Friday, 13 October 2017
Top Billing
In biomedical science, later on in my career, it was rather different. I remember having a one-side-heated conversation with a post-graduate in the ophthalmic genetics lab one floor down. He was raging because he had been placed 5th / 8 in the billing for the lab's latest paper. He was convinced he should be 4th! I was amazed that someone would a) care b) be so precise in the algebra. The other thing that used to annoy me when I worked in a hospital setting was that the consultant surgeon and often his registrar would get their names on the scientific papers when all they had contributed was some very delicate butchery to provide the samples which the real scientists had analysed. I said at the time that you should only get your name on a paper if you could present it at a scientific conference if/when The Effective fell sick at the last moment. You can do this if you've written a chunk of the text, or you're the boss, of you've heard & seen the results thrashed out at numerous lab-meetings. The surgeons are far to busy to attend lab meetings in the research centre so they often haven't a clue how their abstracted tissue is analysed.
Sometimes, the paper results from the collision of two different trains of research. Then you have two young turks, of similar seniority, who have both put their all into the project for the last several months. The solution to that is "joint first author". I know at least one case where, the most ambitious and, let's face it, ruthless of the two has gotten his [almost always a he] name physically first among the joint-firsts. Papers are usually cited as Smith, J. et al. (20xx) so it does make a difference in external perception. So it's very much a case of "Eclipse first, the rest nowhere". In my own case, we were on a collision path when my old boss, who had moved to Nottingham, and my current boss in Dublin found that they were both analysing the same pair of organisms in essentially the same way. My oppo in Nottingham was much younger than me, just starting out and a woman-in-science. Of course, I let her take first-first place in the list of authors. This helps explain why I am a nobody at The Institute while the other actors here cited are Rulers of Empires at home or abroad.
As I said in the hook at the top of this piece, the ambition, the chutzpah, the meanness are all present in Hollywood. The megastars in any film get top billing on the promotional material. Even if it means the order of names bears zero relationship to the mugshots in the back-ground photo. Actors have agents to fight their corner on this, because the order means money. If two monster stars are neither of them backing down, you can stagger the names so that one is leftest and the other is toppest [R] and let their agents fight over how many pixels higher or lefter their client finishes up.
Saturday, 28 January 2017
Gus Grissom Gone
I was reflecting on the costs because yesterday was the 50th anniversary of the Apollo I disaster when three astronauts were incinerated on the launch pad during a practice run on 27th Jan 1967. Of the three dead men, Gus Grissom, Ed White and Roger Chaffee, Grissom's name struck the memory bell loudest. He was Indiana's most famous son and a fighter pilot in the Korean War before he was picked to be a NASA astronaut: one of the Mercury Seven. As with Neil Armstrong and Eugene Cernan there was a lot of Harry Potter 'Eclipse first the rest nowhere" in Project Mercury . The first man in space, John Glenn, became a household name and eventually a US Senator and Presidential candidate. You have to have been around as a small geeky boy to remember the names of the others. Gus Grissom was the second man in space; in those days, the pilot got to name the ship, and Grissom plunked for Liberty Bell 7 [the pair see R]. He almost lost his life, not in a dramatic fireball like the Challenger or Columbia space shuttles but in a botched landing /pick-up after a successful mission. After splashdown the pilot was meant to sit tight until a chopper from the nearby aircraft carrier hooked on and lifted the spaceship to the flight-deck. In somewhat murky circumstances, the capsule door blew off while LB7 was still bobbing about on the ocean, waves slopped in and a lot of expensive kit sank into the depths. Grissom slithered out and nearly followed his command down when his space-suit started to take on water. His buoyancy wasn't helped by having smuggled 2 rolls of dimes onboard to sell as souvenirs afterwards. He ever afterwards denied triggering the explosive bolts, but not everyone believed him. A fellow who could bring half a pound [almost exactly the weight of 100 dimes] of unaccounted weight aboard such a delicately balanced project could have done pretty much any dopey thing. It's similar to the Apollo 8 astronaut who pressed the Don't Press This Button button and unravelled Margaret Hamilton's computer program. There was a tension between the NASA management who wanted the astronauts to be quiet passengers while they controlled everything from Houston and the astronauts, almost all previous test-pilots who wanted to be doing. Doing some daft things like Alan Shepard bringing a 6-iron and two golf balls to the moon and whacking one of them into the distance. NASA believed Grissom had not been tricking about with the door, let alone panicking to get relief from claustrophobia, and that's all the counted. He went up in Gemini 3, becoming the first man to do space twice but was still eclipsed in the public mind and history by John Glenn and Neil Armstrong.
