Lynn Margulis

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.

very very old

In graduate school for one semester, I sat at the feet of the late, great, Lynn Margulis for every minute of her BI504 Evolution course. Her position was that whales, yeast and daffodils were 'essentially the same' and so not worth getting into fine details about. If Evolution was to be an investigation of life's marvellous diversity then we really needed to look for/at life in the remote edges of the earth. We spent quite a lot of time working through stromatolites. These layered conglomerations of bacteria and their residue can be found today in Shark Bay in Western Australia and grow outwards in pillars and columns and mushrooms as photosynthetic cyanobacteria over-grow each other fighting for the light. You don't find stromatolites in Dublin Bay or the Côte d'Azur because cyanobacteria is richly delicious and get eaten by molluscs, crustaceans and starfish before they accumulate in lumps big enough to see. In Shark Bay the sea is so rough that the herbivorous animals get swept clean off the surface twice a day, so the cyanobacteria can make another 2 micron thick layer of greeny-brown. Margulis and her collaborators were fascinated by the fact that fossil stromatolites could be found in great abundance when you looked in pre-Cambrian rocks. The base of the Cambrian is more or less the base of the Phanaerozoic [=manifest destiny animals] aeon when life got sufficiently big and complex to be seen with the naked eye: trilobites, worms, arthropods, chordates and some weird-and-wonderful creatures that are long since extinct. It's called the Cambrian >!explosion!< because in a few inches of the fossil record pretty much all life as we see it appeared, lived, reproduced and died. Before that [let's say 600 mya] life was there but it was much simpler, smaller and less obvious. Hence the interest in fossil stromatolites: they, at least, were Precambrian and bigger than a bread-box.

Margulis tried hard to convince us, and herself and the peer-reviewed scientific literature, that some dots 1μm = a millionth of a metre across were once living creatures, rather than grit or air-bubbles from some purely chemical process. I remember being shown a grainy picture [like R the cluster is about 5μm across] of four little bolupes - one is hidden behind the others as the point of the tetrahedron. Four spoke, and speaks, potently of meiosis and a pair of cell divisions . . . life itself.

You think that 700,000,000 is old? That's nothing compared to microfossils that have just been discovered in Nuvvuagittuq on the Eastern shore of Hudson's Bay in Canada. These aren't tetrads, they are tubes about 20 microns across, and there is an outside chance that they are chemically driven crystal formation with no input from DNA. But the smart money is on them being the earliest, 3.7 billion years ago, evidence of life on Earth. They are close to the Nastapoka Islands if you want to GoogleMap their location. The local concentration of iron suggests that these creatures lived on or in close proximity to hydrothermal vents at the bottom of the sea. They were able to capture the heat and chemical energy and convert that into more of themselves. Photosynthesis, on which almost all the 'obvious' life on Earth today depends, comes waaaaay later. I'd call this pretty cool if it wasn't so smokin' hot down there back then at the dawn of time.

Some of the Nuvvuagittuq greenstone is the oldest rock we know about at 4.3 billion years old. Considering that the consensus for the age of the Earth itself is about 4.6 billion years, that is quite primordial. The rest of solid crust from those dim distant times has been rechurned: subducted into the molten interior to lose all of its layered and crystalline structure. These fossil tubes push back the origins of life; not least because we have to allow them additional time to get from tiny barely detectable - but still autonomously dividing - micron sized dots.

Archaea

I was bigging up Lynn Margulis last year because I knew her well and her course BI504 Evolution had a huge impact as I sat through it with shining eyes in graduate school. In her course, Margulis marginalised humans, indeed mammals, indeed vertebrates as a slightly boring and rather uniform wart on the edge of life's diversity.  She championed a five kingdom division of the living world: Animals, Plants, Fungi, Bacteria and Protochtista.  In 1980, when I took the course, she was happy with the first four bins but acknowledged that Protochtista was a bit of a grab-bag consisting mostly of unicellular organisms that had a nucleus (so were not bacteria) but didn't comfortably fit in the other three kingdoms: including human parasites like amoeba, trypanosomes, giardia but also various algae and things you find in pond-water. But she was wrong, and the timing shows that it takes some time for even a smart, iconoclastic scientist at the peak of her game to absorb new ideas.

Because at the end of 1977, Carl Woese and his post-doc George Fox, had shook all the toys out on the floor and started putting them into different boxes.  They were able to do this by exploiting a new technique for classifying microscopic organisms that didn't depend on growing them on Petri dishes.  It turns out that many, even most, small-small t'ings cannot be grown on a Petri dish no matter how you trick about with the ingredients in the agar. One of the reasons why everyone knows about Escherichia coli, although few can spell it correctly, is that it can be cultivated in vitro (on a glass Petri dish). E.coli, far from being the gut bacterium, in fact contributes less than 1% to your intestinal flora. Before Woese and Fox, microbiologists did nifty things looking at the size, colour and shape of colonies growing on agar in dishes, measuring the metabolic chemicals that went in and out of those colonies and looking at the size and shape of the microbes under a microscope.  I've spent a very enjoyable year in The Institute doing this C19th science with our Yr3 Food and Fermentation Microbiology students.

It took pretty much everyone a long time to take on board this radical shake-up of how we viewed the living world, but like Barbara McClintock, Woese, knowing he was right,  just kept plugging away gathering more data. Woese had been working for the previous decade and a half on nucleic acids DNA and RNA, trying to suss out the genetic code and, when that was sorted by himself and many others, churning out sequence information particularly of structural RNAs in the ribosome.  The ribosome is the biochemical machine, shaped like a teeny cottage loaf, which translates RNA into protein codon by codon.  It consists of maybe 60 different proteins held together with three strings of RNA.  In 1977, Woese and Fox published a classic paradigm-shifting paper in PNAS which suggested that although two bacteria might look identical (oval blob) down a microscope they were as different as two things can be and still come from from the same planet. In particular they recognised that "things without a nucleus" (i.e. different from us) should definitely not be lumped into the same bin. Executive summary and context by Jon Eisen.

This picture is a recent assessment of the state of our knowledge.  4/5ths of Margulis' kingdoms make up the pale green branch pointing upwards and plants / animals / fungi which are effectively the visible portion of the living world are three twigs on a limb of a branch of the whole tree. So you can see why she might have talked up a storm on W&F 1977, but as far as I remember, she did not. [I've gone back and checked my notes from the course and she did mention that the 16S rRNA from methanogens was very different - but that meant that methanogenesis was 'early'; rather than that bacteria of her fifth kingdom were polyphyletic]. The animal 'kingdom' is so well embedded in our language and understanding of life's divisions that the three major groups identified by Woese and Fox are referred to as Domains. It was intitially thought that the recently identified Archaea were ancient hold-outs from a primitive earth living in extremes of temperature, or in weird chemical stews in geologically active ponds.  It being so difficult to cultivate a given microbe in the lab, it's taken a while to realise that Archaea are found pretty much everywhere and that several species are extremely abundant and impact significantly on cycling of carbon (whoop whoop global warming alert) and nitrogen on the planet. Also note the implication that Archaea are more similar to things-with-nucleus Eukaryotes than they are to the rest of bacteria - although this view is under intense scrutiny now.

