Friday 30 June 2017


My Roomie at The Institute is running a meeting this week about nematodes as bioindicators. About 40 of the world's experts in environmental monitoring and sustainable soils with their attendant students (future experts in the field if we still have a planet) have come to Knock-na-bitheolaíocht for a few days networking and presenting their data and analyses. The meeting motored along, on time and well fed, and I dropped in and out to learn about stuff waaaay outside of my field. Someone had the bright idea of inviting an Institute alumnus, founder of Rockfield Ice Cream, to hand out free ice-creams to the delegates - they do weddings as well. I don't do ice-cream, so I was happy to give my voucher to one of our starvin' graduate students.

The first international conference I attended was in 1978 at Siracusa, Sicily. We threw a few things into our leaky old Citroen and drove 3000km across the continent to attend. When we arrived, we camped on the beach and the rest of my party swam, slept and ate pizza while I did science for 3 days. Then we packed up and drove all the way to the Netherlands for the next great leap forward. I didn't dream of getting someone to pay for my petrol and, as I was between jobs, it would have been difficult to identify a target for the invoice. It helped that there was no registration fee for the conference.

It's different now. I met my Roomie on the stairs as she ducked back to the office to photocopy the receipt for dinner the evening before the conference. Lots of delegates were planning to claim that as an allowable cost . . . but needed a receipt for their finance people. They all chipped in to pay the bill but the restaurant only uttered one receipt. I had an image of this same receipt for a few hundr€ds being presented across the free world for multiple payments but was assured that everyone would just claim their own share. The Institute has given up on such claims and give you a per diem if you're away from your desk for more than a certain number of hours. If you choose to dine on chips or out of a dumpster, then you can make a profit. You need to prove that you were away where you said you were, of course, but a copy of the programme is usually enough. After going to Galway to hang out with my mates in 2013, and claiming the per diem and the mileage, I was ahead in the wallet. I am honest (Honest!) but not so pedantically honest that I cause a headache for the accountants. Later that year, there was a meeting in Dublin. As there were a few penniless post-grads who were going as well, I piled them all into my car and drove the 80km to The Smoke to save The Institute 4 bus-fares. The students got to sing Science Songs in the back of my bus. But when I claimed for that, I was told "Duh! didn't you read Institute Policy that travel to Dublin must be carried out by bus or train". No I didn't and neither did my head of department nor the head of school both of whom were required to sign off on the claim. Filling in a form in triplicate is one thing but arguing over €20 is beneath my dignity, so I threw my claim in the bin and learned not to do any of that utilitarian greater good nonsense again.

I was in Dublin a couple of weeks ago to attend a talk given by a palomino - and went by bus. At the pub later, someone told a story about me and receipts that could have been true. In 2014, I organised the VIBE gig in The Institute. - we didn't have the ice-cream gimmick but I did manage to supply tea, a tonne of flapjacks and lunch. No registration fee, so I had to shake down some corporate sponsors for the sandwiches and canapés. The following week, one of my pals the delegates, asked me for proof that he had attended the event, so he could claim the rail-fare from Dublin. I sent him the group photo [above] and invited him to put a circle round his smiling face to convince his college's auditors. I've circled myself above, in case I forget I was there, as I had clearly forgotten my witty and subversive response from 3 years ago. You'll also notice that I have corralled all the delegates into a Y-chromosomeshape to protest the overwhelming hegemony of Men in Science . . . no I made that last bit up.

Thursday 29 June 2017


At The Institute there are several exit strategies. We offer one and two year Diplomas and Certificates, a three year Degree and a 4 year Honours Degree. The difference between the last two options is a research project. Here each student is given a pick and shovel and a section of the Frontier of Knowledge and is invited to hew at the coal-face of science for a few weeks.  It has to be original science - no point in re-inventing the wheel - so the first task is to do a literature survey. Our students' attempts at this task range from poor to appalling. Back in the day, this meant going to the library and finding a recent review of the field and reading that; and reading the references there cited and then going down a recursive rabbit-hole until you're reading manuscripts by Isaac Newton [portrait] or Antoine-Laurent de Lavoisier. In other words it was all retrospective.

I wrote about the process of reading the literature rather than just photocopying papers in February: "Have you tried neuroxing those papers?". There I cited Eugene Garfield for inventing Current Contents and Science Citation Index SCI in the 1960s which made The Literature much more easily accessible. I regret to report that Dr Garfield [See L being enthusiastic] died 26 Feb 2017 two weeks after I wrote that piece; he was 91. Obits: The Scientist - Nature. The Blob is not the place to get The News!

Current Currents was an indexing/abstracting service which allowed you to scan through this week's reports from the Cutting Edge looking for keywords related to your project. Saved having to scan the Table of Contents ToC of 20 key journals each week. More importantly, it allowed you to scan the contents of journals which your institute couldn't afford and send out a reprint request card [prev] to get the one paper in that week's Journal of Molecular Biology that was of interest. The great thing about SCI was that a ramble through the literature could, after its invention, go in both directions: by recording who cited a key earlier paper you could work forward along another branch of research that was developing parallel to, or diverging from, your own interests. It changed the metaphor of a paper from a leaf on a static twig on a branchlet on a branch on a limb on the trunk of science to a more bushy, interconnected and recursive way of viewing the process.

SCI had unintended consequences: as well as making it easier to read the literature, it also allowed data-wonks to treat the citations as meta-data and analyse them. You could count the number of times your own papers were cited [my track record is fair to middling] and be often bemused at which had gone viral and which jewels were languishing unpolished. And prospective employers could tally up your citations to see whether your contributions had made a bigger dent in science-space than Dr Aziz's or Dr Zabriski's.  Garfield's people also invented the Impact Factor for a journal, initially as an internal metric to help them decide which publications to index. Impact Factor is essentially the average citation count for a paper in that journal. That allowed persuaded scientists to try for a pub in a journal with high impact factor in the hope that more clued-in scientists would read it . . . and cite it . . . and boost your employment prospects.

