Back in January I wrote in passing about James Lovelock. He came to give a talk and promote his latest book in Dublin several years ago and I went along with a couple of pals. Afterwards we all queued up to buy, and get signed, a copy each. When I got to the table, I diffidently said that we'd met before, in Boston, in about 1982, in the office of Lynn Margulis. He brightened up (if that's possible for such an ebullient chap) and said that he thought I'd looked familiar. I demurred: we'd met for about 3 minutes nearly 30 years previously. But he insisted that he never forgot a face and we chatted briefly about Margulis before I made way for the next Gaiagroupie.
Margulis was famous for relentlessly promoting three iconoclastic ideas that each became something obvious to all thinking people, at least partly because of her efforts on their behalf. 1) Serial endosymbiosis - mitochondria and chloroplasts and maybe cilia were once independent organisms that were engulfed and co-opted by nucleated cells. 2) That it was fatuous to talk about the Plant and Animal Kingdoms and shoe-horning every-living-thing into one bin of the other. She championed RH Whittaker's idea of not two but Five Kingdoms. 3) Lovelock's concept of Gaia.
A few years after that I bought a second hand copy of a 1st edition of John Brockman's When We Were Kids: how a child becomes a scientist, mainly because one of the contributors was the same Lynn Margulis. After that I decided that it was time to write her a thank-you letter because she had enriched my experience in graduate school more than anyone except my mentor. She taught a course BI504-Evolution that was, shall we say, eccentric. Dinosaurs were not mentioned, indeed the whole of the phanerozoic was bundled into the last two weeks of the semester. As the phanerozoic comprehends everything since fossils appeared about 600m years ago, most of the material on the course was novel. But Lynn's position was that as all fungi, animals and plants are 'essentially the same" in their biochemistry, enumerating their differences was a form of stamp-collecting and so unworthy of real scientists. But she did insist on us each-and-all embracing the reality of the natural world by designating one mid-term class as Organism Day when everyone had to bring something alive to class and talk about its ecology and evolution for 5 minutes. I can barely remember what she told us about the Entner-Douderoff pathway but can remember pretty much everything I found out for myself about Sphagnum moss for Organism Day. And when I came in turn to teach a course about Evolution I hosted an Organism Day too.
The response to my letter was a parcel of books from Chelsea Green Publishers including Luminous Fish: tales of science and love by Lynn Margulis and a note in her almost illegible scrawl to say that she was shortly going to be on sabbatical in Oxford and we might meet up. As Spring turned to Summer the following year, I piled my daughters into the car and took the ferry to Wales, having invited ourselves to dinner with Lynn. I didn't know if either of them was going to be a scientist but I did know that they were both going to be women and that it was going to be relentlessly more difficult for XX-them to make their way than it had been for XY-me or was for their XY-brother. So an encounter with a role-model as positive as Margulis would do no harm.
I wrote yesterday about taking the girls to visit the Earthmother at Silbury Hill and them thereby becoming women, but that was a tad disingenuous. We drove straight from Silbury to Oxford to spend the evening with the midwife of Gaia. And she didn't disappoint: cooking dinner for eight while rattling on about Ireland and Amherst, 9/11, HIV, Emily Dickinson and violin concertos. So the girls did meet her and I'm grateful they got the chance because Lynn died in November 2011. She had a stroke and died with dignity and no intervention at home a few days later her daughter having to insist that the NFR terms of Lynn's living will were strictly adhered to. I miss her.
Monday, 6 May 2013
Sunday, 5 May 2013
Silbury Solsbury
Who is this Bob, then?
I wasn't always Bob and I wasn't always a scientist. I became a scientist rather suddenly at the age
of 16. I have written before about my very
expensive education, and the little good it has done for me since. I spent the years between 15 and 18 in a state
that would have been diagnosed as clinical depression if anyone had cared to
look closely at a teenager who spent 14 to 16 hours a day asleep, who didn’t
eat in the school dining room and might
be found in the lee of a hedgerow writing “poetry” as the sun went down. In those days, you had to decide ridiculously
early whether you were going to join the Arts or the Science stream and your formal
education got increasingly constrained and funnelled as you progressed from “O”
to “A” Levels. I’d been put off science
by an unfortunate early encounter with a well rotted turkey fetus which should
have been fresh for dissection and so was trudging through the curriculum of
History, Economics and Politics. . . and Maths. When I returned to school for my final year, I was called for the vocational interview by the feller who should rather have looked at my lonely and disaffected 16-year-old self and sent me to a psychiatrist instead. John Seymour's Self-Sufficiency had been published earlier in the year and I'd bought its dreamy vision of detachment from unhappy reality. I had also recently discovered a great way to needle those in authority to achieve a rather sad measure of self-esteem: whenever I encountered anyone higher in the elaborate pecking-order (Versailles under Louis XIV was in the ha'penny place compared to the school) I would 'umbly tug my forelock. I'd recently done this once too often with The Feller and he had belabored me about the head and shoulders crying "Don't <tok> ape <thunk> peasant <wup> gestures <wack> boy <ding>!". Yes, the education was so expensive that adults involved were allowed to assault the students. ANNyway, when asked what I intended to do when I left his, and the school's, care, I replied "I want to be a farmer" fully expecting to be struck again or at least mocked for being totally adrift from the practicalities of my situation. Instead, my off-hand remark was taken at face-value, my parents were consulted, and I was untimely ripped from a warm bath of Disraeli, the American Civil War, and Walter Bagehot's magisterial The English Constitution and dropped back a year into Chemistry and Biology. My first chemistry lesson was pure maths - working out exactly how the number of topological permutations of alkanes increased as carbons were added to the chain of organic molecules: methane, ethane, propane, butane, pentane . . . octane. I was in my element. Later the same day I met Mr Wilkinson, my first mentor and role model who had studied biology under the late great Peter Medawar. Wilkinson was pretty odd but so was I and I relished the oddities of biology as he presented them. My off-hand, cynical remark had catapulted me into science.
