Sunday, 31 May 2015

Worrying ignorance

At The Institute we require a 12 week work-placement or internship as a prerequisite for graduation because the education is training people for the workplace not for a life of leisure. About 12 weeks ago, towards the end of my intense relationship with 16 final year project students, I conducted a straw poll of who had found a work-placement. It was black [no placement sorted] and white [no problem].  You can rant about this inequity, and I did, but you can also do something about it and my roomie called a meeting to put in train a scheme to formally offer internships in our own research wing. Only two people were prepared to take on a trainee/intern/gopher - myself and herself - and last week we had eleven (11!) people in the applicants line for 2, or perhaps 3 positions. Those are better odds that getting a place in Harvard but I was till surprised how many of our students had been caught without a place to go.  They have to fit in 12 weeks between now and the end of September which is 18 weeks away.

We set out a timetable to interview 10 [one having sorted himself out across town] candidates on Friday last. We had the cunning plan to have our two MSc students on the interview panel - which will be good training for them and allow them a substantial say in whom they'll be working with all Summer.  But two claimed that they could attend on Friday, so we scheduled them for Tuesday.  Then one fellow e-mailed us the night before to say that he had a job in Wexford, which is short notice and left an annoying hole in the schedule that was too late to fill.  At least he told us! Two of the other candidates just didn't turn up: no word, no apology, no manners. That's quite worrying because these people are now going out into the work-place (if they can get a position) and the Institute's street-cred depends in part on how our ex-students present themselves.

The rest brushed up nicely and presented themselves rather well - as dedicated, competent scientists who were not afraid of hard work. This didn't always jive with my two+ years of experience with them working in the lab under my supervision; so that made me wonder about a) the efficacy of our interview technique and b) the usefulness of interviews in general. Maybe they've developed their sense of competent self by carrying out a final year research project.  They certainly seemed to describe their own brick in the wall of science with some knowledge and insight.

One of the MSc post-graduates asked the first interviewee "If I asked you get me some H2SO4 what would you bring back?" [blank] "it's an acid" [still blank].  Only one of the 5 remaining candidates answered correctly and quickly and another came up with "sulphuric acid" after a  l o n g pause and the supplementary statement. Cripes and jiminy!  If they don't know that after studying science for 4 years in college there's something wrong. I went off to look for a negative control (what answer was given by people who had no formal scientific training) N = 2 people in their 50s + 2 people about 20 years old. One of the oldsters and one of the youngsters got an almost right answer.

Saturday, 30 May 2015

The Numbers behind Numb3rs

In the last year or so of her education, Dau.II spent much of her waking life sitting on the sofa facing the 24" screen absorbing information like it was going out of fashion.  In this sense, she was very like her father who is, even in his declining years, a Prince of Pub-Quiz.  The difference is that my folks paid a king's ransom for me to acquire a headful of triv, whereas Dau.II only cost money once when she downloaded so many GB that we had to pay punitive rates to our ISP for a month. She would watch boxed-sets if she could borrow them but failing that youtube was her lifeline. She was only a week behind Baltimore in watching the latest episode of Masterchef. We also went from Desperate Housewives to House to Scrubs in a sort of free-association word connexion. I say "we" because, although I didn't have the stamina to do a six-hour half-series binge, I was up for sitting down to watch a single episode [not Desperate Housewives, mind, I had to fling out of the room after 5 minutes of that].

47 50m3 57463 w3 4l50 3nc0un73r3d numb3r5 wh1ch w45 r1v3771n6 f0r 4 7u7hr33 3p150d35 bu7 7h3n 607 70 b3 4 l177l3 f0rmul41c.  7h3r3 15 4n fb1 br07h3r wh0 h45 4n 4b5urdly 3xc171n6 l1f3: 3v3ry w33k h3 15 45516n3d 70 4 dr4m471c c453: nucl34r b0mb5, 4554551n4710n5, 53r14l k1ll3r5, 1n73rn4710n4l 5h1pp1n6 5c4m5, dru6 b4r0n5, c3n7r4l 4m3r1c4n w4rl0rd5. h3 15 n3v3r 5h0wn f1ll1n6 0u7 h15 3xp3n53 cl41m5, cl34r1n6 h15 d35k up 0r f1l1n6 l457 w33k5 p4p3rw0rk.
You should be able to read that as we've met l33t before in intriguing road-signs, but it's not fair on you to read wodges of l33t-text when my Ukrainian followers are possibly struggling enough with my idiosyncratic English.

At some stage we also encountered Numb3rs which was rivetting for tuthree episodes but then got to be a little formulaic.  The show, which CBS ran through six TV series between 2005-2010, features an FBI brother who has an absurdly exciting life: every week he is assigned to a dramatic case: nuclear bombs, assassinations, serial killers, international shipping scams, drug barons, trafficked girls. He is never shown filling out his expense claims, clearing his desk-drawers or filing last week's paperwork.  He has a younger brother who, as a childhood math prodigy, left Princeton with a degree at about the same age that normal people are going there. At about minute 15 in every episode, the screen will fade to sepia and a swirl of Greek letters and math-symbols will blurf out to a voice-over of bamboozling science-speak. For light relief, the boys will visit their widowed father for beer and lasagna and Charlie the math-whizz has a mumbling and less symmetrical math-pal who serves as a foil to allow the math to be 'explained'. To leaven the male geeks there are a few attractive women, some of whom are math-anxious but some are clearly as familiar with Riemann zeta functions, Cantor's infinities and Gödel incompleteness as the boy genius. Oh, and there is the obligatory token black. All good fun and far richer than Desperate Suburbia. Rather like House [which was running at the same time over on Fox] really, with a different subset of sciency words: I guess if you watched both series long enough you'd dream of an episode where a topologist developed lupus or a number theorist had a brain tumor.

This post is not really about the TV series, it is about the book of the TV series but I see that Wolfram has also contributed to the math of the series.  I've read a few books about the science behind some other cultural series: the Science of Discworld, co-authored by Sir Pratchett; The Science of Philip Pullman’s His Dark Materials by John and Mary Gribben.  These are often a little wooden and consciously didactic: the kind of stuff that would have my home-educated daughters rolling their eyes at being taught something that they should know, rather than something that the author thinks is really neat.  The Numbers behind Numb3rs leans much more to the second option and although each chapter starts from a Numb3rs episode, the trigger is often left in the dust as the authors zoom off where their passions or obsessions take them. A bit like a good blog, really. Some of the themes:
  • A good explanation of Bayesian statistics (although not as good as Nate Silver's)in evaluating the likelihood that a particular black dude committed a crime, rather than just being the first black dude caught up by a razzia through the nearest ghetto. 
  • A critical investigation of the USA being in a 15 year lock-down trying to protect itself from terrists and how much that might cost and how cost-effective it might be.
  • An important if 100 years too late evaluation of the reliability of finger-prints as evidence.  Nobody seems to have tested the statement that "all fingerprints are unique" or more importantly that the way we code fingerprints give a unique signature for all 70 billion finger-prints that are attached to living people this weekend.
  • For where the paranoia of lock-down met sketchy probability and fingerprints, check out the infamous Brandon Mayfield case where the FBI sacrificed one of their [white] citizens to show that they were on the 2004 Madrid train-bombing case.  Possibly because he is white, Mr Mayfield's prosecution was quashed.
  • An investigation of the 1868 Howland will case, which hinged on two signatures on successive pages of a last-will-and-testament being suspiciously similar. A father and son team of mathematicians called Peirce gathered a few dozen authenticated signatures and analysed the lengths of the 30 down-strokes to determine their distribution. The two contested sigs were far more similar than any other pair of genuine signature . . . therefore one was a tracing of the other. 
I didn't anticipate how much I enjoyed the book; it was published in 2007 - how come nobody gave it to me for Christmas?
I'll mention one

