Showing posts sorted by relevance for query george dawson. Sort by date Show all posts
Showing posts sorted by relevance for query george dawson. Sort by date Show all posts

Wednesday, 29 January 2025

Recumbent nude

I've mentioned George Dawson, my original professor of Genetics before but only in connexion with his monumental study of ABO blood groups in Ireland which posed a relict fire-hazard. But that presents an unfairly1-dimensional view of his cares. Back in the day, after two years being drilled in the basics, students had to choose the department in which they were going to specialize. I opted for Genetics, partly because they could spell evolution, but mainly for

 the collegiate for all-ranks atmosphere fostered by George. Because of the structures he implemented, I was possibly the first person in Ireland to make chili con carne with a dash of cumin

Dawson was also locally famous for his devotion to 20thC art and accumulated an enormous collection of prints, drawings and oils. When my then boss got married in the late 80s, George invited the much younger man up to his rooms in college for a glass of sherry. George pulled out a chunky roll of artworks from under the bed and invited his guest to choose something as a wedding gift. They went through the material and my gaffer said he'd really appreciate this OR this OR this OR this. With an expansive gesture George counter-offered with this AND this AND this AND this. George of the Generous Hand, indeed.

Over 30 years George also blagged his employer TCD into acquiring heavier lumps of crafted metal which were too large to fit under a bed. When I arrived on campus in 1973, extremely green and scruffy, I was not entirely Know-Nothing. I recognised, for example, that the inconnected blobs on a plinth [L] in Front Square Reclining Connected Forms (1969) was the work of Henry Moore.

I knew this because a couple of years before when I was 17, living in rural Essex, and borrowing my mother's Vauxhall Viva to get to parties, I had a crush on a girl from Much Hadham. She was arrestingly pretty despite having been fired through the windscreen of her mother's car as an infant and acquired a a faceful of tiny cicatrixes. She was also the god-dau of . . . HenryMoore, who lived down the way at Perry Green. There was talk of taking me and my louche companion Dom to take tea at Perry Green and see the sculptures. But that never happened, let alone any recumbent nude stuff. The following Fall, I left that part of the world behind to go to college in Dublin.

About three weeks after the start of term, I was hanging out on a sofa [hey, story of my life!] below the left-hand window behind the sculpture in the picture when The Beloved walked into the room and sat on the other end of the same sofa. She was also arrestingly pretty and we've been taking tea ever since.

In 1996, George Dawson made one his last art acquisitions. Seeking to furnish TCD's brand new Smurfit Institute of Genetics he contacted Arnaldo Pomodoro famous for his rotating brass Sfera con Sfera outside TCD's Berkeley [he bin cancelled] Library. Pomodoro, giving back to his early patron, insisted on donating 8 enormous pictures riffing on the dreams of cuttlefish [‽]. I had a quiet word with the Chief Technician at Smurfit and he allowed me to cart off the plywood packing cases in which the Pomodoro artworks had been delivered. All that timber got a second life on our farm as work-tops, partitions and chicken-coops. Thanks Dave! And thanks to George for demonstrating that scientists don't have to be Philistines.

Sunday, 28 July 2013

100K

A couple of months ago, I put up my 100th post on this blog.  I thought that was an achievement - I was never able to keep my Letts Schoolboy Diary going even to the end of January.  So I trawled through the back-catalogue and abstracted all the people who had merited a mention.  I thought that several pairs of people in that list wouldn't appear in the googleverse, and it was so . . . then.  Because Google scrapes the very bottom of the barrel, my abstruse connexions have now become googlechapwhacks (rather than googlewhacks):
Your search - "Lynn Margulis" "Varro Raetinus" - did not match any documents.
now has two hits: both from The Blob.
I now find that I've written more than 100,000 words here since January, so thought I'd put up another summary list.  It's getting rather long (N > 300), so I won't be doing this ever again.  There are more saints than astronauts, more Jims than Bills, the sex ratio is shamefully (41F:267M) skewed and for a republican there are rather too many monarchs.