Whatever you feel about the sinking of Liberty Bell 7, Apollo 1 was a good candidate for a Normal Accident: a cascade of small-small t'ings had to go wrong or go unnoticed. The inside of the capsule was pressurized a little above atmospheric with pure oxygen (!). A smoldering candle will burst into full flame in such an atmosphere. One of the ironies of the disaster was that the door was designed to open inwards - partly because of Grissom's earlier mishap with out-opening doorways. Another door shouldered some of the blame. An access port had, through repeated opening for inspection, stripped off the insulation of a silver-coated copper wire. The inspections were necessary because a tube transporting ethylene-glycol coolant was always leaking. With 20:20 hindsight it was revealed that silver had a positive electrolytic effect on ethylene-glycol and the ignition wouldn't have occurred with plain copper wire. One suspects that the silver coating was there to justify a fabulously inflated price for the material by NASA contractors North American and Grumman. They charged top dollar because they could, but their workmanship was often shoddy, the delivery time-keeping weak, and design-flaws manifold. We remove our shoes in the run up to all air-flights now because on 22 Dec 2001 Richard "Bat-shit bonkers" Reid smuggled a bomb aboard an American Airlines flight in his shoes. Likewise, the NASA contractors stopped using silver coated wire anywhere rather than thinking about the next potential hazard. If ethylene-glycol started the fire, there was plenty of flammable material in the cockpit to keep it going. The walls had been almost carpetted with Velcro which had been recently invented by George de Mestral; this allowed the astronauts to park pretty much everything while weightless but burned very well in pure oxygen . . . likewise the space-suits.
If you read Richard Feynman's story of the Challenger disaster and investigation, and you should, you'll get the feeling that NASA's managers were culpably negligent in heeding the concerns of their astronauts and terrestrial engineers about redundancy, safety, testing, and analysis of complex systems. Mean with the routine but necessary checks and balances, they were spend-thrift with contracts and were always cranking up the ante to make NASA more sexy and pioneering. It was as if they knew Congress would only buy into the idea of space-travel if the projects became increasingly complex and hard to fully comprehend. Feynman concluded that NASA management were almost ideologically incapable of grasping probability and risk-assessment.
In 1999, three decades after it sank, Liberty Bell 7 was recovered from the ocean floor. 52 more dimes were found loose in the capsule. It seems that Grissom wasn't the only one sending souvenirs into space - but he was the only man with the bottle to ride with the illicit payload.
Friday, 6 November 2020
From Askwith to Zátopek
. . . a love and respeck letter from one runner to another. We've met them both before. Richard Askwith's Feet in the Clouds is the tale of a London journalist who is invited to go hillwalking one weekend. It's a long drive on Friday night, Saturday dawns with drizzle, his pals set off up the target hill, he tags along with increasing grumpiness, he's wet, and cold, and unfit and is quite pissed off when they finally get to the pointless peak. And then, with magnificent natural theatre, the clouds are swept apart and the lads are treated to a panorama of The Whole World [Matt 4v8] and Askwith is hooked.
I wrote my tribute to Emil Zátopek for Sunday Miscellany before The Blob and hinged it on the miraculous fortnight in Helsinki 1952 when Zátopek won gold for the 10,000m, the 5,000m and the Marathon, and his wife Dana Zátopková [b. Ingrová] won gold for the javelin. This [R - czech out the two chaps with their eyes on stalks] is one version of The Kiss immediately after Emil powered into the stadium Eclipse first the rest nowhere to win the marathon. It was the first time that he had raced at that distance. But he was an early adopter, if not the inventor, of interval training where he'd run many many multiples of 200m and 400m sprints.I've just finished reading Askwith's 2016 book Today We Die a Little: The Rise and Fall of Emil Zátopek [Grauniad interview; Waterstone's retrospect] which is 200x longer than my vignette on The Blob. There is of course more detail in the book and it's more nuanced in its adulation. Zátopek's fame rests partly on his loyalty to fellow Czech athlete Stanislav Jungwirth who was deemed politically unsound days before the Helsinki Olympics. Zátopek risked his own ticket [and the gulags] by insisting that he wouldn't fly unless Jungwirth went with him. That's the stuff of heroes, as much as being able to go Citius, Altius, Fortius.
But that moral backbone doesn't sit well with a letter to the press written in 1950 by Captain Zátopek which comprehensively agrees with the grotesque judicial killing of Milada Horáková, a respectable political dissident who spoke the truth to the power of the Communist Party, In 1968, the new First Secretary of the Communist Party Alexander Dubček implemented a new policy "socialism with a human face" which initiated The Prague Spring a local thaw in the Cold War. It encouraged freedom of expression, liberalisation of state control of everything, and economic diversity. It was very popular in Czechoslovakia and seen as the beginning of the end in the West until at midnight on 20th August, tanks and APCs from the other Warsaw Pact countries rumbled across the border and occupied the country.
Zátopek had been prominent on the streets of Prague and was an iconic figurehead of the reformists. But at a crucial time as the Spring was crushed, he recanted, much to the disgust of those who didn't. Nevertheless, he was dismissed from the army and the Communist Party without a pension and spent five years in exile in Moravia working as a laborer for a geological exploration company. He was eventually rehabilitated and survived to see the collapse of the Iron Curtain in 1989 and the development of a capitalist liberal democracy in Czecho and the other countries of the Warsaw Pact. In the recriminatory aftermath, it was suggested that Zátopek had been an agent provocateur, a stooge for The Party and spy for the Stání bezpečnost StB, the state secret police. Statistically, this would not have been an outrageous suggestion because one estimate has it that 25% of the state's citizens were bearing tales to the StB. But Askwith, with Dana Zátopková's permission, spent days and days in the StB archives sifting through the evidence for such a denunciation. And >!phew!< came to the conclusion that Emil was a little naive politically but not a monster. It is also possible that the letter to the press about Milada Horáková was written for Zátopek rather than by him. It's pretty clear that many of his party loyalist speeches at youth clubs and factories were scripted because they were so dull dull dull.