These objective metrics are fine as aids to the decision-making process or the progress of science but too often became the tail wagging the dog. If you hire by algorithm you mustn't be surprised if you acquire colleagues who are selfish. sexist, specialist and sententious shit-heads. Impact Factor is a generic metric which generates winner-takes-all harrypotterism; if you follow IF you may edge away from the subset of scientists who work in your [minority] field. If you really want a lot of cites, you should develop a new method rather than discover new primary data. Methods papers get widely cited. Garfield himself despaired at the misuse of his tools, castigating “bibliographic negligence” “citation amnesia” because scientists were too lazy to read the literature that they were citing. Have you ever cited a paper which was cited in a paper you have scanned for the figures without reading the original . . . because you were under pressure to get your own stuff out? If you haven't then the chap in the office next door has. It is partly because life itself is not long enough to read all the relevant papers every working day in 2016, six new papers on TLR4 were published. If you're a TLR4 groupie you wouldn't have time to both read this leaf-storm (ignoring TLR3 and TLR5 papers) and do your own work.

I will here gives tribs to Ken Wolfe, a walking genius and my one-time boss at TCD, who was overwhelmed with the task of separating the literature wheat from the chaff. He invented Pubcrawler to scan the daily updates to PubMed for key-words to the areas of science in which he was interested, and send him the abstracts. This super-useful tool was developed by Karsten Hokamp as a free public subscription service. Try it? - " It goes to the library - you go to the pub(TM)"

Our plagiarism policy document at The Institute is called Credit Where Credit is Due, which is what Garfield wanted us all to take on board. I've reflected on that issue as well. PageRank the Google algorithm also acknowledge a debt of gratitude to Eugene 'Serial Pioneer' Garfield. Really interesting and informative interview with Garfield from 2000.

Wednesday 28 June 2017

Publish or be predated

 I was in Trinity College Dublin at the end of last week witnessing the 2nd graduation of one of my students who passed through The Institute a couple of years ago to get her BSc. Her work was sound and if the money had worked out as she had wanted, it would have been possible to parlay her MSc into a PhD.  But she has now decided that she's not so much interested in hewing at the frontiers to generate some primary data as she is in explaining those findings, Other Men's Flowers [prevs], to Joe and Jenny Public. She wants to be a Science Communicator. Scientists are often woeful at this necessary task, so there is a niche there in the same way as there is a niche managing labs because Principal Investigators are often hopeless with money too.  Those two deficiencies collide when you reflect that there is precious little science that you can do without going cap in hand to the tax-payers and their proxy-funders at Science Foundation Ireland. After the Initium Ceremonia, there were canapés and I explained the maths: her MSc supervisor has had about 35 post-graduate students under her care; academic appointments are at a steady state; so 34/35 of these intellectual children are going to work elsewhere: as drug reps, administrators, secondary school teachers, entrepreneurs . . . science communicators. Your post-grad mentor is thus an unlikely role-model for your future career development. Ego being what it is, all the teachers and mentors you meet going through university have Arrived, ther self-esteem requires them to believe that they have been successful - and other careers will be implicitly cast as not quite top drawer. This is bloody nonsense because most academics haven't worked at all out in the real world so they are not qualified to make any comparisons.

Getting a seat at the academic table, and access to the Senior Common Room, is fiercely competitive and the main criterion for separating the bleaty sheep from the rugged goats is the number and quality of peer-reviewed publications which each candidate, for appointment or promotion, has generated. This is covered by the phrase Publish or Perish. It costs money to maintain an academic journal. Even if it is entirely on-line with paper/printing costs hoofed back on the consumer as downloadable PDFs, the secretary, the telephone line, the desk, the e-mail account all have to be paid for. The Editor is often moon-lighting pro-bono from an academic post, and the referees are almost certain to be working for the journal for free. On the other side of the counter, there are a lot of academics trying to get their stuff 'over the line' and out in the public domain . . . and they're prepared to pay for it. Accordingly, as a storm follows the sun, hopeful entrepreneurs are prepared to set up as an academic publisher to follow the money. Nobody gets nothing unless a paper is published so there is plenty of scope for implicit and explicit corruption. Although seats at the academic table are more or less the same, the generation of papers is going exponential, to satisfy the bean-counters, so it is hard to keep up with which journals are reputable.

At The Institute, the pressure is less intense because, in contrast to Universities, research and publishing are aspirational rather than essential. We spend so much time in class that you have to be extraordinarily dedicated, single and well-fit to find time to do research on top of the billable hours. This is a good billet for me because I lack finish: my attention tends to drift off after the data-gathering and analysis; restlessly moving onto the next puzzle rather than writing up the results and getting them published. The path of my career can be followed by the trail of manuscripts: unfinished, rejected or unrevised. Nevertheless I have acquired a student because he beat a path to my door and wouldn't be brushed off.  This chap has more bottle than me and is energised rather than disheartened when papers are not accepted. Because of this can-do we had a paper published recently in the International Journal of Environmental Research and Public Health. It's sound; it contains a novel methodological insight that might qualify is the fourth good idea I've had in 4 decades of science; the data are noisy because the data are real; that made telling the story less crisp; but that is the nature of biological and environmental science. An earlier draft had been turned down by another journal, which gave us the opportunity to revise and extend the original work. The second version was much stronger and had better figures. Nevertheless we had to address a number of criticisms and comments from three referees and had to work to get the thing over the line. It wasn't a shoo-in.

Last week, restlessly surfing the interweb, I found myself reading a Canadian story about predatory publishing. Dr. Lucy Lee had her doubts about a journal in which one of her students was trying to get published. To make her worries explicit, the journal in question was highlighted in red: International Journal of Environmental Research and Public Health. You may notice that it is the same place where we published our brick in the wall of science. There is a certain amount of reputational damage in that observation, but having bitch-slapped IJERPH, the Canadians moved on to reserve its broadside for an entity called OMICS. I note that IJERPH is indexed in PubMed, so that confers a certain amount of legitimacy. My student's response to the issue was robust: "They can kiss my Irish arse".