The other important consequence of the technique of RNA sequencing is that you can pull up a net full of sea-water or an aliquot from the intestinal flora or a shovelful of contaminated soil and get a good Petri-free idea of the number and types of the invisible organisms that inhabit those environments.  This bears on diagnostics, environmental chemistry and numerous other fields. Woese died a couple of years ago, but today is his birthday 15 July 1928.  Hats off!

3,200.040 years BC

Forty years ago this morning 24 Nov 1974, Don Johanson wrote in his diary that he was "feeling really lucky".  A few hours later, he found a few fragments of the fossil hominid that he was looking for. He was on an expedition with two French anthropologists, Maurice Taieb and Yves Coppens, looking for 'the missing link' - fossil evidence of transitional forms between modern humans and the great apes our nearest living relatives.  At the end of the day, sitting round the camp-fire with the Beatles "Lucy in the Sky with Diamonds" playing again (there was a limited repertoire available in the middle of an Ethiopian desert), someone suggested that the fossils fragments should be named Lucy - and by breakfast the next morning it was so.  Some people claim that, as Lennon was cranked up on LSD when he wrote the song, so drugs had been taken the night our renote ancestor was discovered.  Even after weeks of intensive work in widening circles round the original find, only 40% of the skeleton was recovered and only a couple of fragments of skull.  The picture L from Patrick Clarkin, shows what we know in pink with the rest 'reconstructed' and filled in. The first bits Johansen found were crucially bits of the knee, which showed that his fossil was knock-kneed rather than bow-legged like apes, which can and do walk upright but it's a hirple for them but normal for us and for Lucy.  The other piece of crucial information was the date, which we now agree to be about 3.2 million years ago.  That came from the analysis of the relative amounts of potassium and argon (it's the radio-active decay, stupid) in nearby volcanic rocks.  There is a key leap of faith required because volcanic rocks don't have fossils, and sedimentary rocks don't have the K/Ar clock. A bit of stitch and match is required.

Lucy (AL-288-1 officially) was only 110cm tall but probably a female (the pelvis has a couple of different possible re-constructions) and definitely an adult from the complete ossification of the epiphyses of the bones and the eruption of, and wear to, the third molars aka wisdom teeth.  The skull fragments show that she was small brained like other apes and the knees show that she walked upright, so it settled a debate about brain early or bipedal early. I like this very much because I buy into the idea that the hand drove the brain.  Freeing the hand from any constraint for locomotion means that it can start sewing, flint-knapping, spear-crafting and designing fish-hooks; not to mention make jewellery and other fripperies to impress the opposite sex. It needs an ever bigger brain to cope with these ever multiplying artifacts (bangles to Saturn V rocket, say): we are Homo faber, in the coinage of Hannah Arendt, of banality of evil fame.

As it happens, I met Johanson, about ten years after Lucy changed his life entirely, when he was the guest of my friend-and-mentor Lynn Margulis at BU when I was still in graduate school.  I had just completed a catalogue of hominid teeth, including Lucy's, with another of my friend-and-mentors called Ben Blumenberg.  On the back of cranking some hundreds of tooth metrics through a mainframe computer to generate comparative statistics we said something profound about the human condition - I can't remember what it was though.  Johanson was charming and I didn't bore him too much before fading into the background and leaving him to talk to a real evolutionist like Margulis.  I haven't been there, but I've talked to the T-shirt.

Oxygen - deadly poison

Couple of threads got tangled last night. It turns out that today is Christian de Duve's birthday. He was born in then same month as my Old Man in 1917 and died only last year with a string of fundamental discoveries to his name and a Nobel Prize to polish.  He got the Prize for his discovery and characterisation of lysosomes and peroxisomes: two sub-cellular organelles which have particular and peculiar functions to perform in the metabolism of all eukaryotic cells including our own.  I talk about them in my human physiology course and The Institute in sufficient detail that I have set an exam question on them.  He discovered lysosomes after noticing an intriguing anomaly: the amount of the enzyme he was researching differed according to whether he ground his cell samples in a pestle & mortar or a blender.  Obituaries in the UK Independent and Telegraph contain laughable errors in their description of the science but between the two of them you can work out the source of de Duve's eureka moment.

de Duve and my mentor Lynn Margulis believed that peroxisomes were once free-living microbes that were particularly adept at dealing with the enormous amounts of free gaseous oxygen that was being generated a billion years ago by a new class of microbe that made a living by photosynthesis. They could use the sun's energy to carry out this reaction:

6CO₂ + 6H₂O --> C₆H₁₂O₆ + 6O₂

This is rather nifty.  Converting a lot of carbon-dioxide and water into sugar from which complex carbohydrates might be built is clearly a useful trick even if it requires energy.  If you can evolve a set of structures and enzymes that can capture this energy from sunlight, then it's a bit of a coup.  If we could do more of it today, that would suck up the most significant green-house gas carbon-dioxide and use it to make sugar, starch, cellulose, wood, coal . . . you get my drift: energy reserves built up and global warming set back for a while. Oxygen is a bio-product from this reaction and that sounds like a bonus. But you have to appreciate that O₂ oxygen is so potently reactive that it is toxic to a lot of free-living microbes even today - the germs that cause tetanus Clostridium tetani and gangrene Clostridium perfringens and other bacteria that skulk in dark places a long way from fresh air. The atmosphere is now, and has been steady at for a long long time, just under 20% oxygen and this is evidence for James Lovelock's Gaia - if the concentration was a few percent higher things would spontaneously combust.

de Duve and Margulis noted that peroxisomes are full of enzymes which process and detoxify free oxygen and they independently came to believe that, like mitochondria, these little bodies had once been independent bacteria. The trouble with this hypothesis, which has the ring of truth, is that no trace of any DNA remains which is physically associated with the peroxisome itself.  At least vertebrate mitochondria have retained 16,000 bp of DNA (maybe 1%) from which it can be inferred that they are descended from alpha-proteobacteria like Rickettsia prowazekii. The rest of the original genome has been exported piecemeal and absorbed by the chromosomes of the hosting organism from which we are all [plants, animals, fungi] descended. de Duve reckoned that this process of export had been carried through to completion by the peroxisome, and I'm not going to say any different.