Abraham Lincoln; Ada Lovelace; Adi Roche; Aeschylus; Al Bean ; Alan Shepard ; Alexander Bell; Alexander Friedmann; Alexis St.Martin; Allen Gardner; Amedeo Avogadro; Andre Lwoff; Andreas Ioannides; Andrew Harrington; Anne Boleyn; Anne-Marie Pétrequin; Aoife McLysaght; Aristotle; Arjumand Banu; Aurangzeb; Barbara McClintock; Barry Dalby; Beatrice Gardner; Benjamin Disraeli; Bert Vaux; Bibb Latané; Bill Bryson; Bill Clinton; Bill Liao; Bill Watterson; Brian Owens; Leopold I Belgians; Buzz Aldrin ; Calvin Klein; Carole Lartigue; Cathal Daly; Catherine Aragon; Richard Rich; Charles Babbage; Charles Burnham; Charles Darwin; Charles Dickens; Charles Duke ; Charles Weingartner; Charles-I Stuart; Charlton Heston; Chris Burnett; Chris Corlett; Chris Hayes; Christian Goldbach; Christophe Irmscher ; Christopher H. Calvey; Chuck Merryman; Clyde A. Hutchison III; Craig Venter; Cuchulainn; Cynthia Andrews-Pfannkoch; Dalai Lama; Dan White; Daniel Day-Lewis; Daniel G. Gibson; Dave Brubek; Dave Bruno; Dave Scott ; David Attenborough; David Fahey; David Haussler; David Hockney; David Lean; Debarghya Das; Dermott MacMorrough; DH Lawrence; Dionysius Exiguus; Dorian Pritchard; Edgar Mitchell ; Edmund Burke; Edsger Dijkstra; Edward MacNeil; Elizabeth Marshall Thomas; Elizabeth Windsor; Emil Zatopek; Enda Keane; Enver Hoxha; Ernest Walton; Ernst Röhm; Esmond Harmsworth; Eugene Cernan; Euripides; Evelyn Fox Keller; Evgeniya A. Denisova; Ewan Birney; Francis Coppola; Francois Jacob; Frank Ramsey; Garret Mullooly; Gene Wilder; Georg Wittig; George Beadle; George Dawson; George Gaylord Simpson; George III Hanover; George McClellan; Gerd Gigerenzer; Gordon Ramsey; Gregor Mendel; Gregor Strasser; Gretchen Rubin; Gustav Ritter von Kahr; Gwynedd A. Benders; Hamilton O. Smith; Harold Macmillan; Harold McGee; Harold Wilson; Harvey Milk; HDF Kitto; Heinrich Matthaei; Herbert Terrace; Iain M Banks; Iizuka Sh?kansai; Jack Hawkins; Jack Schmitt ; Jacob Bronowski; Jacob Lewis Bourjaily; Jacques Monod; James Gleick; James Irwin ; James Joyce; James Lovelock; James Murray; James Ussher; James VI/I Stuart; James Watson; James Whelton; Jan Jansky; Jane Goodall; JBS Haldane; JD Salinger; JD Salinger; Jean Anouilh; Jean Danjou; Jim Jones; Jim Kent; Jim Peters; Jocelyn Bell-Burnell; Johan Kjeldahl; Johann Charpentier; Johann Goethe; John Charles McQuaid; John Darley; John Glenn; John Henry; John Hinde; John I. Glass; John Keats; John Lonergan; John McCarthy; John Napier; John Seymour; John Tukey; John W. Drape; John Young ; Jonathan McCrea; Joseph Conrad; Joseph Stalin; Joshua Foer; Joshua Katz; Joshua Slocum; JS Haldane; Julie Christie; Julie Powell; JW Nijman; Karl Landsteiner; Karl Schimper; Karsten Hokamp; Ken Wolfe; Kevin Byrne; Kevin Mitchell; Kitty Genovese; Lambros Lambrou; Laurens van der Post; Lei Young; Leonard Mlodnick; Leslie Liebermann; Li Ma; Louis Agassiz; Lucy Ferris; Lynn Margulis; Malcolm Gladwell; Marcus Rhoades; Marius L. Jøhnda; Marjorie Shostak; Mark Boyle; Marshall Nirenberg; Martin Luther; Martin Ryle; Mary Mulvihill; Matt Groening; Matthew Broderick; Maximillian I of Mexico; MC Escher; Melvin Konner; Michael G. Montague; Michael Pollan; Michael Ramsey; Michael Young; Michel Thomas; Michelangelo Buonarotti; Mikkel A. Algire; Monzia M. Moodie; Nacyra Assad-Garcia; Nan Doyle; Neil Armstrong; Neil Gaiman; Neil MacGregor; Neil Postman; Nigel Slater; Nils Bohr; Nisa !Xun; Oscar Wilde; Paddy Lydon; Padraig Pearse; Patricia Arquette; Paul Crutzen; Paul McCartney; Percy Shelley; Pete Conrad ; Peter Donnelly; Peter Medawar; Philippe II Belgians; Phineas Gage; Pierre Pétrequin; Pope PiusX; Prashanth P. Parmar; Primo Levi; RAB Butler; Rachel Hewitt; Radha Krishnakumar; Raj Padam; Ralph Leighton; Rami Ismail; Ray-Yuan Chuang; Richard Chamberlain; Richard Doll; Richard Feynman; Richard Haldane; Rollins Emerson; Ronald Graham; Ruggero Boscovich; Saddam Hussein; St Agatha; St Aidan; St Barbara; St Cunigunde; St Cyr; St Edan; St Francis; St George; St James the Great; St Lucy; St Martin de Porres; St Martin de Tours; St Mary ; St Patrick; St Thomas Apostle; St Thomas More; Sally Clark; Sally Hemmings; Samuel Wilberforce; Sanjay Vashee; Shah Jahan; Sian Croose; Siddhartha Gautama ; Simon Perry; Sinead O’Brien; Skip Lovelady; Sophocles; Stanislav Jungwirth; Stanley Adrianus; Stephen Fry; Stephen Jay Gould; Steven Brams; Sukiyabashi Jiro; Suzanne Leenhoff; Sydney Brenner ; Terentius Afer; Thomas H. Segall-Shapiro; Thomas Hunt Morgan; Thomas Huxley; Thomas Jefferson; Thomas More; Tony Blair; Tony Hewish; Varro Raetinus; Victorine Meurent; Vladimir N. Noskov; Walter Bagehot; Widukind Lenz; Wilkinson, Mr; Willam Cobbett; William Beaumont; William Hurt; William Marshall; William McBride; William Rowan Hamilton; William Shakespeare; William Wordsworth; Zeve Sanderson; Zhi-Qing Qi