Tuesday 27 June 2017

Tropic of Cancer

I might write about Henry Miller's shockin' and widely banned book Tropic of Cancer at some time, but not now. I am today writing about the line on the globe at 23°26′13.3″ N and its companion the Tropic of Capricorn down South. Why? Because I read recently that the names are a stonkin' great fib. Because the tropics are a movable feast both as to latitude and with respect to the 'fixed' stars. The first people to look up in the sky and pay attention noted that the sun doesn't rise to the same height through the year: it was higher and hotter in the Summer. During Winter in Norway and Alaska, the sun appears to have trouble with take-off and skims the horizon if it appears at all at all. About 2,000 years ago, this phenomenon was observed, tallied and quantified and named. When the sun was at its highest in and around the Mediterranean, the Sun was [just] in the constellation Cancer. And that was the label that appeared on maps and globes

That was a clever piece to deduction, if you think about it, because when you can see the sun you defo can't see the stars in any constellation. I know my star sign is Gemini, because I used to make Birth Charts. That's a convenient sign to be born under because it means that I can regularly view Castor, Pollux and the other Geminian stars in December when star-gazing doesn't require being out after my bed-time. Just like some of my best friends are Jewish, many of them are woowah, tree-hugging alternative types. They are not above saying "Oh, you're Libra, that's why you are so balanced" OR "Aha, Virgo, no wonder you don't have children". Labelling which is somehow acceptable while "Black people are natural runners" or "Fat people are [un]happy" are unspeakable. I really have no idea when the other Zodiacal signs fall during the year and I never read horoscopes in the newspaper - I avert my eyes lest my thinking mind is soiled. Racism is waaaay better than astrology at binning people into groups. [aside Dara O'Briain et al. on Private Browsing]

Well it turns out that when the Sun tips the Summer Solstice nowadays it is in the constellation Taurus having passed through the whole of Gemini since Hipparcus of Rhodes first deduced the precession of the equinoxes. It is hard enough to reconcile the calendar with the tropical year because the day is not an exact multiple of the year and we have to fix the discrepancy with leap days every 4th February . . . except when we don't. And I've attempted to explain perihelion before. The Tropical Year is the length of time between Summer [or Winter] equinoxes. The Tropic of Cancer's shift to Taurus is caused by changes in the Sidereal Year - the position of the sun w.r.t. the fixed stars. Ptolemy, building on the earlier calculations of Hipparcus, worked out that every 100 years things slip about 1° but his time-scale baseline was too short and his estimation of how long the cycle of precession lasts was too long. Consensus now is that it will take ~25800 years to get back to the state things were when Hipparcus was still walking and disputing.

You should also note that the super-accurate 23°26′13.3″ N is slipping towards the equator at a rate of 15m every year so that 13.3" will be 12.8" next year.

The 1970s hit hippie musical Hair sang ensemble "This is the dawning of the Age of Aquarius" but nobody can agree when our solar system will move into that constellation. Indeed it may not have arrived yet, which is s good thing because then we'd be all wet.

Monday 26 June 2017


The Shiants = Na h-Eileanan Mòra are a navigational hazard in the middle of the Minch, the channel between the out Hebrides and the Isle of Skye and Mainland Scotland. There are 3 main chunks: Garbh Eilean joined by a spit to Eilean an Taighe and Eilean Mhuire to the East. The top most point on the map of the Minch [R] is the Butt of Lewis and it is inhabited by the Men of Ness. We've met them before going off on an annual hunt to Sula Sgeir in search of guga - young gannet Morus bassana - for the pot. I wrote about the hunt and the island because it featured a couple of weeks ago on BBC Alba. Now because things always come in twos, guga hunting came up again in my current book The Old Ways by Robert Macfarlane which The Boy gave me for Christmas in 2012. That was unfortunate timing because I was super-busy preparing classes for my new career in The Institute which started, with The Blob!, in early January 2013. The Old Ways sunk beneath a heap of notes about the pancreas, the ozone layer and logarithms.  I'm fairly sure I've read some of the chapters before but, with my two week event horizon, it was all as new.  In one Chapter, Macfarlane and friends sail an open boat from Port of Ness to Sula Sgeir [recently] as a two day there and back trip. When they arrive, they find that they have coincidentally turned up within an hour of the guga hunters - they are met with truculent stares and realise that they are Not Welcome.  Guga is very much acquired taste which is eloquently expressed by a crofter "I gave a piece to my dog and it spent all week licking its arse to take away the taste". Yum!
The previous chapter is about another open-boat voyage out of Lewis: from Stornaway to The Shiants. It is a small-small adventure for Macfarlane and his skipper the folklorist Ian Stephen. They travel the hwæl weg of ancient Anglo-Saxon poetry and indeed meeting a few Cetaceans along the way.  The Shiants are much more substantial than Sula Sgeir. Each square on the Ordnance Survey map above is a = 100 hectares.  The names translate as Rough Island, the Island of the House and St Mary's Island. There is a bothy maintained on, and giving its name to, Eilean an Taighe the Island of the House. The place was privately owned and was made available to anyone adventurous enough to get there [no train, no bus, no airport, no ferry] by Adam Nicolson, grandson of Sir Harold Nicolson and Vita Sackville-West but the archipelago's website now refers to him as the previous owner because he recently ceded the fairy-tale to his son Tom Nicolson. The last year when there was an orderly booking system was 2015.  You will know something of Vita Sackville-West if you have seen Sally Potter's 1992 film Orlando. Which is to be recommended as is Potter's super film The Tango Lesson.

Mais revenons nous a nos oiseaux! It is true that there are sheep on at least one of the islands, but the place is really an amazing bird sanctuary with more puffins - about a quarter million - Fratercula arctica than you can shake a stick at. Confusingly Puffinus spp. refers to much smaller and drabber birds which we call shearwaters. French, sensibly or at least consistently, calls these chaps puffins. Sadly for human and avian inhabitants, the two larger islands are infested with black rats aka ship-rats Rattus rattus. Despite a number of the trapped specimens being brown in colour none of them were of the lab rat Rattus norvegicus species. That paper in the Hebridean Naturalist used a neat, appropriate technology, surveying tool call a rat-stick which is a piece of wooden kindling soaked in margarine and driven into the ground. Teeth marks in the wood indicated the presence of rats!

A few years ago the Daily Mail did a sort of Hello magazine piece on the Islands and the Nicolsons. Maybe put the Shiants on your bucket-list?

Sunday 25 June 2017

Robots and people 250617

Very miscellaneous today
  • Sumo robots losing chunks. [via kottke]
  • Lupus Housepus. You only notice peculiar words if they appear twice in quick succession. Dau.II would never have twigged that the Black Doctor in House was partial to diagnosing any and everything as Lupus if she'd seen an episode a week like Christian. Binge-watching a whole series in a day-long marathon was, shall we say, trigger-happy for Lupus.
  • Dads catch a few; it's not true to say they are mere sperm-donors.
  • Nostalgia alert. AtlasObscura readers share favorite children's books. I recognise none of them which is a rather wonderful celebration of long-tail diversity. There is more to children's literature than Harry Potter and Judy Blume.
  • Medieval roof trusses felled in the noisy modern way by The Blob's favorite tree surgeon.
  • Soldiering. A few years ago I had chose to bicycle the 40km to work because the gear box fell out of the car. We live about 200m above The Institute but it's all up and down between. I was fresh enough to teach my classes when I arrived and set off home in fine fettle. Nearing home there was a stretch where, far from being able to cycle up the hill, my jelly-knees couldn't even walk up the incline. I am a sofa person
  • Kodaline - Brother - [prev All I want]
  • Had lunch with Dau.I on Friday: she suggested Symmetry Breakfast
  • If you like drop of Shagsper [recently], you might like to check out the modern blank verse of Charles III. Trailer.

