Nearly two years ago towards to Birth of the Blob, I wrote a comment on a poorly nuanced RTE report about the association between diabetes and 7up (and other sweetened soft drinks). If true it needed to be stated in a less hysterical fashion to convince me. One of the factors that tuned my skepticism antenna was the fact that diet coke appeared to make you even fatter than regular sugar-loaded soft-drinks. Although, when the increase in diabetes was properly contexted by BMI, the apparent association disappeared. Turns out I was quite possibly >!gasp!< wrong . . . to think that aspartame and saccharine were irrelevant to the obesity epidemic.
It's all in the microbiome, stupid: the 10,000 species of bacteria that we all tote around with us, mostly in the large intestine. On 18th September last year, there was a nutrition report which laid out some pretty convincing evidence that drinks loaded with artificial sweeteners, far from being a solution to our increasing girth might actually be making things worse. Check out the work of Eran Elinav from the Weizmann Institute in Israel. Elinav at the movies! One of the early (that's as long ago as 2006!) studies searched for twins, identical and fraternal, who differed primarily in trouser size. They took twin-paired samples from the twins' intestinal flora and introduced them into germ-free (caesarian-sectioned, brought up in a bubble eating gamma-irradiated mouse-chow) genetically identical mice. The mice receiving the 'obese' bacteria reliably ballooned out, while their cousins who received slim bacteria gained weight at half the rate. Why is this important? Because we have in the last 100 years developed an epidemic of "metabolic disease" - a syndrome involving the woes of Western society: obesity, diabetes, fatty liver, high blood pressure and heart disease.
They have now done similar controlled experiments with mice getting artificial sweeteners in the water and mice getting glucose. The mice taking saccharine.etc. rapidly developed glucose intolerance. If you experience the following symptoms and are not recovering from a night on the batter, you might consider seeing your diabetologist: Feeling very thirsty; Dry mouth; Extreme tiredness Blurred vision; Drowsiness; Frequent need to urinate; Loss of muscle mass. Glucose intolerance essentially means that glucose doesn't get cleared from the blood circulation quickly after food intake but hangs around rather than getting converted into glycogen for future use. Apart from anything else, glucose is a universal currency and you are much more likely to develop septicaemia if you are hyperglycaemic - peripheral gangrene, anyone? Convincingly, this glucose intolerance evaporated when the mice had their intestinal flora eliminated with a short course of broad-spectrum antibiotics.
Perhaps the most important factor that has developed from Elinav's huge sampling of people, their lifestyle, their circulating glucose levels and their microbiome and cross-referencing of these different threads (or tsunamis - we're talking terabytes of information, here) of data is that Folks are Different. The Atkins diet may work a charm for that lady you met at the water-cooler . . . and her sister; but will do nothing at all for you because your bacteria are not her bacteria. When I was working in St. Vincent's Hospital a dozen years ago, we were just beginning to talk seriously about personalised medicine: only 50% of people with chronic Hepatitis C Virus infection will respond to interferon-α therapy, and it costs €12,000+ a year, so we'd dearly like to know who will respond: not least because the side-effects of interferon are almost as bad as the disease. Now we are clearly talking about personalised intestinal bacteria. There are people out there, whom I've never met who have something in common: they have essentially the same bugs as me and therefore the same pitch of glucose intolerance, possibly similar food preferences, the same sort of winter sniffles.
As this intestinal flora changes radically and within a couple of days when we have a change in diet, it is not beyond belief that the bugs inside are telling us what to eat. That, frankly, seems a little invasive.
Saturday 28 February 2015
Friday 27 February 2015
The Lady of the Lead
Her mother had instilled a strong sense of social justice by conspicuously disapproving of such societal norms as lynching black men, child labour and police brutality. So it was not completely out of character when Alice announced that she wanted to be a doctor to help poor people in the slums of the grossly unequal society that was the USA in the early 1890s. To this end, she cobbled together an education in biology, physics, chemistry and anatomy and enrolled in Medical School at U. Michigan. That was a good fit and she found that her bleeding-heart ideas of helping the poor took better focus in the idea of doing clinical and laboratory science to help the poor. She did a year of postgraduate research with Simon "Shigella flexneri" Flexner, one of the giants of 19thC microbiology, at Johns Hopkins U in Baltimore. Then she went on a tour of Germany with her sister Edith: brushing up their languages, doing the galleries and . . . auditing university classes in pathology and microbiology.
On her return stateside she landed a job teaching pathology at Northwestern U in Chicago at the same time as finding a billet in 1897 at Hull House; an extraordinary experiment in living where middle class people lived cheek-by-jowl with the dirt-poor and attempted to bridge some of the gaps between their unequal lives. Such "settlement houses" were loosely modelled on Toynbee Hall in East London. A few years later she was invited by the Governor of Illinois to serve on a committee of physicians investigating industrial sickness in the lead, paint and munitions industries. Work-place sickness was a consequence of industrialists itemising 'labour' as an expendable and seemingly bottomless resource: there was always some fresh chap off the boat from Europe who would work under any conditions to get a foothold on the ladder of the American dream. Health&Safety was a) expensive and b) hadn't been invented yet.
Thursday 26 February 2015
Orcadas
Those of us over the age of 40 should remember the 1982 Falklands War aka La Guerra del Atlántico Sur or even La Guerra de las Malvinas when the Argentine government pushed to see just how craven the Brits would be in defense of their much dwindled empire. The 1970s had seen a see-saw between ineffective Labour and ineffective Conservative governments in Britain, one of whose heads of agreement was that the British Empire was something definitely retro and probably shameful. In Argentina, over the same period, democracy had been put on the back-boiler while a succession of Generals filled out their chests with a nugatory bling of self-awarded medals and threw shapes at each other while authorising the midnight dispatch of any real or presumed leftists. In May 1979, Margaret Thatcher was elected Prime Minister and in December 1981 Leopoldo Galtieri toppled a rival general to become El Supremo. With the finances in total shambles, Galtieri opted to divert attention from the economy by assaulting the sheep farmers of the Falkland Islands. Huge patriotic flag waving in Buenos Aires was matched in the UK and 74 days later the status quo ante was restored. It cost a mort of money and 907 people, including 3 friendly fire civilians, were killed; 2432 were wounded; with Argentine sailors and squaddies a disproportionate chunk of the casualties. Status quo ante included the continuing claims of both nations to sovereignty over the Islands - and by extension its dependencies.
