it is to close it more snugly."  Ogden Nash - his birthday yesterday.  . . . but some of the consequences of having a flat earth discussed by Vsauce [10 mins].  There, who moaned "borrrrrring" from the back of the class when I mentioned the WFD.

Wednesday, 19 August 2015

Tick tock

I acquired a sheep tick Ixodes ricinus [R] a week ago.  It hunkered down behind my left knee in just the position least available for unbendy me to get access and remove it.  The Beloved applied a tissue soaked in tea-tree Melaleuca alternifolia oil which makes t'buggers loosen their hold sufficiently that they may be removed with tweezers. Nevertheless, I had an annoying itchy local inflammation for 3-4 days afterwards. Ticks were an occupational hazard for the girls when they grew up spending large parts of their waking hours going through the long grass in meadows where sheep may safely graze.  When The Beloved picked up a tick on the back of her neck a few weeks ago, we had no tea-tree oil in the house and I used methylated spirits instead. It doesn't work and I botched the operation . . . sorry. The CDC in Atlanta, the GoTo source for global health information has no time for tea-tree oil, vaseline, acetone or the hot head of a match; that say just seize the beast with your tweezers and pull. I beg to differ.  You can count the legs on the unengorged tick [R, above] to convince yourself that it is an arthropod but not an insect. Rather it is, with spiders and mites, an arachnid.

Having an annoying itch for a few days is much less of  a problem than acquiring a tick-borne disease of which there is quite a list. In all these cases ticks serve as vectors for smaller creatures which get into the blood stream and cause trouble. Thankfully, the distribution of these pathogens is frequently quite limited. You won't catch Lyme Disease [R] if you live in Kansas or Alabama. The tick Ixodes ricinus is found wherever it has been looked for in Europe but not always in juxtaposition with suitably pathogenic bacteria. Because it is rare in Ireland, it is often not correctly diagnosed.

Examples of pathogenic tick passengers include
  • Bacteria
    • Borrelia burgdorferi causes Lyme Disease, named for the village in Connecticut where it was first identified. Its range is limited to two hotspots New England-Delaware on the East Coast and Minnesota and Wisconsin in the Upper Midwest. Its incidence has been climbing steadily from about 10,000 cases in 1995 to 30,000 in more recent years.  Lyme disease won't kill you (it has appeared on 100+ US death certificates over those 30 years but only in 25 cases as principal cause of mortality) but may make you feel crook for years.  One of the issues is that your doctor may declare you cured but you know you ain't right and you weren't neurotic before you got bitten.
    • Borrelia spp. including  B. miyamotoi or B. parkeri cause Relapsing Fever, which all cause similar symptoms, rather different from those of Lyme Disease
    • Rickettsia rickettsii which causes Rocky Mountain Spotted Fever which has experienced 4-5x a surge of cases (to about 2000 per year) since the turn of the century.  That's bad news but fatalities have fallen from 25% to less than 1% with effective antibiotic treatment.
    • Francisella tularensis will give you Tularemia [aka rabbit fever, deer fly fever, lawnmower's fever to suggest where you might catch it] which, in contrast to Lyme Disease and RMSF, has been falling off from about 900 cases in 1950 to 150 cases nowayears.  Tularemia can be fatal if untreated but let's not get excited about that until antibiotic resistant strains of F. tularensis emerge.
  • Viruses including Tick-borne meningoencephalitis virus; Colorado tick fever virus; Crimean-Congo hemorrhagic fever virus; Heartland virus.  These viruses come from widely separated branches of the viral evolutionary tree; their only commonality being that they can be carried by ticks and cause pathology in humans.
  • Protozoa. Main badboy here is Babesia microti or B.venetorum. They cause, !surprise!, Babesiosis aka Texas cattle fever, Nantucket fever or redwater fever. These names are informative, because the vector is likely to be Ixodes scapularis, the deer tick (which favours cattle too) and one of the symptoms is the release of haemoglobin breakdown products in the urine - redwater geddit. Babesia is a protozoan in the Phylum apicomplexa which also contains the causes of malaria Plasmodium spp, and the water-borne runs Cryptosporidium. Babesiosis also took a bit of a leap up in incidence, which doubled between 2012 (N=900) and 2013 (N=1800) the most recent years for which data is easily available
President Obama is currently on vacation in the Babesia and Lyme Disease heartland of Martha's Vineyard where he intends to read The Sixth Extinction by Elizabeth Kolbert. Watch out for those ticks Mr President!