Friday, 29 May 2015

Muntjac: a deer with fangs

There is a possibility that, next year at The Institute, I will be asked to teach Molecular Biology and Immunology to our 4th Year Biologists. I had my annual timetable meeting with the new HoD and was boasting about my research record discovering genes of immunological interest in chickens Gallus gallus and cows Bos taurus.  Suddenly I twigged that my roomie has been kicked upstairs to a part-time admin position and was looking to shed her 4hrs/wk MolBol&Imm lectures!  Bottling out and back-pedalling, I stoutly asserted I was a) old and b) hoping to coast quietly down-river to retirement and that c) it would be better taught by some young person more up to date with his/her MolBio. After I thought a bit and acquired a backbone, I e-mailed the HoD to say that I'd be happy to teach MolBolImmunol if that would help the cause. We'll see and you'll hear how that turns out in due course. Then over the w/e El Asturiano sent me a link about the Indian Muntjac and I was kick-started to think that I could do whole chunks of the 4th Year course just talking about cetartiodactyls, a word I find I used without definition [shame] a couple of weeks ago. For starters I could tell them a war story from the battle with morphologists by which molecular evolutionists defined a new mammalian order Cetartiodactyla to include cows, sheep, goats, antelopes, pigs, hippos, llamas, camels and . . . whales.
Mais revenons nous a nos muntjacs. The genus Muntiacus consists of about a dozen species of small deer.  Fossils that can fit into this genus have been found in Miocene [7-24mya] deposits in Central Europe, making it one of the oldest extant types of deer. M. reevesi the Chinese muntjac has been introduced into England through the ineptitude of the Duke of Bedford who allowed these exotics to escape from his estate at Woburn in 1925.  Since then the species has spread to pretty much every county. Munjacs are small, but you can differentiate an adult muntjac from a juvenile some-other-deer by the presence of its tusks - enlarged upper canines most clearly seen on the stripped skull [L above].  That's not so surprising as pigs are cetartiodactyls also although they tend to develop the lower canines into formidable weapons. The most extreme example of canine development is in Babyrousa babyrussa known in English as . . . the babirusa. Their upper canines start development pointing downwards and then, in males, do an extraordinary and elaborate curve upwards to punch through the maxilla to create a fearsome curlicue in front of the eyes.  What are the developmental signals that drive that?  Dunno, but my students next year are going to find out!

Muntiacus reevesi has a more or less normal number of chromosomes at 2N=46, which happens to be the same number as we have but it has a sister species Muntiacus muntjak which is only distinguishable from M. reevesi through very careful scrutiny by an expert 'deerologist'. M. muntjak, in contrast to Bedford's Folly, has the distinction of having the smallest number of chromosomes of any mammal at 2N=6,7.  The 6,7 indicates another bizarre trait: females have 6 chromosomes (2 pairs of 'autosomes' + XX), males in this species have 7 (2 pairs of 'autosomes' + X+Y1+Y2).  Somewhere along the way, their Y chromosome has gotten split into two unequal halves.  Despite this absurd difference in chromosome count, the two species are interfertile, sort of, the cross yields viable offspring but they are sterile in  the same way as crosses between horses Equus caballus and donkeys Equus africanus asinus are called mules or hinnies (depending on which species is the jumper and which the jumpee).

Everybode kno that mules are sterile at least partly because they cannot sort out the discrepancy in chromosome number of their parents 2N=64 for horse and 2N=62 for donkeys and the hybrids have an odd number at 2N=63 presumably with two short chromosomes from horse trying to pair up with a single long one from the donkey parent. In fact not all female mules are sterile and there have been numerous (but still proportionately rare) examples since the time of Herodotus. The Muntiacus hybrid must be a real mess at meiosis when the pairs of chromosomes line up to halve their number to produce the gametes: sperm and egg. Lest you think that the USA has a corner on gun-nuts, you can shoot a muntjak in England if you have a gun and £75.  The deer which I illustrate [R] to show they are but little (and not fierce) are neither sleeping nor smiling, they are venison.

Thursday, 28 May 2015

No: you're mad, not me

John and Alicia Nash are dead. just two out of the 30,000+ people who will be killed in road traffic accidents this year in the USA.  The rate of RTA fatalities [worldwide] is going down both in absolute terms and more so in relative terms as the number of people and vehicles on the roads is steadily climbing along with their carbon emissions. It is about 3x safer on the roads now than in 1940 [R].  The cops in New Jersey were quick to report that neither Nash was wearing a seat-belt and so they were flung from the taxi in which they were returning home from the Airport along the New Jersey Turnpike.  I've advocated that these things should be made public pour encourager les autres with regard to safe behaviour in and about vehicles.  Still it's better to neglect your seat-belt than to be txtn yr pals while at the wheel. The obits show that the film streamlined the Nashes' life a bit by ignoring the fact that Alicia divorced John in 1963 when the madness all got too much and she remarried him 38 years later. For me the point is that John Nash was supported and tolerated by his wife and their Princeton community for a helluva long time because he was a once-and-future genius. That tolerance of The Different could be much more widely expressed. Indeed we should celebrate, cherish and nurture difference because same-old same-old is not going to get our planet out of the nice mess humanity has gotten it into.

Where had the Nashes been?  They'd been to Norway to pick up a half share of the NOK7,000,000 [€750,000ish] Abel Prize which recognizes outstanding scientific work in the field of mathematics. The citation for 2015 talks about their contribution to partial differential equations, of which the easy explanation by Alex Bellos won't be either easy or interesting unless you have a degree or two in mathematics.  We met John and Alicia before on The Blob in a review of A Beautiful Mind the film of the book by Sylvia Nasar. I then had some important things to say about letting the mad alone. If you start the meds, or the Electro-convulsive therapy [alternative positive view], let alone some gung-ho brain surgery, then you are likely to be committed to more and more of the same until the well runs dry or you run out of money.  Nash believed that he thought himself well as his endocrine equilibrium changed with age. “I emerged from irrational thinking, ultimately, without medicine other than the natural hormonal changes of aging,”  Very few of us would have the patience to let things hang for 3 decades until they [maybe] got better.  And we have a very low tolerance threshold for people talking to themselves in public.  I think this is a recent phenomenon as medicine has taken on a supermed mantle that everything can be cured: even things that should be let alone.  In the run up to the Marriage Equality Referendum there has been some retrospective about how homosexuality was 'treated' when it was considered to be an illness a short generation ago. Alan Turing anyone? They still talk about the Turing Test as a lynch-pin of our understanding of Artificial Intelligence. We talk less about Turing's Testes which were rendered 'confused' by judicial injections of artificial estrogen.  Aaaargh, retrospective rage!  Further back in time, today is the anniversary (28 May 1936) of Turing submitting for publication his ideas on the Turing Machine.  This was a key gedankenexperiment / thought-experiment in the maturation of computer science: on the back of a few envelopes Turing laid out how all computers would work. iPhone anyone?

In the run-up to the Referendum, a bright child asked his teacher,"Miss, after we free the gays, who will we help next?".  Let's rephrase that: After we let homosexuals just get on with what seems right and appropriate to them, let's look at doing the same for a rattle of mental illnesses: ADHD for starters.  There may be a condition or a syndrome called ADHD but I know that it is massively over-diagnosed among children who are just not happy sitting quietly waiting for instructions in school - possibly because that is so boring and unchallenging. There are people alive today who were physcially and psychologically abused for being left-handed. It is far too easy to tsk tsk about the past - it is harder but necessary now to look sharply at our unconsidered certainties about where normal ends. Back in the Hippy 1970s R.D. Laing maintained "Insanity - a perfectly rational adjustment to an insane world" and "Schizophrenia cannot be understood without understanding despair." He campaigned against the over-drugging of the 'mad'. It was difficult to hear him shouting that crisp labelling of conditions led to too much money was being diverted to Big Pharma. It was easier to dismiss him as a Marxist; then his 1983 confession in a broadcast interview that he and his parents had had disturbing mental 'episodes' conveniently provided an excuse for him being effectively struck off the register by the British General Medical Council.  If we feel so uncomfortable about our treatment of mental illness that we never see lunatics abroad in society, then it is likely that our diagnosis and treatment of mental illness is needlessly cruel, destructively normalising, riotously expensive . . . and wrong. 

Wednesday, 27 May 2015

A time of her choosing

Now here's an interesting story from the NYT Mag about finding a time to die after a fulfilling life, even if attack ships on fire off the shoulder of Orion were no part of it. Sandy Bem was a writer, a 1970s radical, an academic and a psychologist with a particular interest in gender studies. Just when she was coming up for retirement from Cornell U, she was watching a TV documentary about Alzheimer's and realised, all in a tumble, that she was on that path herself. She braced herself for that and resolved that she wouldn't wait until aluminium plaques destroyed her last vestige of self: she would finish the job herself at a time of her choosing. She would thus be a step more autonomous than, say, murderer Clayton Lockett who was also under a sentence of death for much of the same period.

