Friday 31 May 2013

Data compression

I could have gotten maudlin' and sentimental yesterday as we drove Dau.II off up to Dublin for her new life and I did . . . but not really about her: so full of hope, so full of the future.  But I took the opportunity of being in Dublin to drop into my old place of work.  The boss has decided to shift his traps to the Other University after 25 years man-and-boy in the same place. I bumped into my Venter Code pal as I was leaving and he said they were not taking much of the accumulated rommel to the spare, austere premises in their new workplace.  He asked if I would take "The Genbank Tape" because it was likely to finish up in the dumpster if I didn't take it.  So I brought home one of the last 2400ft magnetic tapes left in Ireland as a souvenir of how it was during the war, back in the early 1990s. Amazingly you can buy "new" still-in-its-packing 2400ft mag tapes on Ebay - a snip at $49.95 + $43.20 p&p. I am told that banks still use such legacy hardware because they are terrified of changing to something handier in case the data gets corrupted in the transition. Genbank is the database of every DNA sequence known to humankind and for the last 30 years has been more or less following Moore's law and doubling in size every 18 months.  The last release of GenBank that we received in the post may well have been Release 74 from December 1992, which contained just under 100,000 different sequences made up of 120,242,234 base pairs (bps).  So effectively that's what I brought home last night. If only I had a machine that could read it.  The database is/was about twice as big in bytes because for every 1000 bps of sequence there is/was about 1000 letters of plain text explaining what the sequence means.  So the tape I now have propped up on top of the piano at home contains about 250 megs of data.  I weighed it on the kitchen scales at 980g - it almost balanced a bag of sugar.  While I was in weighing mode I took my 4GB USB key out of my shirt-pocket and clocked that at 10g.

16x as much data.  1% of the weight.  That's compression.
OTOH, GenBank is now 151,178,979,155bp in size - as near as dammit 1000x bigger than it was 20 years ago in June 1993.   

Thursday 30 May 2013

Launch - loss

I wrote in January about the death of our dog Rashers, brought into our mountainy home ten years ago by the importunities of our younger daughter then aged seven. Today, like her aunt before her Dau.II tied up some few belongings in a small-small rucksack and left home aged 17.  She is going to live in Dublin for the summer giving a hand to the childcare-in-school-holidays problem of her odd-mother - it would be false to call a committed atheist god-mother but that's effectively the relationship.  There are few enough opportunities for a minor to have any significant relationship with an adult who is not a blood-relative, so it's a source of comfort-and-joy that these two women get on well together.  I haven't spoken much about the fact the Dau.II and her sister Dau.I the Poet never went to school.  Our family practiced a fairly extreme example of 'unschooling' - just stand out of the way, close your gob, choke down your own fears and apprehensions and let the kids get on with their own education.  We started off with a house full of books - mostly second-hand - on just about every subject that has appeared in print except perhaps morris-dancing and incest. Later on we got a raft of interactive CDs from the late-great educational publishers Dorling-Kindersley, and a flaky connexion to the interweb.  More recently, we've acquired a reasonable wireless 'broad'band connexion to the interweb.  Since the girls were born we've never owned a television, but with the 'broad'band, Dau.II can play Geoguessr and has watched numerous youtube examples of Gordon Ramsey swearing at incompetents in the catering trade.  She's educated herself and the results are a bit quirky.  Just in the month before she left home she has absorbed a) the name, location and capital city of every country in Africa b) how to make a swiss-roll c) enough Japanese to order food and drink with an appropriate level of politeness d) how to play Dave Brubek's Take Five on her saxophone e) how to repair a broken lawn-mower with duct-tape.  That's a pretty handy set of accomplishments with which to face into this dark world and wide.

So she has just launched herself.  She is funny and sassy, very light on the invective and sharp on the irony, with a well-honed crap-detector . . . and she's loose on the world. To say I'm proud of her would be, in some sense, to take credit for who and how she is - I can hardly do that because I did nothing much more than sit on my behind and watch her become.  So I'll just say that though I'm bereft I'm delighted at how she's turned out.

Wednesday 29 May 2013

The World through Geoguessr

Some time before the Last War, I went on a field trip to gather population genetic data in the Republic of Cabo Verde with two American colleagues. This ex-Portuguese colony is an archipelago 500km West of Senegal off the coast of Africa.  In the evenings two of us would play patience - the one everyone plays.  It passed the time and saved us from talking to each other.  Apparently you can play this in some casinos by paying $10 for a shuffled pack of cards and winning $1 for each card that you can pile on the aces.  We had a discussion about what the odds were on the casino game - which are rather more difficult to calculate than the probabilities of the roulette wheel delivering red (18/37 giving the house an edge of just under 3%).  You can't leave that sort of question unanswered, so when I got home I played the game 100 times on the trot and recorded my score.  In those 100 games, I got the whole pack 'out' for a payola of $52 only 3 times and the other 97 games paid out in dribs and drabs, so I finished up losing about $120 on my investment of $1,000 in play-money. I'd calculated the odds, to my own satisfaction, by simulation; and a  perfectly good and widely employed scientific method it is too.  The take-home is: stick to roulette at casinos, you get better odds and,  especially if you wear a tuxedo, you look more like James Bond and less like Johnny No-Pals playing cards with yourself in a corner.

Geoguessr is, like Klondike solitaire, a way of passing the time. Try it before reading on? A friend of mine had one hit early on at 240m from target (6500points!!) and got a bit hooked.  After his 4th report of his latest score, I told him "STOP now. That way madness lies, you'll have to stop or the wind will change when you're geoguessring and you'll find yourself sitting on a rock in the Atacama Desert wearing a sack."  But there is a mort of educational value in the pass-time.  It really helps to be able to read cyrillic characters, for example, so when you see a road sign saying Владивосток, you know it's not near Athlone.  You get a higher score if the distance is small between the picture displayed and your guess about its location.  So the two are inversely related.  The largest distance possible on the planet is half the circumference of the earth - 20,000km.   I don't know what score you get for that but my worse punt was 16,600km adrift and clocked a pathetic 45 points so maybe 20Mm is rated as 0.  Playing a few games with Dau.II was good fun and our best single guess was 160m (that's 0.16km) from target and netted (whoohoo) 6466 points.  Being a scientist obliges you to try to turn footling anecdotes like that into DATA.  Accordingly, like my sad-sack card-turning with Klondike after the Cabo Verde trip, I sat down and recorded the results from several games:
Us population geneticists are quite interested in the distribution of data and this graph shows an interestingly discontinuous pattern.  The points at the bottom left are all bad luck when presented with a paved road cutting through an uninhabited red laterite landscape and coin-tossing Australia rather than South Africa or vice-versa.  The ones at the top left are when you are beside the Lincoln Memorial in Washington DC, or outside the Walla Walla Vinyard Inn in the other Washington.  The middle bunch represent guesses in the 100 - 1000km range.  You know the country from the road or shop signs, you can guesstimate the latitude and some other facts from the vegetation.  You know that if the picture is pancake flat you're either in Ohio or near the Oder River.  Any mention of silver and you can bet real silver that you're in Nevada or Colorado.  Flags (North Americans are all mad about the ould flags) are, of course, a dead give away.  So that's quite a lot of information about the political and physical geography of our planet, that can narrow the sensible range
Notice the other weird thing about the distribution of points (apart from the patchiness due to the nature of the game)?  It's not linear.  You get way more points than you deserve for getting up close and personal with the target.  The lads at Geoguessr must have a formula to assign scores, and curve above looks logarithmic.  So let's transform the data by taking the natural log of the score:
That certainly makes the relationship look a lot more linear.  Although there is still a distinct fillip up to your score when you're less than 5 or 10 km from target.  I knew I needed more data and particularly data in the range 2,000-12,000km, so I went back to the game.  I had to make some absurd guesses - mid-Atlantic or halfway between ZA and Oz - to get some points in the desired range:
Which when the score is log-transformed shows:
The wonky double bulge in this line indicates clearly that the algorithm/formula is not straight logarithmic with a bonus for really-close. It must be more complex. And I'm sure the answer has been posted somewhere. A final picture shows a zoom into the top left corner of the last picture
What does that all amount to?  My advice, if you care about really high scores, is to work hard to get your distances down from 100km to 10km or 1km, because that has more impact than the much larger change from 1000km to 100km.