So I buy it! Zátopek was a card and a character and worked so hard to achieve his athletic prowess. But he was running much more against his own inner compass than to crush his opponents. He was friendly, hospitable, funny, and generous and those feathers weigh well against the snark and bitterness of those who were less successful in the race.
Silver in London 1948 - That marathon - Ron Clark gets his gold - Marta Kubišová sings Modlitba pro Martu 1968 - She goes again in 1989
Monday, 10 May 2021
Plonkety plonk
"Il meglio è l'inimico del bene" an old Italian proverb quoted by Voltaire means Perfection is the enemy of the good enough. Which resonates for me, as an evolutionary biologist: successful species are a kludge of attributes that work better than those of competitors despite being a long way from perfect. Think the recurrent pharyngeal nerve, or male nipples, the phalanges of your pinkie toe . . .
The Western World has a contemptible obsession with stardom: there is only one [Zatopek] winner of the 10,000m; only one Harry Potter; very few millionaire golfers, soccer players or film actors. In horse racing it's ever and always "Eclipse first, the rest nowhere". The difference between first and second in many fields is not statistically significant or reproducible. Run the race or exam next week and the order will be different: the consequence should be that everyone over a certain threshold is deemed to be good enough . . . and a lot better than slobby old me sitting on the sofa swigging tinnies.
I'm not a black&white bloke, indeed my last true name means 'grey'. My sister briefly shared a flat in London in the 80s with a woman who went on to become one of the top wine-tasters in The World. So I'm inclined to believe that there are people out there who practice enough, and are sensitive enough, to discern subtle differences among wines. Me, I'll trust someone who makes a living visiting hundreds of co-ops and vineyards for LIDL. If the company is going to order 1000s of cases at €100/case then that product is not going to be drain-cleaner . . . it will be good enough for €5.75. In the range €5.95 to €15.95 it's all going to be a matter of taste. I am told by my brother, who's been there, that €50/bottle wines are something else entirely but I'm on the pension now, so I'm not going there.I wrote a few years ago [whoop, whoop, numbers alert] that competitive wine-tasting is largely flim-flam, boondoggle and blackguardry. IF the label is soaked off or the wine is decanted THEN most people can't identify a wine to grape-variety, let alone terroir. I was delirah therefore to discover the 2018 Master Sommelier Exam Cheating Scandal. It is a tale of hubris [overweening arrogance inviting disaster] and huckster. Who knew that there was a Court of Master Sommeliers, Americas (CMSA)? Who cared enough to let it be known that there were fewer Master Sommeliers than astronauts? Whose sense of self is so tied up in the business that they actually append "MS" to their business cards?Answer: people whose interest in wine is conflated with their interest in money.In 2018, and not for the first time, there were shenanigans and insider dealings in the process of accepting new members into The Inner Circle. The examination is in three parts, each section of which costs €1,000 to take . . . with no guarantee of success. Indeed only 1 candidate in 12 passes through the ordeal. It reads like the "servitor" section of the exam is licenced hazing by the judges AND is regressively snobbish in its 19thC ideals about what a Sommelier is. For reasons beyond comprehension, in 2018 one of the judges send out a txt to candidates hinting at which six wines would be on that year's tasting panel: Subject: Heads up // "PG, CndP". Which being interpreted was pinot gris / grigio & Châteauneuf-du-Pape. tl;dr The Court of Master Buffoons decided to cancel the certs of all the successful candidates that year on the assumption that any and all of them could have been given the Heads-Up. Like a typically patriarchal, smug, self-aggrandizing coterie of bluffers they refused to have a proper investigation or an external audit to their arbitrary and capricious decision. The Optics are terrible and the lawyers are rubbing the hands.
Friday, 8 June 2018
Shoulder roll
It is clearly a bit of a problem because one hand is taken up administering the shoulder-roll and there is a limit to what you can do with the one remaining hand. And what about if you want to get stones out of the rear hooves or check for spavin on the back legs? A lot of horse-handling work requires two people, one of whom just stands at the front end holding on - with or without the ould shoulder-roll. One of our Design students has clearly grown up on a horse-farm because s/he's found a solution to this waste-of-hand problem. It's a fist-sized clothes-peg or bulldog-clip which you attach to the horse's neck in the prescribed manner and leave there: freeing up both of your hands for counting the rings on the teeth or whatever it is that horse-copers do. I hope it works into a successful business proposition.
Got all that? Now a quiz:
1. Which of the following is not a disease of horses?
glanders - stifle - bone-spavin - colic - rainscald - strangles
2. When was "Eclipse first, the rest nowhere"
3. Where [the heck] is Shergar?
4. What's the difference between a mule and a hinny?
5. In what sense is it good luck to have a horse-shoe fall on your head?
Whoa! did somebody mention Horse's Neck? My father used to ply us with these when we were kids. Not tots; but not voting age adults either. It's a cocktail made with brandy and ginger ale in about 1:3 ratio. You can fancy it up with Angostura bitters, a snake of lemon peel and ice, but brandy and ginger is the core. Using whiskey in place of brandy is as a bad a solecism as putting milk in the cup first before the tea: it tastes pretty much the same but is just . . . not . . . done.
