Olde Bald's eye salve

My first mentor was my high-school biology teacher, who had a fund of funny, and some downright peculiar, stories to help us remember the facts and relationships in life science. It was years before powerpoint, so the teaching was telling.  Once he read out, county by county, from a 19thC Flora the long list of common names for dandelion Taraxacum officinale. I was entranced. For a European perspective on the issue. For hot dandelion wine.  Another story was about a medieval remedy for a particular sort of mushroom poisoning.  This involved mashing up three rabbit Oryctolagus cuniculus livers, two rabbit brains and some other ingredients and chugging down the brew while it was still warm. Mr Wilkinson pointed out that, although this worked, modern science had revealed that the only active ingredient was the rabbit liver which housed an enzyme that specifically detoxified that species of mushroom. That allowed rabbits to get calories when other foods were scarce.  Those medieval healers hadn't read Claude Shannon's recipe for creativity, so that they never simplified the recipe to its bare essentials and so made application a bit quicker.

A couple of days ago I was browsing researchblogging and found a piece by Rosin Cerate, which brought the redundant rabbit brain story into focus. It's a wonderful collision between the Arts and Science starting with a close reading of Bald's Leechbook by Freya Harrison, Stephen Diggle et al. at Nottingham U. Bald's pharmacopoeia was written in proto-English 1000 years ago and describes infections that we recognise today from the symptoms to be caused by Staphylococcus aureus. The methicillin-resistant variety of this bacteria MRSA is what frightens old ladies going to hospital for hip-replacement surgery and kills several every year. Old Bald didn't know anything about microbes but he recorded a recipe [L] for an eye-salve that worked. Harrison and Diggle provide a gloss for the words shown in the picture “Ƿyrc eaȝsealf ƿiþ ƿænne: ȝenim cropleac ⁊ ȝarleac beȝea emfela . . ." "Make an eyesalve against a wen: take equal amounts of cropleac and garlic, pound well together . . .". This had a certain resonance for me because I was beset with Staph infections when I was a child: boils, styes, carbuncles almost every week: all painful and full of pus.  The recipe combines two species in the genus Allium 'cropleac' and garlic crushed in wine and oxgall and left to steep for 9 days in brass vessel. After this the poultice can be applied to the infected eye with the tip of a feather.

These are not unreasonable things to put into an anti-bacterial concoction, garlic is known to produce anti-microbial chemicals; brass has been long known to be anti-microbial, probably because brass is 2/3 copper [and 1/3 zinc] and the wine will soon turn acid and that will help dissolve the metals into the stew.  The lads from Nottingham have reconstructed the 10th century recipe going to some pains to be todo authentico: 1) using an organic English wine 2) Sigma-Aldrich "bovine bile salts" 3) garlic Allium sativum mixed 4) with either onion Allium cepa ES-O or leek Allium ampeloprasum ES-L to stand in for the cropleac .  What's really interesting is that all these ingredients on their own are not significantly different from the control [L] but that the two full-monty treatments ES-O and ES-L bring down the concentration of S. aureus about a million-fold [L lower values circled in red].  Old Bald and his school knew a thing or two about what worked and what didn't and seem to have developed a recipe that that was sufficiently complex but not too complex. It is the flip-side of Einstein's restatement of Occam's Razor "A scientific theory should be as simple as possible, but no simpler." This whole story is just marvellous: simple, thoughtful, cross-disciplinary and clearly a lot of fun.  If all science was like this, there would be less completely useless unreadable and unread uncited papers to clutter the library bookshelves.

Bones: what counts?

In the certainties of the limited world of Trivial Pursuit and pub quizzes there is one answer to any question. The QM's decision is final; because s/he got it out of the back of the Compendium of Table Quiz Questions and it must be true.  It is bad form to argue at pub quizzes, it's meant to be fun as well as isn't-Bob-clever. and the money is going to a good cause.  But questions with only one answer aren't very interesting and that's why QI, the thinking-person's game-show is in its 13th season. Although, if you see that clip you'll wonder that any of the QIstas have survived. An earlier stodgier version of the concept was a BBC production called The Brains Trust that ran through the 1940s and 50s on wireless and TV and Pathé News; there you could use a word like self-abnegation without blushing. One of the egg-heads was C.E.M Joad, who started many of his answers with "It depends what you mean by . . .".  B'god that's a welcome introduction to almost anything that's worth investigating.