Mais revenons nous a nos Belgiques.  de Duve died in May last year at the time of his choosing.  His wife had passed on five years earlier, he had cancer and heart problems, he was 95 and had recently been injured in a fall, it was time to go. Belgium has the most forward-looking and liberal laws regarding end of life issues and de Duve died with a quiet word and a smile surrounded by his grown up children and assisted by two doctors and a syringe. A lesson to us all.

100-up

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

Clearly these may be gathered into bins or made to form themes (several Haldanes, many geneticists, some film-stars, a surprising number of Jims).  But several of them appear to be, in the tradition of "googlewhacks", un-met by google-light:
Your search - "Amedeo Avogadro" "Sukiyabashi Jiro" - did not match any documents.
Your search - "Johan Kjeldahl" "Emil Zatopek" - did not match any documents.
Your search - "Lynn Margulis" "Varro Raetinus" - did not match any documents.
But it is the destiny of googlewhacks to fade as soon as the spiders of Google find the site that reports them, so there will be soon at least one site on Google that reports the meeting of these unlikely couples.
 

100K

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

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

Darwin's last days

Darwinday today as it was last year and indeed for me every previous year back to 1982 the centenary of Charles Darwin's death. Events that year gave some traction to the canonisation of St Darwin of Downe which is pursued with quite evangelical vigour by some who 'believe' in evolution. When I worked at Evolution Central in a couple of Genetics Departments, I used to bring donuts in to work as a sort of agnostic host. My fellow believers were happy to glom down a donut on Der Tag but generally forgot about the great man for the rest of the year. The trouble is that, to be successful in science, you need to specialise and focus on one area of expertise - like cyanogenesis in plants fr'instance - rather than flitting from one thing to the other as the fancy takes you. I was never a very successful scientist because I was always starting something new before I'd wrapped up and published the previous project. That butterfly mind makes me a successful, or at least prolific, blogger.

As Robert Heinlein said specialization is for insects: you can't understand, let alone explain, evolution unless you know some biogeography, some embryology & development, some taxonomy and comparative anatomy, some geology . . . and some genetics helps too. If you have spent the last 20 years studying mutations in the upstream control control region of a single gene in Bacillus subtilis, you're not going to do well in a TV debate with an intelligent designist.

The final year honours course I taught in Newcastle was a whistle-stop tour marshalling the evidence for evolution a) as Darwin knew it and b) as subsequent developments, like Mendelian genetics, had added to and fleshed out that evidence. Even back then I filled out the Evolution course with nifty anecdotes about mutilated bears and Slijper's goat, rather than sticking strictly to genetics. I was driven to develop, write and deliver that course because one of our students, a biblical fundamentalist [Plymouth Bretheren?] asked me to recommend a book on evolution that she could present at her church's monthly book club. I was completely wrong-footed by this request because, although I could think of a few books, I couldn't there and then convince this young wan that evolution was a better explanation of the marvellous diversity of life than God's Grandeur. And this was just a couple of years after I'd taken BI504-Evolution sitting at the feet of Lynn Margulis in graduate school. Shame on me!

If you ask most biology students - those in the bible-belt of the USA possible exceptions - if they believe in evolution they will say Yes, of course without the least blush of shame that 'belief' is a disturbingly religious word. Furthermore, because they have neither read the Origin of Species, nor taken BI504 or my Evolution from primeval soup to hominid nuts course they are not qualified to assert such a belief because they don't have a coherent bank of evidence to back that belief. Same goes for almost all the teachers of biology in school and college.  Today, in honour of Darwin's birthday you might resolve to read The Origin - you won't be disappointed and you will be blizzarded by quirky facts. If you're French, and that's currently more than half my readers, you might pick up Thomas Glick's The Comparative Reception of Darwin for less than $10. I was lent a copy by Lynn Margulis in the 1980s. That shows that Darwin had a different impact on thinking people on the Continent than in insular Britain where they made Darwin FRS, FLS, FGS and FZS and knighted three of his sons . . . which?:

On dit que Darwin spent 20 years not writing the Origin of Species because he was conflicted by religious doubts and was only goaded into committing his thoughts to paper to avoid being scooped by Alfred Russell Wallace in 1858. That is peculiar because all his children grew up to be agnostics and felt that they had taken that position from listening to their Papa. Nearly 100 years ago a peculiar story was put about that Darwin had a sort of death-bed conversion and invited a bible thumper called Lady Hope to preach to his servants and tenants in the summer house at Downe. The idea of this evangelical busybody pitching up in Darwin's bedroom in the last year of his life to hear his confession has the ring of augmented truth. It's the kind of thing my Great Aunt Lily would have done. That dreadnought lady had a habit of ringing the doorbell of whatever grand house she was passing and insisting on viewing the staircase or the Adam fireplace in the main bedroom. The fact that all Darwin's children [the seven who survived to adulthood are shown above] were adamant that the meeting with Lady Hope had never taken place doesn't fully allay suspicion.

Sphagnum

Sphagnum [above a little more than life-size] is pillowing over my awareness horizon because Charles W. Cathcart was mentioned as part of a wikipedia Did you know: tag. There was a time in 1982 when I knew a helluva lot about Sphagnum from a class assignment in graduate school but if you don't use it you lose it and what I now know about moss can be written on a postage-stamp in the 630 words which you are now reading.

In 1982, I was a star-struck groupie of Lynn Margulis taking her eccentric but brilliant course BI504 Evolution. As part of "Organism Day" we were each requested & required to write an essay on any living species - its biogeographical  distribution, ecological niche and evolutionary relationships - and bring an example to class. That morning everyone made a presentation about their chosen organism and took questions. I had recently read a report by Henry David Thoreau (1817-1862) about Gowing's Swamp in Concorde, Mass. That's Henry "Walden" Thoreau [prev]! Accordingly, I borrowed a car and drove out to find Gowing's Swamp [before GPS, maps.google and smart phones] which was behind a school near Revolutionary Ridge. Thoreau (and I) caught the swamp at a snap shot in its transition from a pond to dry land - a process called succession by ecologists. I scooped a little clump of Sphagnum moss into a tupperware container; ready for delivery in class. But obsessive me was unable to determine which of the ~380 species of Sphagnum I might have in my hand. With a great deal of chutzpah, I arranged to take some of it to the world's expert on the taxonomy of mosses, who was a professor across the river in Harvard. Organism Day was a really good learning experience for us students - Margulis realised that content is the least important part of learning in college - process means much more in the long run.