Thursday, 22 January 2015

Furry bags of genes

Felis catus the domestic cat is handy for keeping down mice and less desirable for killing song birds but these are value judgements that we humans lay on the poor creatures according to how useful they are to us. An interesting and valuable project is being launched today here in Ireland that is based on the fact that cats come in a palette of colours and that those colours are largely determined by variants inherited in a 'simple Mendelian fashion".  The last phrase of jargon means that the genetics of cat coat colour is well understood and that you can tell which gene-variants a given cat carries merely by looking . . . with binoculars if necessary or even by microscopic analysis of a photograph that appeared on the front cover of Journal of Heredity. Almost all other species would require a blood- or DNA-sample to generate any genetic information.

This project is a good example of where a number of observations can be combined to yield some data. Q: "What is the singular of data?" A: "Anecdote".  You can't tell much by determining the genetic make-up of the cat next door; except to hazard a well-informed guess as to which of the neighbourhood cats were its parents.  But if you look at many cats, you can calculate what the frequency of the genes are in that population. This was first done in a scientific fashion by a student of J.B.S Haldane in 1947: A.G. 'Tony" Searle was tasked by the great man to sample the cats of blitz-damaged London as part of his PhD programme.  It turned out that there were a lot of stray cats on  bomb-sites and in SPCA shelters and, in short order, Searle had data on 700 cats.  That sounds like data but on another level it is also an anecdote.  It is just one dot on the globe with rather a lot of numbers attached to it.  A few years later, however, Searle was posted to Singapore and he dusted off his cat genetics tool-kit and found several hundred cats in the streets and bazaars of that outpost of empire . . .  

. . . and they were completely different from the cats of London. Not in the sense that they had extra legs or googly eyes but their gene frequencies were different. In post-WWII London, for example, Siamese cats were exotic and rare but in Singapore they were common as muck. Well, that's interesting: any scientist would start to ask questions:
  • What's halfway between Singapore and London? Ans: Kuwait
  • Will the frequency in Kuwait of, say, orange cats be the average of Singapore and London?
  • Would I expect the frequency profile in Kuala Lumpur to be  rather similar to Singapore's?
  • What about Australia?  hmmmm, maybe those cats would look more like London than Singapore despite geography?
  • Black cats in the tropics?  White polar cats with long hair?
Such questions spawned a cottage industry that covered large portions of the globe in the 1970s and 1980s.  In my callow youth, I was part of that project and it got me an education, lifelong friends and loadsa data.  The data that came in were idiosyncratically patchy: New England, Brazil, Scotland and the Netherlands were exhaustively covered but Africa and Spanish South America were blank.  It all depended on who was prepared to make a run for it in a particular region.

Aoife McLysaght, in conjunction with the Irish Times, is taking up the baton today to bring the field of cat population genetics into the crowd-sourced 21st century. By making it easy for Sean O'Public to contribute a genetic diagnosis of the family cat, they hope to get a mountain of data from across the country and see whether the 40 year old findings in Donegal have held up to the buffets of evolution.  Here's the lead article in the Irish Times which includes an embedded link to a simple web-form that will enable you, or your class at school, or your scout-troop to contribute. One of the questions will allow them to tie your data to a particular county.  This follows an honorable tradition in the footsteps of George Dawson Ireland's first Professor of Genetics who surveyed the country's human inhabitants w.r.t. their ABO blood groups back in the 1950s.  He went to the Blood Transfusion Board and lifted data for something in excess of 150,000 people (1:18 of the whole population) and calculated the frequencies for each county.  Like Searle with his cats, Dawson was gratified to find that there were slight but statistically significant differences in ABO frequencies in the West of the country compared to Dublin.

And what about Ukraine?  A parallel project would mobilise a lot of youngsters into doing some real science.

Saturday, 20 January 2018

Paternity and the patriarchy

IF you're reading this from Abroad [which is likely given The Blob's readership stats R], OR you are our Taoiseach Leo Varadkar, OR you've lived all your life under a stone THEN you may not have heard of the Kerry Babies case which shook the nation in the 1980s. At about the same time, in another part of the country, Ann Lovett and her neonatal child died in the drizzle near Granard. For me, the fact that the head of the current government should admit to ignorance about such a watershed in Irish social development is worrying. George Santayana said "Those who cannot remember the past are condemned to repeat it." which is entirely on the button because a key element of the Kerry Babies was a stitch-up by investigating Gardai, which led to a Tribunal which failed to put the stitchers back in their box, let alone behind bars. Right now we are taking a long time to not find anyone to blame for the stitch-up of Garda whistle-blower Maurice McCabe. The Blob carried the McCabe story in April 2014: that is four years ago and we're still rumbling along looking pointedly in the wrong direction.