It wasn't always so belligerent between the countries and last week marked an anniversary of territorial accord between the nations. It concerns the South Orkneys a little [600 sq.km] archipelago of wind-swept islands about as far South as the original Orkneys are North but with a significantly more brutal climate - bless the Gulf Stream that the Olde Orkneys are not ice-bound for more than half the year. Bob the Island is not a million miles away. The South Orkneys were discovered in 1821 and named and surveyed by the sealer and explorer James Weddell in 1823. You can see [maps R] that his attempt at a geographical survey got the count and relative location of the islands more or less correct but with large topological distortion of their perimeters. 80 years later, in 1904 William Bruce explored the South Orkneys, carried out a proper geographical survey and established a weather station on Laurie Island in the East of the archipelago. The polar establishment of the day, including the revered Robert "Deathwish" Scott and a peculiar eccentric called Sir Clements Markham, chair of the Royal Geographical Society, were terribly gentlemanly - provided they got their own way. Bruce, a Scot, tried to join the club, never fit in and was reviled when he launched the Scottish National Antarctic Expedition without the RGS's permission (cad, bounder).
When Bruce's expedition was forced by end of funds to wrap up the Antarctic weather station he, with the consent of the British Government, sold it as a going concern to the Argentines for 5,000 pesos. They have occupied it continuously ever since with a small community of meteorologists, seismologists and glacier boffins. They are 1500km South of civilisation at Ushuaia, if you can call a town of 50,000 inhabitants in Tierra del Fuego [previously], 'civilisation'. The Argentine position is shown as a red dot on an isthmus of Laurie Island. The current name of the station "Orcadas" is nothing to do with killer whales Orcinus orca but taken straight from the name of the place in Spanish Islas Orcadas del Sur. In 1947, after two world wars, the British established their own weather station, marked with a Kelly green blob above [L] at the head of a sheltered bay on Signy Island 50km further West. I guess there aren't that many options when 90% of the parts above sea level are covered in glaciers. The Falklands War left these outposts untouched.
Wednesday 25 February 2015
Koraalduivel
Now here's a story that some F*@&!ng idiot dumped a gravid female into the warm water off Fort Lauderdale Florida in 1985 (rather than eating her and have done with it) and her offspring have since spread over 4 million sq.km across the Caribbean and down the coast of South America. It has been a lot worse than flushing a Christmas-gift crocodile down the toilet into the NYC sewers [Snopes: not true!] because lionfish eat a lot and grow fast and there are no natural predators on that side of the Atlantic. There seems, however, to be a solution akin to weeding your rose-garden. The things you like (roses, native fish and crustacea) may be in danger of being swamped to oblivion, but can be given a competitive edge by some selective culling. You know that no amount of pulling nettles Urtica dioica and scutch Elymus repens from your roses is going to eliminate the weeds but a little work on that front will let you see the flowers. There have been a number of ventures and competitions to encourage scuba divers and snorklers to take out lionfish because they taste so good but mainly because a prize or bounty has been offered. A controlled experiment in the Netherlands Antillies showed that a culling scheme in Bonaire reduced the biomass of these predators to a quarter of that seen in nearby Curaçao.
The 2002-2003 Victorian Fox Bounty Trial [PDF] is cited as a cunning plan that was expensive and did not work. $A10 was paid out for each fox-tail that was submitted to a score of centres across the State of Victoria in Australia. 150,000 tails were turned in for cash and there was no significant impact on the density or depredations of the foxes Vulpes vulpes (one of several European mammals introduced to Australia in the 19thC. There are even suggestions that the cull increased the number of foxes by disrupting the local social structure or encouraging the influx of foxes from outside the culling area. There is certainly anecdotal evidence that fox-tails were shipped in from outside the State by enterprising bounty-hunters with cousins up-country. Despite the evidence that bounty-hunting in 2002-2003 was useless, the scheme was allocated another $4 million in 2011 for a repeat performance that is still current. Agronomists in these WEA islands are convinced that killing badgers Meles meles is an effective way of preventing tuberculosis in cattle, but this is really more of an article of faith than strongly backed by scientific evidence. There is evidence with badgers that culling in one area will encourage influx of fertile badgers from the surrounding area.
Hello? Research? Evidence?
Tuesday 24 February 2015
One jot or two tittles
. . . that is the question. It is amazing how the vehemence with which a position is held is in inverse proportion with its importance. In the King James Version of the Bible, Matthew 5:18 is rendered as "For verily I say unto you, Till heaven and earth pass, one jot or one tittle shall in no wise pass from the law, till all be fulfilled." Which says that the law will not be changed in the slightest degree. Jot is a corruption of Greek iota, in turn a corruption of yod - י - the smallest Hebrew letter and tittle is the diacritical mark that we put on top of i and j; who says we don't have accents in English? ANNyway, what we are concerned with today is is neither jot nor tittle but the much more important issue of whether you should put two spaces after a " . " [full stop = period for yankee-dogs] or just put one.
Somewhere along the way, I was taught that you should put .<space><space> but ,<space> and ;<space>. It wasn't in school because typewriters weren't invented when I was in school, so it was probably in Graduate School in Boston. But I've heard a lot of people saying that this is just too 19thC altogether and I should get with the .<space> programme. But I don't feel strongly either way and I'm not about to correct it if students follow one regime or the other or even if they apply the two options indiscriminately . . . nope, I have enough on my plate dealing with rogue apostrophe's. I think I'll have to change the habits of a life-time because the blogspot editor translates the first of my two <space>s as " " which is HTML for non-breaking space which can make a mess of line-feeds and carriage-returns and make my posts
look
ragged and unprofessional.