Q. How many bones in the human body?
A. 206!! they all cry with confidence.

At The Institute we have up-graded the Counting Dem Bones practical from a stop gap to a written-in-the-manual item for all 1st Year cell biologists.  We've also found Bob the Skeleton in a dusty cupboard and have that as a resource for the exercise. Most of the ribs on Bob's left side have been replaced with PVC tubing and he is festooned with gobs of ancient glue and crumbly sellotape which have long since ceased to hold him together. It was good fun, getting the folks to think a little and realise that it's quite hard to find where the '206' comes from or is comprised of. One of the key realisations was that, in 206-land, the sacrum and coccyx at the base of the spine are considered 2 bones not the 5 and 4 bones which a cursory examination [L above]reveals them to be. There is indeed a good bit of inter-personal variability here as to the amount of bone fusion and even as to how many bits are present.

Contrast this with the skull which is treated as 22 bones out of 206 rather than two that Josie Public sees with her own two eyes: skull & jaw-bone. N=22 does not include the 3 teeny bones in each ear-hole: the stirrup stapes, [R at something approaching life size] hammer malleus and anvil incus, and N=206 does not include these ossicles either.

If you're interested in your bones - and who isn't? - you should concentrate half your attention on the limbs because they comprise half of the bones: mostly in the hands and feet. Interestingly the front and back limbs have the same number of bones but in different places. Legs have a patella halfway up but there is no equivalent at the elbow joint. OTOH, the ankle has one fewer bone (tarsals=7) than the wrist (carpals=8) [R above]. Otherwise the structure of each limb is uncannily similar: down to the 3 phalanges in the little toe, the smallest of which could easily get lost if you dropped it in the rice.  And the great toe and thumb both have only two phalanges.

I was reading up on the wrist bones and the pisiform (pea-like) was referred to as a sesamoid bone. These are peculiar bones, named after sesame seeds, which develop entirely or partly enclosed in tendon. The patella is the largest of this class of bone and nobody from 206-ville considers excluding either patella or pisiform.  But sesamoid bones are 'commonly' found at the toe-end of the metatarsals [L above as x-ray ghosts] and also at the base of the thumb. I say commonly, because the appearance and number of sesamoids is higher variable between people. Other examples of human osteo-polymorphism in my earlier piece. Why aren't they included in the 206? They are a lot bigger than the ear-bones.  Indeed, there should be N=4 ear-bones as the lenticular process of the incus is a teeny-tiny sesamoid bone with a separate developmental origin. Sesamoid bones got a brief pulse of press in 1980 when an extension of the radial sesamoid got tribbed in Stephen J. Gould's [previously] famous essay The Panda's Thumb and the book of the same name.
The count of bones is thus arbitrary and capricious and very bad science until you get under the covers with Bob the Skeleton. When the Quiz-master asserts that N=206 you are well within your rights to cry "It depends what you mean by . . .".

Mighty Shannon

A few days ago, I was talking about John Cleese and his attempts to get to grips with the act of creation through reading the key sources and relating those findings to his own experience. I've also alluded to the sources of inspiration experienced by mathematicians such as Cedric Villani. On a personal note, in a life time of science, I've had three good ideas, one of which probably turned out to be wrong. I've had a few more Aha! moments, to be sure: it would have required enormous patience and dedication to carry on at the coal-face getting positive feedback only once a decade.  I've suggested that one way to get an idea is to have half an idea and then lob it across the table at some colleagues. Famously, when Sydney Brenner and Francis Crick shared an office in the MRC for 20 years, they had a rule that either could say aloud whatever came into his head.  If you've got no friends, then I've found that cycling to work has delivered, not only mighty thighs, but also a good number of insights and solutions to problems. The exercise increases the circulation to the brain (and everywhere else); to survive a decade of city cycling you have to be alert; that extra brain activity can unconsciously be channelled into problem-solving.  That's handier than Poincaré's solution to having ideas which asks you keep stepping onto buses preferably in Normandy.