Tuesday, 18 August 2015

Mountainy man cries fowl

Bon anniversaire! à Luc Montagnier, the discoverer, with a lot of other people, of Human Immunodeficiency Virus HIV the virus that causes AIDS. Now, if you're white and live in the West, your life expectancy with a load of HIV on board is measured in decades. That's because of the development of at least 20 anti-retroviral therapies which are making money and saving lives. It's a different matter, of course, if you are living in sub-Saharan Africa, where the collapse of your immune system will finish you off rather quickly: because poverty and foul water and poor housing and exotic worms and protozoa and bacteria conspire to a perfect storm of death.

In the very late 1970s healthy young men in the US started to present to their medical practitioners with some really rare, not to say bizarre, illnesses including Pneumocystis carinii pneumonia and Kaposi's sarcoma. The doctors did their best to treat them and scratched their heads as to what might have laid fit young chaps open to such assaults. In 1981, the Center for Disease Control CDC in Atlanta, put out a bulletin describing the condition. That brought to light hundreds of other cases across the country - a worrying epidemic. It's CDC's job to collate reports of disease, so that someone has an overall picture in case there is a pandemic in the making. People at the CDC and elsewhere with a historical frame of mind might have cast back to the 1918 Spanish 'Flu Epidemic which killed millions and seemed to have a preference for the young and the fit.  There was something about both epidemics that made people shake their fists at the heavens at the outrageous unfairness of it.  One current take on the Spanish 'Flu is that it killed the fit because their immune system worked really well - over-reacted really and caused a system wide shut-down in order to control the assault.  The treatment worked but the patient died.

It is really the opposite with AIDS, because it rapidly became clear that in AIDS the immune system was working not-so-good and getting progressively ineffective until something quite ordinary, Candida "thrush" albicans for example, finally killed the patient. Pneumocystis carinii and Staphylococcus aureus are widespread in the environment, including up our noses but a working immune system, including a fully functional flora of 'good' bacteria, keeps them in check. Like William McBride noticing a few kids presenting without arms and connecting that with the fact that their mother's had taken the drug thalidomide, the people at the CDC were putting together a syndrome of symptoms and associations.  Early on they called it GRID - gay-related immune disease - because the dying men often had had sex with other men. That naming didn't stop them wasting away, covered in red lesions and coughing up blood, but it gave the astute a clue about how it [whatever it might be] was transmitted.

Willy Rozenbaum a doctor in Hôpital Bichat in Paris, who had a number of GRID patients on his wards, was sure it was caused by a virus, perhaps one related to another virus HTLV discovered a few years earlier. HTLV [human T-lymphotropic virus] is what it says on the tin - a virus with an affinity for T-cells which are key players in a functional immune system.  Rozenbaum took a trip across town to the Institut Pasteur where Montagnier [R, L] was the acknowledged expert on retroviruses, including HTLV, which have the strange facility to be able to make DNA from RNA in contravention of the Central Dogma. Montagnier quickly dismissed any close association between a) the cause of GRID which appeared to be screwing T-cells over and making them die and b) HTLV which contrariwise caused T-cells to multiply uncontrollably and present as a leukaemia.  Nevertheless, he was intrigued and said that one of his people would look into it if Rozenbaum would provide a biopsy to work on.  One of his people turned out to be Françoise Barré-Sinoussi [R, R] a post-doctoral researcher then in her mid 30s. 

With a hypothesis, an effective and the wherewithal to test it, the answer came back really quickly. Barré-Sinoussi had developed a test for the presence of reverse-transcriptase, the enzyme that makes DNA from an RNA template. What she noticed was that as T-cells died in the Hôpital Bichat biopsy material [they had a test for cell-death too] there was a little burst of reverse-transcriptase activity and this association was predictable and reproducible. This evidence looked like a retrovirus, quacked like a retrovirus, so they called it lymphadenopathy-associated virus (LAV) and rushed their findings into print. At one point they were concerned that their sample would run out of suitable cells for their monster to consume; but a quick trip across the road to the blood-bank kept the experiment going. Despite the title of this key 1983 paper in medical history "Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS)" they were appropriately cautious not to spell out that LAV caused AIDS.