One of the "this is nifty" bits of information I included in my report was the fact that sphagnum was used in WWI as a sterile wound-dressing. It is amazingly absorbant - able to hold 20x its own weight in water. That water is almost always acidic because sphagnum acts as an ion exchange column taking in Mg⁺⁺ and Ca⁺⁺ and sending out H⁺. That acidity discourages a lot of microbes from growing. It also took only 20 years to destroy the copper pipe-work in our mountainy home where the well-water has been filtered through centuries of sphagnum and peat. In addition, Sphagnum cell walls include a variety of phenolic compounds which, like phenol itself and TCP, are mildly antiseptic. Charles Cathcart and Isaac Balfour, the Keeper of the Royal Botanic Garden, Edinburgh wrote an article in The Scotsman extolling its virtues despite the fact that the Germans had been using the stuff for the previous 30 years. In the real-ekonomik of materials in war time, cotton fibres were needed for gun cotton [structure above R] rather than cotton wool AND had to be imported through U-boat wolf-packs AND was less absorbant AND was not naturally antiseptic.  Sphagnum moss otoh grew in abundance across the uplands of the British Isles [they were all British in 1914]. In an early example of crowdsourcing, women and children were mobilised for moss drives to gather the raw material. In Germany this part of the process was carried out by Allied PoWs as well as civilians. The pickers were instructed to box-clever “fill the sacks only about three-quarter full, drag them to the nearest hard ground, and then dance on them to extract the larger percentage of water.” Water is water and it's heavy, so you don't want to schlep it about the world - better to ship orange-juice concentrate from the warm lands of the south and reconstitute from the tap close to final destination.

Triumph of the Free Will

I'm not stupid, but I've definitely worked in places where I was not the smartest person in the room. In the early 90s, I was contributing to the birth of bioinformatics in Trinity College Dublin. Our lab acquired a final year project student who, on the side, used to devise crossword puzzles for the magazine his aunt edited and played contract bridge for Ireland. In contrast to me, in the same department 15 years earlier, he secured a First.  He went to America for his PhD and was peer-reviewed top-listed for one of the five first multi-million Big Biotech grants after the 2000AD foundation of Science Foundation Ireland SFI. That quango cravenly refused to cough up and start his proposal because he was too young. The country is lucky he's not now making waves at Stanford or Yale but is indeed back in TCD cutting edges at the interface of neuro and genetics.

Who dat? It's Kevin Mitchell, assoc prof of [neuro]genetics at TCD. We've met him before. In addition to teaching and research and raising a family, Kevin has also made time [like Luther he can do no other] to write books for Princeton UP. Innate: How the Wiring of Our Brains Shapes Who We Are (2018) and this year Free Agents: How Evolution Gave Us Free Will (2023). I was at the launch of the most recent book [what's not to like when free canapés meet with free travel?] and shelled out a pony to bring a copy home. Pony? That's Buridan's Ass [L] unable to choose between two equally delectable choices.

Can't afford €25? Free Agents is in many Libraries. Can't make the time? Nigel Warburton hosts another debate about free will. 'Is Free Will An Illusion?', joined by psychologist Susan Blackmore and Kevin Mitchell -only 40 mins. Blackmore has acquired interesting baggage on the nature of reality by practicing Zen for 40 years as well as being a skeptic and free-thinker.

Free Agents reads easy, although the middle chapters have a lot of '$10 words' [like salient, instantiate, reify] not always with an appropriate gloss for those who missed out on a very expensive education. Each chapter is split into bite-sized chunks with a helpful contents label. Chapter 4 Life Gets Complicated, for example: The Energy Barrier - E pluribus unum - Big Hungry Beasts - La Familia - Coordinating Movement with Electricity - Neurons - Hail Hydra! - As the Worm Turns - Summary. As you see, a mix of informative with whimsical and assuming that everyone clocks the cultural references . . . and knows the rudiments of Latin. Thus p.75: "Like the Borg in Star Trek, these individuals get assimilated into a collective. It's not just that resistance is futile: it's pointless".  I've only a sketchy idea of what/who/where/when are the Borg [Χ]; resistance is futile is lifted from h2g2 [✓] but I doubt if pointless is referencing Richard Osman's gameshow [Χ]. Comms Fail w.r.t. to me = 2/3, so!

I hope it's a conscious, freely-chosen hat-tip to Robert Heinlein when Mitchell outlines the huge range of things a primate could do after breakfast. It could climb a tree, search for grubs, scratch itself, groom another monkey, look for a mate, go to sleep, bang some rocks together, jump up and down, poke itself in the eye, urinate, start a fight, wave its arms around, stick a pebbles up its nose, eat some dirt, screech . . . and not a lot different from a Man from the West as imagined by O'Grady and Pyke.

I have a lot of respeck for Kevin Mitchell. His book is an attempt to defuse the hot button topic of Free Will by dissing the  black and white  thinking and entrenchments which are normal in the field. Robert Sapolsky [bloboprev] is the latest big hitter to book-bat for No Free Will. Harris Hegel Hobbes and Hume have all had a go, and that's just the Hs! It takes confidence to go public in such august company.

Of course we all have baggage:

• they fuck you up, your Mum and Dad
• all of us have taken a tonk to the head at some stage
• we were [not] bullied in school
• we've had a couple of pints
• or an argument at work.

Whatever life throws up [bloooargh!] we still get out of bed most mornings and make decisions. Some of those decisions are on autopilot: involving only a tad of conscious thought; but others are life changing for us or those around us. For Mitchell [and for me as I fire my fan-boy knickers on stage] choice, agency, decisions, Will are on a continuum of constraint: some lock-and-loaded by our autonomic nervous system; some almost a dice-throw; some the product of deep thought and rationalization. That this accords with our humble not-an-intellectual lived experience doesn't make it less true . . . whatever nifty neuro-psychological experiments may tell us.

It doesn't help that there has been A Lot of recent side-eye towards iconic experiments which purported to expose how the human mind thinks. Too many:

• studies with fatuously small samples;
• W.E.I.R.D. volunteer participants;
• crappy stats;
• shameful nod-through referees (this comes from Harvard: must be sound) of papers;
• wishful thinking;
  
• outright fudged data-sets

Mitchell and Sapolsky have their stalls compared on the pages of Nautil.us: "Yes, We Have Free Will. No, We Absolutely Do Not". Here they biff it out toe-to-toe split-screen on Philosophical Trials.  I've bought Sapolsky's book - it seemed to demand parity of esteem with Mitchell's - which comes to the opposite conclusion about Free Will. I really don't think I have the energy to read it anytime soon. Although I got a lot out of his last book Behave: The Biology of Humans at Our Best and Worst. Here's the thing, we all feel that we have free-will, we behave as if we do, our legal system and society itself are predicated on it. If it walks like a duck, quacks like a duck, and doesn't sink in water . . . then it's a duck we have free will. Clever Free Will is Bunk people are retreating from this common sense, common knowledge; redefining free-will, separating it from agency, and dickering about several incommensurate versions of determinism as they circle their waggons of certainty. Me, I'm 300 pages down on Free Will and right now frankly Scarlett about the whole debate. I'm outside that intellectual waggon corral, dancing with bison and freeeeeee.