Now I'm back off to Кыргыз Республикасы.

Tuesday 28 May 2013

The Venter Code

. . .a challenge.

It's three years to the week since J Craig Venter announced the creation of "the first bacterial genome whose parent was a computer".  As any fule kno the genetic code depends on the order in which four bases A T C G are clagged onto a sugar-phosphate-sugar backbone in a double helix.  Nirenberg and Matthaei took the first step in decrypting the biological reality of the code in 1961.  It took fifty years for Craig Venter to be in a position to announce his Genetics-meets-Genesis achievement.  The press conference of the announcement is interesting because JCV is at pains to elaborate on the glitches, hold-ups, and false trails as well as the clever ideas, breakthroughs and ultimate triumph.

Venter has had some really smart ideas over the last 25 years which I'll get round to covering in due course. On this 3rd anniversary I'll note the hubris in the idea that when his people were creating their new bacterial genome from whole cloth (or from four bottles as Venter has it) they chose to write their own names into the sequence . . . in a code, that isn't necessarily the same as the "universal" genetic code
Their artificial genome sequence contains four "watermarks" each of just over a kilobase. The first water mark contains the code for all letters, numerals and punctuation. The others,
 a) the names of 46 people associated with the project. (The Authors of the 2010 paper N=24 are Daniel G. Gibson// John I. Glass// Carole Lartigue// Vladimir N. Noskov// Ray-Yuan Chuang// Mikkel A. Algire// Gwynedd A. Benders// Michael G. Montague// Li Ma// Monzia M. Moodie// Chuck Merryman// Sanjay Vashee// Radha Krishnakumar// Nacyra Assad-Garcia// Cynthia Andrews-Pfannkoch// Evgeniya A. Denisova// Lei Young// Zhi-Qing Qi// Thomas H. Segall-Shapiro// Christopher H. Calvey// Prashanth P. Parmar// Clyde A. Hutchison III// Hamilton O. Smith// J. Craig Venter//) 
b) a website where you can check in when you’ve solved the puzzle and
c) the following meaningful quotes:
* To live, to err, to fall, to triumph and to recreate life out of life. Joyce
* See things not as they are, but as they might be. Oppenheimer
* What I cannot build, I cannot understand. Feynman

Here’s the data. Your task is to crack the code. When this-all hit the news-stands 3 years ago, I put this task to the smartest young(er) people I knew and only got one "begob I'll give it a lash" response.
Interestingly my technique and his were quite different although the solution was the same. That feller has just landed a lectureship in a different university and I suggest that these two 1000-day-separated events are not unrelated. Solving this puzzle requires a crucial creative insight or two and some grunt work to see the task through to completion.

That's a pretty good summary of what makes a successful scientist.  So hats off to Kevin Byrne!  (I got my lectureship too - hence The Blob)

Monday 27 May 2013

Who needs a radon barrier?

The Beloved's youngest sister has done well for herself.  Through no fault of her own, she went to a different school each year for much of her teens, and so missed out on large chunks of the standard curriculum.  She covered the Young Irelanders in 1848 two or three times but missed out on Jim Larkin and the 1913 Dublin lock-out entirely.  As a teenager she went mad-about-the-nags for several years, and her marginal grades didn't matter much when she was looking for work in the riding business.  After several years of this she found that while blokes with money can do alright in the world of horses, girls with no money just shovel horse-shit.  So she jacked it in and came and stayed with us in England - and promptly got a job in the bar of the student's union to pay for her training in office and secretarial work.  She left when she was qualified, tied her few belongings up in a handkerchief, and went to London to seek her fortune.  She got a job there, made herself essential to an engineering firm, asked for a day off a week to go to college and got a diploma, then jacked in the job to go full time for year and parlay that qual into a degree in networking and systems analysis.  It took a few years (and the kind of guts, determination and ambition that I long ago left on the side of my plate as too gristly to tackle) but her degree got her a job working at the very bottom of one of the huge multinational telecoms companies.  She's now in her 40s and une tres grande fromage out East - VP AsiaPac or Mikado of Titipoo or something.  There are no OAPensions out in foreign: you have to sort that out yourself.  So she's just bought a house in Tramore, Co Waterford as a hedge against an uncertain future and a place to live when she finally gets home (assuming that yellow-jack, pirates, or the HR Department don't do for her first).  Tramore wouldn't be my idea of heaven with it's view of the disgraceful landfill along the Backstrand but that's where she wants to be in 20 years time.

She contracted an engineer to survey the house and recommend the structural, engineering and insulation issues that needed to be addressed.  This feller returned a long list of necessary and expensive alterations to bring a 1980s vintage bungalow up to modern specs.  Item 13 was something like "rip up existing concrete floor and replace with a radon barrier underneath - €8,000".

Now radon is bad news (or rather it's the polonium to which radon decays), so such advice can't be dismissed with a wave of the hand. The Radiological Protection Institute has produced a map showing the radon hazard of each 10km square for the island (thanks to Lloyd-George and Michael Collins in 1921 there is no radon hazard in the 6 counties - which is fortunate for them all in The North). A single step south into Co Louth of course and you're going to get hot, so mind yourself there.  This amazingly handy and informative map shows that Tramore is in a hot square as well as Carlingford up near the borrrder.  For those who are geographically challenged as to the location of small towns in Waterford I attach a red arrow to show where Tramore is. 