Saturday 24 June 2017

First day of the rest of your life

Regular readers will know that I had an absurdly expensive and extended education. Primary school, prep school, secondary school, university (BA), another university (PhD), University of Life (Blob). This has had both good and bad aspects: a) an asset at pub quizzes b) emotional cripple. For neither of my degrees did I dress up medieval (silly hat, pointy shoes, gaudy gown). I might have done it for my parents but I deliberately went to college in a different country, so it would have been faff for everyone. Formal graduation also cost money but my main reasoning was that such ceremonies were a bourgeois charade and/or a silly anachronism, so I probably scotched any suggestion that my graduations should be a family affair.  I have been to graduations every year at The Institute, however, because I have better manners now and more empathy: students want their folks to meet their teachers and I am moderately interested in seeing where they came from. It also gives me access to a bunch of data to analyse I - II. And an opportunity to graze some canapés! For a college (it used to be a Regional Technical College is now an Institute of Technology and will be a Technological University) that is less than 50 years old it is damn-fool silly to confer degrees in faux-medieval costume; so I put on a jacket and tie, sit in with the parents and boycott the academic procession.

aNNyway, yesterday morning I went to my first ever 'Commencements' in Trinity College Dublin. TCD is by far the oldest university in Ireland, and they are hot for tradition, archaicism, and dressing up medieval. The real name of the institution is The College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin. They call the terms Michaelmas and Hilary rather than Winter and Spring, the boss is a Provost rather than a President and graduation is called Commencements not Graduation or Conferring because leaving Trinity is seen as a start rather than a finale. This was all explained by The Registrar as a warm-up to the ceremony proper. She also explained that the entire ceremony would be rendered in Latin! making the claim that when TCD was founded in 1592, Latin was an all-inclusive lingua franca which could be used for dialogue whether you came from Bologna or Bristol. Hmmm, true-dat but it is now 425 years later and nobody - nobody - in the room was fluent in Latin so using that language was now exclusive and alienating. Ironically, for inclusivity, Trinity employs a signer for the hard-of-hearing, so the deaf understood better what was going on than the rest of us. And no, the signer isn't fluent in Latin either: he's working off an English translation - although probably using Irish Sign Language not British [big difference].

I was in TCD because one of my project students at The Institute went on to do her  12 week work placement internship in my old Comparative Immunology lab in TCD and stayed on to work up the project [on olfactory receptors in dolphins] for a M.Sc.  She stuck at it and wrote it all up and was in medieval clobber [a snip at €40 for a couple of hours] to Commence the rest of her life.

Now here's an important multicultural issue that is buried in the use of a deaf dead language. Proceedings are signed off with an envoi "Valete senatores, non diutius vos morabimur; valete candidati novis honoribus decorati; valete et vos, hospites acceptissimi. Comitia solvantur in nomine Patris et Filii et Spiritus Sancti."   . . . in the name of the father, the son and the holy ghost??? We're all inclusive for the deaf [N = 380,000 in Ireland] but divil-and-all for the No-religions [N = 280,000] or Muslims [N = 50,000], of which 'my' candidate was one.  I've had a peg at this unthinking religiosity in our local Credit Union. Let me also say that Sign Language is as opaque as Latin to me and Pat the Salt who are both hard-of-hearing.

That done I went off to lunch with Dau.I who works but a half day on Fridays. That was very nice - we went to the student dining hall - called The Buttery in Trinity! - for cheap and cheerful fish'n'chips. By the time we had finished catching up - since last Sunday in Cork two hours had passed and I noted that a crowd, fat with photographers, was gathering again in Front Square. Turned out that Bob Geldof was getting a celeb Honorary Doctor of Laws Degree. Other important people [see above with President Mary Robinson] were also getting tribbed. When the procession trooped past, the paparazzi called "Bob, Bob" and Geldof turned to the cameras to wave. Me-the-Bob muttered to Dau.I " My Public, my Public". The nearest photographer rounded on me and said "You cynical old man . . . but I do agree" and went off to his next assignment. As must I.

Friday 23 June 2017

little wedges

I've said this before but I'll say it again; the mighty Georges Cuvier (1769-1832) summed up his expertise as "À la vue d'un os, d'un seul morceau d'os, je reconnais et reconstruis la partie de l'ensemble dont il provient". Essentially this translates as "your toe bone's connected to your foot bone, your foot bone's connected to . . . everything you are and do: what you eat, how you move to get what you eat, how old you are". This assertion of knowledge is partly true because of evolution and context. My thigh bone, gracile but strong, says that I am a runner [or could be if I'd only get off the sofa], the thigh bone of a hippopotamus says "plodder" and because of this "vegetarian". My thigh bone is far more similar to Usain Bolt's and Emmanuel Macron's than it is to one of our sheep grazing 50m away. Simply measuring and analysing teeth metrics we used this concept of homology [descent from a common ancestor] to assert something about Australopithecus spp. and the eruption of the genus Homo = humankind.

Archaeologists are capable of similar feats of deduction. From a series of blackened back-filled holes in the the ground, a pot-sherd, an axe-head and some pollen analysis, they can infer the life and times of a neolithic village and mourn its savage destruction. But about 6,000 years ago information became immeasurably richer because someone invented writing and history emerged from pre-history. After 4,000 BCE, therefore, we can begin to name [a few chosen] people and get another source of data about the life and times of people who are long dead. The written data is still super-patchy but nevertheless adds to our understanding on top of pottery fragments and a few crumbly skeletons to autopsy: like ourselves, the pharaohs were prone to TB, malaria, dental caries and thrush.

Denise Besserat was born in 1933 at Ay in NE France where they make the Bollinger >!cheers!< and made herself the GoTo person for understanding the birth and development of writing systems in the Near East. In 1954 she married Jurgen Schmandt, a philosopher and policist, and added his name to hers: Denise Schmandt-Besserat [L].  A couple of weeks ago here was a nice programme about her revelatory insight on BBC World Service which you can read or listen to [with annoying and unnecessary bingly-bongly background music].