I was talking about this at The Institute yesterday and made a jeering comment that if Smithers used .<space><space> he was showing his age: "must be over 40" I said. But, as you do, I promptly went to google with "period two spaces" and found a gratifyingly shouty variety of opinions. Including one which proved that I had plagiarised someone (as you do) "Nothing Says Over 40 Like Two Spaces after a Period!" [and see L]. Well that's pretty clear. A nerd from Slate is rather more cross and certain with "Space Invaders: Why you should never, ever use two spaces after a period." There is, of course, a counter-position [without which there would be no war] from the Chicago Manual of Style blog : "About two spaces after a period. As a US Marine, I know that what’s right is right and you are wrong. I declare it once and for all aesthetically more appealing to have two spaces after a period. If you refuse to alter your bullheadedness, I will petition the commandant to allow me to take one Marine detail to conquer your organization and impose my rule. Thou shalt place two spaces after a period. Period. Semper Fidelis." Ooooh frighty me! Lifehacker warns about .<space><space> age discrimination in preparing CVs/resumés.
The standard trope is that we use .<space><space> because that was the only way that you could give more weight to the full-stop with an old fashioned typewriter that for mechanical reasons had to deliver fixed-width fonts like Courier: in which I've written this sentence. But you might reflect that such crude typography only held sway for about 120 years between, say, 1880 when typewriters replaced a clean copperplate hand written with a quill pen and, say, 2000 when my aged-77 Uncle embraced a word-processor to write his letters. In my research into the question, I've had an education in whether the tail or the dog was wagging the spaces.
Here is an interesting short overview of a couple of centuries of typography showing that the conventions evolve. And hey, they are just conventions like its vs it's [see last para of my review] and the sky won't fall if you encounter someone who marches to a different convention/drum. Moveable type, however, has been spreading the word since 23 February 1455, the traditional date for when Gutenberg published his Bible; [R ALEPH quomodo sedit sola civitas plena populo facta est quasi vidua domina gentium princeps provinciarum facta est sub tributo BETH] that's a staggering 560 years ago yesterday.
But you should always go with the flow if it doesn't cost you too much: "As a practical matter, however, there is nothing wrong with using two spaces after concluding punctuation marks unless an instructor or editor requests that you do otherwise." This is what scientists do in response to the inane and ill-informed comments that referees have made about their papers when they come back from a round of peer-review. It's galling to accede to their fatuous suggestions but easier for everyone if you just rewrite your paper to tick their boxes. When their helpful suggestion will require your student to soend another 6 months at the lab-bench - that's when you polish off your Diploma in Assertiveness and start fighting your corner.
Somewhere along the way, I was taught that you should put .<space><space> but ,<space> and ;<space>. It wasn't in school because typewriters weren't invented when I was in school, so it was probably in Graduate School in Boston. But I've heard a lot of people saying that this is just too 19thC altogether and I should get with the .<space> programme. But I don't feel strongly either way and I'm not about to correct it if students follow one regime or the other or even if they apply the two options indiscriminately . . . nope, I have enough on my plate dealing with rogue apostrophe's. I think I'll have to change the habits of a life-time because the blogspot editor translates the first of my two <space>s as " " which is HTML for non-breaking space which can make a mess of line-feeds and carriage-returns and make my posts
look
ragged and unprofessional.
The standard trope is that we use .<space><space> because that was the only way that you could give more weight to the full-stop with an old fashioned typewriter that for mechanical reasons had to deliver fixed-width fonts like Courier: in which I've written this sentence. But you might reflect that such crude typography only held sway for about 120 years between, say, 1880 when typewriters replaced a clean copperplate hand written with a quill pen and, say, 2000 when my aged-77 Uncle embraced a word-processor to write his letters. In my research into the question, I've had an education in whether the tail or the dog was wagging the spaces.
But you should always go with the flow if it doesn't cost you too much: "As a practical matter, however, there is nothing wrong with using two spaces after concluding punctuation marks unless an instructor or editor requests that you do otherwise." This is what scientists do in response to the inane and ill-informed comments that referees have made about their papers when they come back from a round of peer-review. It's galling to accede to their fatuous suggestions but easier for everyone if you just rewrite your paper to tick their boxes. When their helpful suggestion will require your student to soend another 6 months at the lab-bench - that's when you polish off your Diploma in Assertiveness and start fighting your corner.
Monday 23 February 2015
Glycogen
Gerty Cori died in St. Louis Missouri in 1957 a long way from where she was born (Prague). It took 50 years before she was commemorated with a stamp in her adopted country. When the USPS, not known for the subtlety of its designs, published a series of stamps acknowledging scientists in April 2008, she was the only woman. The others were John "Transistor" Bardeen, Edwin "Red Shift" Hubble and Linus "Alpha Helix" Pauling. Two of these boys won two Nobel Prizes and one won none. Guess which! I've had occasion to be critical of Linus Pauling for running waaaay beyond the evidence about vitamin C. No such complaint was ever levelled at Gerty Cori for the work that led to her Nobel Prize in 1947, of which she shared a half share with her husband; Bernardo Houussay got the other half. There was a bit of a clever-clogs media show in 2008 because a chemist noticed an error in the representation of the molecule that is acting as a sort of speech bubble on the stamp. That molecule is glucose-1-phosphate, a breakdown product of glycogen, whose identification was one of Cori's contributions to science. The error lies in the fact that the phosphate group on Cori's shoulder appears to be joined to the glucose ring by the wrong oxygen atom! Shock, it took me five minutes of staring at the stamp knowing there was 'an error' to not see what the problem was. That was partly because my chemistry has been rusting for nearly 40 years, but partly because the 'error' fails to acknowledge that the picture is just a cartoon representation of the molecule - a gross simplification of what it really looks/behaves like. Whatever, printing errors give you pause to think - so that's a good thing.