For all you biological determinists out there, remember there is, even at this moment, a butterfly in Haiti stamping its foot saying "I refute it thus"!

postscriptsgripes:
Q? why oh why do we need to know that John "Inequalities"  Bell [no relation!] was born in Belfast and not be given parity of birth insight to John Nash, John von Neumann, Jean "Ass" Buridan or Hans Jonas?
A! because none of the other Johns wear the green jersey. By flag-wagging the sole Irish contributor to the book's bibliography, Ireland's collective deep thinking capacity is rather diminished than bigged up.

Lynn "Endosymbiosis" Sagan shd not be "née Margulis", she was née Alexander. Carl Sagan was her first husband, Thomas Margulis her second. Ask me how I know.

Prochlorococcus

Q. What's the most abundant living thing on this our blue planet?

I recently read, through tears of frustration, Atlantic by Simon Winchester.  I found it worthy, erudite and informative . . . but scrappy and ultimately dissatisfying. But 430/490ths of the way through the book, he devotes a couple of pages to the - to me -wholly unexpected researches and calculations of Dr Penny Chisholm [R at the time when she made her remarkable discoveries] which sent me off down the rabbit-hole to fill in the details. I didn't go further than last year at the University of Illinois at Urbana-Champaign for a symposium Looking in the Right Direction: Carl Woese and the New Biology tribbing [bloboprev] UIUC's most famous scientific faculty member. Dr Chisholm led off the event with a stunning talk about her life on the ocean wave. If you can spell evolution, this is definitely worth the hour of your time (and stick around for the post-talk questions).

I spent 12 years of my life discovering genes in an immunology lab and being bemused by the instruments, experiments and mind-set of my immunology colleagues. Eventually I got to understand what they meant when they talked about CD4⁺CD8⁺ T-cells, CD4dims, side-scatter and gating. This is the language flow-cytometry, an instrument that immunologists use to characterise individual cells and count them under different experimental conditions. In 1985, Chisholm and her collaborator Rob Olson took one of these delicate monsters out into the wide Sargasso Sea and ran samples of salt water through it. They were looking for a blue-green alga BGA aka cyanobacteria called Synechococcus which had recently been discovered in marine samples. What they found as well was a smaller [0.6μm] amazingly abundant [10⁵/ml] photosynthetic bacterium that eventual got the name Prochlorococcus marinus. Even if you only count the upper 200m of the oceans where sunlight penetrates there are a helluva a lot of mls of sea-water and the best estimate is that there are a Carl "Billions" Sagan number of Prochlorococcus - 3 billion billion billion = 10²⁷ - out there; making them probably the most abundant species of which we know.

Math aside - there are lots of Prochlorococcus but they are very small and I think Homo sapiens has about the same biomass and rats Rattus norvegicus probably out-weigh us both.  Calculating the mass of all humanity is an exercise I do with my 1st Year Quant Methods. If we take the average weight (the clinically obese balanced by the starving infants) as 50kg and 7.4 billion of us in August 2016 [more today!] then there are 0.370 billion tonnes = 4 x 10⁸ tonnes available to carnivorous aliens from the Planet Zorg.  otoh, each Pcc weighs 2 x 10^-19 tonnes and there are 3 x 10²⁷ of them. So they tip the scales at 6 x 10⁸ tonnes. Not so tasty as humans and much harder to catch: got a sieve, Zorgistas?

Finding so many so tiny photosynthetic organisms in the ocean made us radically re-think our view of the carbon cycle, which up until then had been focused, with a sense of awe, on tropical rain-forest which includes some of the largest living things on the planet. The annual amount 5 Gtonnes of carbon fixed by Prochlorococcus is in the same ball-park as the excess 6 Gtonnes we are adding to the atmosphere by burning fossils fuels. Our carbon footprint is still increasing but the density of Prochlorococcus is remarkably stable year after year, despite doubling about once a day, so we must conclude that half of each day's reproductive bounty is promptly scarfed up by something else for dinner. As food, its carbon-based structures - protein, glucose and lipid - are quite quickly metabolised back into CO₂ and so are unlikely to be a major player in locking up the carbon which we are hosing into the atmosphere as we drive to work and heat homes in ludicrously unsuitable living spaces like New England, the whole of Canada, Scandinavia, and much of Russia.

One of the things that makes Prochlorococcus suitable for a lifetime's scientific research is that some strains can be cultivated in the lab while they can also be studied in their natural environment. The first such tame strain was SS120 [Sargasso Sea 120m down]. By flipping focus between the data generated by these different approaches, Chisholm has built up a startling picture of this tiny organism's place in the wide wet world. Small as it is, they have discovered it shipping fluid-filled vesicles out from the surface membrane for purposes intriguing but not yet fully understood. These vesicles contain DNA, RNA and proteins and could be regarded as mobile workshops spreading out from the minuscule mother-ship. It seems that Prochlorococcus lives in a complex commensal relationship with other bacteria that have only a tenuous physical connexion - it's really dilute in the sea. These other bacteria are able to scavenge the limiting elements, mainly nitrogen, phosphorus and iron, in a marine environment. It's almost as if Prochlorococcus is paying its taxes in fixed carbon and receiving the key N, P, Fe building blocks for making more DNA and protein as it doubles its numbers every day.

And please, please be extremely skeptical of people, even 'scientists' who propose that, by seeding the ocean with iron or one of the other limiting elements we can boost the carbon-holding capacity of oceanic life. That reductionist single-factor analysis is likely mad bad and dangerous to implement because it will boost some unknown and unculturable microbes at the expense of others and upset the equilibrium of the n-dimensional [Fe, P, N, pH, salinity, conductivity, day-length, light intensity, depth, unknown-but-important-1, unmeasurable-but-important-2, intangible-but-vital-3 etc.] hyperspace that is an ecological niche. That niche is just one species characterised for what we can measure. But an ecosystem is an interlocked set of niches involving thousands of interacting and inter-dependent species. To the nearest whole number, the best estimate of how much we know about how an ecosystem works is . . . nothing.