So it looks like the engineer is correct in his advice unless you're going to critically evaluate the evidence.  Radon is radioactive and itself the product of radioactive decay from Uranium-234, which as it decays over millions of years gets depleted, so the only source of Uranium that hasn't already decayed into Radon is what has come up from the earth's interior as a volcanic eruption. If the rock over which your home is built isn't of volcanic origin, you're pretty much in the clear with respect to radon.  But lets look at the detail:
This is another nice map showing the geological bed-rock for Co Waterford.  You can follow the link to get similar maps for each of the 26 counties. Here's the key: Light purple: Precambrian metamorphic rocks; Pink: Ordovician; Dark blue: Ordovician volcanic rocks; Green: Silurian sediments; Beige: Devonian sandstones and conglomerates; Light blue: Lower Carboniferous limestone.  So it's the dark blue volcanic rocks that are loaded with radioactivity including radon and its desperately dangerous descendant polonium.  So if you live a couple of miles N and W of Tramore you really do need a radon barrier, but if you're in town you don't.  You just have to deal with drunks urinating in your garden when they spill out of the Grand Hotel in the (aptly named) wee hours.

Sunday 26 May 2013

Gathering geography

Years ago, we lived in the North of England and, during the Autumn midterm one year, I announced that me and The Boy were going to Cape Wrath - the very-top-left-most corner of Scotland. We set off North and, as dusk fell in the middle of Scotland, we needed to find a) food and b) a place to camp.  The first was easy because we were only 34, 30, 25, 17 miles from Braemar: famous in song and story, seat of the Highland Games, where Elizabeth Windsor Sr. was known to down a few G&Ts of an evening.  So we fell into a drooling discussion of what we'd eat when we arrived in town.  I was for chicken curry and he was for pizza, but I was prepared to concede my druthers if there was pepperoni.  So imagine our disappointment when tally of Braemar's restaurants had an N = 0.  There was a tea-shoppe (closed) two pubs and a couple of grand hotels.  No pizza.  So we tightened our belts (we weren't talking much to each other, certainly not about food, by then) and drove on-and-on-and-on to Grantown-on-Spey where The Boy had his first deep-fried pizza and I had scotch-pie and chips.  We felt a bit cheated by Braemar's reputation.

Years later, but still years ago, I was the Irish representative of a European consortium and we had our AGM in Vienna.  Our host and shepherd had booked the 40 of us into a cheap and cheerful hotel near where he lived and scheduled the business meeting to start at 0900hrs in the University on the other side of the city centre.  At about 0830, he strolled into the lobby and said that we could catch the next tram going north.  He was completely confident that a rush-hour journey involving two trams and a bus could be completed in time - and it was so.
It just felt so civilized, if a little alien for one who was used to Dublin buses arriving in flocks at very irregular intervals, and no trams at all - this was before the wonderful Luas arrived.  Vienna also felt very central because on the way out to airport, we passed under the sign shown to the left.  I was just thrilled to be told by the cabbie that Bratislava is only 60km from Vienna.  Indeed Bratislava should be your airport of choice if you're going to Vienna with Ryanair because it's much closer than the three Austrian airports (Klagenfurt 236km, Linz 152km , Salzburg 253km) served by Ireland's Own Carrier.

 Mais revenons-nous a nos moutons.  After all the travel, we should try to bring this back towards the title.  When we returned to Ireland in 1990, after a dozen years in foreign, the country was staggering out of the end of the 1980s recession and it was still poor, rural and whatever is the opposite of multinational.  There were, as I said above, no trams; there were no motorways and certainly no nighttime buses to the airport.  Since then, we've acquired all three and so it's much easier to get around.  Now imagine that you're new to the country and heading North on the M9 from Waterford. You're all hank-marvin and the kids are wrangling in the back, so you'd be delighted to see Exit 3 leading to Baltinglass, Athy, Timolin and Moone.  Moone or Timolin (the nearest to the junction) would surely have a choice of places to feed the children.  But if our travelers thought that then they would be disappointingly Braemarred.  Because the National Roads Authority sees fit to give villages parity of esteem with the cities and large towns that appear on motorway signs in continental Europe. Let's look at the statistics using population as a surrogate marker for markets, restaurants, t'ilets, Irish dancing studios.  Because I really deprecate spurious accuracy we'll give the figures to the nearest 10,000 people:
Bratislava 460,000 Athy 10,000
Budapest 1,740,000 Baltinglass 0
Prague 1,260,000 Moone 0
Schwechat  Vienna airport Timolin 0
European distances from WolframAlpha; European populations from Wikipedia and the Irish pops from Table 12 of the 2011 Census summary reports at the Central Statistics Office: "Alphabetical list of towns with their populations".  This says that Baltinglass has 2,000 inhabitants (rounds to zero).  Neither Timolin nor Moone feature in the list, so they must be smaller than Arthurstown, WX N=135; Ballyedmond, WX, N=116; or Cromane, KY, N=115. 

Now here's an idea that will ignite The Gathering this year, Tourism Ireland could run a competition for identifying the least significant Irish hamlet that features in letters 50cm tall on motorway signs.  First prize: a weekend in Inch, Co Wexford (one of the candidates).  Second prize: a full week.

Saturday 25 May 2013

Coderdojo II

I went along to the CoderDojo at The Institute again this morning after the fun I had last week.  I was better prepared: I'd found a handy set of tutorials in javascript the evening before, clipped some simple code examples into a word file and printed it out.  Then I'd fallen asleep into my dinner (it had been a long week) before I'd had any chance to see how js (that's what us javascript mavens call it) syntax differed from perl, a programming language of which I have some experience.  So I was not much better prepared.

I gave myself a roving brief and spent some time in the Scratch room drag-and-dropping code fragments with the tinies and some next door with the keyboard coders.  As last week, it was a pretty good learning experience because I knew virtually nuttin' but was prepared to have a plunge at what might work.  First hand up was a little chap in the front row who couldn't start because he didn't know where Scratch was hiding in the operating system, so I turned to the 8 yo girl at the seat next door and asked her and she showed us how to type "scr" into the search box.  That was great, that's how I learned perl 12 years ago.  I had just started in a lab that spoke perl almost exclusively.  I didn't know anything: either about perl or about the work we were doing with perl so I asked the (bit older that 8 yo) girl at the seat next door and she was very helpful.  Lesson 1.  Ask the girl next door.

After a few weeks, I was the class whizz at making pictures with perl and GD because I'd robbed some picture-making code from my helpful neighbour and modified it and tweaked it and experimented with it until it would do my bidding.  Lesson 2. When you have robbed some code, try changing it and see what happens.

And it was Lesson 2 that I concentrated on when I was next door with the javascripters.  Not exclusively, mind, I also had to push the gospel (this will change your life) according to ctrl-C and ctrl-V.  The assigned task was to design a web page with a handful of clickable buttons, each of which would reveal a different picture.  As before that meant typing in a bunch of code (40 lines this week rather than 120, so that was an improvement) and then running it to see what happened.  That took a while and there were lots of typos to correct, but eventually a number of working programs emerged.  I took it upon myself to point to a section of their code and suggest changing it:
<img src="gandalf.jpg" height="320" width="160">
* what happens if you change 320 to 160
* what will happen if you write: height="160" width="320"
* what happens if you have it: hieght="320" width="160"
* what about: <mage src="gandalf.jpg"
Soon enough everyone knew what was an internal variable, which was an external variable (the red code only works if there is a file called gandalf.jpg outside of the code you've just written), and which is essential syntax - what some languages call 'reserved words' - that will generate an error message. Of course, none of the kids knew the terms (reserved words etc) but they had a sound idea of the principles.