The stamp story generates a vision of USPS bureaucrats, under some affirmative action protocol, looking to identify and trib a female scientist - possibly crying "find a woman in a white coat . . . any woman so long as she's a scientist . . . any of these broads have a Nobel Prize?" [picture of 'lady scientist' looking intently at a flask of urine] One could wish that, rather than pedestalling Gerty Cori, they had realised that she'd have been happier sharing her stamp, as she had shared her Nobel and as she had shared a lab-bench for 25 years with her husband Carl Cori. Over a life time, they carried out a wide ranging series of experiments setting out some of the fundamentals of biochemical science, especially in the area of carbohydrate metabolism. Glycogen is a polymer made up of numerous glucose molecules that is reasonably inert and so serves as a reservoir of energy for the body, in much the same way that starch serves plants. The Coris sorted out the mechanics of the biochemistry of Glycogen breakdown and made a good fist at revealing the complex of cells and hormones that control the process. The Cori Cycle where lactic acid, produced from anaerobic activity in working muscles, is transported to the liver, rebuilt into glucose and sent back to the muscle for another go-through, is named for them. Our sports science students learn all this at an early stage in their career as gospel truth, and I don't think they are really invited to remember Carl and Gerty Cori and their work. I don't them being mentioned when I went through college 40 years ago.
Gerty Cori had to tolerate, by-pass, ignore and overcome the most outrageous discrimination to pursue a career in science, starting with school in Prague before WWI where women were groomed to be a doormat or a mattress for a future husband. She married Carl, whom she had met in graduate school in Europe, and shortly thereafter they escaped to the free world and much better food in Buffalo, NY. But, like Jocelyn Bell Burnell, it was always following his career opportunities largely because she had, for much of the time, no career opportunities. At least no honoured or honourable opportunities: she worked for some years as her husband's 'lab assistant' at a tenth of his salary; even as she was co-authoring most of his papers and publishing a few on her own. She only got a properly paying job in Wash U. St. Louis a few months before she was awarded the Nobel Prize. Having experienced hardship and prejudice in post-WWI Europe in the 1920s, they held a sort of open house for brilliant dispossessed scientists in post-WWII St Louis. It didn't matter whether they were male or female, Jew or gentile, if they could cut the mustard, there was work and funding with the Coris. Six future Nobel Prize-winners passed through their lab [page 5], including Christian de Duve, Earl Sutherland, Edwin Krebs, Arthur Kornberg.
The same year she won the Nobel, Gerty got a diagnosis of Myelofibrosis, a fatal bone cancer where the cells that make blood cells in the bone-marrow get converted into a mass of connective tissue. She carried on pushing the frontiers of science for as long as she could stand and think straight through the pain, fatigue and anaemia and died at home at the shocking young age of 61. Six months later, at an even earlier age, Rosalind Franklin pegged out of the science game as well.
Sunday 22 February 2015
Beriberi Eijkman
- make up a litre of MacConkey Broth (Enzymatic Digest of Gelatin 20g; Lactose 10 g; Oxbile 5 g; Bromocresol Purple 0.01 g) which because of the bromocresol starts off an agreeable royal purple in colour. Only a few organisms will grow happily on lactose (milk sugar), and the Ox bile inhibits the half of the bacterial world, some of which can handle lactose, that are blue after Gram-staining. The digest of gelatin (ox hooves, possibly from the same animals that contributed their gall-bladders for the bile) provides all the other nutrients - a bit of protein, some vitamins. There's a century of science behind this: originally the indicator was litmus, which was replaced by 'neutral' red, which in turn was found to inhibit a bunch of the bacteria that poor MacConkey was trying to grow.
- dole it out into 10ml test-tubes.
- sink an inverted Durham tube the liquid in each tube.
- sterilize them all.
- add your possibly contaminated sample (we use sheep shit and other likely sources)
- Incubate at 40oC for a day or two.
Eijkman was born in Nijkerk on the shores of the Zuider Zee in the Netherlands. He trained as a medical officer for the army and shipped out to the Dutch East Indies in 1883 at the age of 25. He caught a dose of malaria and within two years shipped back home sick. It was good timing because he was able to go back to college and studied for a time under the giant of the microbiological world, Robert "Postulates" Koch in Berlin. While there, he met Professors Pekelharing and Winkler who had been tasked to work out the causes of beri-beri: a devastating disease of the tropical East Indies which was a huge drain on the Dutch colonial economy. Eijkman joined their team and in short order found himself on a boat back to Batavia. When the Big Guns went back to Europe, Eijkman stayed on as the newly appointed director of the Medical Laboratory; having resigned from the army, he could devote his energies to scientific research.
I think he was a great scientist who looked to the evidence for his understanding and wasn't swayed by what Everybody Knew To Be True. He carried out some careful metabolic and physiological studies of Europeans and 'natives' and could find no significant difference. This put in the dustbin a lot of protocols for 'acclimatizing' white men to the tropics. Actually, it probably didn't - you may be sure that many people persisted in doing the same-old same-old in the face of scientific evidence that they were wasting their time. More importantly he cracked the puzzle of the cause of beriberi, a progressive and often fatal neurological disease which killed native soldiers and prisoners in disproportionate numbers even if they were young and fit. Everyone had a theory, including 'vapours', rotten fish, and excessive perspiration. The Pekelharing and Winkler Commission followed the "it must have been something I ate" theory and tentatively identified a bacterial coccus as probable cause before they went home. Eijkman more of less accepted this, evidence based, theory until he noticed that the hospitals chickens developed a condition that looked suspiciously like beri-beri after they were fed on rice which was used to feed the native soldiery. They recovered when some martinet in the army refused to allow military rations to feed civilian birds! That was Eijkman's cue and after further research (convenient lab 'rat' now available) he was able to show that brown rice had a beneficial active principal that was lost when the rice was 'polished' to remove the husk.
Eijkman was successful in his endeavours at least partly because he paid attention to what was happening around him and he wasn't prepared to accept what other people considered certain - because they were all too often wrong. He is recognised by the Indonesian Government in the Eijkman Institute for Molecular Biology in downtown Jakarta. The Eijkman-Oxford Clinical Research Unit (EOCRU) was created in 2007 as a collaboration between the EIMB and Oxford University. There is also an Eijkman-Winkler Institute for Clinical Microbiology attached to Universiteit Utrecht where he was working when he won the Nobel Prize. He died the following year in November 1930. Laten we ons petje te verwijderen.