Meanwhile across the pond, Robert Gallo, the doyen of American retroviral work, was hot on the same trail. Gallo's team had discovered a molecule, IL2, which allowed them to culture T-cells in the lab rather than feeding their viral samples with fresh blood.  In addition they had identified HTLVs which caused leukemia and Gallo had won the 1982 Lasker Prize for this work.  Americans regard, with good statistical evidence, a Lasker as a prelude to a Nobel. In 1984, Gallo published a clatter of papers in Science, putting out his stall for HTLV-III being the cause of AIDS. It transpired that LAV and HTLV-III were the same thing and what we now call HIV.  It also turned out that HTLV-III was rather too identical to LAV!  The way RNA retroviruses reproduce is inherently inaccurate and so they evolve really fast. The probability of two independent samples from unrelated gay men on different sides of the Atlantic being so similar was vanishingly small and it looked like a bit of industrial espionage might have crossed the line from rivalry to fraud.  A forensic study of archived samples in the two laboratories showed that the Americans had gotten their virus from Paris rather than vice versa and the French called 'foul' and took the high moral ground. Gallo is Italian for rooster hence the fowl/foul pun in the title.

Why did it matter? Because the Americans had been quick to develop their findings into a golden goose and had taken out a patent for a reliable test for the presence of HIV in people who presented with Kaposi's sarcoma. One of the grounds for challenging a patent is the concept of prior art: if key knowledge is out there already, the applicants for patent can't claim they have invented something unique. Surely Barré-Sinoussi's 1983 paper constituted such a challenge?  But nobody wanted to fight that line too hard because it would kill the patent and allow everyone - Ivoiriens, Tanzanians, Mozambiquies - to develop their own test and not pay royalties to Gallo's employers. It was a huge, ugly and very public argument that spattered the ivory tower of science with mud. It took an intervention by the Presidents of the two countries François Mitterrand and Ronald Reagan to iron out the ruckus and agree that the income stream would be divided 50:50. Eventually further meticulous investigations cleared Gallo of misconduct and he and Montagnier published a joint 2003 paper in the NEJM New England Journal of Medicine "The Discovery of HIV as the Cause of AIDS". But it is as easy to recall the sped arrow as the flung mud of moral indignation and Gallo's rep was irretrievably tarnished.

In 2008, the Nobel Prize of Physiology and Medicine was awarded to Montagnier, Barré-Sinoussi and . . . Harald zur Hausen (!) a German virologist who had done nifty work on human papilloma virus which causes cervical cancer. Montagnier acknowledged that this was a bit unfair as he knew that Gallo's contribution to the discovery of HIV and working out how it nobbled T-cells had been enormous. But the committee-men of the Nobel Prize knew better because their sense of moral certainty was yet more enormous.

Still and all, it's Luc Montagnier's day today. 83 candles to blow out. Félicitations from all the people who are not dying of AIDS.

Monday, 17 August 2015

Flixborough 1974

At tea-time on Saturday 1st June 1974 a seeping cloud of cyclohexane vapour reached a distant ignition source and deflagrated. As the leak and the ignition occurred in the middle of a chemical production facility the explosion rapidly propagated through the plant and killed or injured almost everyone at work at the time.  It went down in the history of health and safety, chemical engineering and North Lincolnshire as the Flixborough Disaster.  That was the end of Flixborough's two generational record of being thankful for sparing its inhabitants from sudden death.