150 minutes passes real quick when you're having fun.  We've been told that today was the last session before The Institute closes for the summer.  So I'll have time to learn a little bit more, and bring something useful to the table.

Friday 24 May 2013


Today, in large parts of the world, is Vesak or Vesakha  - a celebration of the birth of the Buddha.  This is decided by tradition and fiat rather than any evidence - very similar to Christmas in the West.  But it is more like Easter in that it is a moveable feast, being celebrated on the 8th day of the 4th month of the Chinese lunar calendar OR the day of the full moon in May OR the second Sunday in May. These can't all be in agreement let alone right, and I point out that NASA reckons the full moon is tomorrow 25-May.  Vesakha is equivalent to Hanamatsuri (Flower Festival) in Japan although that is celebrated on a different day again.    No matter, it's okay if we designate one day in our year to reflecting on our good fortune in being alive and thinking about those less fortunate.  No harm if we do something about the dispossessed, either, and many Buddhist temples lay on some tea and free food on the day.
I like the picture of the Buddha on the left, I find it/him restful and calming, somewhat austere - protestant even.  A lot of the statues and pictures of Siddhartha Gautama (as he was born) strike me as prim or supercilious, or over-coloured, or facetiously fat-and-jolly.  But that's just me embedding myself too rigidly in my own cultural clutter.  But whatever the language, whatever the culture, whatever the country we could all do worse than resolving to bring the following into focus/foreground of our lives:
* Right beliefs
* Right intention
* Right speech
* Right conduct
* Right livelihood
* Right effort
* Right mindfulness
* Right concentration
I've been swept up in a little bit of a flood-tide of Buddhism over the last 10 years or so because of The Beloved's involvement in the practice.  I won't go on about it here except to note a rather heartening teaching that I heard from a very young very calm Vietnamese monk in a dharma-discussion a good few years ago.  He was explaining the five mindfulness trainings or the eight-fold path (see above) or  the ten precepts or the four noble truths - I forget which.  But the point he made was that they were aspirational and if you could get through the week having achieved 2 or 3 out of the five (or 8, or 10, or 4) then you were a lot better (off) than if you'd booted them all and you shouldn't beat up on yourself too much.  From 3/5 you could push on to making 4/5 at some future date.  In the christian tradition, there are similar rules but the balance is too often reversed - one strike and you're a sinner.

What is mind? -- no matter.
What is matter? -- never mind.

Thursday 23 May 2013

National underpinnings

I do love a good polemic.  So I appreciated the sustained contempt in this essay in Slate about the lack of choice and/or grotesque lack of imagination which the several United States have sunk into designating their state bird. If the state legislatures are going to do this, could they not pick a different one each?  Clearly not: 10% of them have chosen a single species: Mimus polyglottos, and seven (!) others have chosen Cardinalis cardinalis.  Nicholas Lund has some great and eye-catching ideas for a complete re-jig of the system.  And what is the point anyway?  What do you do, if you live in Peoria IL, with the information that your elected reps have chosen the Cardinal to represent your state?

Europeans have got to remember that the United States are just that, not really much more like a single country than is the EU.  So you can see why each state might need a flag, an anthem, a motto - states have had such things since their leaders wore armour - and modern states probably need a website. After that it becomes a little twee.  Most of the states have a state . . . bird (as above), flower, tree, butterfly, rock, gemstone, animal. I'm not judgmental, so I'm not going to opine on where twee-but-sort-of-useless slips into absurd. And sometimes it's not so much the category - loads of (dairy) states choose milk as their beverage and Florida pushes OJ, all fairy nuff - as the choice. Wouldn't you cringe to know that your elected reps had designated kool-aid (NE) or Moxie (ME)?  Is that what they serve at state banquets in Maine?  Those of us who are old enough can remember certain murderous associations with kool-aid, so we're not surprised to learn that Utah has designated a state fire-arm. Browning M1911, seeing as you ask.

It's well known that Europe, particularly anglo-phone Europe, has for the last two generations been slavishly aping the USA in all things cultural, so I'm proud to report that the countries of the EU have stolen a march on Uncle Sam.  In an Order-in-Council published by the European Commission this week, it is announced that each of the states of Our Union now have designated underwear.  These choices are all unique, and informed by geographical area, climate and culture.  Note also that the order of precedence in the EU is determined alphabetically by the name of each country in its own first language.  So Austria is demoted from the top.  India has a similar system and West Bengal, fed up with being the last state called to vote in parliament and other indignities, is in the process of changing its name to Pashimbanga to get further up this list.

Belgium European union-suit Bulgaria pair of boxers
Czecho gingham pants Denmark lungi
Germany freikorperkulturohne Estonia felt long-johns
Ireland green combinations Greece sandy monokini
Spain boyshorts France cambric French-cuts
Croatia cheekies Italy cheekini
Cyprus copper drawers Latvia V-string
Lithuania T-back Luxembourg G-string
Hungary rice-paper briefs (1) Malta C-string
Netherlands hemp bloomers Austria red & whitietighties
Poland European midways Portugal Brazilian bikini
Romania wresting singlet Slovenia Slovoggis
Slovakia Bratislingerie Finland bark long-johns (2)
Sweden woollen long-johns UK Viyella Y-fronts
(1) if they're hungry they need something to eat (2) well 'ard the Finns
 Phew, I'm glad that's over!  I've spent more time this evening finding out about underwear than I've spent shopping for the th{i/o}ngs in my entire life. Other folk spend much more time on these matters. The Underwear Expert, as he is proud to call himself has some advice for those making their 2013 purchases.  But is it “This season, many brands are embracing the most natural of spring colors with a number of green underwear styles and designs that emphasize man’s natural bounty.”  OR “While hot pink was a big trend last season for underwear for men; lighter shades of pink underwear as well as pink’s cousin, fuchsia, have emerged as the new trend for the spring season.”

And after all this unscientific nonsense, let's reflect on the cost of a G-string compared to, say, a kilt. You can buy a kilt length of McKurosawa 100% wool tartan for about £50 - 100cm long by 140cm wide: £35 per sq.m.  You can buy teeny underwear online from Victoria's Secret, for about £12.50.  Let's guesstimate the dimensions - I don't have such a thing about my person - generously at an equilateral triangle with 15cm sides. As everybode kno the area of a triangle is half the base x the vertical height.  The vertical height can be calculated with trig: sin60 x 15cm OR with Pythagoras: AF2 + CF2 = AC2, so the height CF = SQRT(225 - 56.25) = 13cm, and the area is (13 x 15/2) or about  There are 10,000 in a sq.m, from which you can cut 100 undies.  That's £1,250 a sq.m !!  You can see why the Scots (supposed to be near with their shillings) don't bother.