The problem was: when?  It's like there is always a better time in the future to try for a baby . . . until you run out of time at menopause.  In Professor Bem's case, there was a grandchild to see, and projects to finish and, in order to help that happening, she paid some $000s for medications of doubtful efficacy to maybe slow down the cognitive decline. When she did finally chug down 100ml of liquid pentobarbital, comfy in her own bed in her own home with a trusted friend to hold her hand, she basically didn't know what day of the week it was and certainly wasn't in a position to sign an informed consent form.  But she had printed out all the relevant e-mails and signed enough paper-work while she still had her marbles.

Clayton Lockett was tazered then left alone for 8 hours before being strapped down on gurney by 5 prison guards and used a pincushion by a stressed out paramedic and a totally unprepared doctor to administer an absurdly complex exit protocol that smells of scienciness and not at all of 'humane'.  A long time ago, the authorities in Athens decided that they'd had enough of Socrates and his thinking about everything and handed him a glass of hemlock juice to drink. Would anyone think to offer the likes of Clayton Lockett 200ml of pentobarbital instead of the ghoulish convention of a last meal of choice?  It might be more convenient and dignified, and cheaper for everyone.

Tuesday, 26 May 2015

The bones betray

I've suggested that, for about 100 years, anatomy has been considered rather old hat, all the namers-of-parts being long dead:
  • Islets of Langerhans (1847-1888)
  • Malpighian (1628-1694) pyramids
  • Purkinje (aka Purkyně 1787-1869) fibres
  • Golgi (1843–1926) body
  • Broca's (1824–1880) area
  • Fallopian (1523–1562) tubes
  • Haversian (1657–1702) canals
  • Crypts of Lieberkühn (1711-1756)
But with 3-D printing and other technologies, anatomy has moved front and centre in competition for the limelight of medical sexiness. Comparative anatomy has always been a minority sport because it's hard to find anything monetisable=useful in knowledge of the homology of a bat's wing, a whale's flipper and the hands which are now diligently hunting over the key-board.  I guess that's fair enough but I still find it all fascinating.  Perhaps it's just that I find any deep knowledge fascinating; heck, I could spend an hour listening to someone who collects match-boxes or is the county Donkey-Kong champion.

Neil Shubin is the Robert R. Bensley Professor of Organismal Biology and Anatomy [POBA?] at U. Chicago and also Provost of the Field Museum of Natural History, so he's Emilie Graslie's boss.  He's written a book Your Inner Fish and this is a review.  I'm sure you can find other reviews [Grauniad] on line and if you live in the right part of the world you can see three PBS episodes based on the book.  Or for a flavor of the issues and their resolution try this youtube lecture. It's a wonderful story of a serendipitous encounter with an atlas which sent Shubin and Co. to the Arctic to look at 350 mya tropical river sediments. There they found Tiktaalik roseae a strange Devonian lobed-finned fish (it's definitely a fish with scales and gills) that could do push-ups: it has a structural rib-cage and pectoral girdle that would have allowed its fore-fins to propel the beast across the land between ponds. The rib-cage also contained lungs Importantly, it has a neck so it can look around and admire the view from topside.  These missing links are important for understanding where we came from and the descriptive paper made Nature although not the cover. Your Inner Fish is a wide-ranging discourse on how the past can explain the present notably by using the concept of homology - the shared ancestry of structures that don't obviously look as if they have much in common.

There are three tiny bones in each of your middle ears: incus, malleus and stapes [anvil, hammer and stirrup to chaps who didn't have Latin in the education]. The incus and malleus form a hinge/lever that gives mechanical advantage to the sound waves that strike the ear-drum.  That hinge has been re-purposed from the articulation of a reptile jaw!  The hinge was too useful to discard when mammals developed a new jaw with fancier teeth stuck into a single bone called the mandible which articulates directly with the skull and so streamlines the engineering of chomp. That's how evolution works: by tinkering around with what we already have to create something new.  "Tinkering" in English implies rather feeble piffling about; François Jacob's French equivalent bricolage sounds to my ear more like giving some recalcitrant thing a few good dings with a hammer to make it fit.

Like Gollum Shubin gets weaker as he gets further from the magic seams of Devonian (420-360mya) fossil beds but he deserves credit for putting an evolutionary gloss on a great many puzzles of the vertebrate-mammalian-human condition. Coming from the United Theocracy of America scientists need to launch the SS Evolution whenever possible into the complacent warm waves of creationism. But pushing out a leaky, poorly manned vessel is just providing food for the biblefish. He 'explains' obesity and heart-disease . . . and hemorrhoids for good measure in 2.5 pages! An explanation of obesity without mentioning the gut flora is wrong inadequate. I have more to say on the nuance of obesity.  The last third of Subin's book is like a blog without a good sub-editor:  whatever-you're-having-yourself is run out into the public domain without it being properly developed and almost immediately segues into another intriguing sort-of-related topic. In Shubin's case the obesity+ chapter is followed immediately by a trivialisation of the connexion between sleep apnea (which is indeed more frequent among the obese), choking and our ability to speak. Much the same sort of problems beset The Blob but I'm not selling it (yet!) for £9.99. But it's okay in this sense: if Shubin makes you think "hmmmm, that's odd" then that makes him worth the read and he is scientist enough to have 12 tiny-print pages of references to help us follow things up at the end of the book.
"The most exciting phrase to hear in science, the one that heralds 
new discoveries, is not 'Eureka!' but 'That's funny...'"  Isaac Azimov.

One of those "can that be true??" anecdotes concerns a peculiarity of cetacea [whales and dolphins] whose ancestry we were recently reporting. All mammals have something in excess of 1,000 different olfactory receptors [proteins that sit in the membrane of cells in the olfactory epithelium] up our noses.  They are interesting because we have almost as many as blood-hounds and yet we don't consciously pay much attention to smells. Yes, yes, we all hold our noses and shriek when farmers are spreading pig-slurry and most of us respond to fresh-brewed coffee or vanilla or geraniums but we don't know when our partner is ovulating and we scrub our armpits far too much and far too often. It's probably true for many heterosexual blokes that she is receptive when he is drunk. But it's clear that some part of our brain is indeed taking in olfactory signals: mothers can identify their children's clothes in the dark; sororities synchronise their cycles or not; and apparently we sniff our hands a lot.  Nevertheless, a great many of our olfactory receptor genes have become "pseudogenes": mutations have accumulated so that the genes are no longer functional.  Shubin asserts that all the olfactory receptors in whales have become pseudogenes as their nostrils have been bricolagé into a blow-hole at the top of their heads. There is nothing useful to smell top-side and when submerged the epithelium is awash with salt-water which somehow has made the air-adapted olfactory receptors non-functional. That seems to be the argument aNNyway. I feel an under-graduate research project coming on: there are two reasonably complete cetacean genomes that have been sequenced; Dolphin Tursiops truncatus and Sperm whale Physter macrocephalus.  We can trawl through the sequence data to see just how broken their smell-repertoire is.

Monday, 25 May 2015

Methinks 'tis like a camel.

There is an interlude in Shagsper's Hamlet, when the Prince of Denmark unmercifully rags a sycophantic courtier by forcing him to agree with every daft statement made by the head of state:
HAMLET God bless you, sir!
LORD POLONIUS My lord, the queen would speak with you, and presently.
HAMLET Do you see yonder cloud that's almost in shape of a camel?
LORD POLONIUS By the mass, and 'tis like a camel, indeed.
HAMLET Methinks it is like a weasel.
LORD POLONIUS It is backed like a weasel.
HAMLET Or like a whale?
LORD POLONIUS Very like a whale.

