Francois Jacob - gone.

Francois Jacob was one of the great scientists of the 20th century, and a huge hero of mine. He was awarded the 1965 Nobel Prize for Medicine and Physiology for carrying out an elegant series of experiments which explained how bacteria (and by extension us) control gene 'expression'.  How, in other words, the information in our DNA is mobilised to modify the biochemical machinery of the cell to achieve something/everything useful.  He thus helped articulate the Central Dogma (which like all Dogmas has utility but is flawed in its monolithic certainty):  DNA makes RNA; RNA makes protein; and protein makes everything else.  That statement hopefully becomes clearer to non-scientists if I add the gloss that all enzymes are proteins and all biochemical activity goes much much more precisely and efficiently if enzymes are involved.  The Nobel prize was awarded to Jacob and his lab-partner Jacques Monod and their boss Andre Lwoff, they all worked in the Institute Pasteur that teeming hugger-mugger incubator of Francophone brilliance in the middle of Paris.  They worked out how E.coli controlled the metabolism of the milk sugar lactose and the explanation 'invented' or discovered the lac operon which has a chapter to itself in every genetics textbook since.  The E.coli on which they worked was isolated from a stool sample contributed by Lwoff - not a lot of people know that.

Jacques Monod went on to write an influential book which was translated in to English as Chance and Necessity. For years I had a first English edition with its MC Escher inspired cover-design.  I read it when I was 17 and it was really too dense and philosophical for me but I sort of twigged that it was deterministic and materialist and it curtly dismissed any need for reasons for our existence. Confused as I was at the time: an wanna-be atheist reading Augustine's City of God while trying to find the zen of Akira Kurosawa's films (dang! I'm confused now even thinking about what I was at back then) - I knew Monod wasn't for me.

A few years later I encountered The Possible and The Actual, Francois Jacob's antidote to Chance and Necessity.  Now that book sang to me: short, crystal-clear,  clever, simple.  Here Jacob brought to Anglophone science the quintessentially French concept of bricolage, haltingly translated as "tinkering".  Every village and every neighbourhood in France has (or prolly had) its bricoleur: the Mr Fixit, the handyman, the jacques-of-all-trades who can re-purpose a broken washing-machine as a chicken-coop and never throws anything away.  Nature is just like that, she doesn't invent a wing from whole cloth, she takes an existing running/grasping limb and over a few hundred generations turns it into a flapping/flying appendage.  It works at a  molecular level too (well everything works at a molecular level): an enzyme that can process lactose has an accident, or two, or three, and ka-ching! it is able to process maltose as well or maybe process maltose only.

And Jacob was a war hero, escaping from France on the last boat from Bayonne and joining the Free French in England.  Later on he was blown to fritters by a bomb and spent months having fragments of shrapnel removed from his right side.  That put paid to his career as a surgeon and so he went to the Pasteur to do fundamental research instead.
The rest is history and so, since 20th April 2013, is Professor Jacob - quel type merveilleux.

Teenstatistics

At The Institute, things have been very quiet this week.  It's officially the last week of the teaching year and. although our HoD has been stalwartly insisting that no classes will be cancelled without his express clearance, many class just haven't happened.  It's like rag-week all over again when classes were officially carrying on as normal but the students were out getting wasted and/or pushing bedsteads along the roads for charity.  I had a last revision session with my 1st Year Human Physiologists, to nail the concept of homeostasis for the half dozen who thought they wanted it.

But it was a mad-busy morning with a free lunch because I volunteered to help judge the teenage entrants to SciFest in the Sunny South-East; teen-boffins from Donegal were reporting their results in Sligo IT.  Like the Student Enterprise Awards which The Institute hosted in March, it was great fun, and I wished I'd had more time to talk to ALL 57 entrants rather than the random pick of 7-8 which me an my co-judge Aoife were assigned.  She's a graduate student, and in that rich tradition, was doing it for the lunch.  I was once a graduate student (yer yer: before the first war), and have never been as hard-up financially or as stoked in every other way.  You never lose your nose for free food if you've trained by need rather than desire.