Now here's a novelty: we live on - are the only inhabited house on - Shannon's Lane in the Blackstairs Mountains hills.  It's named for the family that used to live in our farmsteading. The most famous member of the Shannon clan is surely Claude Shannon the mathematician and engineer. He became the Father of Information Theory FIT by applying Boolean logic to circuit-boards while working in Bell Labs. We'd probably have got to universal mobile phone usage and rockets to alpha-Centauri without him but it would have taken longer.  During WWII, he met Alan Turing and had a conversation in which half ideas were lobbed back and forth across a canteen table. Part of me wishes I'd been a fly on the ketchup bottle taking notes, but the other half knows I'd have been unable to follow the Smart Guys as they romped through ciphers and circuits way above my head. It turns out that a re-found friend of mine is also interested in the trappings of creativity. His father wrote A History of Engineering and Science in the Bell System, so knew a thing or two about The Shannon. As well as being a whizz at information theory, code-breaking, robotics, juggling, unicycling and chess, Shannon had thoughts about where the ideas came from. His piece on Creative Thinking, written in March 1952, is pages 529-538 of Claude Elwood Shannon Miscellaneous Writings edited by N.J.A. Sloane and Aaron D. Wyner which is available as a mammoth PDF (half Gbyte!). I've filleted out the relevant pages as a separate, much smaller, PDF.

Here's the executive summary of what Shannon, a true creative genius, had to say on the matter of thinking creatively.  Back in our Geordie days in the 1980s, there was a radical Scottish theatre group called the 7:84 Company; named for the observation that 7% of the people owned 84% of the wealth.  Shannon believes this to be true of creative people: most of the useful ideas come from a tiny subset of the whole population.  The same power law applies to word use in any language and to publishing where Harry Potter sold as many copies as the whole rest of 20thC fiction.  He believed that three attributes needed to be present in a truly creative mind.

• Experience, training, knowledge.  You have to know something about the field before you make earth-moving contributions.
• Smarts, nous, IQ. Creativity is not for dullards.
• Drive, curiosity, motivation. Creative people like to find things out, how things tick.

He then goes on to elaborate on attributes, some of them possibly trainable or learnable, that increase the hit-rate; perhaps particularly through early experience when we are little more limber in the brain.

• Positive dissatisfaction.  A hard-to-shake certainty that we could do better . . . at everything. If we tweak this and try that, it might all work more efficiently.  It is the opposite of a lazy-arse, pragmatic "If it ain't broke, don't fix it".
• A deep appreciation of a neat&nifty result, even if you haven't arrived at it yourself.
• A terrier-like determination to finish things off, even if it means missing lunch or staying late. [I was never so alive as when I was in graduate school working all the waking hours].

Shannon then lists his toolbox, the tricks of his trade that had helped him find solutions to the most intractable of problems.

• Simplification. Trim the fat off the problem and reduce it to its bare necessities. Identify the key issues and stop being distracted by details on the surface. Having sorted the core, you can re-clothe the whole with refinements and additions.
• Seek similar.  This is where deep knowledge of the field pays off: you have in your head hundreds of previous problems and their solution. Andrew Wiles saw the similarity between two utterly different branches of mathematics to solve Fermat's Last Theorem.
• Restate, review, look sideways.  Get a different perspective on the problem: go for a run, write it all backwards. This is where a [smart] greenhorn, with no experience (but no baggage), can make the key contribution.
• Generalisation. Take your narrow, limited, specific solution and ask, with a creative person's restless curiosity, if it is applicable in other cases, under other conditions in different fields.  "Can I use this same clever idea represented here to solve a larger class of problems?"
• Deconstruction.  If you think hard you may be able to show the essential structure and connectivity of the problem.  That will help break a lumbering monster into chewable slices which can be knocked off piecemeal.
• Clunky is okay.  A first working model may be a kludge, held together by chewing gum and string, but, hey, it works.  See above for how positive dissatisfaction will streamline your monster into something more elegant and efficient.
• Turn it over.  Sometimes the different perspective is to take the solution and work back to find the problem.  Our technological world is full of inventions that had no purpose until they existed as solutions: the glue on post-its, thalidomide as therapy for leprosy, teflon, Sugru.