If you're in the 'Shaxpere was a bloomin' genius' school, you'll infer that the Bard knew more about the genetic inter-relationships of these disparate mammals than anyone up to 1994.  Except for the weasel!  That puts a spanner in this Arts/Science hypothesis because it is only the camel and the whale that have a close genetic similarity. Indeed Professor Tonks from Maritime Whoowah University has suggested "weasel" is an First Folio typo for "Sei Whale" Balaenoptera borealis.  In 1994, Dan Graur and Des Higgins published an extraordinary paper mustering the molecular genetic evidence that first pointed at this relationship.  Genbank the DNA database was established in 1982 with less than 600 sequences. By late 1993, there were 150,000 sequences available for study . . . but even then very much under-analysed. Now there are 250 million sequences and we are drowning in data for which there aren't enough effectives on the planet to properly analyse.  Dan and Des decided to gallop across the 1994 data-prairie whoopin' and hollerin' to gather themselves some sequences with which to answer an interesting evolutionary conundrum: where did whales come from?  They downloaded the sequences of a number of proteins including beta-haemoglobin, crystallin-alpha-A and insulin and some transfer-RNA genes from a selection of whales and a selection of artiodactyls - the mammalian order that includes cows, sheep, deer, antelopes, pigs, camels and llamas.  Actually, given that the N=150,000 database was diluted by sequences from bacteria, worms, flies and California condors, they didn't have much choice and their panel of sequences was limited to what was available.

When the sequences were aligned and a tree of relationships was constructed, they were gob-smacked and excited to see that whales were closer to cows and sheep than either of those species were to pigs. They put their arguments in good order with text, tables and figures and sent it off to Nature, Europe's premier general science journal. An editor at the journal looked at the title and sent it off to a whale taxonomist to be refereed.  A scathing review came back.  I paraphrase: "these authors have disappeared up their own backsides with their clever-clogs tinkering around with such irrelevancies as DNA sequences. A child of six knows that artiodactyls have cloven hooves and many of them pronk about in the Serengeti; on the other hand whales have fins and live in the oceanPlease don't waste my time like this ever again."  D&D read this critique, realised that whale-mavens looked at the world through baleen blinkers and later that year the paper was published in MBE Molecular Biology and Evolution.  It didn't quite sink without trace like a dead whale but it didn't make enormous waves either. Des Higgins has achieved mega-fame for writing the nifty software that enabled him and Graur to align their sequences and getting cited for this more than anyone else in Irish science. Dan Graur OTOH wrote The Textbook for the field which is still in print and available for a king's ransom [$75] and holding its price well in the 2nd hand market. But I think their Origin of Whales story is better value.

Two years later, more data had come on stream [Genbank's size then N=850,000 sequences] including a number of casein milk-proteins.  A group led by Peter Arctander constructed a phylogenetic tree [L based on beta caseins] for about 20 mammals including a couple of whales and such artiodactyls as sheep, cow, camel, deer, pronghorn, pig . . . and hippo. >!kaCHING!< and, like, duh!  The far-fetched story told by Graur and Higgins that whales were a sort of cow now made intuitive sense.  In 1963, Ted Hughes wrote a Kiplingesque Just So Story called "How the Whale Became" Higgins and Graur and their tidy-up-afters had an answer 30 years later. Once there was a hippo . . .

Be a hoopy frood today

We read each other when we meet.  Eye-gaze-trackers show that our glance flicks over key areas of the body of people we encounter: face-hands-genitals. Women also check out the shoes! Blokes don't give a hoot about shoes - for them it's all hooters. I have two pairs of shoes. a) some Hi-tec hiking boots worn until worn out: I'm on the 4th pair since they faithfully carried me from Portugal to France via Santiago in 2004 and b) black leather, slightly too small, interview/funeral/wedding lace-ups which I inherited from my father when he died in 2001. I guess I'm scoped as a climbing nut by women I meet.  Blokes, gay and straight, do check out the package of other blokes they meet - everyone in the room needs to know who is the alpha male: it avoids unnecessary blood-shed.

Here's another thing that I picked up from TYWKIWDBI this week: we spend a chunk of our lives sniffing our own hands and we do this more often shortly after we have shaken hands with someone SLYT.  This behaviour is modified according to whether the hand shaken belongs to someone of the same or opposite sex. Same sex and you're 2x more likely to sniff your own left hand (for reassurance?). Opposite sex and you're 2x more likely to sniff the right hand (to check that dude out?). This study, carried out in the Weizmann Institute in Israel, cries out for a further investigation of how gay-people react wrt opposite/same sex.

This is all by way of preparing you for the day ahead.  It's Towel Day, which has been celebrated for the last 15 years on 25th May: a respectful 2 weeks after Douglas Adams died on 11th March 2001. If you like being part of a movement check out WTF is this all about? It's all blown up from a trope in Hitchhikers Guide to the Galaxy describing how useful a towel is when travelling through the further reaches of the Universe: " . . . wrap it round your head to ward off noxious fumes or avoid the gaze of the Ravenous Bugblatter Beast of Traal (such a mind-bogglingly stupid animal, it assumes that if you can't see it, it can't see you)".  By their towels ye shall know them.  I know that several of our 4th Year students at The Institute are h2g2 fans and today half of them are making their research project presentations.  I've made a batch of my famous flapjacks for the tea-break.  I'll put the tin on a respectfully folded towel and see if anyone checks out my shoes.
And I almost forgot: 
So long and thanks for all the fish.

Sunday, 24 May 2015

Free the Gays

The details may not have been reported in Kiev or Qatar but the Irish people voted YES for an amendment to their Constitution on Friday.  The results were finally delivered at about 1900hrs but the No campaign had conceded defeat many hours earlier, possibly when Sligo-North Leitrim was the first constituency to declare with a 53.57% Yes vote. If people in the depths of the country were coming out [sic] for YES, we knew what the overall result would be.  As it turns out Roscommon-South Leitrim was the only constituency that leaned NO: apparently someone threw in a 'miraculous medal' with their ballot paper and it may have moved enough of the pencilled crosses to another box. The Beloved was out in darkest rural South Carlow almost every evening for the last ten days canvassing with a YES and a Tá button one on each bosom.  All her fellow canvassers had relatives or close friends who were gay [we all do] and that's not the really point but putting a face to the people who might be directly affected has been the biggest factor in pushing people towards Yes=equality.  TB was asked for an extra bumper-sticker by a chap who confessed that it was for his house-mate and they intended to 'avail of the constitutional change'. At another front-door, a father said that his teenage son had come out a few days previously and that he was still reeling.

On the wireless yesterday, the Saturday morning talk show host Marion Finucane devoted her entire programme to the count with a panel of pundits and also fielded a number of phone-ins.  People had travelled enormous distances to be get home to vote. Dublin to Clare; a trainload from London arrived at Dublin Ferryport at 5pm on Friday and were driven home via the polling station; one chap flew back from Australia to Be There on The Day.  But Finucane betrayed herself and the feeling of the occasion by asking these returned ones "d'ye mind my asking, are you gay?".  They responded, not without pride, that indeed they were.  But nobody berated her for being crass - voting YES is not about self-interest it's about community; about doing a little for people who have been given stick for so long. Young people and students from Roscommon-South Leitrim [L above] are in for an unmerciful slaggin' over the next several years. Before you join the baying mob, Donegal-SW only scraaaaped into the Yes bin by 33 votes and more than 1/3 of our neighbours voted Nil/No.

In the evening, after a day of visits and grass-mowing, we buffed ourselves up and went to Carlow for a drink with some of TB's fellow campaigners. I didn't go out doorstepping, I was too busy bloggin' up the vote in Ukraine and France. So many war stories; such feel-good; such bouyancy.  A 101 year old went out to vote in a pride scarf.  60,000 people voted on supplemental registers round the country: they went and got themselves registered to vote on something that they felt really strongly about. The turnout in both relative and absolute terms was the highest it has even been for a referendum.  It has been a great day for the politicisation for the Youth. This includes Dau.II who mobilised all her pals in Cork to get registered to vote for the first time in their lives. Everyone agrees that the youth vote has been key in swinging the pendulum.  But equally it is not only Youth, or only Dublin, or only people with 3rd level education or only the affluent.  The turn out and the margin was effectively the same in Dublin's ghettos as in her leafy suburbs. The map shown above is almost entirely green.