A final word on genetic diversity. What they call Prochlorococcus marinus is a sort of universe in itself. Small cell has a small genome - 2,000 genes = about half that of E.coli - but the genetic complement = biochemical capability is wildly different between any tow randomly selected individuals from the "same species". When the US Dept Energy were planning to sequence the genome of Prochlorococcus marinus Chisholm insisted that they sequence two different genomes, to get a handle on 'allowable variability' in the species. Now there are 40 ecotypes fully sequenced. They all have a core genome of about 1,300 genes which make the proteins to do the 'housekeeping' tasks all living cells do every day. The rest - the flexi-genome - do different things, presumably related to the peculiar niche in which they serve/thrive. 200 m down is really different from 2 m down and the concentration of phosphorus is 10x different between the Atlantic and the Pacific.  If you sequence a genome and find nitrate reductase, then you know that bug will do well near an estuary where nitrate is flooding off the agricultural land upstream. With Prochlorococcus every time they sequence another isolate they find dozens or hundreds of new genes with novel functions. Collectively they have a "pan-genome" of 80,000 genes making them 4x more complex than, say, humans.

But then, my mentor Lynn Margulis [prev] often said that, given the astonishing diversity of life on Earth,  all mammals are 'essentially the same', each of these 5,000 furry lactating viviparous species are trifling variants on the same fundamental system. Molecular genetic comparisons have shown that there are several extra species of giraffe, rhinoceros and elephant and we now lose sleep over the likelihood that we cannot save them all from poaching and habitat destruction. On the Margulis 'essentially the same' argument we could lose all members of all three mammals and it will have less impact [biochemical, ecological, evolutionary] than the loss of a small fraction of the variants that are currently binned into species Prochlorococcus marinus. Bonnets off to Dr Chisholm for comtinuing to bowl this hoop along the road!

More Women in Science

Potential energy

Today is Ada Lovelace Day.  This annual reminder about the fact that there are women working in Science, Technology, Engineering and Mathematics (STEM) has been running since 2009 but I only heard about it on Sunday. Check out Aoife McLysaght in today's IT.  We really must change  

ST[XX]EM << ST[XY]EM 

into something more like  

ST[XX]EM = ST[XY]EM

There's a huge reservoir of creativity and talent that is just not being tapped. I checked out the ADA website and the founder, and discovered a link asking for inspiring essays about inspiring women in science.  So I thrust The Blob's views on Barbara McClintock, Lynn Margulis, and Jocelyn Bell Burnell at them.  I've called that all-too-short list an occasional series. As it's exactly 3 months since the last entry, and for the day that's in it, I'll write a few words here about Cliona O'Farrelly.  She is a scientist and a woman and a mother. I mention the last qualification because this attribute had a significant impact on female professionals of her generation and none whatsoever on their male contemporaries.

She is now Professor of Comparative Immunology in TCD.  When she was appointed six years ago, she was not the first choice of the chaps on the committee, because her publication record was solid but not stellar.  First they offered the Chair to a high-flyer from Foreign, who had forgotten to ask his wife, a professional in her own field, and family if they wanted to up-stakes and move to the edge of Europe (rotes Gesicht zu Hause).  Then they offered it to a local man who used the offer to blag himself a better position at the place he was then working (and good for him).  Finally, and possibly with a sense of desperation, they offered it to a woman.  Maybe it wasn't exactly like that, my memory is woofly, but many professional women who read this will hear a small ring <ding> of truth.

I'm sure that one of the reasons she made it to the short-list is that she is a great teacher.  She's not a narrow specialist, but has many interests including things beyond science.  She is thus able to draw her explanatory metaphors from a much wider experience than the specialist scientific literature.  I remember going to one of her seminars a decade ago; the pictures for her talk came with her on a CD. This disc was put into a Mac computer which dutifully ate it up and choked.  Nothing anyone could do would either release the CD or bring the Mac back to life.  Only marginally daunted, she carried on with her talk, which was mainly about the work her molecular evolutionists had been doing on computers, showing the multiple sequence alignments with vigorous horizontal sweeps of both hands, the conserved sites with precise vertical chops, and the Hidden Markov Model with similarly appropriate theatre. Eee, it were great! So clear, such fun.  Every year she visits her local girls-only secondary school to talk to them about science - careers in science ostensibly - but really, passionately, about science.

When COF came to TCD, she found a catch-as-catch-can Transition Year work experience programme.  If you or your neighbour or your cousin knew one of the faculty members then you could ask them to take your teenager under their wing for a week.  Each youngster, as they came in, would have a session with the Safety Officer, a tour of the building, and other infrastructural essentials. Taking in such would-be scientists is paying your taxes to the aspiration that Ireland has a future as a technological nation.  Like taxes it is an imposition on your time and resources, so it is easy to shirk the responsibility.  COF codified the program so it happened on two specific weeks in the year.  Positions had to be competitively applied for, all the Faculty had to contribute and a program for the whole week was formalised. Half of the available hours were actually in laboratories experiencing work and half were group activities, tours, demonstrations and lectures - and the Safety Officer could efficiently give her talk to 18 people at once. It was great, not least because I was asked to devise a scientific scavenger hunt round the campus. I love treasure hunts.

Before TCD and after Harvard, she was for a decade the Research Director at the Education and Research Centre in one of the Dublin teaching hospitals.  The ERC had several  purposes but one of them was a place for consultants to park their graduate students while they were in theatre or doing rounds of the wards or rounds of golf.  Accordingly COF had an important role mentoring not only her own research group but also these orphans.  In the lifetime of any doctoral training, there will be at least one moment of despair, when the work is stagnant, the ideas have dried up and blown away, the avenues of advance are all obscured by thickets.  One of her mentoring SOPs was to fish the student out towards the edge of the Slough of Despond and get them to go through their first lab books with her.  Even for one at the lowest ebb of self-esteem, it is a revelation to see just how plug-ignorant and clueless you were when you started.  You cannot but feel better when it is clear that you have learned so much, and that your toolbox is so much better filled with sharper tools now.  Sometimes that helps and sometimes so does an ultimatum and a quite brutal shove and when that seemed necessary she didn't shy away from it.

The purpose of a PhD programme is not really about generating results, although that is a key deliverable for the funders. It's much more of a training in how to reason, how to marshal evidence, how to present data and how to solve problems . . . regardless of what those problems, or that data, are.  Even at this top level of formal education there is a wide range of abilities, some students are stellar and some are nearer our good green earth.  It's easy to supervise the ad astra chaps; they are as smart as you or smarter, they get up in the morning raring to go, they work all the hours that the day sends and they have ideas in their sleep. If you are brilliant and successful yourself you may never have to draw your students from the per ardua cohort.  COF sees her role as getting each of her people to fulfill their potential: to go as far as they can . . . and a little bit more. So it's not a doss or a doddle, no PhD can be that and be worth having, but it is clear to her that a good PhD contributes to progress as well as a brilliant PhD.  The narrow path blazed through totally new territory has to be braced and supported by work that comes after and builds in the same direction.  Exactly the same rules apply, over a shorter time-scale and a broader range of ability, to final year undergraduate projects.  Mobilising all this, especially per ardua, potential takes time and effort but the cost-benefit analysis is definitely positive. There can seem sometimes to be a relentless enthusiasm about Professor O'Farrelly, but that doesn't mean that the process is cost-free.  Such commitment to the necessary infrastructure upon which the high-fliers climb for launch is essentially  invisible - it should at least be acknowledged.  Rewarding it would probably be too much for society as we currently arrange things.  Nurses, primary school teachers, refuse collectors (do I mean mothers here?) are also often invisible and all get paid buttons.