The Kerry Babies boiled to the surface this week because someone decided to look at the DNA evidence . . . 34 years after the necessary tissue samples were gathered. That showed conclusively that Joanne Hayes, despite confessing to his murder in elaborate detail, was not the mother - not even a close relative - of Baby John whose body was washed up on a beach near Caherciveen. Sufficient details of the events in Kerry in 1984 can be found in The Indo.  Indeed even back in 1984, the dogs in the street knew that Joanne Hayes could not have been the mother of Baby John because he was blood group A but Ms Hayes, her own dead baby and the baby's father were all blood group O. I think we can be sure that if Baby John had also been blood group O, then Joanne Hayes and/or members of her immediate family would have been convicted and imprisoned and the relevant Gardai would have been congratulated on a brisk and efficient investigation.

How likely was that? How close did an innocent woman come to being banged up in chokey in a stitch-up that required so many bizarre and unlikely events to be true. Let's look at the numbers. If you have no idea how ABO blood groups work, I refer you to my tutorial on the genetics. Today's investigation is about probability and gene frequencies which I've looted from George Dawson's famous survey of Irish blood groups from the 1950s, which I've cited before. Each of us has two copies of the ABO gene - one from The Mammy and one from The Dad. If you tally up a bunch of them as A, B or O and divide by the total number of genes counted, then you can calculate the frequency of each variety in Ireland [see chart L]. You can see that blood group B at 7% was very rare in 1955 and also in 1984 a generation later. It's a bit higher now insofar as we've welcomed people from *istan and the PRC where this variant is much more common [see map in my prev cited tutorial]. To be blood group O you must have inherited O genes from both parents. But there are two ways you can be B - either with one B gene or with two - pedantically but necessarily for the maths to work there are really 3 ways you can be B - BB, BO or OB. Similar arguments apply to those who are blood A. Finally you are group AB if you get A from The Mammy and B from The Dad = AB or the other way round BA. This is no discernable difference between the two cases except their history.

Many people get a bit confused about the gene frequency and the frequency of the blood groups. It's mostly because manifestation of a particular blood group - called the phenotype - depends on the presence of two variants of the ABO genes. You can verify from the table above that the chance of being blood group O depends on independently acquiring two copies of the O gene:
0.738 x 0.738 = 0.545
So that's how close Joanne Hayes got to being convicted. All other things being equal, 54.5% of Irish people, including murdered neonates, are going to be blood group O. It's like Fortuna tossed a coin and it came down heads-for-exoneration rather than tails-for conviction. Phew!

Well, at that stage I got an attack of the datas and put together a comprehensive study of ABO blood groups as they impinge on paternity testing. Apart from the odd cock-up with wrist-bands in maternity hospitals we know who is the mother. The following tables and charts are based on the frequencies found in Ireland, the conclusions will be slightly different if you come from elsewhere in Europe and quite a bit different if you're tracking Aztecs or Han Chinese. First lets look at when a man and a women love each other very much . . . and have a child. We can calculate how many of each sort of mother-father-child triplets we can expect. The numbers in the coloured part of the table are the product of the frequencies along the table margins:
There are six possible 'genotypes'. As far as we know - and it has been investigated - there is no assortative mating: you choose your partner because s/he wears the same sort of shoes as your mother or because s/he smells like your Uncle Jim; not because s/he has the same (or different) blood group as you. From the top part of the table above note that in 0.297 (just under 30%) of all 'marriages' in Ireland both parents are blood group O. otoh, only 0.001 (or 1-in-1000) involved two people who are both AB.  The bottom part of the table imagines that there are 4 children to each liaison and lists out their blood groups. Of course, it doesn't work out with strict determinism: all the kids of Mr AB and Ms AB could be AB . . . or A . . . or B - or any combination. But the probability is as outlined in the chart. Some interesting outcomes
  • If you are group O, neither parent can be AB
    • If you are AB you cannot have a child who is group O
  • If one parent is B and the other A then any sort of child could be legitimate
  • If one parent is AB and the other is O then none of the children will be like their parents
We can summarise the Exclusions [chart L] as those children who cannot be the offspring of the declared parents. You may choose to suspect the golf Pro or Mellors the garrrrdener. I've had some thoughts about non-paternity in a case, much more recent than 1984, where the gardai and society-in-general were jumping to conclusions about people who lived a bit outside of a rather narrow definition of normal.

And because I am nerdy like that I have put down [Table L] each combination of parents and the proportion they comprise of the population: from the colour coded blocks in the third table above. My codes for combination are short-hand: A=A also includes A=O cases where one parent is group O - the orange colour really means parents who cannot have a child who is B or AB etc.  I've then cross-referenced the Exclusion table to tally up the expected proportion of people in the Irish population who have the attributes which are excluded by that combination of parents. The bottom right cell = 0.273 = 25%. It's reciprocal of that number which is important: 75% of the time ABO blood groups will,  on their own, have no utility to exclude paternity. YMMV in Kazakhstan but not by much: as group B gets more common in Asia so group A frequencies fall. This is why the Kerry DNA data is so important; by looking at dozens of different independent variants it becomes vanishingly unlikely that you'll make a wrong call on who the parents are.