Monday, 11 December 2017
Top Ten Human Genes
We had a paper in the 00s, for example, which showed that genes expressed in the liver (or heart or kidney) are scattered all over the genome. The long genes aren't all found on the longest chromosome. Olfactory receptors are clustered in little groups, it is true, but there are lots of these OR clusters and toll-like receptors TLRs are all over the shop. We'd be mad if we only wrote papers about receptors and ignored enzymes. Kerpedjiev was curious about which genes/proteins occupied the collective time and energy of science and wrote a simple-enough script to snag this information for each and every one of the 27,000 protein coding genes we know about. It's exactly the same idea as I've been progressing with the Masters of Imm up in Trinity over the last several years from 2012 until they sacked me in 2016. I called it the Most Sexy Immuno-protein competition. We didn't aspire to be comprehensive because we couldn't write a simple-enough script without a lot of help. Nevertheless, we showed that some TLRs were stupidly more popular than others because science puts a lot of handicaps on doing original research: everyone - HoDs, funders, editors, reviewers and referees - is happier if you mullock along in the footsteps of others. Wenceslas science, we might
A few proteins acquire legs and outstrip their trudging rivals for the attention of scientists. Aled Edwards from Toronto did a similar study ten years ago in which he showed that the $1billion Human Genome Project had been effectively useless in generating new targets of research to ameliorate the human condition. Researchers found it easier to fondle each other's work than to strike out into the unknown. Working within the herd is safe but not very exciting. Going all maverick makes funders nervous and the results require too much effort to assimilate and tend to get ignored. I could ask you to guess which genes are most highly cited in the scientific literature, but even if you are full time in bio-science you likely won't have the breadth of interest to know them all, let alone put them in the correct order.
Well here they are [L]. I'm surprised that TLR4 isn't there but that's only because we discovered a minority interest TLR and so I think that TLRs are bound to be interesting to everybody and I acknowledge that TLR4 trumps our 'umble TLR15. But all TLRs are collectively a bit of a side-show. Even among the top 10, p53 is Eclipse first, the rest nowhere, but in a way that is reminiscent of Zipf's distribution laws for letters or Benford's for numbers. So who are these celebrity boys and girls of biomedical world?
p53 is the guardian of the genome a tumour suppressor which is found to be mutated in about 50% of all cancers. The implication is that, when fully fighting fit it is preventing the development of cancer.. Several of the other genes reflect the biomedical world's obsession with cancer - which affects the family and friends of the affluent white males in power in the West - rather than possible targets for infectious diarrhoea, TB or malaria. The million black babies a year who succumb to each of those diseases can't afford to pay for drugs. #2 is TNF whose name tumour necrosis factor says it all: it works to gee up the immune system to kill tumours. VEGF vascular endothelial growth factor is the source of another nifty insight to treating cancers. As a tumour grows through out-of-control cell division it demands to have more oxygen and glucose to fuel its energy demands. If we can suppress the develop the growth and development of the local matrix of capillaries then we can suffocate the traitor in our midst. EGFR epidermal growth factor receptor works on the same process from a different angle. If we can jigger the receptor of a growth factor, then we can also suppress growth. Note the GF in TGFB it's another target for growth factor control. Note the R in ESR1 the oestrogen receptor which is involved in ovarian and breast cancer and tell us the oestrogen has more role in life than just shedding an egg a month for 30 years.
I'll refer you to the original article for a really neat graph of the timeline of trendiness. When I was in college 3% of all the publications were obsessing with beta haemoglobin HBB, mutations in which led to the first genetic disease sickle cell anaemia. Hey, before President Richard Nixon signed the National Cancer Act in 1971 and diverted $billion$$$ towards the War of Cancer, biomedical science cared about black babies. You have to talk % impact because in absolute terms publications were a trickle back then compared to the tsunami of tosh today. I say tosh because the average citations for a scientific paper is less than one: more than half of all papers published bob up and promptly sink without trace effectively unread by everyone including the authors.
1980 280,000
1990 410,000
2000 532,000
2010 940,000
2016 1,259,000. Heck and jiminy there are even 13,000 pubs for 2018 out there - I guess mostly from the Journal of Clairvoyant Studies and Prognostics.
Monday, 25 June 2018
Literati Indiana
India, then World's largest democracy, covers about 3/4 the area [3.3 million sq.km] but has more than twice as many citizens [1.3 billion (and rising)] as the EU. There are currently 22 languages on the Eighth Schedule to the Constitution of India. Here they are alphabetically: Assamese; Bengali; Bodo; Dogri; Gujarati; Hindi; Kannada; Kashmiri; Konkani; Maithili; Malayalam; Manipuri; Marathi; Nepali; Odia; Punjabi; Sanskrit; Santali; Sindhi; Tamil; Telugu; Urdu. Don't know about you but I could only have named a handful of these and even with the list would have difficulty writing them ordered by the number of native speakers. But I would have been quite sure that it would be, like Eclipse, Hindi first, the rest nowhere. And I'd be right: 44% of Indians speak Hindi as a first language 5x more than Bengali, Telugu and Marathi the next highest contenders.