We have known about cuneiform since archaeologists started unearthing barrow-loads of decorated clay tablets in Mesopotamia in 1929. These tablets, frozen in time, predate the writing systems of MesoAmerica, China and Egypt possibly because clay survives better than wood, paper or papyrus or more probably because this really was the first method of recording stuff in an abstract way. Writing things down precludes any possibility of the he said she said which is always a real possibility with a verbal agreement. One thing that supports the antecendence of cuneiform is the suggestion that early examples were impressions of tokens pressed into the wet clay.  Later, everyone who mattered agreed that a stroke with a stylus could double for a pressed token and was far quicker and neater to inscribe. That break-through also allowed abstraction for larger numbers. V rather than IIIII and X not IIIIIIIIII is on familiar almost modern territory.

For a generation after these cuneiform tablets [R section of one] started to be gathered, recorded and compared, nobody had a clue what they meant. Because archaeologists tend to be educated in the Arts Block, they were imagined to be poetry or messages between kings and commanders. DS-B had a hypothesis that they were an example of correspondence counting. This is used by cricket umpires who transfer a pebble from one pocket of their dazzling white trousers to the other whenever a ball is bowled: when six pebbles have been transferred the umpire calls 'over', everyone troops to the other end of the pitch and the six-ball cycle continues. What if the accountants in the marts of Uruk had little blobs of clay to represent a sheep, a firkin of ale, a bushel of barley, or tray of loaves? Scanning a table of pots containing the various tokens was a lot more convenient than going outside in the blistering sun to see how many sheep the merchant had to trade. One firkin/sheep/bushel = one token but it takes two to tango a transaction, so the receipt for sheep became a clay tablet impressed with the correct equivalent of tokens. They have found an inventory of about 300 different commodities represented by tokens.  Read this essay on the evolution of writing from U Texas. Actually, the tokens were initially stored in a ball of clay = bulla for convenience, which was ++ inconvenient because you couldn't see what was inside (they would have paid a lot of barley-cakes for a supply of ziploc plastic bags). So the accountants would write the contents of each bulla on the outside. It took a long time to appreciate that 10 chickens, 10 wine-skins and 10 loaves all had something in common - 10 - and mathematics was launched.

The idea of correspondence of two written records for a transaction/trade is captured by another lovely essay in BBC series 50 Things That Made the Modern Economy. This is about tally sticks: small (20cm long) billets of willow-wood upon which a series of notches were cut to represent the amount of the debt. The stick was then split lengthwise, half retained by the creditor and half given to the debtor. The notches and the grain of wood matched uniquely and so made an incontrovertible contract. One unintended consequence of these sticks was that they could be traded themselves for other products. The BBC story includes a neat summary of the 6 month long Irish bank strike of 1970. The economy managed quite well for half a year because people - publicans, shop-keepers, feed-merchants - would accept cheques from people whom they knew and use those checks to pay their suppliers and employees. A local peasant economy could make it work with that amount of trust. It brought into focus what money really is. Old banknotes had a flourishy statement "I promise to pay the bearer on demand . . ." signed by the president of the issuing bank. They have dispensed with that in multi-lingual Euroland leading to a further level of monetary abstraction. We've come along way since a handful of clay tokens were the sheep they represented.

Thursday 22 June 2017

old and gnu

eee but we do love our megafauna. The logo for the World Wildlife Fund is a giant panda Ailuropoda melanoleuca [the black&white cat-footed one] rather than a nematode worm because pandas pass for cuddly in a way that no nematode can. Although a case could be made that the nematode Baylisascaris schroederi which parasitises pandas makes as much impact on the ecosystem as the cuddly furry one. Let's hear it even louder for the microbial community of those bamboo forests upon which the whole visible habitat depends . . . indeed let's change the logo for the WWF [R].

We've been to the Serengeti before sifting Zebra shit; it is the quintessence of  ecosystem not least because there is a wide variety of fauna bigger-than-a-breadbox which makes it more sexy than Louis Agassiz's back yard in Cambridge MA. A few weeks in East Africa appeals to a certain cohort of the well-heeled travelling public. I think that, in terms of Serengeti biomass, the wildebeest Connochaetes taurinus is probably the top dog. Wildebeest is [duh!] a dutch loanword but we also call them gnu which may be borrowed from the language spoken by the !ung san [prev]. Actually, purists and pedants will point out that if the word is from the San people it is naming Connochaetes gnou the black wildebeest Gnou à queue blanc not the blue variety C. taurinus  gnou à queue noire [See map L: C. taurinus in blue, C. gnou in yellow, C. both-species in brown].The San had been driven to the margins squeezed by the Bantu coming South and the Voortrekkers coming North met on the Orange River. And the only intersect between San speakers, Anglophones and gnus occurred Cis-vaal rather than Transvaal. Did you know there were two species of gnu? I didn't: it's like African giraffes and elephants - there is more diversity than a cursory glance would make you suspect. otoh, maybe the Connochaetes genus has been over-split because the karyotype is essentially the same for both species and fertile hybrids have been obtained. Maybe the French have it, one type has a white tail the other black and that is enough to make them different species. The history of civil rights has been an action to dismiss a similar exaggeration of superficial difference in Homo sapiens - emphatically a single species.

A nice consolidation of some wildebeest links on Metafilter brought on some droll commentary. One author compared 6500 dead blue wildebeest to 10 dead blue whales, which elicited a laconic "Degree of difficulty: getting the whales across the Serengeti." Seems that the restless gnus in the Serengeti and adjacent parts of East Africa go round and round on an annual migration following spells of rain which bring out a flush of grass upon which the gnu, and their attendant artiodactyls and perissodactyls feed. Millions of walking herbivores chomp through thousands of tonnes of vegetation every day. This wall of flesh pushes forward over hill and dale but pauses at rivers, especially if they are in spate or have naturally steep banks or are thronged with tourists in land-rovers hoping to get some snaps for their holiday album. At every river-crossing some gnu get snagged by crocodiles [death-porn link] or miss their footing or are elbowed off the ford by the conspecific press . . . and drown. A couple of hundred rotting gnu carcasses [pic!] are a bit poooeeee but only for a month or so as their protein is recycled. The skeletons last longer and provide slow-release phosphorus for everything downstream for many months. It is surprising how many species depend on these accidental deaths. Each death is a tragedy for the individual  but collectively they happen with sufficient regularity that they can be banked on.  Not just the crocs and the fish, but the hyaenas Crocuta crocuta and hunting dogs Lycaon pictus which haul joints out of the river where what's left nourishes the trees and bushes. And of course the buzzillion flies lay eggs and the maggots feed the birds and the cycle of death goes round. More glossy and more data at Atlantic.