Saturday 21 February 2015
Wrong turn for the dragon
For a while, I've been wanting to write about Don Knuth who wrote TAOCP The Art of Computer Programming which is for computer geeks what ZAMM Zen and the Art of Motorcycle Maintenance is for philosophy geeks. TAOCP was conceived in 1962 as a finite book of 12 chapters and spawned into an infinite book that yielded volume 4A in 2011 having released Volume 1 in 1968. Knuth is now 77 and doesn't seem to be stopping anytime soon. He's an interesting version of nerd:
years ago he offered some advice about life-strategies Don't be a sheep - find your true self. Part of his true self was being a Lutheran and one of his books was a systematic sampling of The Book: 3:16 Bible Texts Illuminated abstracts, discusses and illustrates the sixteenth verse of the 3rd chapter of every book in the bible.
I like that; it reminds me of my 2813184 project which never got beyond the concept. Our phone number in Newcastle upon Tyne was 091-2813184 and I thought it would nifty to phone all the other 2813184s in British telephone districts . . . and then? ?Invite them to meet me at the geographic centre of Britain on Walpurgis Night? Now really, was it kind inviting to folks to have a party in the middle of a peat hag in Lancashire when you could accept the assertion of the people of Haltwhistle in Northumberland that their town was the centre of of the world Britain, or anyone of a number of other claimants depending on how you define the parameters - the big island only, the whole archipelago, the bit that has Mrs Windsor as Head of State. Haltwhistle, conveniently for the 2813184 party, has a railway station but isn't named for that fact, as some believe. The name antedates railways by a long stretch of time: Hautwesel (1240), Hautwysel (1254), Hawtewysill (1279), Haltwesell (1610) and probably indicates a hill [haw] near the divided [twy] stream [wella].
Knuth is famous for offering $2.56 for anybody finding a typo in one of his books. Why 256? because that is a hexadecimal dollar (16x16 rather than 'normal' 10x10). He claims to have written more than 2,000 checks under this project and would be $20,000 in the hole if everyone had cashed them. In fact, almost all of them are kept safely in a drawer for the grandchildren unless they are framed and stuck up on the wall of a basement machine room. It's a bit like my claim to be in an exclusive club of people who have found errors in PHYLIP, Joe Felsenstein's software for calculating phylogenetic trees. That took time, attention to detail and a refusal to accept that what was delivered was true, and I am, accordingly, still dining out on it. Occupying pride of place in Knuth's home [R] is a grook by the Danish scientist's poet Piet Hein:
But the hook on which I'm hanging Don Knuth now, is that I was in the pottery zone last Sunday and there's a lovely story about tiles and Knuth, called Wrong Turn on the Dragon on the Numberphile channel of youtube. I'd leave it at that if I didn't know that virtually nobody follows through on the copious links which I shovel into The Blob. The deal is that Knuth built a new house and had a geeky fractal design in mind for filling a central wall. His design showed a particular sequence of 2^9 = 512 folds/turns which could, according to the algorithm be either mountain or valley folds / left or right turns. The size of the design and the size of the wall required about 1000 tiles [many blank] 2x2in (5cm x 5cm) in size. They took their design up the coast to Sausalito where their favorite ceramicist had his studio, and were gutted to hear that they only made tiles 3.5 inches across. But, said the potter brightly, they were going to close the place down for a week in June for vacation and the Knuths were welcome to use their clay, glazes and equipment to make their own tiles to whatever daft size they wanted and these custom tiles could be fired when the kiln had its first run later in the month. And it was so. The twist in the dragon's tail was that, years after the house was built and the tiles put up to intrigue all Knuth's mathy pals, he realised that he'd made one incorrect turn and back-flipped half of the design outwards. They say that Persian carpet weavers put in one deliberate error when making their 900 kpsi (knots per sq. inch about 135 k/sq.cm) carpets; lest they offend god with their hubris.
years ago he offered some advice about life-strategies Don't be a sheep - find your true self. Part of his true self was being a Lutheran and one of his books was a systematic sampling of The Book: 3:16 Bible Texts Illuminated abstracts, discusses and illustrates the sixteenth verse of the 3rd chapter of every book in the bible.
The road to wisdom? Well, it's plain & simple to express
To err and err and err again, but less and less and less
I think a lot of scientists and engineers could sign up to that.But the hook on which I'm hanging Don Knuth now, is that I was in the pottery zone last Sunday and there's a lovely story about tiles and Knuth, called Wrong Turn on the Dragon on the Numberphile channel of youtube. I'd leave it at that if I didn't know that virtually nobody follows through on the copious links which I shovel into The Blob. The deal is that Knuth built a new house and had a geeky fractal design in mind for filling a central wall. His design showed a particular sequence of 2^9 = 512 folds/turns which could, according to the algorithm be either mountain or valley folds / left or right turns. The size of the design and the size of the wall required about 1000 tiles [many blank] 2x2in (5cm x 5cm) in size. They took their design up the coast to Sausalito where their favorite ceramicist had his studio, and were gutted to hear that they only made tiles 3.5 inches across. But, said the potter brightly, they were going to close the place down for a week in June for vacation and the Knuths were welcome to use their clay, glazes and equipment to make their own tiles to whatever daft size they wanted and these custom tiles could be fired when the kiln had its first run later in the month. And it was so. The twist in the dragon's tail was that, years after the house was built and the tiles put up to intrigue all Knuth's mathy pals, he realised that he'd made one incorrect turn and back-flipped half of the design outwards. They say that Persian carpet weavers put in one deliberate error when making their 900 kpsi (knots per sq. inch about 135 k/sq.cm) carpets; lest they offend god with their hubris.
Friday 20 February 2015
Mudlarks
Who owns the kit? If you have or are given something ex officio - in your professional capacity - do you own it personally or should you hand it on to your successors? The former Archbishop of Canterbury Michael Ramsey thought various archiepiscopal gifts were his but in the austerity of old age they became burdensome and he dumped a lot of golden clutter into the River Wear at Durham. Yes, yes, he'd tried selling it for the poor (archbishop). Having written about that nearly two years ago, and given my thing about beachcombing, I'm surprised I haven't had more to say about combing the foreshore for ancient artifacts. Time to redress that today.