It has been compared to Italia '90, the Summer 25 years ago when the Irish People pulled themselves out of the worst recession of the late 20th century by watching their soccer team claw its way up a few rungs of the ladder during that year's World Cup.  The laughed, they bought rounds of drink, they slapped each other on the back and they felt feckin' mighty about themselves and when they were finally knocked out by home-team Italy on 30th June, they still felt great.  Getting a job was easy after that and the economy started to make sounds that eventually became a roaring Celtic Tiger.  The Marriage Equality is the watershed for this generation.  It's not about marriage, it's not about gays, it is about inclusion, it is about helping the dispossessed, it is about tolerance. It tells the world that Ireland is a good place to live. It will still be unfair being gay in Ireland, it is unfair being a woman, it is unfair being black.  There will still be people who are afraid to come out, and with good reason. But we have collectively made a statement that we will resolve to do and be better.

We have also had a debate, the children hanging off the railings in Dublin castle yesterday evening [Top] have been talking over the issues, they've had to rethink what a family looks like. Not their family that will still be the same, but other families will be different and that is okay. Eileen Gamble blogger at was talking over some of the referendum issues with her class [must have been Civics] last week and one tot piped up "Miss, after we free the gays, who will we help next?"

Saturday, 23 May 2015

Death - the final frontier

While participating passively in an amputation the other day, I reflected briefly about how anaesthesia in the sheep was not an exact science. That required that I go and find out something about it.  But the idea was ringing distracting alarum bells along two threads in a disturbing skein of news from across the Pond. The Boston Marathon bombing had particular resonance for me at the time: that story has been wrapped up a few days ago with Dzokhar Tsarnaev being sentenced to death.  He may hope that the federal authorities in Massachusetts make a better fist of it than Oklahoma did for Clayton Lockett [long-form article in The Atlantic]  The sciencification of our lives can get a little wearing - having the right iKit to communicate is far more important than actually communicating with another person: the medium is the message.  But the sciencification of death is an offense to science.

Somehow, the medical profession have managed to claim that terminal anaesthesia is nothing to do with them: they have all dressed up in medieval gowns and chanted the Hippocratic Oath "primum non nocere; primum non nocere; primum non nocere" when they got their licence to practice.  So they couldn't possibly help to off the sweepings of their society.  This high moral ground trembles with irony given that US medicos manage to kill between 50,000 and 100,000 of their fellow citizens each year from 'medical misadventure' aka a cock-up by Hippocrates or one of his minions. If the best teaching hospitals manage to achieve a costly adverse drug event for 2/100 of their admissions, what can be the rate in Bohunk County Hospital, Backwoods, Appalachia?  If the doctors won't do executions, a different class of people must take on the task and where do they get their training? Even the US States most gung-ho for the death penalty only get through a few every year, so where is the poor thanatotech going to build up the experience?  The most recent public scandal in Irish healthcare involves a statistical excess of neonatal deaths in the maternity ward in a regional hospital (Portlaoise, as you ask, but it could be any similar place).  The preferred solution is to close such small throughput entities and consolidate maternity care in a few centres of excellence where the midwives and obstetricians can meet all the rare-but-challenging presentations and know what to do the next time.  That seems logical from the perspective of minimising death, but is a royal pain in the tits for all the mothers and babies who will be required to deliver their babies 100km from home.  Maybe that's okay: mothers-and-babies get shoved out of hospital within a very short space of time nowadays: let the unsupported uteruses fall where they may.  The centres-of-excellence argument is more burdensome for long-term cancer or diabetes treatment: its hard to visit every day if it is a 200km round trip to bring tea-brack and love.

The sciencification of deathing [let us mangle the language to draw attention to the mangling of logical thought here] is being driven by a curious statement in the 8th Amendment to US constitution which they lifted from the Bill of Rights of a century earlier 1689 in England "That excessive Baile ought not to be required nor excessive Fines imposed nor cruell and unusuall Punishments inflicted".  Somehow a high-tech solution has become synonymous with 'humane'; although we are quite happy to by-pass this with other creatures that we feel the need to terminate: from thorough-bred horses (who have the misfortune to break a leg) worth upwards of $10,000 to a 40kg spring lamb which might fetch $100 at the factory. These animals are offed with the >!klunk!< of a captive-bolt human-killer to the brain-stem. They don't feel anything for very long.  In contrast Clayton Lockett took 100 minutes to die as a scarcely competent and inadequately trained technician was unable to find a vein (in the arm, the neck, the thorax or the groin) and the doctor who was there on an over-sight boondoggle wasn't able to help her either.  The serial cocktail of drugs sodium thiopental [barbiturate general anaesthetic], lidocaine [local anaesthetic], midazolam [sedative], vecuronium bromide [paralytic] and finally potassium chloride [which will upset the salt balance of the cardiac muscle so badly that the heart stops] were eventually administered in sufficient quantities to kill Mr Lockett. And I should add that he was woken up and tazed more than 12 hours before he finally died so he had a whole day to reflect on his crimes. This is what passes the test for nor cruell and unusuall Punishments inflicted in Oklahoma and 31 other States.

In 2014, 35 people were judicially killed in the USA, all by lethal injection.  The average difference in age between the time of the offense and them time of retribution was 20 years with a range from 10-39 years. Dzokhar Tsarnaev is off to a secure federal holding unit where he will be confined, alone for 23 hours a day for the next several decades, in a cell 2.1m x 3.7m with a concrete bed, as his appeals work their way up and down the courts. That isn't cruell and unusuall Punishment either. Between 1972 and 1976, the US Supreme Court had declared the death penalty unconstitutional. Science has not served execution well, there is a very long list of botched executions [harrowing reading alert] since they became constitutional again in the USA in 1976.

For a nation with such a high proportion of gun-nuts, it's a wonder there isn't more active advocacy for death by firing squad, a method preferred in Utah and allowed in Oklahoma. Although the sample size is tiny (N=3 since 1976), this is the only method method that has a 100% track-record of successful administration. In the interests of 'transparency' most of the States allow journalists and even the families of victims to sit in to witness the last minutes of the perpetrator. I'm sure there would be no shortage of volunteers to make up a firing squad: submit CV with evidence of at least 2 dozen clean kills on deer and other large mammals?  The 'paramedic' [as above, I prefer my coinage thanatotech] who terminated Mr Lockett got $600 for his pains, the firing squad might well be happy to divvy that amount up amongst themselves. Talking of money, three days ago the Irish Department of Justice released the figures for the cost of incarceration = €86,000 every year. It can't be cheaper in the US, so Justice is costing on average 20 x $90K = $1.8million before execution - and I haven't yet found out who pays the defense lawyers.

Friday, 22 May 2015

Democracy? I think not

In Ireland we live in a democracy.  This means that, every few years we go to polling stations and vote for our political representatives.  The politicians want to get elected and the custom has built up that candidates attach election posters to telephone poles and lamp-posts to raise their profile in the consciousness of the electorate.  The standard posters are printed on a sheet of corrugated plastic about 900x1200mm and are often shockingly inept - unintentionally humorous hair-style, fat tum bursting out of shirt, vacuous expression, apparent aura or halo, illiterate slogan.  More 'happening' candidates have recently taken to airbrushing the wrinkles and photoshopping the jowls to such an extent that they are unrecognisable on the doorstep.  The posters are an eyesore for a month before the election but are really useful about our farm afterwards, making compost bins, covering wood-piles.  I do try not to put the politician's face next to the dung - I'm not totally insensitive: even about Fianna Fail.  There is a limit to this allowable littering of the street-scape: nobody may put up a poster within 50m of a polling station.  Likewise, you may not in person encourage people to towards your political beliefs anywhere near the polling station. Nobody wants to run a gauntlet of hectoring party apparatchiks on the way to vote. And of course you cannot carry a poster or a flag into the polling station itself.

This time round, however, we are being warned by the [independent] Referendum Commission that you shouldn't go to vote wearing your position on your sleeve as a rainbow scarf or as a Nil button on your lapel. Furthermore, we are being forbidden to take selfies in the polling booth - the legislation clearly needs to catch up with the social media deluge in which we are now drowning. Posters in the polling-station are one [undesirable] thing but stripping off my Tá button?  Where will it stop?  Will they take my Fáinne?  As it happens, Carlow-Kilkenny is going through a bye-election at the same time as the referendums.  Apparently, outside the Carlow County Courthouse this morning, a security swat-team from the Referendum Commission over-stepped their brief on keeping Yes and No buttons off lapels and arrested a man who turned up to vote in a blue shirt.