Tuesday 21 May 2013

Nirenberg and Matthaei 1961

Thar she blows, as it appears in every biochemistry or genetics textbook.  An iconic image for our molecular biological times.  But have you ever asked why UUU is always shown in the top left-hand corner, as if that codon was first?
Nobody really knows why, but to a very close approximation, all proteins in all organisms incorporate just 20 amino acids and the same ones at that. Since Crick and Watson sorted out the structure of DNA 60 years ago this Spring, everybode kno that the information in DNA resided the linear ordering of just four 'bases'.  We all now familiarly refer to them by their initials A T C and G.  (It is too much for this post to explain but in some nucleic acids T is replace by another base designated U, so sometimes this list is written A C G T/U).  C&W showed that the thing worked as a replicator if A always paired with T and C always with G. But it was a mystery as to how the linear ordering of DNA bases translated (now a technical term for the process) into the linear ordering of amino acids in proteins.  Elementary (my dear Crick) math shows that two bases weren't enough to code for 20 amino acids because there can only be 16 of these 'dinucleotides': AA AC AG AT - CA CC CG CT - GA GC GG GT - TA TC TG TT.  It seemed extravagant to suppose that 4 bases AAAA AAAC AACA etc. were required because there are 256 possible permutations there.  Triplets (AAA AAC ACA ACC etc.) on the other hand seemed like Goldilocks' porridge to be 'just right'.  Those 64 possibilities had a comforting biological redundancy.  Crick the unarguably brilliant theoretician and others sat down with pencil and paper to work out how the encoding could happen.  The first coherent internally consistent solution came from left-field - a physicist and cosmologist called George Gamow came up with a diamond code which hinged on the fact that, if you squinted, the structure of DNA could be seen as a repeated series of diamond-
shaped indentations. Gamow accepted as necessary-and-sufficient that the coding was triplet-based and further that was that each hole was symmetrical so that CXG would determine the same amino acid as GXC and further still that the middle base for a given amino acid could be either of the complementary pairings A or T, C or G.  So CAG CTG GAC GTC would all code for "Z" while CGG CCG GGC GCG for "Y" etc etc.  When the end bases were the same as each other there were only two possibilities for each encoding rather than four as above - ATA or AAA for amino acid "N", ACA or AGA for "M" etc.  Remarkably, and I can imagine Gamow getting the shivers when he realised this, such an arrangement yields 12 four-way codings (accounting for 48 DNA triplets) and 8 two-way codings (accounting for 16 triplets).  12 + 8 being <shazzam!> just right to service the known 20 amino acids.  It was so neat it had to be true.  For various reasons of compelling permutational math Sydeny Brenner and others later showed that Gamow's code couldn't be true.
Francis Crick then stepped up to the plate with a hypothesis that a) the code was triplets b) the order didn't matter - so ACC CAC ACC all coded for amino acid  "J", ACG, AGC, CAG, CGA, GAC, GCA all for "I", solo AAA for "H" etc.  His solution required 4 one-way codings (4 triplets); 12 three-way codings (36 triplets) and 4 six-way codings (24 triplets). This mathematically compelling and biologically more reasonable solution cleanly explained the presence of 4 + 12 + 4 = 20 amino acids and 4 + 36 + 24 = 64 DNA triplets!  Begodde it was neat, and if poor Gamow had been deluded, this just had to be true.  Some of the excitement of the time is conveyed by Sydney Brenner's eyebrows in this series of soundbyte interviews at the wonderful archive of interviews at webofstories.  If you want more details of the math, you could do worse than read this great essay by Brian Hayes at American Scientist, where several other zany-with-hindsight codes are described in colour.

Meanwhile back in 1961 at NIH, a couple of more-or-less-unknown biochemists Marshall Nirenberg and Heinrich Matthaei, instead of looking at the ceiling thinking, were looking at the lab-bench experimenting.  They put together the contents of a typical cell in a test tube, fed into the sludge a molecUUUUUUUle consisting entirely of the base Uracil and generated an artificial protein consisting entirely of the amino acid phenylalanine. The first step, UUU=Phe, in cracking the code had been made, like Thomas Young's insight that cartouches in hieroglyphic script represented proper names. The other codings were knocked off over the next tuthree years by Nirenberg, Matthaei and many others and the real genetic code was revealed to be a robust but quirky kludge of contingency, accident and evolution. Nirenberg shared the 1968 Nobel prize with Holley and Khorana, and Matthaei didn't, adding to the list of controversial awards associated with Mr Dynamite's legacy.  I've always supposed it was because nobodaei could spell his name properlaei.

Sunday 19 May 2013

Map of the Nation

Ever wondered what the circumference of the world is?  It's 40,000km to the nearest couple of miles.  And that's not a coincidence - it's a definition.  In the turmoil after their revolution, the French Academy of Science decided to put manners on us all by replacing yards, cubits and Flemish ells with a single universal measure of length, which they chose to define a the 10,000,000th part of the distance between the North Pole and the equator.  It took the designated engineers Mechain and Delambre the best part of seven years to triangulate between Dunkerque and Barcelona and extrapolate the distance to make the calculations. With the best science of the day, they made some assumptions about the shape of the earth which meant that their official meter is out by 200 micrometers (about the width of the dot on this i).  Tsk!

At about the same time, the British Government decided it would be a sound idea to make accurate maps of the South coastal counties of England, so that if the revolutionaries decided to swarm across the channel in a waft of garlic, the local militia could get to invasion beaches in the shortest possible time.  And out of this, the project to map the whole country was born.  It also explains why the mapping was carried out by a branch of the army.

All this is amply explained by the wonderful Map of the Nation: a biography of the Ordnance Survey by Rachel Hewitt, which was given to me by El Asturiano as I left Dublin at the end of 2012 to start work at The Institute.  It's taken me nearly six months to finish it partly because I've been somewhat busy, but mostly because the font is miserly small and unaccountably hard to read.  But it's worth it for the introduction to the technology and hardship of cartography in the olde days when you had to get out in the rain with your Gunter's chain and theodolite and hope that the gales wouldn't carry away your sail-canvas tent in the night.  The Ordnance Survey started in the South of England (Sheet 1, Kent 1801), and it took them two generations to work their way North and West to knock off Sheet 108 Denbigh in 1870 and cover the whole island.  It is one of the peculiarities of history that Ireland got served first and the Other Island was fully surveyed by 1845.  Which is handy because we thus have an accurate record of what the country looked like when it supported 8 million people before the famine. For example, the field you must walk through to see The Ringstone is called Crowe's and if you look at the 1840 map you can see a black square at the bohereen end of the field.  That was presumably the cabin where Mr and Mrs Crowe and their (numerous?) progeny lived. 5 years ago when we dug up part of the field to plant trees we unearthed lots of broken china at that spot on the map.

After independence, Ordnance Survey Ireland continued to work away in Phoenix Park and they have released an amazing zoomable historical map resource which allows you view the original 1825-1845 survey, the update 50 years later, and a sample of modern satellite pictures which you can over-lay.  I've picked the two views of Borris Co Carlow on the left because they show the rise and fall of the railway in Ireland.  In 1840 (in colour) the South of the village was barely populated, but the advent of the the railway changed
all that.  The GSWR branch-line lasted almost exactly 100 years 1858-1963 but only the viaduct is left now.

Rachel Hewitt's book is the offspring of her PhD thesis and a trove of data and history and vignette and technology.  William Wordsworth and William Rowan Hamilton both feature prominently in the Irish part of the tale. Read it to find out why you need two 20-foot-long glass rods if you want to start mapping a nation.