I was reflecting on this because, in my restless surfing of the interweb, I came across the Jnanpith Award, India's Premier literary prize. It has been awarded annually since 1965, sometimes shared when the committee appointed by the Bharatiya Jnanpith cannot agree. The BJ is a literary think tank endowed in 1944 to carry out research into India's dead languages: Sanskrit, Prakrit, Pali and Apabhramsha. The Jnanpith Award, is given to an author who has written something in an Eighth Schedule language, or in English and is worth ₹11 lakh = 1.1 million rupees. That's 'only' worth about $20K USDs, but a lakh goes a long way on the sub-conitinent. The JA is thus like the Nobel Prize for Literature, the Man-Booker Prize or our own Bord Gáis Energy Irish Book Awards. Richard Flanagan (and others) has been scathing about the concept and execution of these events: "Literary prizes exist to give dog shows a good name . . . National prizes are often a barometer of bourgeois bad taste." Success as a writer is chaotic - as in 'sensitive to initial conditions' - Two writers, both alike in dignity, in fair India, where we lay our scene . . . have very different career trajectories if one (and it can only be one) wins a LitFest Prize.
So I thought, I'd have a look at the data of the Jnanpith Award to see if there was evidence of skull-duggery. There could be two sorts of error: one language could be garnering too many prizes or minority languages aren't getting their day in the glare of publicity. The JA committee are compelled to give weight to the Buggins Turn - if a Malayalam writer wins one year, his/her co-linguists are excluded for the next two years. There is a suspicion that Rudyard Kipling won his Nobel because no English-language writer had won in the first seven years of the Nobel Prize for Literature.
I think it's clear from that plot that you're at a significant disadvantage if you choose to write in Hindi, the lonely dot in the top right-hand corner. Demographics indicate that Hindi should win 44% of the 57 so far JAs but they've only landed 11.
I should add that, in a separate analysis, I have also incorporated data from The Moortidevi Award another Lit and Phil Prize given out annually by the lads from Bharatiya Jnanpith. But adding another 29 datums doesn't begin to address the stochastic effects and most of the minority languages remain un-prized. My advice: stick to Bodo, it's the language of the future: looks easy enough.
Monday, 28 April 2014
One's Company
All of these books have two things going for them: they give an idiosyncratic and evocative view of events distant in both time and place and they are really well written. People who have been taught to write grammatically correct English tend to snicker at the Da Vinci Code and other books by Dan Brown: the illiteracy is sometimes enough to stop the flow of the racing narrative because you can't follow who is doing what to whom. When Fermor left England with a copy of Horace as one of two books to carry him across the continent it was in Latin. Before dropping out of his fancy school he had been formally educated in the ancient tongue. That meant that he could recognise a gerund, a subjunctive clause, a preposition or a phrasal verb in either Latin or English. The Horace for a contemporary 18 year old to take Inter-railing round Europe would be more likely Rumpole of the Bailey. I also went to a fancy school but was useless at Latin and I was unable to translate its formality into better writing in English. Having O'Manch staying with us for 4 months learning English as foreign language has been an education for us all. When I was at school I thought all that grammar was just an impediment to the communication; I now realise that grammar is essential for communicating your ideas unambiguously.
I've had occasion to remark about our unconsidered certainties - the background that cannot be seen and so is never questioned: that homosexuality is a kind of curable disease, that it's okay to hit children with sticks, that life is sacred, that boxing is a sport in which civilised people might engage. It would not be true to say that there is a vein of anti-semitism in One's Company - nothing compared to what central Europe was getting geared up to in the 1930s - but casual use of Jewish racial stereotypes (salesmen, clever) has modern readers brought up all standing. Nobody nowadays thinks that a pipe is an essential piece of kit to take to the Brazilian jungle. You will notice this of many books written before WWII. It would be about as true to say that Peter Fleming or Agatha Christie was anti-semitic as to say that the Iona Institute is homophobic or that the driver of the Clapham omnibus (and most of his passengers) is racist. After WWII, of course, in Europe there was rather less point in uttering casual racial stereotypes about Jews because there weren't any.
There's a nice critical tribute by Ben Downing to celebrate Peter Fleming's centenary. And here's an attempt by Robert Ryan to bring him out of eclipse by his younger and ultimately more famous brother Ian '007' Fleming. But forget all that, go and get any of Fleming's books out of the library: real life on the edge trumps fantasy however fantastic.
Sunday, 2 April 2017
Da Nags
All that ignorance about Da Nags hasn't stopped me writing about them in the past:
- Policy affecting fertility
- Work-horses 1940s
- Antient artistic representations
- Antient liguistic representations
- As political assassins
- Risking my life for
- Thoroughbred
- Βουκεφάλας Bucephalas
- Copehagen
- Dawn Run
- Desert Orchid
- Eclipse first [and R] the rest nowhere
- Incitatus
- Marengo
- Seabiscuit
- Shergar
- Whistlejacket
It takes a helluva a lot of pall-bearers to carry a horse coffin . . . and you have to make the box yourself because there doesn't appear to be a market for horse-coffins. Why no market? Because most horses are 'put down' when their care becomes too troublesome to their owners. Danehill Dancer [R] was, for example, was euthanized due to the infirmities of old age, just last month in Ireland.