Wednesday 21 June 2017

Every light blazing

My late lamented father was a complex chap. Never mean about money but having a few bonnet-bees about certain aspects of the household budget. He was a danger to leave out in a shopping precinct alone on a Saturday morning because he was certain-sure to come back with a device for punching aeration holes in the lawn or a gadget for exercising the calf-muscles. He didn't seem to appreciate that, IF he used the lawn-aerator THEN his calves would get sufficient exercise pushing the thing up and down between the herbaceous borders. Periodically (after he'd seen the monthly bank-statement?) he'd tear through the house switching things off and crying "Every light in the house blazing!" in the hope that his family would rally round and help fight the haemorrhage of kWhs.  I don't think he got much support and things would quieten down after a couple of days - possibly because he decided it wasn't worth the effort. But I'm pretty certain his crusade was not really evidence-driven. In any case he realised that pinching pennies was really quite alien to his sense of self.

In 2012, I had a rather abrupt pay cut as the research money that was supporting me was running out and I was down to one paid day a week. Being time-rich but cash-poor had its advantages and me and Dau.II spent a lot of quality time with her grandparents. It also gave me an inkling of hope for my future in retirement because two old age pensions was way more than I was pulling in for on€-day-a-w€€k. Nevertheless, having but a trickle of money meant that there was no slack in the budget and that is when I stopped drinking. The 2011 data suggested that The Beloved and I might well knock off a couple of bottles of wine a week if we had a glass each with dinner each night. That would be okay if we lived in South Africa where Chardonnay is cheaper than bottled water or in France where they have low taxes on booze pour encourager les viticulteurs. But in Ireland back then, a bottle of Old Red Biddy was at least €5 and two bottles a week was therefore €500 a year. Which was lot for a man on €1,000/mo; so it was farewell to plonk.

I fell to those reflections because we had a morning of post-graduate student presentations and when we all left I noticed that the last presenting student had left the computer on; so I switched it off. As I walked back to my office with one of my colleagues I wondered aloud how much electricity was being wasted by such "someone else will do it" bystander effect.  I know that every Monday last academic year I had a QM quantitative methods class at the very end of the working day. At about 1700hrs we'd all leave and as far as I was concerned all 20 desktop computers would be on-standby for 16 hours until 0900hrs the next day.  A computer in sleep mode is using 25W or about the same as a lightbulb. Not so much you say but 25 * 20 * 16 is 8 kWh which costs, in Ireland about €2. That's a tenner a week or about €500/yr which was doing much less good to me or the planet than €500 worth of wine. I feel a guesstimation exercise coming on for next year's QM class:
  • Is it worth employing someone to switch off all the lights/computers in The Institute at the end of the working day?
And that's just one computer room, there are probably 20 such room-equivalents on campus = 400 there are 400 faculty and support staff, each one with a desktop computer. If half of all the computers are left on all night that's (400 + 400)/2 * 16hrs * 25W = 160kWh each night or €40. Many of my colleagues leave their computers on each night because the boot up takes so long which is a real deficit if you have a 0900 class and want to print out a quiz for 30 students . . . after a forward-planning failure. I used to do the same thing - and piss-and-moan at the inefficiency of it until I spoke to our IT support person. He said that the boot-up delay was because my computer was under RAMmed so he came over in the afternoon and replaced the 4GB chip with an 8GB version: the boot up then took 10 seconds. Moral: just ask - you may be pushing at an open door.  And switch the bloody lights out, of course.

Tuesday 20 June 2017

Now dry your hands

Having two daughters in the catering trade and teaching biology and human physiology in The Institute, I have views on hand-washing and not washing them.  Clearly I R confuse about the matter. I'm much firmer about the art of drying your hands, however. I'll give the students a broadside about arbormort if I see them pulling out fathoms of paper towel to dab their fingers dry. If the kids have to wash their hands before and after lab-class that is a lot of paper towel and we habitually get through the annual quota about 6 weeks before classes finish. Outside the labs, in the "bathrooms", some bean-counter has decided that air-blowers are more economic than paying for paper towels.

On our Cultural Weekend in Cork (march, film, dance, bonding) we went out to dinner before the ProdiJig gig. After a certain amount of geopolitical debate we wound up in Koto: Our Asian inspired menu has been created to soothe, nourish, and inspire . . . you get the picture. We got perfectly acceptable tasty bowls of noodles and polished our plates, so that was okay. But waiting for the bill, we all went up many flights of stairs for tinkle before a couple of hours in the theatre. The hand dryers in the gents were just pathetic and I finshed up drying my hands on the back of my shirt. This is a known thing among blokes. As we walked across to the Cork Opera House, I asked my three favorite women, on the hypothesis that the ladies hand-'drier' was as useless as the blokes',
Q1, How did you dry your hands?
Dau.I. On my skirt, of course.
Q2. How did you dry your hands?
Dau.II, Duh, on the seat of my jeans.
Q3. How did you dry your hands?
The Beloved: I used toilet paper.
All.  Mega-fail! What about the trees? Were they organic, even?
All that intra-family barney and diequilibrium could have been avoited if the restaurant had installed a system that not only saved paper but actually dried hands . . . more effectively than having someone breathe on a glass prior to polishing it. There's no excuse here because Koto has only been open since March

The air driers at work are noisy and hot and almost do the biz in the time allotted. The newest building dubbed the Haughton Teaching and Learning Centre has Dyson blade driers which really do work better than the sclerotic warm-air machines installed in the older parts of campus. a) I wish to receive a gratituity from Dyson for this affirmation b) I intend to take a short walk in the rain next time I need to wash my hands . . . or bring a table-napkin to work - fits folded in the back-pocket and serves as a personal hand-towel. Epic Win!

Monday 19 June 2017

You can sing it

We've finished exams at The Institute - big phew! all round. Almost all my hours nowadays are practical classes in biology and maths, so I only have to write, have reviewed and mark one Summer exam: Human Physiology for 1st Year Pharm Tech PT1. With all my courses, there is a certain amount of Imposter Syndrome - none of it really taps into my peer-reviewed expertise in the migration of cats; hominid tooth metrics, synonymous codon usage; gene discovery in chickens or operons in the human genome.  There are no operons in the human genome!  I used to get nervous submitting exams in Human Physiology knowing they were to be reviewed by two external experts in Pharmacy.  Then for several years, the feedback was entirely complimentary "good paper, well developed syllabus, fair questions" so I started to believe that I really did know and was effectively explaining important stuff about how the human body works.