Saturday 18 May 2013


I was in a dreary workshop earlier this week and my eyes drifted off the task and onto a whiteboard saying but one word  Coderdojo (yes, in red) and suddenly I was alert.  Because CoderDojo is the coolest, possibly the most important innovation to come out of Ireland this decade.  The brain-child of James Whelton when he was a schoolkid in Cork and midwifed into a global phenomenon by global phenomenon Bill Liao, CoderDojo is a forum to encourage young people to write computer code rather than coat-tail on the millions of person hours that other people have put into writing computer code for you.  I'm not saying that young fellers aren't "active" as they steer Lara Croft by the hips through a labyrinth filled with Uzi-toting heavies; their brains (and other parts) are engaged in the process with problem-solving, planning, and imagination necessary for many of the games they while away the hours at.  It's not the same as TV, which is utterly passive.  But the quality of the graphics and the complexity of plotting must make an aspirant coder feel like s/he's at the foot of Mount Unsurpassable.  CoderDojo is billed at the antidote to that sense of disempowerment.

CoderDojo the template, the concept, the dream has spread to more than 75 places in Ireland (not to mention Burundi, Slovenia and Sweden) and one of them is The Institute every Saturday morning.

With my background, at various times capable of coding in six different languages, if I failed to volunteer, I'd lose my own face.  So this morning, I made myself a CoderDojolunteer badge and turned up in terminal-suite A313.  As Scratch and Javascript are about as opaque to me as Sanskrit, I didn't think I'd be much help . . . and I wasn't.  But I was able to tell the kids that ctrl-C and ctrl-V beats footling about with a mouse and, that cut&paste&modify is quicker and more reliable than typing similar lines in again and again.  I know now that making a working analogue clock appear on the screen requires typing more than 100 lines of javascript.  That's pretty onerous, given that javascript knows that testobj is different from testObj, but a lad of 12 might not.  But I also know that several of the Codistas had the bottle to keep plugging away for two hours and catch their numerous typos to create something nifty that can be built on.  If you can create a black clock you can surely make a green one or a smaller one; but can you make one that runs backwards?  Or a 24 hour clock?  And if you can build a clock face, you've got the speedometer and the rev counter sorted for your own Grand Theft Auto.  But you've got to slog it out at the beginning.  If you can put the graft in with programming, you suddenly find that you can put the graft in on other difficult or time consuming tasks - learning french irregular verbs, or cleaning your room or telling the school bully that you're not having it any more.

More next week!


I was up in Dublin again on Thursday - this is getting to be a habit - and after a heavy day's meetings we went off to the pub to celebrate a new a job (not mine, I just got one) and a new child-in-waiting (not mine, I've been genetically dead this last decade) and so I missed the bus home and had to wait for the next one. I elbowed my way past all the young people and got a seat in the front of the bus and, as often happens, another senior sat in beside me. Folks over 60 like to see where they're going and view public transport as an opportunity for a natter, while those under 40 see it as something to be endured.  While waiting for The Off, this bloke (slightly the worse for dhrink but far from legless) tried to blag his way onto the bus, because "he'd lost his wallet" and "sure didn't the driver know him" and "wasn't he up-and-down that route all the time".  The driver, quite properly, wasn't having any of this.  His job is to take money for the company and deliver us safe to where we want to go.  I've stuck my hand in my pocket before in such cases - who'd want to go to Castledermott in the middle of the night unless they had to? But despite assurances that I'd get the money back, and being compelled writing my address on the various scraps of paper, I've never seen folding-money in the post.  Nevertheless, what can you do?  Well you can do nothing and as happened a few years ago when I had to catch the bus in a hurry to get home and didn't have my phone to arrange a pick-up from the bus stop. I went up the aisle asking if anyone would send a txt on my behalf and the dozen or so me-people on the bus all resolutely looked out the window.  ANNyway, I was geeing myself up to do the human thing again, when the old dear beside me leaned forward and said she was good for a tenner.  It was too complicated to offer to go halves as I had intended and everyone knows that I am near when it comes to cash. So she stumped up, the bus-driver calmed down, the indigent got on and insisted on making tipsy-gracious small talk and asking for the lady's address.  Well, it being Ireland and a narrow corridor of Ireland at that, they soon established where their people were buried and a rattle of acquaintance was topped by the fact that his god-parents (deceased) had been her next-door neighbours.
So she has a better chance of retrieving her investment in kindness than I ever did.

Tuesday 14 May 2013

pee glorious pee

warm water and nitrates . . . but not immediately.  The nitrogen in urine is mostly urea (NH2CONH2) and ammonia (NH4+) and so not easily or directly usable by your plants.  They much prefer to obtain their nitrogen as nitrates (NO3-), so depend on the microbes in the soil to do the conversion.  This is done in a two-step process:
1) ammonia to nitrite: carried out by Nitrosomonas
2) nitrite to nitrate: carried out by Nitrobacter.
So that's a reason why it's not efficient to pee straight on your vegetables, the intermediates (and some time) are necessary.  Back of an envelope calculations and a bit of scoping out the internet suggest a) that the average adult voids 1.2 lt (make that 3 yankee pints) a day, mostly water but including about 10g of nitrogen.  This is enough, if spread about judiciously and through the year, to provide 50-100% of the nitrogen requirements for plants sufficient to feed an adult. So that's kind of neat in a self-contained way. But a 1% solution of this stuff is muy potente, not least because urine is also rich in salt, so it's better to cut it 1:10 with water.  I'm glad I found that all out, and therefore I'm glad I got to teach The Nitrogen Cycle for the Environmental Science Module at The Institute

Monday 13 May 2013


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.


I spent much of the day interviewing Mature Students.  They were none of them older than me, but they were all older than your average school leaver.  A third (!) of the people I interviewed today have been made redundant in the last 12 months.  This anecdote * 3 doesn't qualify as data, but it does suggest a recent slump in the economy; banks, telecoms and pharma were all letting my people go at the end of 2012.  Of course, they're not my people . . . yet.  But people who have managed euromillions (as in loadsa money, not the lotto), who have run departments, who have applied themselves to hard work for a decade or two - such folks bring something to the table.  They may not be 100% sure that they want a Cert in Pharmacy Tech, but they're certain-sure that they're not going to sit on the couch waiting for dole day.  So I look forward to meeting some of them again after the summer.

Sunday 12 May 2013

Celebrating the Ordinary

On dit que one of the most important lessons to learn before you reach 10 or 11 is to know that excellence only comes from application. Malcolm Gladwell is famous for codifying the rule that you can only achieve excellence by putting in those 10,000 hours. This sort of ex-cathedra opinionating makes me feel queasy because I have baggage.  My poor father was always on and on at me to “concentrate“ but I never could sit down and practice the berluddy piano, never stick at my coin “collection”, never finish reading Pickwick Papers.  It was obvious to me, my family and my teachers, that I was not about to achieve excellence.   Although I want better for our children, and wonder when they are about to manifest their own version of excellence, I've been careful not to 'help them' crank up application to achieve this.