The Beloved has a long-time thing about William Morris and the Arts and Crafts Movement. Morris saw himself as trying to hold back that juggernaut of the Industrial Revolution by crafting beautiful and functional material artifacts that may cost a bit more but a) would last longer b) look nicer and c) employ people living just down the road for a respectable wage. Here's an example [R "seaweed"] of his fussy, detailed wall-paper, fabrics, book-endcovers. I like it; I don't think I could handle a roomful of it as wall-paper but you can order it as a 150x150mm ceramic tile that would serve nicely as a coaster. Actually, this design as many "William Morris" patterns is probably the work of John Henry Dearle a talented employee of the Morris company who started as a tea-boy and finished up as head designer and art director. Morris was quite shiny-eyed about design and craftmanship and persuaded a number of people to give up the day job and work with their hands.
One of these apostles was T.J Cobden-Sanderson, a friend of Morris who was also a college drop-out and not particularly successful barrister. He was convinced by Jane Burden, Morris's wife [and a person in her own right!], to give up aspiring to 'take silk' but rather take up book-binding. TJCS founded Doves Bindery in Hammersmith, West London, named for the pub next door. Around 1899 he went into partnership with an arty-crafty printer and photographer called Emery Walker. Doves Press produced some iconic Arts and Crafts books including a five volume Bible, typeset in a font called Doves. Indeed all of the books produced by Doves Press used this font. I don't know what all the fuss is about: not all fonts are suitable for all purposes, but I'm sure any designer or type-setter could find a font that was good enough for any purpose without having to trick about with the details of a font like Bembo (1495), Baskerville (1757) or Bodoni (1798) and call it something different because the serifs on the descenders are now 5 degrees off horizontal. Here are a selection of letters from Jenson Venetian Roman (1470 above) and Doves (1900 below), can you tell the difference? And don't say than Jenson Roman is bigger:
TJCS and his partner Walker felt very strongly about their font which, in the spirit of who owns the ideas, both considered to be their creation. When the partnership collapsed in 1909 in a furore of recrimination and sense of betrayal, their respective lawyers allowed Doves to be used by TJ in the Press but stipulated that the font would eventually revert to whichever partner out-lived the other. As Walker was 11 years younger, it looked like he would finish up with the prize. Doves Press struggled along for another 7 or 8 years but finally folded in 1916 when TJ was 76 years old. Rather than let his rival to have the font, he made 170 nocturnal trips to nearby Hammersmith Bridge and dumped it all, including the punches and matrices for making new type, into the River Thames. The whole 'bequest to Father Thames' weighed more than a tonne, or more than 5kg each night. According to his diary (!), it took him about 9 months to destroy his baby piecemeal.
A great number of people, pre-Raphaelite groupies, Arts&Crafts buffs and the like, have claimed to be gutted about this loss to posterity but they sat there sad. Robert Green, designer and typographer, cared enough about it to recreate a digital version of Doves - it took him 3 years. It then nagged him that there might be a few fragments remaining on the riverbed from the great typographic holocaust of 1916-1917 . . . so he went and looked . . . and found 3 letters in a mere 20 minutes on casting about on the bank at low tide. Proof of principal established, a larger search involving scuba divers has found 170 pieces of type in pretty good condition [L from Sunday Times] after a century in the drink.
Nice piece about other (romantic) material that has been flung into the Thames.
One of these apostles was T.J Cobden-Sanderson, a friend of Morris who was also a college drop-out and not particularly successful barrister. He was convinced by Jane Burden, Morris's wife [and a person in her own right!], to give up aspiring to 'take silk' but rather take up book-binding. TJCS founded Doves Bindery in Hammersmith, West London, named for the pub next door. Around 1899 he went into partnership with an arty-crafty printer and photographer called Emery Walker. Doves Press produced some iconic Arts and Crafts books including a five volume Bible, typeset in a font called Doves. Indeed all of the books produced by Doves Press used this font. I don't know what all the fuss is about: not all fonts are suitable for all purposes, but I'm sure any designer or type-setter could find a font that was good enough for any purpose without having to trick about with the details of a font like Bembo (1495), Baskerville (1757) or Bodoni (1798) and call it something different because the serifs on the descenders are now 5 degrees off horizontal. Here are a selection of letters from Jenson Venetian Roman (1470 above) and Doves (1900 below), can you tell the difference? And don't say than Jenson Roman is bigger:
Nice piece about other (romantic) material that has been flung into the Thames.
Thursday 19 February 2015
Tin Day
Neither Tintin nor Rin Tin Tin are made of tin. Tin-foil in the kitchen is not made of tin, but aluminium; and tins as it tin-cans aren't either, although some of them are steel coated in tin to make more resistant to corrosion. A lot of the tin-cans that go through out kitchen look like they are painted on the inside rather than tinned. But maybe that's because almost all the tins in our kitchen hold tomatoes which are corrosively acidic and have been known to eat through the metal(s) when stored for a few months in one of our damp sheds. We can use tin in this way because the metallic element and its inorganic compounds are not toxic.This is not true of organotin compounds which are used in a wide variety of biocidal situations: TBT tributyl-tin has been widely used as an anti-fouling paint on boats until it was finally banned in 2008 and TBT-oxide is impregnated into wood as a preservative.
For millennia tin was a highly tradable commodity because of its importance in making bronze an alloy of copper [90%] and either arsenic (initially) or tin (later) [10%]. Bronze was stronger, harder and more resistant to corrosion that either of its constituents. Enormous quantities of tin, as Cassiterite (SnO2) had washed out of the granite uplands in the South West English counties of Devon and Cornwall. It is believed that Phoenician sailors voyaged the whole length of the Mediterranean, past Gibraltar and up the wild Atlantic to trade for 'white' (metallic) tin. The ancient metallurgists put a premium on tin because they were fully aware of the toxicity of arsenic vapours generated by bronze-smelting. Indeed, the everything-makes-sense brigade makes a case that Ἥφαιστος Hephaestus the blacksmith to the Greek gods was, with his skin cancer and limping neurological deficits (Κυλλοποδίων) the embodiment of arsenic poisoning. The fact that tin has so many isotopes provides another channel of information to the archaeologists. In most deposits of tin the 120Sn isotope is most common but the precise cocktail of abundance of the other isotopes varies characteristically from location to location. Find a bronze arm-ring in Turkey and a chemist can tell you that the tin came from Cornwall. 4000 years ago, some brave and enterprising spirit put time and comfort on hold and journeyed to the end of the known world to bring back tin. Not quite the same as driving the car to Tesco to buy some 'tin' foil.