Good luck, I hope you have good more ideas than me.

The Rights of Women

"It was the best of times, it was the worst of times, it was the age of wisdom, it was the age of foolishness . . ." is how Dickens' Tale of Two Cities launches into a story of romance and honour set in the midst of the French Revolution. It was certainly interesting times, when everything was thrown up in the air and [the] people were invited to choose what to keep and how to arrange the pieces into a coherent and fairer world. In August 1789, the French National Constituent Assembly published a "Déclaration des droits de l'homme et du citoyen!" - the Rights of Man - enumerating what seemed to be the natural rights of Everyman.  If we were to follow the precepts of the Declaration, we'd all get a fair crack of the whip rather than a relentless lashing from those who held the reins of power. The stamp of Thomas Jefferson is all over the document although seemingly channelled through General Lafayette [aka Marie-Joseph Paul Yves Roch Gilbert du Motier de Lafayette, Marquis de Lafayette for the full monty]. It includes such wisdom as Art 4. "La liberté consiste à pouvoir faire tout ce qui ne nuit pas à autrui . . ." or "Your rights end where my nose begins" It was stirring and inspiring stuff until someone pointed out that it only applied to half of humanity.

Olympe de Gouges [on the left where she was happiest] took two years over it - she was busy surviving the buffets of a revolution as well as having a lot of other material to get down on paper - but in September 1791 she launched her counter-blast to reset the scales of justice: Déclaration des droits de la Femme et de la Citoyenne. You can get the full text in English to see whether you agree.  Such a statement as "Art 17. Property belongs to both sexes whether united or separated; it is for each of them an inviolable and sacred right, and no one may be deprived of it . . ." was not implemented in English law [and by UK extension in Ireland] until the Married Women's Property Act of 1882. It would have been infinitely frustrating for Olympe to see her aspirational and inspirational Declaration ignored for the best part of a century.  But she did not live in this frustrated state for long.

She wasn't about to go quietly along with the political flow; no, she was going to continue her prodigious output of plays, essays and pamphlets.  All of them vehicles for what she believed to be right and what would make France and the World a better place. She was, for example, an abolitionist decades before it became mainstream.  I don't suppose Jeremy Bentham, another early abolitionist, was any more accepting of her ideas than he was over Les droits de l'homme - "nonsense on stilts". Like a lot of our current ideals, Olympe's polemics were only partly universal and for all time; and partly limited by her own imagination of what was possible living in the 1790s, not the 1590s or 1990s. Although an independent and original thinker and writer she was associated in the political/public mind with the Girondists. When the balance of power tilted towards the Jacobins in the Summer of 1793, the Girondists were swept up in a razzia and banged into jail, Olympe de Gouges amongst them. She continued to write from jail until on 2nd November she was put through a show-trial worthy of Stalin or McCarthy and on 3rd November 1793 she mounted the scaffold to be guillotined. It's quite hard, at this distance in time, to appreciate the ideological, let alone the practical and effective, differences between Jacobins and La Gironde; surely not enough to execute people about. That's what I mean about trying to see things from outside your own certainties.  On a cosmic scale of politics there is no difference between Republicans and Democrats in the US or between Fianna Fail and Fine Gael here. Each party has a tale, told by an idiot, full of sound and fury, signifying nothing. If we get all hot and bothered [Ireland must hold a general election before the end of February 2016] about minute differences of policy we are condemned to living the same-old-same-old for ever.  Bring on the dancing elephants, let the circus begin.