The exam papers are reviewed by the externs in February and the answers are reviewed at the beginning of June.  For the first time, all my PT1 students had passed the course, although I'd had to be a bit generous towards some in the trailing tail of the class.  To be honest, a handful of them had done shockin' bad on the exams and had only passed because they had done okay on the numerous MCQ quizzes that I'd put them through during the year . . . and done surprisingly well on their essay on lysosome storage disorders. So I was little defensive talking to the extern and I found myself gabbling about the artificiality of examinations: learn learn learn, cram cram cram, blurf it all out in two hours and forget it forever the very next day.- as shown by some of these university graduates retaking the teenage maths exam. I asserted that my students would remember the information about their lysosome storage disorder for longer than anything that had appeared on the May exams.  It made me resolve to have more project work next year but I also resolved to make some of the key facts more sticky.

At the beginning of the month I was unavoidably listening to adults talking about the berluddy Leaving Certificate, the exam ordeal to which every 18 y.o. in the country is subjected.  As a bit of light relief two presenters were remembering what was top of the pop charts during those fateful two weeks long long ago. Loadsa people txtd and phoned in to report the song that was still buzzing round their heads decades after they had forgotten The Calculus, the terms of The Treaty of Paris 1783 or who signed The Treaty of Paris 1951.

Then I heard an interview with George Hammond-Hagan [similar on the BBC] who has devised a mnemonic resource call Study Tracks.  He is song-writer who had a son going through the goddam exams and so he wrote and sang some songs using the text-books for lyrics.  It has the ring-a-ling-ling of truth. It's got to work for some kids some of the time.  It's a business but here are some samplers renaissance - R&J. Such rapology doesn't sing to me, but it may well work for The Yoof. This is not an original idea: here's Mrs Martin making her maths pupils dance to her tune. And years and years ago Tom Lehrer [bloboprev] nailed the Elements to a song so that Daniel "Potter" Ratcliffe could recite them.

I've introduced my PT1s to The Memory Palace for blood pressure but there are lots of ways in which something will happen that will make more sticky the ideas, the lists of attributes, the main players in Human Physiology.  If I was deliver myself slightly late to class in a bright red leotard, brandishing a huge hot-water bottle and moaning about the pain d'ye think they'd remember the four attributes of inflammation . . . forever?

Sunday 18 June 2017

The Dadical

Dadical is a new coinage, as far as my daughters are concerned, having been applied to me yesterday. 'Popsicle' would have been possible except that it is already a word for something cool and refreshing: hardly applicable to The Da. Back in  April, Dau.I and I went on the March for Science in Dublin. The agreement was that she'd come out For Science if I would come out for The Gays. That was tentatively fixed as having a date with the Dublin Pride March on 24th June 2017. But 2 months is a long time in radical politics and I washed up in Cork this weekend because a) it was my birthday yesterday b) therefore Dau.II had bought us tickets for ProdiJig, a hoofer troop of which she is a fan. Here we are, Dau.I and her Dadical [Left for Rights! close-up below] wearing identical repealthe8th badges.
Because good things always come in threes, it turned out that Dau.I could get her pay-back and we could have a family outing round Cork city centre, by going on the local Repeal the Eighth rally, which kicked off at 1330hrs yesterday. Here  I explained the issues about the 8th Amemndment to the Constitution back in March. With two daughters in the 20s, I get to hear about those issues from the horse's mouth as one might say. A case could be made, and the girls are quite keen to make it, that only women of child-bearing age have a locus standi on the matter and they invite nuns, grannies and blokes of any age to just hold their whisht about the rights and wrongs of abortion. My late lamented, and rarely PC boss had a phrase "your rights end where my nose begins" which I am inclined to take up on his behalf. That's  a trip-off-the tongue way of articulating an overarching tolerance of diversity. Matter-a-damn what you do at home - eat pray or love whomever or whatever you wanted because it was none of my business. It's not a literal nose as the boundary - mowing the lawn or raising cain at 0300hrs on a week-night is not tolerable unless your neighbours all have ear-plugs.

One problem with Rights is deciding who is to vindicate them. I don't think that normal people would have much tolerance for a return to trial by combat in which the strongest, fastest or wiliest fighter was demmed to have found favour with the deity. We still haven't cracked the closely related problem of trial by lawyers because it is clear statistically that the richest person wins disputes a disproportionate amount of the time. It is more or less a sham to appoint a lawyer to fight for the dispossessed because they are hobbled by lack of money.  ANNyway the effect of the 8th Amendment as it has come to be interpreted is that the right to life of the unborn trumps pretty much any right of the mother except avoidance of her death. The vindication of this right has led to one high profile case, Savita Halappanavar's, which killed both mother and child and that doesn't seem to be the best possible outcome by an objective assessment. The right to life was brought into focus again in 2015 when a woman, 17 weeks pregnant was kept on life-support after sustaining a catastrophic internal blood clot that left her brain-dead.  The Hippocratic Oath is specifically against abortion but we don't need to adopt wholesale the ethics of ancient Greeks whose civilisation had a foundation of slavery in the silver mines of Athens. We could move to the 19thC with Arthur Clough's verse advice "Thou shalt not kill / But need’st not strive / Officiously, to keep alive." which I've trotted out before on end-of-life issues.

Here's the thing, right now we are in an 'every sperm life is sacred' era: caught between a life is cheap time when a child could be hanged for stealing a handerkerchief and an uncertain future. The trouble with Rights is when they are prefaced by a starement like "We hold these truths to be self-evident . . .".  To which the skeptical reply is Whoa! no we don't. Rights that were obvious to all thinking people at some time in the past are now considered repugnant to many. The rights of the unborn are a super-polarising concept about which it is hard to have a rational discussion. Discussion degenerates into a recital of anecdotes (I gave two, Savita H and life-support,, in the prev para); young women fall pregnant for all sorts of reasons and travel to the UK for a termination - at a rate of 10-30 every day so they already have the ability to safely become unpregnant. If The Patriarchy would just shut up, this Irish Right could be vindicated in an Irish clinic. Another place to start the discussion might be to suggest that we throw out the Absolutes - because we don't give an unqualified right to life to Syrian refugees, or starvelings in the Sahel or Somali pirates. We now live in a 21stC where 7.5 billion people are eating their seed-corn and despoiling the planet. Fewer people please: coral reefs, rain-forests and every species on the IUCN red list have rights as well as every person or proto-person on the planet.