Fast forward 30 years; my travels in Science had taken me from England to Dublin, to Rotterdam, to Boston, to Newcastle upon Tyne and back to Dublin. In 2001 I was, to my considerable surprise because my scientific output hadn't been stellar, hired to work in one of the first labs funded by the lavishly endowed Science Foundation Ireland. SFI had a new policy to cherry-pick the smartest handful of bioscientists and give them some million$$$ to really push the frontiers by hiring the brightest and best people who were prepared to work in the Republic. The new lab was no warm bath, it was HOT, and populated by native and repatriated Irish, with a short handful of continentals and me - and I was definitely not the smartest boy in the room.
I was at my desk early one the morning (I had to start early just to keep up) when the (brilliant) eSpanish post-doc arrived for work. He asked if he could run something by me for feedback and pulled up a chair. For the next half hour I sat and nodded while he tried to articulate the abstruse conundrum that was wrecking his head. My contributions were "uh-huh . . . mmmm . . . yes . . . no, of course it couldn't . . . errrm . . . ???". After a while he paused, cried "Of course! that's it!, THANK YOU SO MUCH" and went off to write it all down. I came to the conclusion that every lab needed a stuffed dummy in a white coat called, say, Bob The Scientist that could be wheeled about to help creative people thrash things out. The other creative people being busy enough with their own problems. When not in use Bob could be parked in a director's chair with his name on the back.
Fast forward 30 years; my travels in Science had taken me from England to Dublin, to Rotterdam, to Boston, to Newcastle upon Tyne and back to Dublin. In 2001 I was, to my considerable surprise because my scientific output hadn't been stellar, hired to work in one of the first labs funded by the lavishly endowed Science Foundation Ireland. SFI had a new policy to cherry-pick the smartest handful of bioscientists and give them some million$$$ to really push the frontiers by hiring the brightest and best people who were prepared to work in the Republic. The new lab was no warm bath, it was HOT, and populated by native and repatriated Irish, with a short handful of continentals and me - and I was definitely not the smartest boy in the room.
I was at my desk early one the morning (I had to start early just to keep up) when the (brilliant) eSpanish post-doc arrived for work. He asked if he could run something by me for feedback and pulled up a chair. For the next half hour I sat and nodded while he tried to articulate the abstruse conundrum that was wrecking his head. My contributions were "uh-huh . . . mmmm . . . yes . . . no, of course it couldn't . . . errrm . . . ???". After a while he paused, cried "Of course! that's it!, THANK YOU SO MUCH" and went off to write it all down. I came to the conclusion that every lab needed a stuffed dummy in a white coat called, say, Bob The Scientist that could be wheeled about to help creative people thrash things out. The other creative people being busy enough with their own problems. When not in use Bob could be parked in a director's chair with his name on the back.
Saturday, 4 May 2013
New Map 1:25000 - brilliant
You might not think it would make a big diff, but cranking up the scale from rural motorist's 1:50,000 to rambler's 1:25,000 gives a whole other level of utility. Barry Dalby of Eastwest Mapping has just brought out one of the latter Blackstairs Mount Leinster & The Barrow Valley. It is wonderful and available on-line for €9.95 + €1.50pp. This contrasts with the €8.60 which the government mapping monolith seeks to charge for their 1:50,000 Discovery Series. I have no idea what the P&P is with OSI because they don't tell you until you have AddToCarted a product, and given them your e-mail address, your grand-mother's maiden name, all your credit details and half a litre of blood. Here is a teeny sample to indicate the extra data that you get with EastWest's products:
Information differential here is about 10:1. And the Knockroe Desert outlined by the OSI (right, above) is revealed as a richly populated landscape of historical, archaeological, geological and religious interest. Barry has been all over the area on foot; talked to the Oldest Inhabitant in each locality to get down the names of the ruined steadings and the location of the neolithic art-works; integrated data from satellites, GPS, and olde mappes. I don't see how it can be an economic proposition to spend months obtaining the data, weeks making the map, as well as paying for the printing and have a print-run of, say, 1000. But it will improve the prospects of this extraordinary entrepreneur if you go online and buy your own copy. You won't be disappointed. And if you live in Dublin/Wicklow you can buy similar maps of your own area.
Friday, 3 May 2013
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.
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?
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?
Thursday, 2 May 2013
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.
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.
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