 Two things I have chosen to embrace as an adult have helped me develop me a position on this.  And even as I write, I realise that I never really chose the piano, the coins or Dickens as a child: they were sort of surrogates for actually applying myself.  About 30 years ago I enrolled in a book-binding course to put some spine into the rough-handled collection of second-hand books I’d picked up at yard-sales during our American years.  My teachers, fine craftsmen and enthusiasts, were frequently at me to go beyond the workaday robust library style bindings that I was making week after week.  And, to please them, I did create a couple of rather good leather and gold bindings with marbled end-papers.  But my real happiness was, over 3 or 4 years of Tuesday evenings, putting a few dozen old books back into a usable state.
I’ve also devoted a lot of time (maybe One,000 hours?) to samba (Weds) and djembe (Tues) drumming.  One Wednesday, the biggest of the samba teachers gave us an earful about how beginners must realise that even the best drummers in the group need to achieve their own goals; that tyros shouldn’t pester the “effectives” too much with requests for help when we were all in the process of becoming better Sambistas; that even the best percussionists needed space to apply themselves to achieve excellence.  Naaah, I said to myself; I don’t want to become an excellent sambista, I just want to hang out and do a bit of samba.  

That was very liberating. And you know, I did get better. My bindings got more symmetrical, my drumming got less ragged without me striving for excellence. It’s okay not to be centre-forward and I like to see my scientific career as having providing the infrastructure to help others make their great leaps forward. As an evolutionary biologist I find that quite comforting.  To succeed in life you don't need to be The Best, you just need to be good enough.  The accident that Darwin happened to live in an age of  galloping capitalism has informed our understanding and especially our metaphors of how the natural world functions. "Nature red in tooth and claw", "the survival of the fittest" rather than the survival of the fitter.  But I don't think that success need be defined as being better than your neighbour, just "good enough".  I am happy seeing my girls achieve the ordinary.  Just by being, they flourish.

Silver Linings

For about five years just after the turn of the century, I was percussing every Wednesday with a Samba School in Dublin.  We drummed.  In the marching season, we provided colour and spectacle for parades all around dull rainy Ireland: Ballymena, Clonegal, Drogheda, Dublin, Kilmuckridge, Maynooth, Waterford. We ran workshops for adults and we encouraged excellence in a youth wing whose membership is drawn almost entirely from the flats of Inner City Dublin.  Rehearsals were open to all but you could get elected to “membership”, and save a dollar on the weekly sub if you were good enough and attended 4 consecutive rehearsals in any six-week period.  You’d get bumped from membership and have to re-apply if you missed 4 consecutive rehearsals without a “sick-note”.  Membership was fluid, turn-over high and critical mass sometimes hard to achieve, but the School is still going (without me) now after running for nearly 20 years.
One spring, one of our most effective and experienced drummers, who was also one of our two really effective social facilitators, went abroad for a couple of months.  When she returned, she did her 4 consecutive rehearsals and came up for election to membership . . . and she was dumped! damned by a determined group of long-standing members.  For whatever reason, they just didn’t like her.  It was a heavy, ugly scene at the meeting and, in the aftermath, 4 or 5 more sambistas, including two members of the steering committee and the other effective social facilitator, resigned.  As fortune would have it, I was off that night doing science instead of shaking.

Several weeks later, I met Ms Blackball in the street, gave her a big hug and apologised for having failed to be there at the traumatic meeting.  She was much more upbeat about the night of the long knives than I was (so resilient and insouciant is yoof) and said that she was quite happy and drumming elsewhere.  As we chatted, I realised that, dreadful as the experience had been, it was not without its silver lining. 

Without her manifest social and musical skills, the rest of us had had to grow.  We could no longer just follow her lead in the riffs, but had to engage more fully with the music, pay better attention, and take responsibility for even less experienced drummers.  We also had to contribute more to the social glue of the group.  When new faces appeared it was up to me and the others to step up and introduce myself, make small talk and make welcome.  Indeed, at the next monthly meeting, we formally introduced a buddy system so that each rehearsal night someone was there, with an “I’m the buddy” badge, who was prepared to do this social facilitation.

What to learn?
1) Nobody is indispensable.
2) It shouldn’t take a pogrom or disaster for people to step up to the plate.
3) Samba, like soccer, is a team sport.  It’s not only about, not even mainly about, the centre-forward or the bloke with the biggest drum.  Without the likes of me quietly but reliably going shukka suhkka on the chocalho in the background, the guy hefting the Number One Surdo is just a big NOISE.

Saturday 11 May 2013

The Madness of the Inclined Plane

I wrote just now about the humiliation of failing my Physics "O" level.  I'm not stupid, my folks paid a great deal of money to send me to a school that had above average science teachers - one of whom started me off on a lifetime embedded in science.  But there were elements of what physicists know that were plainly bonkers and so my rational head revolted at having to embrace them.  The analysis of the forces involved in a block (or a car, a wheelbarrow, a bloke) sitting (or sliding or just about to slide) on an inclined plane is a standard problem for teenage would-be physicists to tackle.  So standard indeed that I had a choice of hundreds of pictures of the problem to loot off the internet.  The wee arrows show the forces that have to be considered: f(k) is something to do with friction which normal folks kind of take for granted and ignore but which can be explained by pointing out that a block tends not to slide down a slope while a ball of identical weight does.  So that's a useful insight.  And of course the block is pressing down on the inclined plain - because that's gravity and it would be a shockin' shame if Isaac Newton had lived, and his pet apple had died, in vain.  And because physicists tend not to be math-anxious, I can sort of understand why they might want to resolve the force W into two vectors (I think W.sinθ and W.cosθ are called vectors and maybe W is a vector too) so that they are at right angles to the plane.  So the block is pressing down on the inclined plane (tick, gottit) but physics expects us to believe that the inclined plane is pushing back on the block!  See what I mean?  Daft.


Richard (Dick to his pals) Feynman has been dead these last 25 years, but would have been turning 95 today had he not been caught in a pincer movement by two species of the dreaded crab in 1988.  Since 1982 - the centennial of Charles Darwin's death - I've been celebrating Darwinday at wherever I happen to be working. One 12th Feb I brought pizza to the lab with the cheese cut to shapes representing the Galapagos Islands but the oven smartly reduced this OCD aspiration to the Blobby Archipelago. Eventually the annual party settled down to me buying a few dozen donuts and pushing them at folks over coffee.

If I hadn't failed my physics "O" level I might instead have been making a reg'lar knees-up on the 11th of May because Feynman was made of the same stuff as heroes are. There were very few places where he wasn't the smartest man in the room and we should be in awe of this intellectual prowess.  I wrote in March about his intuitive feeling for numbers and how this helped hone his crap-detector. 

But he brought a number of other talents to a level far above the mean.  He was a natural percussionist who was co-opted into an authentic Samba School in Rio and played with them during Carnaval.  He modestly maintained that they liked his style because he played with a 'foreign accent' that was as attractive to them as for us hearing a French girl speak English.  Quite independently of my admiration for Feynman, I spent about 5 years of my life playing chocalho and repinique very badly with a samba school in Dublin, so my respect for his skill is informed by knowing how hard it can be to do it at all, let alone well.  