Irony warning: this post is intended as satire.

It's two years if a day

When I started a new job in The Institute in January 2013, I thought it would be interesting to blog the process of transition from working one day a week the Ivory Tower of Trinity College Dublin to hewing at the coal-face in The Institute. Starting at the bottom of the scale as an Assistant Lecturer was a bit of an etymological tumble from Senior Scientist.   With the anomalies of Irish tax credits and allowances, the financial deal also seemed to be invidious - I was invited to work five times as many hours for twice as much money.  But twice as much money is still the difference between eating stir-about every day and having a cheese sandwich on Sundays.  But it's not about the money

I called the blog Science Matters because it does; but that title is a little fraudulent because the content, all too frequently, lurches off into left-field bucketting over tussocks of remote island groups, biographies of women, and castigation of iniquities - let's kick Fritz Haber again.  With all this off-topic material the banner title became The Blob, at least in my head.  When I started the new job, I had to prep a bunch of totally new classes with support from my colleagues that was 'patchy' (some mighty, some totally hands-off) and so I was busy every evening and every weekend clagging together enough material for next Monday.  All good fun and reading the early posts brings back some of the excitement and some of the panic.  After a frenetic Jan, Feb, Mar 2013 things started to settle down and I found more time for The Blob although I was still mad busy at work and several days might pass without anything posted.  For example, on 21st May 2013 I wrote a historical piece about Nirenberg and Matthaei and the birth of the genetic code which has garnered over 1000 page views and is the most popular post on The Blob.  On 23rd May 2013 I was on about fashions in European underwear which is more important [every knows about Nirenberg and Matty except how to spell Matt's name; but not many know what studs and hotties are should be wearing next to their skin] but has only clocked up 67 PVs. The problem with blogs is that they are ephemeral; blogspot puts up the most recent 7 posts but, to the nearest integer, 0 people go to the second page let alone browse through the archive.

There was a gap between 21st and 23rd May 2013 when I was mad busy marking exams but every day since then, I've posted something for posterity.  Well done me! When you do something regularly and often the material clocks up and I'm happy to report some statistics.
  • Content: 600,000+ words is 1.33 LOTRs and more than War & Peace, Moby Dick, or Ulysses.
  • Average post is about 600 words: in the Summer I'll put out a 1,000th post
  • In about a year's time, I'll tell you when I've passed out Potter (a million&something words)
But it's not about the word count.  Much of The Blob is about as interesting as a roomful of monkeys typing away until they've re-written Hamlet.  I must confess that sometimes I read a piece in the archive whose the logic I just cannot follow - brows furrowed but it might as well be written in Magyar. Another way of looking at it is
  • Impact/sales: a very humble 160μPotters 
    • J.K. Rowling has shifted 450,000,000 units
    • The Blob has about 77,000 pageviews
I like the units, it's like Francis Galton's unit of millihelen - the amount of beauty required to launch a single ship.  Actually I can't get nearer than 'anonymous'  for an attribution for this witticism.  But Galton was definitely interested in the matter and invented an event recorder to surreptitiously tally up the number of beautiful women he encountered [don't shed the o!] in British cities: London had the highest index of pulchritude, Aberdeen the lowest.

I don't undertake to post every day hereinafter but I don't intend to wrap The Blob any time soon either.

Thursday, 21 May 2015

Droits de l'homme

The Rights of Man.  People in revolutionary France felt so strongly about this concept that they named a ship after it, which was destroyed on its way home from an attempt to foment rebellion in Ireland.  Jeremy Bentham famously called the Rights of Man "Nonsense on stilts".  I think I agree with him on a lot of such statements. The UN Convention on the Rights of the Child to an Education used to worry us as Home Educators.  It sounds unexceptionable until you ask The Man to define 'education' and suddenly all our children are taken into care because they don't know the square root of two or the name of the President- two facts about which most adults would have a "Frankly Scarlett ..." attitude.

So what about the franchise?  That's a Right.  Everybody in Ireland over the age of 18 gets to vote nowadays, even people in prison, although that option is not extended to prisoners in England.  Also excluded from the franchise in the UK are 'idiots', 'lunatics' unless 'in a lucid phase' and members of the House of Lords.  I can't easily track down a definitive answer but, as 'idiot' and 'lunatic' are both politically incorrect, I suppose that neither blithering idiots nor mad-women are excluded from the franchise in Ireland.  Even if I am wrong in the details, we have close enough to universal suffrage here. I reckon that certain blithering idiots should not be allowed in a polling booth but don't want to push that sentiment too hard in case they turn around and take away my right to vote.

It wasn't always thus. In 1831, the population of England and Wales was just under 14 million, the electorate was 336,000 = 2.5%.  You had to be worth 40 shillings in property and have XY chromosomes to vote.  In Scotland it was even worse: in a population of 2.6 million only 4,500 people were enfranchised = 2/1000!  How pished aff would you be if you lived North of the borrrder, to realise that the democratic odds were so stacked in favour of the Home Counties? The 2.5% needs to be taken with a pinch of skept because the % is adult men but the baseline population includes women and children; here's a graphic of the steps to full suffrage. The first step occurred in 1832, when the Great Reform Act cleaned up the worst of the anomalies and exceptions and grossly corrupt election practice.  Further extensions happened in 1867, 1884, 1885 and 1918, when finally, with the Representation of the People Act 1918, women got the vote.  Not all women, mind, they had to be thirty (30)!  Men of 21 were men, but women of 21 were something less. How pissed off would you be if you be if you were a young woman and saw your idiot younger brother being treated as adult.  It wasn't until 1928, fully ten years later, the women were given parity of esteem in the polling booth.  It was decades before equality was achieved in other spheres of life - indeed most people I know would deny that we are there yet.  Jeremy Bentham had laid it all out 100 years before: calling for votes for women in his "Plan of Parliamentary Reform, in the form of Catechism with Reasons for Each Article, with An Introduction shewing the Necessity and the Inadequacy of Moderate Reform" of 1817. 

So far, so what?  Why the potted history?  Aren't we all for the future?  We are . . . but we need in Ireland to reflect on history tomorrow because we get to vote on two constitutional amendments where we'll get a chance att full equality for one section of society but not for another.  How pissed off would you be if you were gay and you saw your idiot younger brother being allowed to marry his girl while you had to be content with a sort of halfway house which didn't address important issues of inheritance and next-of-kin.  The tide of history is with the change, lets not have another referendum in 2025 when Uganda and Saudi have long ago embraced full tolerance for homosexuals.  The Beloved has been out almost every evening this week canvassing for YES in the darker rural backwaters of South Carlow, one of the householders was still in shock because his teenage son had come out

As for the other [minority interest] referendum on Friday we are being invited to allow people of 21 years to become President. This is all wet and everyone should be ashamed for laying this half-hearted half-arsed option before us. If we want to live in a gerontocracy then we can continue to have a minimum age for the Head of State, currently set at 35 years. The youngest people we've ever elected were both a full ten years older than that: Mary Robinson was 46 in 1990, and Mary McAleese was also 46 in 1997.  If we want full equality of opportunity then the minimum age must be 18 - the age at which we define adulthood. It is the principle. 21 is neither fish nor fowl nor good red herring. "Inadequacy of Moderate Reform" which Bentham catechised and castigated 200 years ago is what we have with this Friday's Presidential Age referendum and with the current Civil Partnership nonsense. Plunge on The People,we have nothing to lose but our prejudice.

Wednesday, 20 May 2015

Galena - a pretty name for a girl

It's been a week of two nights, two late nights, so far.  On Monday, I skipped going to work and spent the morning at home doing some desultory marking of project reports. The weekend had been busy with the Blackstairs Walk, pushing the goddamn mower about the haggard to keep the grass in check, and Sunday sheep surgery. In the afternoon on Monday, I set off by bus, with an apple in my pocket, for the Pint O'Science gig in Dublin . . . and promptly fell into a drooling sleep which bypassed Gorey and Arklow.