Wednesday 18 February 2015
there were no complaints from workers
Our trade union at The Institute has signed up to a number of austerity measures as part of a series of agreements with the government, the management and the Teachers Union of Ireland. As public sector pay workers, all members of the TUI are dependent on how much the besieged Irish tax-payer is prepared to cough up each month in order that their children can get an education at second- and third-level.
Q. How much is that? A. Not very much, given how much more than the minimum wage teachers get.
ANNyway, the negotiators for the TUI shamefully agreed to a clause that allowed the pay of assistant lecturers who started after 1st Jan 2011 to be 90% of their peers who started before 31st December 2010. Thus the senior TUI people at the Haddington Road table sacrificed the youngest, least articulate, most vulnerable and most recent members of their own union to ring-fence the pay-and-conditions of the Old Soldiers who got their knees under the table years ago. The nursing unions signed up to a similar pact with the devil. We the TUI could have spread the the necessary cuts over all members, so that everyone lost a little. But they chose to make their constituency less equable. That's rather a long way from the starry eyed, socialist, financially equilibrating, ideals of unions when they were founded as bands of brother-workers in the 19thC.
Now get this: since a long time ago, teachers on the Lecturer grade do 2 contact hours of work less a week than beginners on the Assistant Lecturer grade. Why is that? In my socialist paradise you'd remember just how hard it was to get going in a new job with new courses to prep, the t'ilets to locate, new faces to meet and new conventions to learn . . . and cut beginners some slack with fewer hours. Believe me, it's far easier to teach the same course the second time around. Thus the TUI condones the fact that older people, whose valuable experience would benefit the students most (!?), work less for more money. Is that fair? Is that efficient?
Over in England, the CWU shop-stewards hand out the new Royal Mail delivery routes according to seniority! The oldest people on the rota get first dibs on which round they fancy doing. The desirable rounds include Chetnole and its delightful surroundings: ye village greene, ye antient churchyard, ye antient old ladies living in detached houses who give you folding money or a voucher at Christmas. Mick Leak, pal of my mother and all the world, was being closed out of his bailiwick by another chap who had 3 months seniority on him.
Mick diffidently mentioned that he was being shifted and that it took a bit of getting used to: after the 24 years, and all. The response of his customers was less diffident and more ballistic, as in: The End of Ye Antient Worlde as Wee Know Itt! Petitions were signed; tea was made; scones were baked, cakes and books were sold in the village hall; posters were hung; irony was employed . . . and the CWU and its restrictive practices were seen off; the would-be new postman affected to be frightened (by the prospect of being hand-bagged by some elderly and scrupulously well-brought up pensioners) and Mick Leak was reinstated. Identical story last June in the next County. An anonymous apparatchik from CWU blustered 'It's disgraceful that customers have been allowed to intimidate a postal worker out of his new delivery round,' he said. 'The changes applied in Royal Mail's Sherborne office were voted through by the staff and there were no complaints from workers about the agreed changes'. "No Complaints" doesn't mean that everybody is happy; some of the workers may have
Picked up from BBC; The Daily Mail; Reactograph; Western Daily Press
Tuesday 17 February 2015
Boys and Girls
Sex ratio allows for an interesting classroom exercise in Ascertainment Bias. The sex-ratio of Fisher's direct progeny was about as skewed as our lambs last year - 2M:6F; except in the other direction. We'd have been delighted to get 75% ewe-lambs. Many people associate Fisher with sex-ratio because he articulated (he was neither the first, nor the last, nor the most clear) the idea that sex-ratio naturally equilibrates at 1M:1F. His argument ran thus:
- If males are less common than females, a random male is more likely to have offspring than a random female; some of whom will be left "on the shelf" in a monogamous society
- Any parents which then acquire a mutation that makes them have sons will have more grandchildren
- Therefore these male-bearing genes will spread through the population . . .
- . . . until males are more common than females or until their minority-report advantage dies away as sex-ratio approaches equality
- Same reasoning applies if you start with females being less common.
Actually, it turns out that sex-ratio at birth is not quite 1:1 - in all societies where these things are recorded (and that is all societies which can count up to two), there is an excess of boys at birth: something around 105M:100F. Boys are fragile in the neonatal period and their mortality is higher than their sisters. Statistics on still-births and from abortions show that this post-natal mortality among boys is a continuation of a trend in utero with the primary sex ratio (at conception) estimated at 130M:100F. That 130 figure is widely cited but it's quite hard to find the data on which this fact is based. Later on, in many societies including Ireland, the sex-ratio takes another nose dive as boys start to drive cars (far too fast); commit suicide, which may be the same thing; and do silly dangerous things to impress girls and prove that they are well 'ard. By some age between 25 and 40 the sex-ratio is really 1:1. Thereafter women consistently and increasingly outnumber men of the same age: there are between 5x and 9x more female centenarians.
Monday 16 February 2015
ASCII v EBCDIC
a 1100001; b 1100010; c 1100011 etc. a=97; b=98; c=99
The last two dots at the right of each row in the picture represent 25 (32) + 26 (64) = 96. Accordingly lower case 'a' 1100001 = 97 in decimal. ASCII is logical and has the capital letters encoded with consistency exactly 32 places lower than their lower case equivalents :
a 1000001; b 1000010; c 1000011 etc. A=65; B=66; C=67
You might expect that the numerals start the whole series off, because numbers is what computers 'do', but they don't: they start at 49:
1 0110001; 2 011010; 3 0110011 etc. 1=49; 2=50; 3=51
and, as you ask, zero: 0 0110000 24 (16) + 25 (32) = 48. the lower codes are for a number of essential computer control features like
CR 013 0001101 (carriage return)
LF 010 0001010 (line feed)
BS 008 0001000 (back-space)
BEL 007 0000111 (bell that made the >!ding!< sound)
here the computer was being instructed to behave in ways that were mechanically achieved by its predecessor the old fashioned manual typewriter including the >!ding!<
This is all concerned with how letters and numbers, which humans can easily read, are represented by binary ON/OFF or 1s and 0s, which was all the subtlety that computers were able for. The internal consistency means that it is easy to convert lower-case to upper [subtract 32] and vice-versa [add 32] or determine if a word begins with a capital letter [if 65<First<90] and so treat it like a proper name.