He learned to speak Portuguese fluently enough to be able to give lectures on particle physics to Brazilian university students in that language.  He started learning the language when he was a young faculty member and took advantage of his institution's evening extension programme.  All set to enroll in Conversational Spanish (always useful in the US where it's the second language), he signed up for Portuguese instead when he saw two pretty girls going into the room next door.  Quite independently of Feynman, and indeed years before I discovered Samba, I also spent several years struggling with Portuguese which I first took up in preparation for a field-trip to the Cape Verde islands a generation ago. I loved it, and was eventually able to read a newspaper and write a few simple grammatically correct sentences but I was as far from being able to lecture in the language as I am from being able to play a concert flute.

He had an artistic eye and was accomplished with charcoal or a pencil and a large sheet of paper or with a biro and the back of an envelope. Coherent with the anecdote about evening classes above, he was particularly drawn to drawing women clothed and especially unclothed.  I suppose that my XX readers will find this a bit seepy but suggest that the directness and openness of his love of women and of the female form has some redeeming qualities.  It is no coincidence that one of his great contributions to the understanding of physics was his Feynman Diagrams which represented the dynamics of particle physics as cartoons.  Oh and while we're on his physics I should mention that he shared the Nobel Prize in 1965 for his work on quantum electrodynamics.  I can't even reliably spell that, let alone explain it.

Ever since it was published in 1985, I've been buying (especially when I find a stack remaindered for less than half the list price) multiple copies of Surely You're Joking Mr Feynman - adventures of a curious character and giving them away to anyone whom I thought might benefit.  It's sort of autobiography, sort of ghost-written or taken-under-dictation by a sambista friend of his called Ralph Leighton.  Most people think it and he is brilliant but a substantial minority find endless anecdotes of Feynman's multiple talents intensely irritating.  So I'll recommend more whole-heartedly Genius - the life and science of Richard Feynman by James Gleick which is more balanced, less adulatory and which you can buy now 2nd hand on Amazon for $0.01.  Don't read?  Then another aspect of his interesting life is covered in the filum Infinity with Matthew Broderick as Feynman and Patricia Arquette as Arline his tragically dying first wife: it's available for €3 on

Thursday 9 May 2013

Today - The Smoke

Today, Ascension Day, is an Holy Day of Obligation.  Bizarrely, for a deeply multicultural place, The Institute declared it a holiday and closed for business.  At school in the 1960s, at the very centre of the Anglican communion, we also used to have holiday on Ascension Day.  But apart from the son of a Jewish shop-keeper from Dagenham and a diplomat's son from Sierra Leone, the school was 100% protestants, so there was an excuse to celebrate one of the key events in the Christian year.  Ascension Day marks the return of the resurrected (that's Easter - 40 days ago) Lord to heaven and is not to be confused with The Assumption which is when his mother Mary left our plane for a higher one (that's 15th August for you unbelievers).
ANNyway, my old Boss in Dublin sent me an e-mail suggesting that "there's no better way to spend a HDoO than in an extended lab meeting" . . . and it was so.  I caught the early bus up and spend the whole morning and much of the afternoon talking science with once-and-future colleagues.  Eeee, it were great.  Lots of catch up for me as I tried to recall what I was working on last year.  Lots of new faces who turned out to be interesting and engaged.  Some of the old guard still still there so I didn't feel totally adrift. 
The turn-over among young scientists can be disorientating.  When we worked out in StVs Hospital 10 and more years ago, one of my tasks was to run the weekly Journal Club: I assembled a mailing list of eligible presenters, decided on a batting order (cricket metaphors are okay if you've been educated at the very hub of the CoE) and sent out timely reminders.  I did that for a couple of years and then someone else took over and then they left so I took up the task again and dug out my previous list to edit.  Of the 59 people on the original list there were only 8 left after 3 years elapsed time.  You don't notice the drip drip turn-over as post-grads write up and move on; technicians fall pregnant and don't come back after maternity leave; people emigrate to Australia.  But if you have a written record of the changes it's like giving a patronising €2 to a child of 10 and next seeing them as they tower above you at 15.
Today we had a rolling succession of productive meetings.  One of the tasks that my HoD  at The Institute is attempting to frighten me with for next academic year is the care and education of six (6!) final year undergraduate project students - 3 x 10 weeks before Xmas and 3 x 10 weeks afterwards.  So I need to source some data for these lads and lasses to analyse and Schmallenberg and H7N9 flu virus are looking like strong possibilities for two projects.  Four to go!

Wednesday 8 May 2013

Pilcrow beats mouse

Introducing the pilcrow or, less elegantly, the paragraph mark.  I wrote earlier about keyboard shortcuts and how they can change your life: "...mouse-work requires a lot of static muscle activity from wrist to shoulder, which leads to lactic acid build up (it's hard for this by-product of activity to flush out if the muscles aren't pulsed), which increases fatigue, muscle mass, deep-vein thrombosis and death...". Now that the teaching year has finished I can expand a little in this arena.  A table of the life-enhancing mousifuge shortcuts that I use every day:

<ctrl>+b:  bold
<ctrl>+u: underline
<ctrl>+i: italics
<ctrl>+c: copy
<ctrl>+x: cut
<ctrl>+v: paste
<ctrl>+z: undo last cmd
<ctrl>+s: save
<ctrl>+p: print
<ctrl>+l: left para
<ctrl>+e: centre para
<ctrl>+r: right para
<ctrl>+ ]: increase font
<ctrl>+<shift>+=: superscript
<ctrl>+j: justify para
<ctrl>+ [: decrease font
<ctrl>+ =: subscript
<ctrl>+g: goto [page]
<ctrl>+ h: find&replace
<ctrl>+ k: make hypertext
<ctrl>+<shift>+*: pilcrow

Edit 27/05/2013: Want a € sign? <ctrl>+<alt>+4 or <ctrl>+<alt>+e both work or (ευχαριστίες (tnx) Chris Ergatides) <AltGr>+4.
<ctrl>+h find & replace is normally used to replace all instances of psuedogene with pseudogene, but, with the handy <ctrl>+a to highlight the whole document, you can better control document format.  In the <ctrl>+h world ^t is a tab, ^l is new line, ^p is a paragraph. Most people create white-space between paragraphs by hitting the <return> key twice. With <ctrl>+h you can [replace all] the, lazy, ugly, uncontrolled rtn+rtn paragraphs with a single rtn:
Find what : ^p^p
Replace with: ^p
WTF who cares??  You will care if you have to cram your florid prose into a specified number of pages - say for a form, a 2 page CV or a grant-application, or to get the page-count down to a multiple of four that you can print as a booklet. You can then specify/reduce the space between paragraphs, so that there is white space enough - 6pt, say, rather than the default 12pt - but not so much as to require another page in your document.

And finally <alt>+o,t will take you to the tab menu.  From there you can control your tabs and make your documents neater and more readable and not prone to schlub into a mess if you increase the font-size or change it from Times New Roman to Calibri.    Here's a more comprehensive list of  of shortcuts; thanks bernd and amp.  TMFS? Sure!