It worries me, the discrepancy between our treatment of end-of-life issues in a) any human b) any animal. If terminating your favourite horse/dog/cat is called putting the creature out of its misery, why are we so determined to keep people alive whatever their prognosis or level of suffering . . . except if we really don't like them.
And did you notice the War Admiral and Man o' War connexion. Stables and studs have a tendency to re-use names and name fragments, presumably for branding purposes.Seabiscuits sire was, for example, Hard Tack, effectively a synonym. But there are limits to what you can call your horse. Or with more Mental Floss obsessive detail.
- Not more than 18 characters including spaces
- Names can be recycled after death; famous horse-names are retired out of respect
- No naughty words
- No obvious commercial advertising
- No racing venue may be included
- Nor the words stallion, dam, sire
- Nor, without permission, the name of any living person
Sunday, 8 August 2021
Mixum gatherum
- Eclipse first [prev], the rest nowhere - Anna Kiesenhofen [R] wins gold
- Bogota - BMX madcaps cycle downstairs
- Apartment living - those neighbours upstairs
- Grady on cranes, collapse of
- Mitholz-sur-Munitions what could possibly go wrong?
- Like The Ploughing, NaneNane 2021 the big aggie day out in Tanzania is cancelled
- Aspiring creatives - Ira Glass advises don't give up
- Osaka to Kyushu by capsule ferry
- Boats? The Evergiven has arrived in Felixstowe most of the foodstuffs will be uneatable if not ignitable.
Saturday, 5 October 2013
What day is it anyway?
The sun and the moon and the rotating earth are in all other respects annoyingly out of kilter. Wouldn't you think that the day (one turn of the earth) would be exactly 1/30th of the the month (one turn of the moon) and that would be exactly 1/12th of the year (one turn round the sun)? Well it's not and it jiggers us all up in ways great and small. But then again, maybe the niggling irregularity of the tides being scarcely predictable (by the per gene product for example) may have pushed some poor fish out of water to become the first effective tetrapod. One could, and The Blob will, go on and on about this but we'll pause today and reflect on the discrepancy between the lengths of the day and the year.
The Sidereal Year is the time taken for the earth to make one circuit of the sun with respect to an arbitrary fixed point (pick any star: Sirius is particularly bright). This is just over 365 and a quarter days: 365d 6h 9m 10s. This is different from the Mean Tropical Year (365d 5h 49m 16s), which is when the Sun returns to shine down the orifice at Newgrange, by about 20 minutes. Depending on how precise you need/desire to be, you must adjust the number of days in the year or suffer having key dates (like Easter, the foundation of The City or the Battle of Clontarf) slip through the seasons. In 708 AUC Julius Caesar rejigged the Roman Calendar to alternating months of 30 and 31 days and a short late winter month Februarius of 28 days (most years) or 29 days (every fourth year). This created a year that was 365.25 days, was easy to calculate and was for most practical purposes a pretty good year.
370 years later, the 1st Council of Nicaea was convened, by the first christian Emperor Constantine I, to decide when Easter was to be celebrated. Tradition clearly had the crucifixion happening at the Jewish Passover but the Council agreed to a) have all Christians celebrate the feast on the same day and b) no longer rely on Jewish authority for determining the date. Those precepts were not enough to unite the whole church because the RC and the Orthodox churches still have slightly different methods of calculating Easter - this year my Greek room mate was celebrating Easter 5 weeks after the rest of us but next year both churches will pick the same date (20th April, as you ask).
1500 years later, the Council of Trent was convened (in Trento, in the Italian Alps not Nottingham!) to wrench Easter back to the time when the Holy Fathers at Nicaea had said it should be. It had drifted because the Julian Calendar's pretty good adjustment had been accumulating a drift of 10 minutes a year for 1.5 millennia, so was then about 10 days off. It was clearly important because the Council of Trent was actually Councils: the senior clerics, their scribes and mitre-carriers, met for 25 sessions over a period of 18 years and three papacies. The final decrees were signed by more than 200 prelates. That's about 8 person years for filibuster and preening and a couple of days of actually getting stuff done. Although I agree that there was more on the Agenda than the calendar.
There were two issues: a) get the calendar back on track b) make sure the drift wouldn't happen again. Both problems was solved by a doctor from Calabria called Luigi Lilio. He proposed reducing the number of leap years from 25 per century, Julian style, to 97 per 400 years: century years 1700, 1800, 1900 would not have a leap year but millennial years 1600, 2000 would. He also suggested that the first problem be solved incrementally by omitting the next 10 leap days. Christopher Clavius (born Christoph Clau or Christoph Schlüssel) took up cudgels for Lilio after the latter's death writing his arguments into an 800 pager. I don't know how these guys would have coped on Twitter. Clavius argued for a one-fell-swoop adjustment of the Calendar and the next-Pope-but-one Gregory XIII (born Ugo Boncompagni) agreed.
Accordingly in 1582 4th October was followed immediately by 15th October and Cardinal Alessandro Farnese (b 5th October 1520) didn't have a birthday that year - he must have been a bit hacked off.