Monday, 13 May 2013

100-up

100-up is much better than Bib-Label Lithiated Lemon-Lime Soda which was the first incarnation of 7-up - less fizz but more substance.  This is my hundredth post and I'll indulge myself in a tiny Retrospective.  It turns out, as near as dammit, that I've dropped about 100 names in those hundred posts.  I've sorted them by first name because we now seem like old friends and the good people at blogspot/blogger provide a search function for Science Matters that will satisfy your curiosity about "What could Bob possibly have to say about Gene Wilder?".  In many cases the answer will be not very much! Sorry.
Abraham Lincoln; Ada Lovelace; Alexander Bell; Amedeo Avogadro; Andre Lwoff; Andrew Harrington; Aoife McLysaght; Barry Dalby; Benjamin Disraeli; Bill Clinton; Charles Babbage; Charles Darwin; Charles-I Stuart; Chris Hayes; Christian Goldbach; Craig Venter; Daniel Day-Lewis; David Attenborough; David Fahey; David Haussler; Dionysius Exiguus; Edsger Dijkstra; Edward MacNeil; Emil Zatopek; Eugene Cernan; Ewan Birney; Francis Coppola; Francois Jacob; Frank Ramsey; Gene Wilder; George Dawson; George McClellan; Gerd Gigerenzer; Jacques Monod; James Gleick; James Joyce; James Lovelock; James Murray; James Ussher; James Watson; Jan Jansky; JBS Haldane;Jean Danjou; Jim Kent; Jim Peters; Jocelyn Bell-Burnell; Johan Kjeldahl; John Hinde; John Keats; John Lonergan; John Seymour; Joseph Conrad; JS Haldane; Karl Landsteiner; Karsten Hokamp; Ken Wolfe; Leslie Liebermann; Lynn Margulis; Malcolm Gladwell; Mary Mulvihill; Matt Groening; Matthew Broderick; Maximillian I of Mexico; MC Escher; Michael Ramsey; Michel Thomas; Michelangelo  Buonarotti; Nan Doyle; Neil Armstrong; Paddy Lydon; Patricia Arquette; Paul Crutzen; Paul McCartney; Percy Shelley; Peter Medawar; Pope PiusX; Ralph Leighton; Raj Padam; Richard Chamberlain; Richard Feynman; Richard Haldane; Ronald Graham; Saint Cunigunde; Sian Croose; Sinead O’Brien; Skip Lovelady; Sophocles; Stanislav Jungwirth; Stephen Fry; Sukiyabashi Jiro; Tony Blair; Varro Raetinus; Walter Bagehot; Widukind Lenz; Wilkinson, Mr; William Hurt; William McBride; William Shakespeare; 

Clearly these may be gathered into bins or made to form themes (several Haldanes, many geneticists, some film-stars, a surprising number of Jims).  But several of them appear to be, in the tradition of "googlewhacks", un-met by google-light:

Your search - "Amedeo Avogadro" "Sukiyabashi Jiro" - did not match any documents.
Your search - "Johan Kjeldahl" "Emil Zatopek" - did not match any documents.
Your search - "Lynn Margulis" "Varro Raetinus" - did not match any documents.
But it is the destiny of googlewhacks to fade as soon as the spiders of Google find the site that reports them, so there will be soon at least one site on Google that reports the meeting of these unlikely couples.
 

Wednesday, 3 April 2013

Jan Jansky - 140 candles today

Jan Jansky born Prague 3rd April 1873.

I think we're all interested in forgotten pioneers: those who gave the frontier a damned good shove but we just can't seem to recall, let alone celebrate, today.  There's a longish list of people who should have gotten a Nobel Prize and would have had one if they hadn't been a woman or hadn't come from a minority country or hadn't been a graduate student or a mere technician.  I'll write about Jocelyn Bell Burnell later, perhaps in July to celebrate her 70th birthday.  But as an example of what I mean, ask yourself who was the last man to set foot on the moon?  Neil Armstrong throws a long shadow, doesn't he?  So Eugene Cernan is all but totally obscured.

So the knee-jerk answer to who discovered ABO blood-groups is the late great Karl Landsteiner.  For his 1900 discovery and subsequent research on agglutination of blood and transfusions he was awarded the 1930 Nobel Prize.  "Late great" is fair enough because, in addition to ABO he also isolated the polio virus (Landsteiner & Popper 1909) and discovered Rhesus incompatibility (Wiener and Landsteiner 1937).  But get this: Landsteiner recognized only 3 classes of the primary agglutination factor, which he called A, B and C.

Jan Jansky OTOH recognised four blood groups which he called I II III IV in a 1907 paper in Czech Hematologická studie u psychotiků.  This classification agrees with our current understanding which recognizes A, B, AB and O. I think we could bring this all to centre stage, not least because it's an early example of publishing negative results.  Jansky had a hypothesis that blood groups were the cause of, or associated with, certain types of psychosis (he was a neurologist and psychiatrist by trade).  But when the data revealed no such association, Jansky tooled up and shot down his cherished theory in the 1907 paper.  An American medical commission sat in 1921 to sort out the science and priority and acknowledged Jansky's claim to the earliest and correctest classification of blood groups.  He is remembered in his home place - regular blood donors in Czecho are eventually awarded a Jansky medal for their half-litres.