21 seconds to empty

. . . the bladder.  The Ig Nobel awards have been running for 25 years now.  They were set up by the team from the Annals of Improbable Research [not to be confused with The Journal of Irreproducible Results]to give tribs to scientific papers that "Make you laugh . . . and then make you think".  We've had Benoit Mandelbrot giving a talk at the award ceremony previously.  When you consider that serious science is full of sleepers that are never heard from again (45% of scientific papers are never cited), then the hit rate is far higher at the quirky end of the spectrum.  If your reaction is WTF would anyone want to spend time over such a problem, or even harrrumph!: waste of tax-payers money. then you're quite possibly wrong.  We know not where the next inspiration and the next great leap forward will come from.  It is almost certainly not going to come from science funded by government agencies that are trying too hard to get short-term results.

One of the 2015 awards that caused a brief flurry in the press several weeks ago was the finding that all mammals that are bigger than a breadbox [3kg to 3000kg aNNyway] take the same time to empty their bladders.  Much of the coverage was a perfectly dreadful soup of coyness, archness and cheap jokes. Livescience was one of the better takes on the reportage. It seems that David Hu of Georgia Tech was changing a particularly brimful diaper and wondered about the bladder-capacity of an elephant. Whatever the reasons for starting the investigations, the results are definitely counter-intuitive.  Lots of things scale up as dimensions increase and not always in a linear fashion.  For example, a newborn baby weighs about 3kg and is about 0.5m long. Over the next 18 years, the length will increase by 4x but the weight by 20x (or more if obesity is at issue).  But the size of the cells doesn't change: a red blood cell is 8µm across from cradle to grave.  Indeed r.b.cs are the same size across the whole range of mammals.  It's because the physical chemistry of gaseous exchange between the rbc and the walls of capillaries [which are also 8µm across) is so clever, intricate and complex that it hasn't been invented twice; it's just been increased in network size.  Same for cells-in-general, they are an average of 30µm across, so mice have fewer cells than we do rather than the same number of smaller cells.

It's a different constraint in the neck.  All mammals have seven (7) cervical vertebrae: all of us from pygmy shrews Sorex minutus to hump-back whales Megaptera novaeangliae have the same neck-bone count. It is these cross-species similarities and scalings that allowed Georges Cuvier, the father of comparative anatomy to say that he could reconstruct the whole animal from a single bone.  The humerus of an elephant is built like a tree trunk because they both have to support enormous weights; a bat's humerus not so much.

Most of us would think that an elephant's bladder, at full 18 lt capacity, would take a considerable time to void and a cat's rather less. That's working on the assumption that the urethra [the tube between bladder and out; not to be confused with the ureter the tube between kidney and bladder] would be, like a capillary, be about the same size in all species. But Professor's Hu's team has shown that this is not so: urethras are all in a length to width ratio of 18:1 regardless of absolute size. They are vessel-emptying devices.  For mammals smaller than a bread-box, the rule doesn't hold: at small sizes the physics of water, including surface tension, comes to the fore and, although rats and mice have bladders, they tended to be dribbly.

Last month at Wexford Science Café we discussed a cunning plan by the Irish Times to carry out a massive crowd-sourcing project like their scheme earlier in the year to gather genetic data about domestic cats.  That persuaded more than 10,000 people to share these data about their cats, without any of them paw-signing an informed consent form. If you're in the science zone, it shouldn't be hard to think of a question that can be addressed scientifically without needing any expensive kit or hours of time. The sample size being beefed up, and the scientific value thereby enhanced, by multiple participants. With 21-seconds-to-pee somewhere near the fore-front of my mind, I'd spent the previous several days counting "1 battleship, 2 battleship, 3 battleship ..." - but not necessarily aloud - every time I took a leak and was accumulating data. The headlines about the Georgia Tech study have all been about the average length of time it takes to empty bladders of all sizes. But biology is at least as much about variability as it is about the mean and the central tendency. Indeed it is the variability that makes life so interesting. This will strike those who know me as far far too much information TMI but I'm quicker than most - about 16 seconds.  In a week you could get a sample of 20 emptyings each with a time-of-day.  10,000 people, male and female, young and old, diabetic and post-partum could generate a dataset worthy of analysis.  Who's with me?