Pint of Science was a good buzz, very modern, with lots of instant social media going on in parallel with the formal talks.  It was kind of weird to find out afterwards that, even as I was waving my arms and clicking through some powerpoint slides about chromosomal anomalies and pathogen-host interactions, one of the PoS organisers was pushing out pictures of self on Twitter. I consciously used the event as an opportunity to push The Blob out but I've seen effectively no hint of going viral . . . yet.  It was the same nil response that I got when I posted something on the Royal Society website.  I don't care, The Blob is a near infinite resource now: everything I know is there, so it's an easy seam to mine for a presentation about Science.  Pint of Science was meant to be scientists explaining their passion to The Public but when the first speaker asked "Who doesn't know what a transcription factor is?" only one bloke put up his hand.  The rest, by elimination, did know about TFs and so could hardly be classified as the [drooling] Man on the Wexford Omnibus.  It's less vital and important for scientists to be talking about their stuff to/with other scientists but still useful; if only because it forces you-the-speaker to imagine what it could be like not to know what you take for granted.  In the mill afterwards I was introduced to a young chap who had done science in TCD several years ago and was now working in biotech.  He said that he met me before when he was a chap and I'd harangued him for 30 minutes about the Joy of Bioinformatics . . . and that it had changed his life!  That was nice, and they gave me a pint glass etched with the Pint of Science logo; that was nice too.

On Tuesday evening, it was off the The Wexford Science Cafe after another morning reading and marking project reports in The Institute.  I brought my lappy and a 24" TV flat-screen in a mail-sack in case anyone wanted to hear about chromosomes and diarrhoeia. They didn't. But we did hear about a recent visit to the halls of the Royal Society, which has been in the news The Blob recently.  One of our number has been recently co-opted onto the editorial board of the Philosophical Transactions of the Royal Society B and had been in London last week at the annual editors meeting.  That was pretty awesome, to be in the halls of an organisation civilised enough to be talking and publishing science 350 years ago. When she was there (the power of smart-phones) she sent me an e-mail saying she was sitting in the Council Chamber of the RS under a portrait of Sir Isaac Newton (1642-1726).  The two things everybode kno about Newton is A is for Apple and b) he claimed to stand on the shoulders of giants. I suggested last week that she get off a selfie with herself standing under Newton's feet. Bwwahahahaha. Turns out that the RS portrait [L above: it has no feet] is by Charles Jervas an Irish portraitist from King's County, which is where my people are buried. More connectedly, Jervas also painted a picture of Lady Mary Wortley Montagu (1689-1762) which hangs in the National Gallery of Ireland.  I haven't talked about Lady Mary yet but I have talked about two blokes who stood on her shoulders later in the 1700s.  Montagu, Jesty and Jenner made the first scientific steps towards eradicating smallpox from the planet - the last case of smallpox (1977) was covered in The Blob last October.  We heard at the Pint of Science gig on Monday that 500 million people had died from smallpox in the 20th Century.  That doesn't seem credible . . . must check sources . . . science is finding out.

Meanwhile back in Wexford, we had been promised to hear something about Galena from Our Man in Radio Telephony. Galena is a crystal, not an element as part of my brain was claiming - I was confusing it with Germanium; probably because they are both semi-conductors.  Galena [R in crystalline form with a spike of calcite in the background] is a heavy rock 7.5x denser than water at least partly because it is loaded with lead; chemically it is PbS or lead(II)sulphide. It is smelted to obtain metallic lead although much less now that previously because we are trying to minimise the lead in our environment. It all made me think of the wonderful chapter "Lead" in Primo Levi's book The Periodic Table: it should be in the library: must read! Galena has been useful unsmelted in the past because the crystal is a semiconductor with a handy bandgap of 0.4eV, that allowed it to help sort signal from noise in early wireless transmission. It was the crystal in crystal wireless sets of 100 years ago.  This-all was just fascinating but we couldn't agree on much because the five of us couldn't muster much information at our finger-tips in a bar in Wexford. But that's the point: science is hearing about something that sounds a little 'off' and the hounds are off after that fox.  I think we agreed that Galena was a pretty name for a girl and resolved to find out more about the tumbled clatter of things that had cropped up over pints. I feel alive.

Tuesday, 19 May 2015

The Palace of Pressure

I've just marked the Human Physiology exam at The Institute and it has been more or less unsurprising, the results for continuous assessment tracking closely the May exams.  In the last session of class four weeks ago, I gave the students some study skills including a glimpse into The Memory Palace of Blood Pressure: how to remember the names and inter-relationships of a lot of long words.  As pharmacy technicians, they should have some clue about the modes-of-action of all the ACE inhibitors, beta-blockers, statins and diuretics they push across the counter at large people with a predilection for junk-food. The great thing about constructing your memory palace is that you don't need to know how to draw, it's all in the mind's eye.  The bad thing about explaining it is that one picture is worth 1000 words, I can't draw and it's hard to find suitable images.
Not many people realise that three unlikely organs play a key part in the endocrine regulation of blood-pressure. The first is the liver which produces a precursor protein called angiotensinogen [Angelina Jolie/Tenzing Norgay/Gin]: an α-2-globulin and larger than average (about 450 amino acids) which is 'always on': it is leaked out into the circulatory system pretty much all the time. The key to BP activity resides in the first 12 residues: DRVTIHPFHLVI

But angiotensinogen is kinda useless, in the same way as fibrinogen can only help to clot leaking blood when it is cleaved to make fibrin.  What cleaves angiotensinogen? Renin! a hormone produced by the kidney hence the wren Troglodytes troglodytes jumping in the kidney-bowl swimming pool in the basement of the palace. Renin is produced when the kidney detects a fall in BP and goes off to find some angiotensinogen to cut up.

Renin clips off  the first ten amino acids leaving Val-Ile on the cutting room floor DRVTIHPFHL this hormone is called angiotensin I and it has minimal detectable activity.  It's there as an intermediate.  Presumably renin can operate on the whole precursor protein and the 10 AA flops into a different shape that the next enzyme can get its teeth into.

What is that next enzyme? ACE! and it is produced in a third tissue - the lung.  Angiotensin Converting Enzyme removes another two amino acids from the diminishing chain. The ACE-inhibitors, of which tons are prescribed each year to people with The Blood Pressure, are interventions in normal BP regulation, which is all about bringing BP up, for when BP overshoots and needs to have a stop put to its gallop.  These drugs are named like escapees from LOTR:  Perindopril, Captopril, Enalapril, Lisinopril, and Ramipril, the louche cousins Tom Bombadil.  Another set of dorky names from Big Pharma.

ANNyway, ACE converts at-I to angiotensin II by clipping off another pair of amino acids giving DRVTIHPF.  This is the mother of all control in the BP department and where most text-books (and my human physiology course) leave it.  But there are further fragmentary products of at-II, at-III,, at-IV etc. which are better at some of the manifold tasks that angiotensins carry out.  Aha, it's more complex than they say in the text-books?  No surprise really.
Three of these effects are shown in the collage [L], angiotensin acts:
  • first [LL] on the hypodermicthalamus and the  posterior pituitary gland to release anti-diuretic hormone ADH. POST+PIT bull: with ADH you pee less.
  • second [LM] on the adrenal cortex [an ADvert for Gortex as mnemonic] to trigger aldosterone [more ads for aldi and steradent]: aldosterone promotes water re-absorbtion in the kidney.
  • third [LR] it directly affects the smooth muscles that line the arteries to cause vaso-constriction [its a vase with a snake - not Boa constrictor but you know what I mean].  ADH's other name is vasopressin - a double-whammy for constricting peripheral arteries to crank up BP.
There you have it!  In an exam you have to lash down what you can remember about the process and try to spell the long names correctly. Simonides, Cicero, Matteo Ricci and the other ancient memorialists found that telling a story helped stick the details into the mind so that they could be easily recalled and in order. The pictures I've told you about are not what's actually in the story I run over in my own head because that is barely fit for a medium read in five continents by women, children and servants. Matteo Ricci recommended using 'dirty' or shocking images - they stick better. Tenzing Norgay with his kit off is not a pretty sight but it is surely more memorable than an unrecognisable dude with an ice-axe.  And I hope nobody wakes up screaming at 0300hrs having a nightmare about small birds drowning.

Monday, 18 May 2015

Lying with the sheep

"Neither shalt thou lie with any beast to defile thyself therewith: neither shall any woman stand before a beast to lie down thereto: it is confusion." Leviticus Ch18v23.
I beg to differ, I was lying with the sheep yesterday forenoon, and there was no confusion about it at all.  I had a role to play when Mike the Vet came for a bit of radical chiropody. If getting covered in sheep-dribble, a bit of blood-spatter and sundry other sheepily fluids is defilement, then I was defiled.