But before we get toooo indignant about the Nobel committee dissing the obscure but insightful genius from Prague, we should note the facts.  Nobels are only awarded to the living and only after sufficient time has elapsed to show the context and scientific impact of the cited discovery.  So if you want one you need at least a touch of longevity.  Jan Jansky developed ischaemic heart disease and pegged out at the age of 48 in 1921.  The Nobel committee wasn't ready to acknowledge the significance of his and Landsteiner's work until nearly a decade later.

Credits: I wrote about student projects and presentations in January.  To the best of my knowledge I'd never even heard of Jansky (shame on me) until one of my first year students dug him up in her researches into ABO blood groups.  So I've been hopping from one foot to the other ever since to write this celebratory birthday post.

And it might be nice to acknowledge here my old (late-great, indeed) professor of genetics George Dawson who published a massive study on the distribution of ABO blood groups in Ireland in 1964.  He recorded the blood group and county of origin of 1/18th of the population of Ireland and mapped their frequencies. I passed through the department a decade later and benefited enormously from my peripheral contact with this old-time scholar.  When I returned to the old department in 1990, the colour-coded 3x5 index cards for this project were still stacked in the warren of inter-connected rooms and cupboards down in the basement. That was something in excess of 600kg of tinder-dry paper.  I'm glad we were less sensitive about fire-safety in those days because that's where I found the acoustic coupler that made my life as a DNA database pilot much easier.

Tuesday, 4 October 2016

Big Foot

If you've been delivered here by Google in your search for a hot date with a sasquatch, may I respectfully send you on your way. There is nothing of that sort to see here. But there is something rather interesting which popped up out of Research Methods class over the last couple of weeks.  As Quantitative Methods = QM is what The Institute calls remedial maths, so Research Methods is beginning statistics and data-crunching. It is taught in two parallel streams: a) a series of lectures about the theory and probably a few worked examples b) a 2 hour session each week where students can get down and dirty with some data.

What data? Why not real data? Why not real data about or from the punters? This year I have two ResMet classes full of 2nd Year sporty people [working towards degrees like Strength & Conditioning or Sports Rehab] and I asked them to record a) their shoe-size and b) their height in cm. These are the same people with whom we investigated reaction times and body-proportions in 1st Year 12 month ago. They are used to me foibles. In my round-the-house Intro to the exercise, I gave them some life-coach advice. When I was born, girls wore dresses and pink and had long hair, while boys wore blue trousers and a buzz-cut. By the time I'd grown up these demarcations were considerably blurred. I floated the idea that if a young person wished to check out a long-haired creature walking down the street in jeans, then the key was in the feet, rather than at the other end of the jeans. Teen and adult boys just have bigger feet, I asserted. We were also gathering real data so that we could test a hypothesis such as "Women are shorter than men" - [with an unmatched t-test or a Mann-Whitney U test] or "Str&Condit attracts more men that SportsRehab" [using Chi.Sq].  But if we have two sorts of related data it is possible to make a scatter-plot to see how they are related:
If you ignore sex M/F, you can see that there is a rather strong trend: Tall people have big feet and vice-versa. There's a lot of scatter, though, which is the variety among humans that makes life so interesting. Nor can we exclude the possibility that someone has made a mistake converting 5ft10in into cm. When you take sex into account something much more interesting turns up. Although the smallest man is shorter than half the women; no man has smaller feet than any woman. Within M or F, the height = foot-size trend is still there [I've dishonestly added a "trend-line" to sex up the effect] but the line for girls is parallel to, and lower than, the trend among boys. I was delighted to see my off-the-cuff assertion so clearly borne out by the data.

The title I've stuck on the diagram is Human Allometry, which is relevant here. Allometry is differential growth rates and the concept is pervasive in the living world. I showed last year that a human skull is essentially the same as a baboon skull, except that it retains features more typical of a child: we are neotenous.  As we grow, some things grow faster/bigger than others. At birth we are about 4 skulls long but as adults the relative height is about 7.5 skulls. For reasons which are not clear, men's feet have a different, cranked-up sensitivity to human growth hormone.

I was sharing these ruminations with one of my colleagues, who said she knew all that already because she bought shoes for both herself and her sons (that's weird - they can vote but they can't buy their own shoes?). She then went on to say that she has spent a life time shopping for shoes in sales in Galway and Dublin. She could never find [ladies] shoes in size 7 in Galway or size 4 in Dublin. Seemingly the country people in The West have bigger feet than the sophisticates of Dublin on the other side of the country. We know, from George Dawson's massive study, that there are differences in the ABO blood group frequencies [last week] between East and West. Now it appears that they are built differently too.