Flixborough was a massive chemical campus owned and operated by NyPro, a joint venture between Dutch State Mines (DSM) and the British National Coal Board (NCB) to produce caprolactam, an essential precursor in the manufacture of Nylon.  The plant had initially been set up to make fertiliser from the coking-furnace byproducts of a nearby steel factory. When the price of Nylon went up and the price of fertiliser came down, one line of the system was re-engineered to process cyclohexane, a colourless and highly flammable [think octane] organic compound with a distinctive 'cleaner' smell. The oxidation by compressed air was carried out at about 8 atmospheres [0.86MPa] and 155oC but it was still quite inefficient. The cyclohexane was passed through a cascade of six pressurised reactors [L above] each holding 25 tons of hot seeth - it boils at 80oC at atmospheric pressure: see Gay-Lussac's Law for the relationship between temperature and pressure.  The 'wort' went down the cascade under gravity and each pass converted about 6% of cyclohexane into cyclohexanone which was bled off.  The 94% unreacted cyclohexane was sent back to the start for another go-through.

In April 1974, routine inspection and audit showed that the cascade was leaking and stripping off the lagging of reactor 5 showed a crack 2m long its the outer shell. Time was money, the plant was way behind on its production targets, the government had capped the price of caprolactam to help the nylon industry and management called for a quick-fix.  The chemical engineers decided to by-pass reactor #5 with some pipework between #4 and #6.  They couldn't find any 700mm pipe in the yard so they bodged in some available 500mm, to accommodate the fall between #4 and #6 a dog-leg drop [cartooned in red in the annotated photo above L] was mitred into the tube.  To the chemical engineers who made up the  caprolactam working group and most of the senior management it looked okay on paper.  So they shifted reactor 5 out of the way and installed the bypass supported by scaffolding. But NyPro's mechanical engineer had retired at the beginning of the year and not been replaced, so there was nobody on site really qualified to critically evaluate the effects of turbulent flow, fluid-hammer, and joint-loading: the bread and butter of engineering engineers.  Anyway, the fix-up worked, so the chemical engineers thought they knew as much as they needed to know about the system.

A few weeks later, the cyclohexane line was switched off to fix more niggling leaks, inspected, repaired, relagged and  . . .  powered up on the morning of 1st of June. On a Saturday, there were far fewer people about the plant, including 18 shut up up in the central control-room. So nobody noticed the distinctive smell of leaking cyclohexane until it reached a furnace in another distant part of the plant and >!WHOOOMPH!< the explosion destroyed the reactors and ripped through the factory breaking and shattering and causing a cascade of supplementary fires and explosions. Nobody knows exactly what happened because everyone in the control room was killed and all their log books were burned to cinders. The only survivors were those who made a quick exit in the right direction immediately on hearing the alarm and/or the first bang. Every window within 2km was broken and structural damage was sustained as far away as Scunthorp 5km distant. 28 dead, 36 injured (burns and flying glass, mostly), a handful of workers shaken but alive. Forensic engineers moved in even before the fires were finally extinguished (things were still smoking on 10th of June) and tried to piece together what had occurred by the position and sustained damage of the parts, which were scattered far and wide. The Rotor of fan #9 [L above], for example was blown out of the plant and into the waste ground. Two hypotheses surfaced: the 20 inch theory which laid the blame on failure in some part of the the complex 500mm bypass OR the 8 inch theory based on finding a rupture in a 200mm pipe which originally joined two nearby separators; the explosion that broke the narrow pipe shook out the 500mm reactor #5 bypass or its Heath-Robinson scaffolding support. There is, inevitably, a  minority opinion that the investigation was a stitch-up to exonerate the company, limit the damage and get everything back into production asap. One member of the investigating committee was 'let go' when he insisted on bringing management and protocols before the board of enquiry.  My father, after he retired from the navy at age 50, secured a sales manager job in another British industrial combine.  His stories of management incompetence in his firm had him occasionally incandescent: ". . . if those buggers had been that stupid and careless aboard any ship of mine, I'd have taken their stripes and sent 'em down to the fo'c's'le". So the idea of men [it was always men back then] drawing a comfortable salary to make cavalier decisions beyond the level of their competence is not entirely without plausibility.

Nevertheless, the Board of Enquiry did find that "All engineers should learn at least the elements of other branches of engineering than their own".  Amen to that, specialization is for insects.  Here's another piece of advice: when management announce that they are going to re-start the production line after some down-time . . . that's the day to pull a sickie.