Wednesday, 3 October 2018
Wallflower genes
It's a fair approximation to say that all progress in medicine is now based on genes and proteins: how they differ in health and ill-health; how they can be encouraged, unplugged, interfered with, replaced and mimicked. Over the last 40 years we have developed a toolkit for clocking these variations. But it turns out that some genes are more equal than others - in terms of the attention they attract from scientists, funders and Big Pharma. I've a neat Most Sexy Protein exercise to do with students which shows how some proteins have had more than 10x more interest than other, related, probably equally worthy, potential targets. I've been here before tribbing the work of Aled Edwards in Toronto for showing that the human genome project delivered [to a close approximation] NO new gene targets. As the HGP a) cost $3 billion of tax-payers money and b) was billed as helping understand our molecular/medical fundamentals; that's a bit of a bust. Scientists, for all their talk of pushing the far frontiers of science, are quite risk-averse: they tend to tweak and polish the same old same old system that they worked on for their PhD when they had all their hair and fewer children. One reason for this is that they follow the money, and funders are even more risk-averse than scientists. The chaps who make the funding decisions have a bean-counting monkey on their backs whispering "Remember, adjudicator, your decisions must bear fruit for the tax-payer".
The conservatism of science got hot 'n' fizzy in September because of a new massive bibliometric study of all the genes we know about in the human genome. Large-scale investigation of the reasons why potentially important genes are ignored was published in PLOS Biology by a small group from Northwestern U headed by Thomas Stoeger and Luis Amaral. I gather that it was Stoeger's original idea and he mobilised Amaral the Portuguese Megaquant (who has an office in each of The Institute on Complex Systems (NICO), Dept of Chemical and Biological Engineering, Dept of Molecular Bioscience, and the Dept of Physics and Astronomy at NWU) to help crunch the numbers, which quickly became formidable.
When I launched into the waves >!plooof!< of molecular evolutionary analysis in 1989, it was fairly calm. I was assigned to a) develop useful software for analysing some classes of DNA sequence b) apply that software to human genes. Only 1064 protein coding genes had been sequenced by Christmas 1990: I know; I collected them carefully. Those genes were cherry picked because they were interesting and analyzable: they had been tracked down because a mutation in their DNA was associated with a disease state. They were not, therefore, a random selection of the 20,000 genes which we now believe exist. The NWU team have flagged 15 basic bio-chemo- physico- attributes which are strongly associated with Interesting genes. That's 15 out of 430 (!) things that you can measure/record about a gene [see R for some of them graphically displayed]. They whittled the list to those key attributes with "gradient boosting regressions with out-of-sample Monte Carlo cross-validation" whatever that it. It seems that most of these measures are derived from street-light science: they could be measured with the techniques which were then available. They had to a) be expressed in bucket quantities b) across a wide range of tissues especially HeLa cells c) have signal peptides so that they were exportable from the cell for access d) tolerate non-fatal variants. If a gene scored strong in these features, it was likely to be discovered and characterised in the last century. In horse-racing parlance, those genes were racing along on the back of Eclipse first the rest nowhere. With that early start, funding-fondling and inertia [continue in its existing state of rest or uniform motion in a straight line, unless that state is changed by an external force] would kick in and a disproportionate amount of
When the human genome came out in 2001, it should have levelled the playing field because the gene sequence and predicted protein were available for all 20,000 human genes, including the wall-flowers and shrinking violets. But it didn't. Obviously there are exceptions to this rule. Six johnny-come-lately genes are identified in Stoeger&Amaral Fig2a [L]. I know a lot about IFNL4 - interferon λ4 - one of those "Sexy Genes". Its existence wasn't even suspected until January 2013. One of my three useful ideas in science was to predict the existence of IFNL4 close to IFNL3 [also sexy see L] from a close analysis of that part of the genome. Our interest was piqued because a series of studies showed that variants/mutations in that region were associated with the clearance of Hepatitis C virus. The bioinformatic evidence, as I presented it at a lab meeting, was so compelling that the boss pulled a graduate student off her own project, where she was quietly minding her own business, and had her try to prove the existence and activity of the predicted gene in real cells in a test-tube. The quest consumed about 1.5 person years and came to nothing. I left that group in December 2012 and started work at The Institute in January 2013. The same week The Blob launched, a far better resourced research group scooped up the prize for discovering IFNL4. And while we're looking at Fig1a, check out C9orf72, it hasn't got a proper name yet [it's the 72nd Open reading frame on Chromosome 9] but it's very strongly associated with ALS [Lou Gehrig] and FTD frontotemporal dementia, and we have only a hazy idea of the how and the why. It was invisible in the 1980s and 1990s because it's not active in HeLa cells and doesn't have a signal peptide. Nevertheless it has huge potential for making money in the development of therapeutics.
Okay that was all good fun, but what to do about this ludicrous, wasteful, boring, use of science funding? Stoeger&Amaral have some [ain't gonna happen] suggestions:
- "In order to counter the career forces currently pushing towards conformity, there would be a need for stable, long-term support for such innovators to focus on the unknown".
- For gawd's sake keep up the basic research - in flies, frogs and nematodes - they have been a rich seam for identifying novel ways forward in human health.
- Reductionist science - where you control for all variable but one - is only sporadically successful in making progress through the complexity which is us and our habitat. Fund multi-gene science with interaction terms in the equation.
- Look carefully at the NWU data, it will help you identify the wall-flowers that could do with a dollop of dollars from NIH.