In the post-WWII Computer Age, IBM was first out of the gate to implement a binary to letter/number/punctuation code for their early electronic computers. They realised that fitting everything (TWO alphabets, a clatter of punctuation, the ten digits and all that carriage-return infrastructure into 7 bits (0-127) would be tight and so used an 8-bit code called EBCDIC (Extended Binary Coded Decimal Interchange Code) which grew out of a minimalist BCDIC 6-bit code used on the very earliest computers that were programmed on stacks of punched cards or paper tape with holes in it. 6-bit only allows for 0-63 different symbols/functions and so never allowed lower case letters. This is why early programming languages COBOL and FORTRAN are written entirely in UPPER-CASE and so read a bit "SHOUTY" to modern eyes. With an extra two bits to play with (0-255) EBCDIC spaced everything out and weirdly shoved the alphabet into three separated blocks
abcdefghi 129-137 10000001-10001001
jklmonpqr 145-153 10010001-10011001
~stuvwxyz 161-169 10100001-10101001
Written like that you can see where they were coming from: each alphablock is 24 (16) higher than the previous one. But this is a total pain in the tits for coding: you can't ask one question to determine if a character is part of a word; you must ask three separate questions. But EBCDIC was the way that the phenomenally successful IBM/360 series of business computers operated, when launched in 1964, and so they nearly swept the board with their clunky choice of encodings. When I was programming an IBM/370 in 1980, I had to get my head around EBCDIC encoding but I also had to get to grips with ASCII which had started slimmer (7-bit for each character) and was out-running the EBCDIC monster. ASCII's inadequacies as to insufficient slots to have açcéñted léttêrs or Greek and Cyrillic characters was addressed when it was expanded into UniCode and even IBM have long ago signed up to that international standard. 85% of what you read on the WWW is written in UTF-8 which combines the efficiency of ASCII with the universality of Unicode by encoding each letter with 1,2,3or4 8-bit bytes. If the text is straightforward American it all compacts into one byte; want accented letters you foreign-johnnies? - add an extra byte; want to write in Hindi - add another byte. UTF-8's 1,112,064 different letters will suffice until we start talking to other planets.
Sunday 15 February 2015
Throwing pots
- Whichford Pottery - showing how a factory makes the functional
- Chris Bowen "Born not made" - starts with a great lunch served on the master's plates
- Mike Dodd "Potter" an investigation into quality
- Anne Mette Hjortshøj from Bornholm "Honest paying attention" - title says it all
- Nic Collins on woodfired pots where the vapours supply the glaze
- Lisa Hammond: 'A Sense of Adventure' studio in a railway ticket office!
scanning the ewes
Last year about this time, the ultrasound man came to scan the ewes and predict who would give birth to what. The data:
Total 17 ewes 19 lambs; average 1.2.
Compare that with this year's data which we obtained around tea-time yesterday evening:
Total 14 ewes 19 lambs; average 1.4. So the rate is better but we'd still have gone bust if this was a commercial undertaking rather than a penance for our sins in a previous life. The ideal is to have an average pretty damned close to 2.0 but not higher; and you want a peaked distribution: all twins, no empties, few triplets. The runt of our triplets is still very small despite us feeding her supplementary milk for months (at €15 the bag for Lamlac powder). Last year we needed (or had) four people to run, heave, push the ewes into the scanning chute - our good-neighbour Carmen dropped by to deliver some cakes for O'Manch and found herself writing numbers with a spray-can on the flanks of 17 sheep. Since then we've upgraded our sheep handling unit to incorporate a sheep-chute half a metre wide and 10 metres long. This more or less forces the ewes to form an orderly queue following each other through the scanner to freedom. Somebody said that we should do this necessary scanning with the least possible stress to the ewes which aspiration was a long way from the reality of stress levels for either two- or four-leggers. We all did commendably well, all things considered.
Not least, we separated the empties and put them in with last years (un-tupped) lambs and a sentimental pensioner, where they can survive on whatever grass there is. We can thus concentrate our concentrated feed into the mothers. Turns out that we had 4 ewe lambs not 3, which only came to light when we were loading the second batch of ram-lambs into the trailer for the butcher. What are we like? So we now have eight not-load-bearing sheep in our haggard saving me from having to mow the lawn for a few weeks . . . win! And we have reconciled the lamb-count numbers on the flanks with the official numbers on the ear tags, so we'll keep proper fertility records from now on - promise.
We are now accepting applications, from people with small hands and no need to sleep, to come help with the lambing starting at the beginning of April. Actually that coincides with a two week gap in the Institute's teaching term over Easter; and I think that several members of the family will be home over that period. Must remember to buy some Lamlac.
| Empty | Single | Twins | Trips |
| 5 | 6 | 5 | 1 |
Compare that with this year's data which we obtained around tea-time yesterday evening:
| Empty | Single | Twins | Trips |
| 3 | 4 | 6 | 1 |
Not least, we separated the empties and put them in with last years (un-tupped) lambs and a sentimental pensioner, where they can survive on whatever grass there is. We can thus concentrate our concentrated feed into the mothers. Turns out that we had 4 ewe lambs not 3, which only came to light when we were loading the second batch of ram-lambs into the trailer for the butcher. What are we like? So we now have eight not-load-bearing sheep in our haggard saving me from having to mow the lawn for a few weeks . . . win! And we have reconciled the lamb-count numbers on the flanks with the official numbers on the ear tags, so we'll keep proper fertility records from now on - promise.
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