The quality of the presentations was 'mixed'.  The thing that gave me most hope for the future of Ireland as a technological nation (FITNa?) was the creativity.  Lots of good, weird, mad ideas out there, a couple of which were directly in my line of competence, so I think I was able to give good feedback and encouragement.  But the absence of any sensible statistics in the dozen or so projects I was able to get to was, shall we say, disturbing.  A subsidiary prizes was on offer for the best use of maths in science and that was a shoo-in because there was only one entry that could fit such a category.  Almost all of the other projects treated some sort of biological data.  Now here's the thing: biological data is noisy; any underlying trend is buffeted by genetic, meteorological,, temporal and plain accidental contingency.  With all these externals, the black and white of your hypothesis slumps into several shades of grey.  Real scientists get round this by beefing up their sample size and thinking of a sensible experimental design before turning one anecdote into the first datum.  The noise is still there, but its fluctuations look (and are!) less serious on an ocean of data than they are on a plateful.

Maybe the Leaving Cert Biology curriculum doesn't deal with variation?  I know, when my boy went through the LC mill 20 years ago, the first page of the text-book was all about the Nitrogen cycle but never thought to mention that although all cows urinate (aqueous solution of urea) some produce more N and some less.  That the measurement of such an item might, accordingly, need to be made a few times - on different cows, at different times of day, at different distances from the river . . .  But that same textbook shamefully relegated Evolution to the final chapter of the book AND made it 'optional for Pass Level'.

So what to do?  This year the kids were edutained by Scientific Sue for an hour after lunch and clearly had a lot of fun.  Maybe, next year, we could corral their teachers in a parallel session and share the rudiments of parametric/non-parametric, Student's T, Mann-Whitney U, Pearson R and Chi-Squared. I haven't written Statistics For Dummies but in the last job I did knuckle down and write 6 pages of notes called Statistics For Immunologists.  Mebbe that would be a start?

Recording the data

In science, the lab-book is a sacred thing.  It is a record of what you have done at the frontier, why you did it, a record of the results and an interpretation of what it all means.  When someone is accused of fudging or nudging the data to better accommodate a cherished hypothesis, their lab-book is the only record that can be scrutinized: the original solutions and samples have long since been flushed down the sink with copious amounts of water. So the lab-book must never be amended, pages must be numbered, none may be removed, errors may be crossed out but not whited out.  In the course of a PhD, you might build up a dozen lab-books, all numbered on the spine, fat with stuff stuck in.

My old boss (who like all my bosses was younger than me so not that old) used to use the early lab books as part of the loco-parental therapy session when her students, each in turn and some regularly, experienced La noche oscura del alma and wondered if they were mad, and bad, to have embarked on such a crazy and frustrating voyage.  When they complained that they had done nothing nothing in the last three years that amounted to more than a hill of dead animals uselessly sacrificed, she showed them through the books just how painfully ignorant and incompetent they had been when they came to her.  Paradoxically, ladling on of more evidence of uselessness was a great fillip as the students all recognised that progress had been made, if only in their development as a thinking reed and a good pair of hands.

Yesterday was my last class with my quirky, disparate and wholly lovable 3rd Year students.  I've had them for four different classes since January, rarely have all 10 of them been present, but it's a different 5 or 6 or 8 who turn up each week ready to find something out.  Their collective attendance has been patchy and their discipline in handing up their lab-books for scrutiny and marking has been sketchy.  So I used the last class to request-and-require them to submit any remaining material by Friday at the latest because that was the last day of the teaching year.  They get credit for this as CA (continuous assessment) and it's an easy way to accumulate a platform of marks from which to leap at the exams. Lab-books of all colours and classes began to appear from bags and satchels and the xerox box which we used as submission station was soon full. 