Monday, 27 November 2017
Just passing through
< The hats off thing about astronomers is that from a record of movement of a dot across a series of 2D photographs, they can calculate the 3D trajectory [See picssource] of an object in space. It helps if they have studied conic sections in high school or college.
The deal here is that the curve tells the star-gazers whether the object is coming back, which it will if the curve is [part of] an ellipse. Edmund Halley's calcs and historical research told him that "his" extraterrestrial traveller had an elliptical orbit and so would return . . . in 75 years time - and it was so. 'Oumuamua won't. They are confident that the trajectory is hyperbolic. That means that 'Oumuamua was travelling in a straight line through space minding its own business when it encountered a vastly more massive object's gravitational field and was sling-shotted round the Sun and sent off in another direction.
'Oumuamua was first observed a month ago on 19th October 2017. Back-calculations led astronomers to make a couple of earlier precoveries [been there before] when the object was more distant and sufficiently faint that it didn't get flagged. It seems that perihelion (closest approach to the Sun) was back on 9th September. Being close to the Sun creates a whole other raft of observational difficulties as we heard about burned retinas during this year's solar eclipse.
Reportage: Michelle Starr at ScienceAlert and Uncle Tom Cobbley across the Internet who is collectively on the story like gravy on biscuits. More Blobby astronomy: Sedna - Eris - Mina Fleming - Annie Jump Cannon - Pleiades - By Jove - Star Boks - others
Sunday, 25 January 2015
Pluck
- tripe, the washed lining of the stomach, is absolutely standard fare, in umpteen variations, on menus in Portuguese cafes and restaurants but is foreign to most Irish larders
- drisheen, a variety of blood pudding, is claimed to originate from Cork but is nowadays only of minority interest in Cork or anywhere else in the country for that matter
- crubeens, pig's trotters, are greatly relished by The Beloved's mother who prefers to wrastle with her food but is more or less universally rejected by anyone under the age of 50: the pale things look altogether too biological
- pork bodice are spare ribs in a long rack and rarely seen outside a Chinese take-away
- ox-tail which makes such exceedingly good stews because long boiling works tasty miracles on the connective and nervous tissue of the diminishing run of vertebrae - but it looks too much like anatomy for most modern tastes
But today is Burns Night the birthday of Rabbie Burns the poet of Scotland. Just as Poles, Greeks and especially Montserratians wear a green tee-shirt on St Patrick's day, a lot of people with only a tenuous connexion with Scotland will try a morsel of haggis on this day in late January. Haggis is made from the 'pluck' [heart-liver-lungs] of a sheep minced and mixed with oatmeal, onions, suet, salt&pepper and stuffed into a stomach, preferably of the same sheep. Genuine versions of this dish are disconcertingly biological with strings tying off the base of the oesophagus and the pyloric sphincter at the other end. But it is tastey enough and traditionally served with plain potatoes and boiled turnips "neeps & tatties" . . . and single-malt whiskey. We can't say fairer than Rab Burns:
And dish them out their bill o fare,
Auld Scotland wants nae skinking ware
That jaups in luggies:
But, if Ye wish her gratefu prayer,
Gie her a Haggis!
Thursday, 17 November 2016
Not even close
Q13. The volume of a sphere is given by the formula 4/3πr3. If a soccer ball is 22cm in diameter, what is its volume in litres? Everyone in the room has handled a 1 lt carton of milk or orange juice and a soccer ball or seen one on TV.
A. It is just bonkers to assert that the volume is 44,000lt. That's about the size of the largest road tanker we have on the roads in Ireland. Nevertheless 2 students offered this as an answer. Actually they offered 44,602.2 lt. Which showed that they didn't know the difference between a diameter and a radius and that one had probably copied the other's answer.
Q16. Given that the period (tick . . tock) T of a pendulum is given by T = 2π*√(L/g), that g the acceleration due to gravity is 9.8ms-2 and the length L of the pendulum is 50cm, how long does it take for the pendulum to swing one complete cycle?
A. I can't claim that everyone will have seen a pendulum up close: only a minority of a homes have a grandfather clock. But we have all been in a children's play ground with swings. The almost universal answer to this question was 14 seconds; because they treated the length as 50 rather than 0.5m. You can run 100m in 14 seconds; how could a pendulum half a metre long take that long to swing forward and then back?? In the post-mortem I whipped out my car-keys and swung them from their lanyard - which is about 50cm long - to show that it takes a tad under 1.5 seconds.
Somehow, I/we have to get kids to realise that the units count! Merely plugging numbers into a formula is the easy part, evaluating the answer for sense is another level of competence altogether. We should have a class in guesstimation, like in Mathsemantics Home Ed class. It might include numbers like counting the spaces for receptor proteins in a typical mammalian cell. More:
- The full moon was super big on Monday, how far from your eye do you have to hold a dime to eclipse it?
- Is it possible for all 7.5 billion people to stand comfortably in Co Carlow = 900 sq.km?
- in the Republic of Ireland 70,000 sq.km?
- many of them all small
- If a cell is mostly water and so are you, how many cells are there in a bloke weighing 70kg is the average diameter is 30μm?
- How thick is a sheet of 80gsm A4 xerox paper if a 500 sheet ream weighs 2.5kg?
- How many blades of grass did Louis Agassiz inspect during his Summer beetle collecting?