It would be a poor show if we allowed the talk of passing water to pass without recording a hilarious example of Dublin street wit. In 1966, to celebrate the 50th anniversary of the Easter Rising, Dublin City commissioned a statute of patriot Thomas Davis [R] incorporating a fountain representing the heralds of the Four Provinces showering the country with the good news of national identity. The installation was instantly christened Urination Once Again.  On a more serious note, if you're a young chap you will not need instructions about how to empty your bladder but this link will explain that not everyone can take this essential life-skill for granted.

Sunday sofa 011115

• Yesterday was Ali Farka Touré's birthday, or it would be if he hadn't died in 2006 [bummer]. You might try this or this or with Ry Cooder for a little background music from Mali.  You'll be happier all day.
• Here's a nice little film about ultra-running - Ultra-trail du Mont Blanc, through 3 countries.  You have 46 hours to finish.
• The importance of jumping in rivers by Alastair Humphreys who has done longer journeys and recommends cold-showers if rivers are not conveniently available.
• The least dreadful clip I could find about the Milford Track; some of the others would make you want to walk somewhere else . . . anywhere else. The blue duck Hymenolaimus malacorhynchos is said to go down nicely poached in red wine.

First Counties in Aotearoa

I have friends&relations on the other side of the World, so have an interest in their demographics and politics flags. When New Zealand / Aotearoa was first colonised, the Islands were divided into 9 administrative provinces. On 1st November <today!> in 1876 these provinces were replaced by 63 counties and 7 boroughs.  My source can only identify 62 of the counties.
Counties and Boroughs in New Zealand 1876 with population:

Mongonui	1204	Wanganui & boro.	6308	Geraldine	13164
Bay of Islands	1489	Rangitikei	3690	Waimate	4269
Hokianga	419	Manawatu & boro.	5730	Waitaki	11595
Hopson	2171	Hult & boro.	25960	Waikouati	10826
Whangarei	2906	Wairarapa West	7163	Peninsula	2195
Rodney	3122	Wairarapa East	1100	Taieri	41318
Waitemata	3424	Waipawa	4721	Bruce	6814
Eden & boro.	32491	Hawke's Bay	9559	Clutha	3731
Manukai	9152	Sounds	570	Tuapeka	7109
Coromandel	2053	Marlborough	6117	Maniototo	2801
Thames & boro	10375	Kaikoura	782	Vincent	3937
Piako	34	Waimea	13641	Lake	3533
Tauranga	1550	Collingwood	1477	Southland	16315
Whakatane	783	Buller	3557	Wallace	3261
Cook & boro.	2745	Mangahua	2970	Fiord	13
Wairoa	809	Gray	7767	Stewart Island	245
East Taupo	95	Westland	11606	Auckland	13758
Waipa & boro.	3259	Amuri	458	Wellington	18953
Waikato & boro.	2460	Cheviot	117	Nelson	6604
Raglan	797	Ashley	12842	Christchurch	13425
Kawhia	69	Akaroa	4364	Sydenham	6510
Taranakai & boro.	7369	Selwyn	50720	Dunedin	22525
Patea	2988	Ashburton	6123	Invercargill	3761

In the 1878 census, two years later, the authorities chose to enumerate all the Chinese [N=4382] and half-castes [1932] but not the Maoris, who in this register are invisible, except in the naming of counties, more than half of which have Maori names. All the 'cities' have names from back home. The population is now [4.6m, the same as Ireland] about 10x what it was 140 years ago. You'll be struck by how small the population of some of the counties is.  Fiord County is now called Fiordland and still has a tiny resident population [N=20, in 2001] and a lot of fiords <surprise!>. The first thing The Boy did on his 2005 arrival in New Zealand for his working year for young people was slog along the Milford Track in Fiordland: a +50km limited access trek in one of the beautiful areas on the planet - I've seen the pictures.