Sunday, 10 May 2015

O'Hara's 1959-1993

I spent the whole day yesterday in a cellar.  A very well appointed cellar, with tea and biscuits supplied and sandwiches for lunch, but a cellar without natural light nevertheless.  It was all about the retirement of David McConnell, the Professor of Genetics at Trinity College Dublin. A selection of his colleagues and students came 'home' to tell war stories about The Old Days in O'Hara's the building [L seen the day it was scheduled for final demolition] that housed the Genetics Department as well as O'Hara's the eponymous builders' merchant, a dance studio, a dental engineer and a variety of other enterprises. The building was owned by Trinity College but parts of it were leased out to raise some rent.  It was hideous from the outside, rendered in grey cement with bars on the lower windows against potential burglars.  Inside was a different matter as the centre of this modest-sized corporate building was taken up with a gorgeous stairwell running up to a 1st and 2nd floor. Each floor had a generous three-sided landing that could accommodate an intense scientific conversation and a technician pushing a trolley of used glassware for sterilisation.  Those conversations were where the frontiers were pushed and if boffins were shoved aside every time a trolley passed, it might hold up the progress of science. I mention this because, in the early 1990s the TCD Biotechnology building had been designed by premier Irish architects Scott Tallon Walker and built next door. Its corridors were built to the minimum width allowed by building regulations to allow most space to laboratories and was therefore, in the opinion of many who worked there (including myself 2007-2010) a failed enterprise.

O'Hara's was designed by Sir William Wilde, Oscar's father, as an ophthalmic hospital, just round the corner from his enormous house at #1 Merrion Square.  He wasn't 100% sure that there would be enough business to support the intended business and specified that, as a fall-back position, the building could be easily converted into a Methodist chapel: hence the generous landings which would presumably have had tiered seats like in a court-house.  By the time I came there as a student in 1975, the building was shabby and run down but punching above its weight in science.  At the retirement festival yesterday, one of the frontier-pushers of the old days was talking about a mammoth project that required the screening of thousands of petri-dishes to find very rare, but crucially interesting, mutations in a key bacterial culture.  The desk-top 37oC incubators were fine for classes but wholly inadequate for an early example of industrial throughput mega-science. They conceived the idea of converting one of the small offices into a walk-in incubator, heated to 37oC by Bunsen burners!  Apparently TCD had a fire-safety officer in those 1960s days and seemingly he gave his appro for this clearly-bonkers plan.

In that case nobody died, but it did make me think about fire-safety in O'Hara's, where I spent about 5 years of my life every-working day.  For starters, there were the bars on the ground-floor windows. With a fire raging in the laboratory you might have no other exit but out through those windows.  Then there was the gorgeous central chimney stair-well over the cellar where I threw my bicycle every morning.  That was an Aladdin's cave of discarded equipment, old papers, not-used-very-often chemicals and looping electrical wiring. There were, for example, boxes of 4x6in index cards from George Dawson's 1959 survey of ABO blood groups.  Each person who had ever donated blood in Ireland had been given a colour-coded index card and these were grouped in boxes by county. This sample was 1:18 of the population which was then about 3.5million. At 160gsm, these cards must have weighed in at 500kg of tinder dry paper right under the chimney stair-well.

My near-death experience was nothing to do with conflagration, however. When I came back to Genetics in 1990, I was working in the bioinformatics / molecular evolution lab on the top floor just under a loft that was full of pigeons because there was always a loose slate or two on the roof.  My section of lab bench faced the wall between the lab and the gaffer's office.  Remarkably we had only 3 computer terminals but 4 people, so we had to take turns to get access to the data.  That was fine, because there was lots to do apart from tricking about with data - reading the literature, thinking, writing the next paper, thinking, having a cup of tea, thinking.  One morning I was getting antsy to get a bit of code up and running and I asked Liz if she could let me have my turn at the key-board.  After asking a couple of times, she wrapped up and went off for her turn at  reading, thinking and tea-drinking.  I had just settled my enormous bottom on the stool in front of the screen when 2.5m of 3-tier shelving detached itself from the wall and crashed onto the bench where my hands had been holding a book 5 minutes earlier. The shelves were mostly filled with books and papers but also had stacks of glass sheets for running electrophoretic gels.  Because I wasn't there my arms weren't crushed and my arteries weren't severed by a glass guillotine, so nobody died.

Round about that time, the College appointed a real Heath and Safety Officer, who wasn't a Trinity chap and so could look at the whole place with fresh, and highly critical eyes - that's what he was paid for.  In due course, he turned up to inspect O'Hara's with his clip-board.  Chief technician and head of department came out to meet and greet him. In my memory, he didn't get a third of the way through the ground floor before his clipboard was covered in crosses and he announced that the building would have to be closed down immediately for flagrant abuse of fire, chemical, electrical, radioactive and environmental safety regulations. Needless to say, that didn't happen: he was new on the block and didn't yet realise how the power-structure of an old style university functioned. I guess we did tidy up some of the most obvious deficiencies so the optics were better but the building was not fit for purpose and the damning safety audit quite possibly expedited the replacement of O'Hara's by the swish new Smurfit Institute for Genetics, which arose like a phoenix on the foot print of the [dear] old building.