Ewe "A for Annabel" was the first of our flock to deliver as expected.  The rogue teens who fell pregnant but shouldn't started from the other end of the alphabet: Z for Zoe and Y for Yvette.  Annabel became obviously lame about three weeks ago and eventually we called the Vet for an opinion.  He reported a deep-seated infection that might yield to an assault with intravenous antibiotics but he felt that the infected offside 'claw' of the right rear foot would have to come off at some stage. Yesterday was Der Tag and the operation required some rope, a pallet, a bunch of medical kit, a saw and a patient. As a fainter at the sight of blood I was told off to hold the front end while Mike-the-Vet and The Beloved played "scalpel please nurse" at the far end.

The pallet serves as both operating table and, with the rope and some handy knots and splices, as a restraining device. And no, a sheepshank is of no use in the circumstances. A dash of i.v. ketamine and xylazine put the old dear into a state of zzzz, a torniquet (old inner tube and a stick as a Spanish windlass) was applied to the affected leg and the distal end was filled brimful of novocaine. Analgesia in sheep is not an exact science.  They aren't valuable enough to have been worth experimenting on to ensure the correct dose, so you hope to give enough that there isn't too much unnecessary pain but not so much that it takes ages to flush out - there is a lamb attached to the system which needs to be taken into account as well.

It was pretty clear that the drugs weren't going to last forever and as there was a stirring of consciousness [as she started to kick off] I was required to hold her head down with a full body press and do what I could to supplement the knots which were immobilising the front legs not-so-good - where are the sailors or the boy-scouts when you need them? It would probably have been okay if I did faint, as I was really only dead-weight on the head and neck. Did I mention a saw? I was expecting a handy tenon saw such as my grandpa used on the finer details of boat-building in the 1930s, but not so: Mike brought out a wire-saw worthy of Bear Grylls and made short work of the task with that. A bit of antiseptic spray and some industrial veterinary bandages - the outer layer a fetching royal blue - and Annabel was ready for discharge. Untying the knots was even more trouble than tying them, which again made me wish for a sailor, not someone who has no intention of sailing ever again. All that then remained was to wring out my slobbered-on sleeves and so to lunch. Washing the blood-spatter off the pallet could wait.

If you were ever unsure about what to do at calving time, here's the answer: Calving under the moon by Sarah Ann Winters. But wait! We know that Vet.
Back-chat on sheep in 2015 I, II, III, IV, V, VI.

Sunday, 17 May 2015

Pint of Science

I don't expect you to make a special trip from Braunschweig [Brunswick] or Полта́ва [Poltava] but if you're in the area, you should get yourself down to South Main Street in Wexford on Tuesday 19th May where the 4th meeting of the Wexford Science Cafe is meeting in The Sky and the Ground. A couple of the participants at that monthly meeting for science-chat and booze have been invited to be part of a Pint of Science gig the day before [Mo 18th May 2015] in the Odessa, Dublin. They might be prevailed upon to reprise those talks - with added powerpoint! - in Wexford on Tuesday.  Pint of Science is the brain-child of Seán Mac Fhearraigh, it's not original to him but he has a corralled an idea born in England and brought it back to Ireland; so tribs to him and the extensive team [N>30] keeping the show on the road.

In recent years, scientists have been expected to engage with the public with 'outreach'. We can no longer look out at the landscape from the top of an ivory tower.  Public engagement is the quid pro quo to ensure that Seamus Tax-payer has the opportunity to know what their tax-dollars are going to support.  Science is mostly expensive and if there is no tangible benefit to show for it at the end, at least we are now expected to be able to explain ourselves to normal people. Scientists are stereotypically incapable of being unable to explain themselves to each other, and their peer-reviewed papers are, by convention, written in a lumpy third-person passive-voice style which is the opposite of easy-to-read.  Most of the grant-giving bodies insist that applications for money include an Abstract - an executive summary - that reviewers can eyeball to get a sense of the scope and direction of the project before they get down to the logistical and methodological details.  Nowadays, the poor boffins are also required to write a Lay Summary for an intelligent person who knows little or no science.  Steven "Curse of Knowledge" Pinker has characterised the ideal Lay Reader as his college room-mate who was sharp as a tack but studying in the Arts Block.  In my experience, scientists are mostly lousy at any Lay Summary task at least partly because they think we all understand their long words. 

I look forward to seeing how well we all do understanding each other this coming week.

Up and Down

It's not the Appalachian Trail, but it is a good day's walk and it trekked past our yard for much of yesterday.  "It" was the 2015 Blackstairs Walk which has happened every year since we've lived here.  It is about 30km in length and involves a cumulative climb of 1670m, which means a cumulative descent of 100m more as the walk starts at 150m and heads South toward the distant coast to wind up in a pub in Glynn which is 60m above sea level.  Many of the walkers camp on the green in St Mullins which is close to the tide-head of the River Barrow.: ie sea-level. The logistics are organised by the Wayfarer's Association: there are checkpoints and registration cards, so it is unlikely that anyone will fall into a drain and die on the mountain.  In return for this solicitous care, you-the-walker have to undertake to be fit enough, to start between 0730-0830 and finish before 1830 hrs.  If you cannot do 30km in 10hours you are not fit enough.  But it's not a dawdle: a relentless 3km/h including breaks, doesn't allow for endless admiration of the view or selfies with a cloudy backdrop.
When the girls were small they would occasionally bake some cookies and put them out in the lane on a tea-chest with an honesty box next door and raise a few shillings from weekend walkers.  I sometimes wonder if that is what got them both into the catering trade.  The first we knew about the Blackstairs Walk was one May morning when there was a disconcertingly large number of people coming off the mountain when it was more usual to find folks starting upwards.  The following year we filled a 25lt drum with the finest Knockroe Springwater and left it on a chair in the lane with a sign saying 'Free Water - Enjoy'.  About half of it was gone by the end of the day. After a few years of remembering to do this in a rather hit&miss fashion, the day of the walk was forecast to be broiling hot and the Wayfarers contacted us prior to ask if we could provide a water-stop. That year it was 27oC at lunchtime and the water was necessary. 7 or 8 years ago we extended the plumbing to a tap in the yard very close to the main gate.  That made everything easier; a plastic mug on a piece of string made it easier still.  I made a finger-post saying <water< and whacked that into the ground beside the lane, in case someone hadn't gotten the message.

We did the same-old-same-old this year and the first customers dropped by at 0930hrs!  That's pacing it to finish in less than 5 hours at a sustained 6km/h which is a good brisk walk on the flat.  I guess they yomp along on the downhills and make what speed they can going up.  They were dressed in shorts and runners each with a dinky black back-pack.  Over the next 3-4 hours a couple of hundred people drifted by and several dozen stopped in for water. A good few also decided to climb various of our gates to have a pee in the fields.  That wasn't quite what I'd offered; next year I'll direct them to the compost heap where their excess nitrogen will do more good.

I do find the commodification of walking a little tedious.  Time was when you'd put on a pair of boots, maybe cut an ash-plant to discourage bears, put a sandwich and an apple in a pocket and set off. There isn't a hill in Ireland that doesn't have water running off it somewhere except in the driest of Summers. People take far too much water anyway: it is not the Gobi Desert. That's why they are urinating all over our farm. Why would you carry an extra 3kg if you didn't have to?  The item I find most disturbing is the fashion for carrying the water in a bladder that slips into a special pocket of your ruck-sack: it comes with a sucky tube.  When filled with one of these absurd Tartrazine yellow energy drinks, it looks like nothing so much as the distal end of a catheter. Then there's the gaiters, the gortex ®, the walking pole (a commodified ash-plant really), another walking pole, sun-screen, dark-glasses, a compass, map and mobile phone, a wind-cheater, rain-proof over-trousers, a sweater, an aluminized bivvy bag, 250g of Kendal Mint Cake ®, a complete change of clothes, a hat and a feather boa.  I was joking about the feather boa. Bearing in mind our 10 y.o. Dau.I walked to the top of Mount Leinster and back barefoot, you might consider all this kit a bit excessive.