Then one of the students asked me if I'd marked his Food&Ferm book, which he said he'd handed to me in class several weeks before.  This was way beyond my two-week event-horizon, so I had no recollection and the mark book showed that I hadn't marked it, so it was a worry.  The labs we use are busy with classes all day every day and some will have a throughput of hundreds of lab-books each week. In the search, I turned up the 1st Year Biology lab-book of another of the students in the same 3rd Year class.  So its clear that you are hunting down through an archaeological dig as well as widely through contemporary material.  Class dismissed and I settled down to mark through the backlog of my 2nd Year group, which I've had for two wholly different classes and who have been quite as patchy and sketchy in their turn-in scheduling.  After a couple of hours and a cup of tea, I mooched back to the F&F lab and looked in the wrong direction and there was a blue lab book tidied away on a shelf near the centrifuges - bingo!

There's got to be a better way.

Not shrimps, the legionnaires

Today is the 150th anniversary of the "Battle" of Camaron in Mexico, a long day for a small detachment of 65 members of the French Legion etranger who held off an army of at least 2000 Mexicans during the French Intervention in Mexico.  Captain Jean Danjou, the French commander, died in the process along with 2/3rds of his men.  Only two unwounded soldiers remained at the end of the day and they refused to surrender unless they could keep their arms and escort the body of their Capitain off the battle-field. It was an iconic moment in the history of the Foreign Legion and is celebrated by them each year on this day.  Two peculiarities attend the ceremonies.  The officers make coffee for the ranks because in 1863 the soldiers were interrupted by the Mexicans just as they were about to have theirs and spent the whole day without water, let alone coffee.  The Hand of Danjou is also reverenced.  Captain Danjou, a career soldier and graduate of St Cyr had blown off his left hand in an accident in 1853 and sported a wooden prosthesis painted to look like a gloved hand.  This was discovered after the battle and found its way back to the Legion's head office in France.

The French Intervention was an abortive example of Imperialist politics which seems appropriate to celebrate the day before MayDay.  A group of Mexican monarchists came to Europe looking for any member of any royal family for hire and offered the crown to Maximillian: a rather bright, fairly liberal nephew of the Hapsburg Emperor Leopold I. 

Maximillian declined, preferring to go to Brazil botanising - he was an accomplished scientist as well as being fluent in at least six languages. But when Napoleon III of France (just possibly Maximillian's genetic half-brother) started the Mexican adventure,  Maximillian was blagged into taking up the post as titular head of the Mexican 'empire'.  He was deposed and executed a mere three years later.  The event being 'recorded' back in Paris by Manet in the famous picture which seems more designed to fit on a commemorative postage stamp than a realistic depiction of death by firing squad - if it happened as represented, Max's shirt would be in flames.

So today, if you refuse to eat blood pudding at least sing a few lines of Le Boudin the legionnaire's anthem. Don't know the words?  Try: Tiens, voilà du boudin, voilà du boudin, voilà du boudin Pour les Alsaciens, les Suisses et les Lorrains, pour les Belges y en a plus, ce sont des tireurs au cul. . .Au Tonkin, la Légion immortelle / À Tuyen-Quang illustra notre drapeau / Héros de Camerone et frères modèles /Dormez en paix dans vos tombeaux.Don't know the tune?  Listen: Le Boudin.  Stirring stuff for chaps with a Y chromosome and/or a HUGE beard.

Unexpected books

I confess: I've bought books through Amazon.  Accordingly, I get info-mails from them - today "New books for May", pushing a score of books that I might think of buying.  As I've also bought books through Amazon for my creditless teenage daughters, there's some diversity there.  But not half enough as 20 books is about 1/1000th of the publishing output for the month, from Britain alone.  Google tailors its searches according to the IP number of the computer asking, Amazon tailors its recommendations according to previous buying habits, so we are sheltered from the unexpected. I'm sure this makes for more efficiency most of the time but I do feel sometimes as if I'm already back in diapers.