Tuesday, 5 December 2017

Code-buster

You know what they say about women in the professions: they have to be twice as good to get half as far as their brothers. Here on The Blob, I write about a very mixed salad of topics but one of the themes is women in science, of whom I've written 60 short biographies. I do this because I want more women in science because they are another county heard from, and more diversity means more and more creative ideas about how the world ticks. I hope that some of them will be read by a teenage girl who might thereby aspire to be a top chemist or nanotechnologist. It embarrasses me when I hear, for the first time this late in my life, about a woman who has made a key discovery in science. Take Nettie Stevens, for example who surfaced in the blogosphere last week, she discovered sex-chromosomes right at the beginning of Genetics . . . never 'eard of her. Maybe my old prof ,George Dawson, who was huge fan of Barbara McClintock, mentioned her but her name rang no bell. With my training in genetics and interest in history, I shd have flagged Dr Stevens - tsk!


But today we're down with Elizebeth Smith Friedman [L in hat], peerless cryptographer in two World Wars.  I have a little bit more excuse there because her work was politically sensitive and for a variety of reasons was kept under wraps. Her work was also appropriated by some of the men around her. Jason Fagone discovered her a tuthree years ago as well as a treasure trove of her personal and professional papers and has just published a biography The Woman Who Smashed Codes which has been gathering rave reviews.  Easily confused with A Life in Code: Pioneer Cryptanalyst Elizebeth Smith Friedman by G. Stuart Smith. Except that Smith's April 2017 biography is trailing at 565,000th on Amazon while Fagone's September 2017 book is 1,700! Poor Mr Smith must be chewing his beard in frustration at the Harry Potterness of it.

Elizebeth Smith was the youngest in an extensive family of Quakers and grew up on a farm outside Boondocks, Indiana. She got a degree in English Literature and was all set for quotidian career as a small town school teacher until she got married. That was one of the sunnier options available for women born in the 1890s. But she yearned for something more interesting and, quite by accident, found herself deciphering Shakespeare for an eccentric millionaire on Riverdale his extensive estate outside Chicago. "Deciphering" rather than reading or studying The Bard because her boss was certain that Shakepeare's works were written by a cunning cryptographer Francis Bacon who had left clues to his identity in the texts themselves. Although it is hard enough to crack things that are obviously encrypted, it turns out to be easy to find hidden messages in documents that are not encrypted . . . if you are prone to confirmation bias or delusion. You should filter 'quite by accident' through the lens of all those people you know who are lucky because they make their own luck. It turned out that the US government of the day, in one of their isolationist phases, had essentially no cryptologists on the payroll, so they rolled up to Riverdale as and when needed.  One of the other Effectives there was a young chap called William Friedman and he and Elizabeth clicked over the codes and soon got married. In 1920, they shipped out from the Midwest and settled in Washington DC, she working for the US Coastguard.

The Coastguard was the front-line in the Prohibition War as The Mob tried to import illicit liquor in almost unimaginable quantities. You'd have to wonder what sort of a democratic decision the Volstead Act was if there was such a demand for illegal booze. The Hoods made rendezvous on and off the coast by wireless and because that was open-mike, they conversed in code. And Elizebeth was able to crack these with reliable regularity even as the Opposition increased the complexity of the ciphers as part of the arms race. Between 1925 and 1931, she worked the entire gig with only one other (female) employee. After that Uncle Sam recognised the value of the work to the extent of sending her more hands for work and training. These were almost all men but such was her demeanour and no-nonsense efficiency that “Many times I’ve been asked as to how my authority, that is the direction and superior status of a woman as instructor, teacher, mentor, and slave driver, even to commissioned and non-commissioned officers, by these men was accepted,” she said. “I must declare with all truth that with one exception, all of the men young or older who have worked for me and under me and with me, have been true colleagues and have never been obstructionists in any way.” [source]

Elizebeth was definitely of sterner stuff than her husband William, who later on suffered stress fractures in his mind. He was working to break Japanese military ciphers during the war when failure was likely to result in thousands of extra US casualties. But like Alicia Nash, she added his care and attention to the list of tasks which she had to address on a daily basis. Whenever she felt like slacking off or taking a holiday, some government department or other would rock up to her door with an unsolvable conundrum and she often found it easier to solve the puzzle than Just Say No. We only know what we know because the Friedman's bundled up their entire archive and donated them to a local library. This was after the NSA had descended on their home and seized wodges of their papers in a security sweep in the 1950s. But for the Friedman's proactive stand, everything would have been boxed up and shipped to a warehouse in Area 51, Nevada.

What I find interesting is the kind of Arts Block creativity was what was looked for in code-breakers back then. They recruited for the Enigma project by having potential cryptographers do the Times crossword. You were in if you could knock that off in 5 minutes; or if you knew the complete works of Shakespeare by heart. They were looking for creative people who could see connexions between disparate things and recognise patterns. It's true that maths is all about recognising patterns as well and so the Enigmatists were also looking for math-whizzes form Oxbridge. Now cryptography is almost all brute force - persuading a massive computer to find prime factors of enormous numbers: no role for quirky cross-referencing there. Whatever her original training, I am owning Elizebeth Smith Friedman for STEM.
If you like Fagone's style you might enjoy this essay about another extraordinary woman 'solving'  gunshot wounds in Philadelphia.