So, as an alumnus of that institution, which makes me a sort of psychological share-holder, I think TCD got a good deal in their third choice. 
The Blob's women in science: Florence Nightingale - Barbara McClintock - Maude Delap - Cliona O'Farrelly - Lynn Margulis - Rosalind Franklin - Jocelyn Bell Burnell

Jocelyn Bell Burnell turns 70

Continuing an occasional series on inspirations (Lynn Margulis, Barbara McClintock) for young wimmin in science, let's celebrate Jocelyn Bell Burnell's 70th birthday which falls today.  JBB is perhaps the most widely discussed case of not getting a Nobel Prize which she could/should have shared with her supervisor Tony Hewish and his boss Martin Ryle for the discovery of pulsars. The wags dubbed 1974's the No-Bell Prize in Physics for "pioneering research in radio astrophysics".

JBB was definitely a pioneer in the sense of a military engineer because the early part of of her PhD programme with Hewish required her to help whack hundreds of wooden posts into a 4 acre field outside Cambridge, then string wires from these posts so that they became the Interplanetary Scintillation Array which Hewish had dreamed up and secured funding for as a way to measure high-frequency fluctuations of radio sources - aka quasars - Out There.  Swinging a sledge-hammer was only the start of JBB's contribution to the project.  She was also required to scrutinize and analyse a hundred feet of computer printout generated each day. 

One day, she noticed a quarter-inch "bit of scruff" on the printout and thought it was interesting enough to tell Hewish about.  He said the scruff must be man-made and told her to ignore it and please stay focussed on her project. He was certainly focussed on the project: he had a hypothesis, he'd asked a cash-strapped British government for a mort o' money and he was using it to get the data to test that hypothesis.  There were deadlines to meet, a thesis to write and this was no time for side-lines.  But JBB just couldn't leave the bit of scruff, it was nagging at her,  so she went back to the printouts after hours when Hewish had gone home, and got out her ruler and saw that the scruff appeared regularly with a frequency of just under one blip per second.

What she had discovered was the first known pulsar, which later turned out to be a neutron star:  a dense gravitationally collapsed once-upon-a-star that crams the mass of our sun into an incredibly fast revolving sphere 10-20km across, emitting strong electromagnetic pulses as it turns.

In the summer before she came to Cambridge, JBB had held a Summer internship at the Jodrell Bank radio telescope near Manchester.  There, she had been required to do a lot of arithmetic because the main-frame computer in Manchester was always fritzing out or being used for other work. So she'd built up her math-muscle then as she built her red-meat muscle with the post driving. Soon enough, because she worked very hard and was diligent and mathematically competent, she discovered the second, third and fourth pulsars, and was able to convince Hewish that what she had discovered was much more interesting than what Hewish had been looking for.  It took them a lot more time to establish that these pulsing scruffs were genuinely Out There and not rogue signals from Pirate Radio, traversing earth-orbit satellites or sparks from an arc-welder down the road.  One of the top Soviet astronomers later sought her out at a meeting of the International Astronomical Union to say: "Miss Bell, you have made the greatest astronomical discovery of the twentieth century."

That was 1967, Miss Bell got married the next year and spent the next 20 years trudging round Britain as her husband was posted to one civil service job after another.  Each time they moved, after she had unpacked the tea-chests, sorted out a school for their son, located the shops and the laundrette then she looked around for a local job in astrophysics, because that's what she did; usually part-time, because that's all that was possible. In 1974, there was the No-Bell prize kerfuffle, which seemed to exercise everyone else a lot more than it did her.  Indeed she was delighted about the Nobel because it was the first recognition by that committee for her field of astronomical physics.

She has not been without honour, indeed without honours, in science. She's been given a string of medals and prizes including the quintessentially British CBE, DBE and FRS.  And she's been awarded 20 honorary degrees including one from Trinity College Dublin in 2008.  She spoke then about the brief intense joy (in the idyllic Arthurian Garde-Joyeuse sense) of knowing something that nobody else in the world knew, after she discovered the second pulsar.  Different part of the sky, different frequency, they couldn't both be a malfunctioning thermostat in the lab next door.  That internal satisfaction and hard-won conviction seems to have been much more important to her than the external trappings of recognition and, indeed, fame.

If she'd been a bloke, would she have had to wait more than 30 years between "the greatest astronomical discovery of the twentieth century" and getting a CBE or joining the Boy's Club as Fellow of the Royal Society?  If she'd been a bloke though, she wouldn't have had to put her career on free-wheel while she changed nappies and put plasters on small knees. Someone with less equanimity and more cynicism might suspect that she'd now become Jocelyn Bell Bandwagon as universities fall over themselves to give her honorary degrees.

The thing that far too few people acknowledge about JBB is her 30 year association with the (wonderful, empowering, facilitator of heroes) Open University: first as a tutor because she could do that while working part-time from home and much later as an inspirational Professor of Physics; infamously at the time doubling the number of such Chairs in Britain who had two X chromosomes..  She far more than doubled the number of teacher-researchers (rather than teacher-teachers) in her sector of the OU, because she believed that active researchers made better teachers.  There's much more to this woman than pulsars.

You don't have to be a rocket-scientist to succeed in science - the young Miss Bell failed her 11+ exam and so wasn't eligible for a free Grammar School place under RAB Butler's 1944 Education Act and she didn't get a 1st Class Honours degree from Glasgow.  Would her Upper 2nd Class Honours degree have anything to do with the fact that she was the only woman in a class of 50 taking Physics?  How about the fact that for two years, every time she entered the Physics lecture theatre she was greeted with hoots and cat-calls and coordinated foot-stamping?  Her response?  She learned quickly to control her blushing and got on with the physics.  The men who participated in this ritualised bullying, and not only in Glasgow, will also be about 70 now, and only a few of them will have joined the dinosaurs underground.