I used to work on Trinity College Dublin. It has the distinction of being one of half a dozen Copyright Libraries in the British Isles, authorised to request a copy of any and every book published in these islands.  That's a LOT of books: about 200,000 each year. And the sad truth is that the Library doesn't chase up all the books to which it is entitled. In the basement of the TCD Library is a section where the books which have been acquired under the rules of copyright are stored after being catalogued but before they’re shipped out to wait-for-readers in a warehouse out by the Airport.  They are shelved by accession number - as they came in – rather than by author or subject.  It’s wonderful down there: an Al-Addin’s cave of treasure peppered through the dross of hydrodynamics, Hogwarts, and history.  I often used to dive down there to choose my weekend reading and always surfaced with an oyster and occasionally a pearl.

I've written before about the increasingly finite Universe of the internet as mediated by Google and Wikipedia for our convenience. If I'm not given more windows to the outside of my internet bubble, I may burst out and go on a merry dance through the dangerous but colourful jungle of the unknown.
 

Happy BirthDay-Lewis

Happy Birthday - Daniel Day-Lewis.  I mentioned him in passing because one of the parts he has played in film - Abraham Lincoln - shared a birthday with Charles Darwin. It's not for lack of commitment that he won an unprecedented 3rd Best Actor Oscar for the part: he is famous for taking method acting to extremes - learning Czech, skinning a deer and contracting pneumonia for his craft. It is said that he even saw the ghost of his own father while playing Hamlet, blew a psychic gasket and hasn't appeared on stage since.  We have a neighborly connexion in that the same (ghostly) father was born near Stradbally, Queen's County while my grandfather was born across the border near Birr, King's County.  There's hardly anyone left alive who would care enough about their Anglo-Irish roots to affect to deny the existence of Offaly and Laois. I don't know if DDL cares a button one way or the other.
I haven't seen Lincoln yet, and am not in a tearing hurry to do so but still have strange dreams about DDL's buckskin-clad thighs pumping up and down as they leap through the woods in the steps of Chingachgook (or was it Queequeg? or Umslopogaas? I forget)

The end of the line

DauII and I arrived in England by plane this morning, having left home at 0230hrs.  We went down to visit my mother, who was born in Dover in 1920.  Her mother had been born in Limerick in 1893 and was living in Dover in July 1909 when Louis Bleriot landed on the cliffs of Dover having completed the first aerial crossing of the English Channel; she lived to see, albeit on the the telly rather than in person, Neil Armstrong take his own giant step 60 years later.  Some progress in her lifetime, no?

In the late 1950s, my mother was living, with three small children, in a house in Norwood, South London.  Her husband, serving since the age of 14 in the Royal Navy, had secured a rare home posting and was working in Whitehall on a joint defense staff committee.  It was at height of the Cold War and things could get a little jittery.  Some politico would point to a map of the world and ask. innocently enough, what would happen if the Russians turned up here.  The Da and his committee would turn to and find out what was available in the way of Avro Vulcan bombers in Cyprus, associated army units on the same island, surface ships and submarines in the Eastern Med  and work out how quickly they could get enough oil-tankers to Malta to fuel up the rag-tag armada that would keep the world safe for democracy.  Nobody wanted to get caught with their pants down, so they put in the hours; frequently working late into the night.  No overtime.

One night, after a few weeks of this rigmarole had worn everyone to a frazzle, my mother was woken at 2.30 AM by The Da. 
"I'm really sorry, but could you pick me up from Elmer's End?  I caught the last train South from Charing Cross."
"Okay," she replied, "where is Elmer's End?"
"I don't know."
In the middle of the night, in a strange metropolis, my mother abandoned her sleeping children (you could do that in those days) and set off  in the Austin to repatriate her bloke.  Nowadays it would be no problem: Gmaps and GPS would sort everything and indicate the quickest route for reuniting them.  They were well 'ard in them days.