It helps if you have supportive parents who won't accept that at school boys do science-science and girls do domestic-science.  An inspiring science teacher also makes a huge difference - Henry Tillott in JBB's case.  You have to be prepared to work hard, with a pick-axe and wire-strippers if that's what it takes, or with a slide rule and deep maths if that is required.  Being at home with numbers and order-of-magnitude is useful: "I guess what I’m saying is, even in that first exam I had learnt to check that my answers seemed sensible, that when I came up with a numerical value, that it was reasonable, whatever reasonable means". You have to put in long hours . . . after the working day and at weekends if necessary.  You have to be able to park your certainties and see things with a fresh eye. You have to be agreeable . . . but not a push-over - some assertiveness training will help you hold your corner against authority figures when it matters.  OTOH, you don't have to treat kids and career as an either/or choice.  Juggling family and science is hard work but so is twirling a sledge-hammer.

Much more detail in a long interview.
The Blob's women in science: Florence Nightingale - Barbara McClintock - Maude Delap - Cliona O'Farrelly - Lynn Margulis - Rosalind Franklin - Jocelyn Bell Burnell

Guinea worm gone

I got a real good education in Graduate School in Boston. It was partly the formal courses which I sat on "subjects" that we didn't know existed in TCD back in Dublin: a whole semester on 'evolution' with Lynn Margulis, ditto 'mammalogy', ditto 'physiological ecology', ditto 'multivariate statistics'. But I also learned a lot from my fellow students: eating ice-cream & loading a salad bowl, for example. My boss, a man of wide interests, recommended that I read his old Parasitology text-book, which was on the shelves down in the basement where I was living. He was an aficianado of Dracunculus medinensis the Guinea worm.  You can hardly admit to loving this parasitic invader, but you can nevertheless be fascinated by its life cycle and the peculiar methods used to rid patients of the adult worms.  Dracunculus lives part of its life in tiny copepod crustaceans which swim about in tropical fresh water. When they are consumed my mammals, including people, who drink the water, the copepods get dissolved by the stomach acid and the Dracunculus larvae burrow through the wall of the intestine and develop into adults among the wobbly bits over the next 3-4 months. When a female worm meets a male, they love each other very much, the male sinks back exhausted and dies from his exertions, the female begins a slow shoving journey through liver and lights, muscle and fat, until she comes to rest just beneath the skin. Somehow this creature, knows where the legs are and tends to come to rest in the lower legs. But occasionally she gets blind-sided by other low hanging appendages and heads for the hand or <eeeuuuw> the scrotum. Her journey is exquisitely painful to the unwilling host.

Evolution has shaped the female Guinea-worm's behaviour to facilitate the continuation of her life cycle. If the skin above the lurking female gets wet, then she burrows rapidly to the surface and sheds thousands of eggs into the water in the hope that some of them will encounter a copepod. This sensitivity to water can be used to start a cure: wrap the leg in a wet towel then when the end of the worm breaks the skin surface you can seize it and e v e r  s o  s l o w l y draw the whole worm out. As she can grew to 80cm in length, this pulling can take several days.  You wrap your winnings round a twig or pencil to stop the whole thing slithering back into the flesh.  If you pull too hard then the bloody worm breaks and you have a serious case of septicaemia on your blistered legs. I'm sure that there were experts at these delicate extractions in many sub-Saharan villages.

I use the past tense advisedly, because at more or less the same time I was reading about Guinea-worms in Boston, retiring President Jimmy Carter was thinking about what he was going to do for the rest of his life. His existential solution was to endow the Carter Centre on some derelict urban blight in Atlanta, Georgia. This institution was established with the brief "to advance human rights and alleviate human suffering".  Grand for a mission statement but What to do next in detail?

• First build a complex of offices and auditoria, a library and museum, all set in lovely parkland, 
• Then appoint a Board of Trustees packed with the great and the good and capable of networking their way to solutions.
• Have the Board appoint Effectives to do committee work and decide how the substantial, but not infinite, endowment can be most effectively leveraged.
• Launch some specific projects: preferably those that will yield tangible results within the life time of the soon to be ex-President.
• It's also important to have projects that can be written up in a headline + 600 words by the Washington Post.

And it was so. Tuberculosis, Malaria, HIV/AIDS were left to other groups [Gates Foundation for example] with far deeper pockets. Along with election watching, the abolition of the death penalty and conflict resolution, the Carter Centre decided that they would take on the dreaded Guinea-worm which at the time in the mid 1980s infected 3.5 million people, mainly in sub-Saharan Africa. The map shows countries in which the worm was endemic in 1985, the hatched countries are those that still had worms 20 years later.  Now I read in Nature 10th Feb 2016, that Dracunculus has almost gone the way of all smallpox.  A combination of Carter Centre monogrammed winding-pencil distribution [kidding!]; water filters, education and political barracking has reduced the disease Dracunuliasis to a mere 22 cases in four countries for calendar year 2015: an astonishingly effective 100,000-fold reduction.  At one point, President Carter bluffed his opposite number in Ghana that with his clout he could persuade science to start calling Dracunculus the Ghana-worm.  “There isn’t a Guinea worm left in Ghana now, Carter told journalists with a grin . . . "  The remaining four benighted nations - Chad, Ethiopia, Mali, and South Sudan - are beset with civil wars that not even Carter's mediators can stop.  Civil war rides with pestilence and makes it really difficult for health-care workers to get where they are needed.

Lovelock gorn, dang!

Guardian reports that James "Gaia" Lovelock finally pegged out 2 days ago at the age of 103 . . . exactly. He was born on 26th July 1919. He made a modest fortune early on by inventing devices to measure minute quantities of specific chemicals in the atmosphere. With the money set himself up as an independent scientist and researcher (and prolific author) with his own lab on his own farmlet in the English West Country. Because you could, in those days, before the possession of property was polarized so fiercely between haves and have-nots. We made that cut also by purchasing, at public auction, a ruined farmstead and 7 hectares in 1996. Because Lovelock was a bigger person than I will ever be, he planted 10 hectares of his gaff with native English trees. We have contributed the twentieth part of that as our own arboreal carbon sink. He beat himself up about doing his planting wrong. But we should forgive the error as the logical nicety of a passionate but critical-thinking advocate. 

I met him twice, for a fleeting minute or two each time. Both times Lynn Margulis was in the room, actually or metaphorically, and it is appropriate to show these two maverick iconoclasts in the same frame:

There will be obits all over the place because, although regular scientists scoffed at the idea that our blue dot planet was a coherent homeostatic super-organism, nobody hated on him for questioning the status quo. I don't think he will have gotten any pleasure from dipping out before the most frighty of his predictions [agricultural failure and mass migration]came true. Although, at that talk I attended, he did implicitly compliment us for living in a place [Ireland is an island surrounded by water] that was likely to become an Ark for The Saved against the coming armageddon.

Chapeaux!