Techno Sunday 180617

A few bits on technological solutions to making things.

Saturday 17 June 2017

Use it or lose it

Can you hold a pencil? Although not recognised as such by the Transportation Security Adminsitration, pencils can be used as a lethal weapon, if hexagonal they can also be used when there are no dice available, or to fish termites out of a hole for dinner. Chimpanzees could carry out any of those tasks but only humans can use a pencil to write their name . . . or The Grapes of Wrath. That's because we can use our thumb, index and middle finger in a 'power-precision grip' PPG and manipulate the pencil to make marks of tiny precision and delicacy - not only writing but drawings, graphs and diagrams that accurately convey and record meaning. Some drawings are so realistic that you wonder why the perp didn't use a camera. The PPG isn't only used for pencils but for lifting jam-jars, bullets, day-old chicks and baseballs. It is hard to program a robot's computer to pick up an egg without crushing but your muscle and mind achieve this without a conscious thought. It takes time to get these tasks right, babies are clumsy, can't get the spoon into their mouths and make a sloppy mess all round them until they learn how. Letting Petal feed herself is a long haul strategy but it pays dividends. Baby led feeding, adopted by The Boy and his family, saves a mort of money because the kids pick over the family dinner rather than being catered for with Gerber Glop, Materna milk puddings or Cow&Gate creamed rice. But BLF also drives the development of the mind, autonomy and a sense of self.

One of the things that neurologists are discovering is that the doors of perception need to be opened and closed, and frequently oiled, if they are to develop and retain utility. The brain is plastic and there are many potential calls on a neuron. After a stroke, you may laboriously recover the use of your limbs and the power of speech by re-purposing and recruiting other neurons to filfill the functions ablated by the ischemic event.  If you are born without eyeballs then the part of your brain destined to become your visual cortex is effectively snapped up by other functions and put to good use. This is an argument for embracing hearing-aids - to stop the auditory cortex closing shop altogether.  If you don't use your hands to carry out finely dextrous tasks then your don't get to keep the motor neurons and that may have negative impact on your general cognitive development.

When I was growing up we played with wooden cotton reels, saucepan lids and sticks, It was like reading the book rather than watching the film of the book. Our imagination filled in the bits between saucepan lid and shield; between Lego and Bridge of the River Kwai; between a plastic airplane and Dresden Valentine's Day 1945. Children then lived in their heads and could subvert efforts to make them play in particular ways - as exposed by Saki's story The Toys of Peace. The youth of today have no patience with wooden blocks or cardboard boxes because they have Lara Croft [bloboprev] to steer through somebody else's imagination.  David Gaul and his boss Johann Issartel at Dublin City University have got some data [PMID 26735589] on how the modern world may be turning the digital generation into blobs unable to zip up their own coats or pick their own noses because the only fine motor skill FMS they can carry out is a swipe or a tap.
Next time you see someone tying the shoe-laces just look at the task sequence required: it's a wonder that we can carry it off at all and I know my twin sister had to do this for me when we first went to primary school. Gaul and Issartel measured 250 kids divided between 2nd, 4th and 6th classes = aged 7, 9 and 11 and found that they got better at a standard set of motor coordination tasks as they grew up. That's good, you'd hope the young shavers were learning something over those 5 years.
Key: fine motor precision (FMP), fine motor integration (FMI), manual dexterity (MD) and upper-limb coordination (ULC). The bars are mean and for 2nd, 4th and 6th class. Quite a lot of variation there.  But concern developed when they compared the skills to the normal average for children of the same age:
Key: [annoyingly different from the tasks in Fig 2 above] fine manual control (FMC) and manual coordination (MC) units and Total Fine Motor Composite (TFMC). You can see that 2nd class students start off close to the average [the 50 line] but steadily fall behind 'normal' as they grow up. David Gaul was on the wireless the other day and he suggested this increasing deficit was a) disturbing and b) possibly due to the swipiness of the youngsters environment decreasing their capacity to do up a button let alone sew another one on when they oafishly rip the original one off trying to force it through the wrong button hole [I paraphrase!]. Skeptics among you will note that the error bars are all large and comfortably embrace the 50%=normal point on the standard score axis. Trouble with social science and medical experiments is that it takes yonks to gather up any kind of sample at all at all and even then it may not be statistically robust. The blue 2nd years are different people to the green 6th years and the difference in the means may be a statistical artifact. I hope that the authors aren't going to park the project having gotten this publication out because there is a longitudinal study crying out to be done: same kids tested at two year intervals. And of course, we need someone from Montpellier or Bordeaux to replicate the study in French schools. And a control set of home-educating children to see if school is sapping the will to live of the children who are ground through that inexorable mill. This reminds me of another place where the external environment impinges disastrously on neuro-musculat development - the myopia epidemic driven by the absence of sunlight.

Friday 16 June 2017

Anti-inflammatory in the balance

Inflammation is a good thing, it is the body's response to physical and biological assault and mostly it works a treat. The other day I was yanking my boots out of the car-trunk and nicked my finger on a tooth of the chainsaw.  It didn't hurt but bled quite a bit and the hole was sore for about 24 hours. A nice clean cut; any bacteria flushed out by the blood flow; some local white blood cell activity to mop up the remaining bugs involved a little swelling, a little tenderness and a little redness. Sounds like inflammation to me - I share an old Latin mnemonic with my Hum Physiol students:
  • Calor heat
  • Dolor pain
  • Rubor redness
  • Tumor swelling
Sometimes, however, inflammation can be a disastrous over-reaction. Cholera toxin is no fun - it's a toxin after all - but the body's response to the presence of Vibrio cholerae is to flood the intestine with fluid to flush out the toxin producing bacteria: flush flush flush until the cistern and the header-tank run dry and you die of dehydration. They say that fit young people, with active inflammatory /immune systems died disproportionately during the Spanish 'flu pandemic of 1918: the treatment worked but the patient died. One of the consequences of developing an auto-immune disease - rheumatoid arthritis; multiple sclerosis; psoriasis; psoriatic arthritis; lupus; Goodpasture syndrome - is that there is tissue damage. Tissue damage means an inflammatory response which means calor dolor rubor & tumor which is a bloody nuisance and makes you feel utter crap for much of the waking day.

What if, some medical researchers asked, we could damp down the immune response. That would alleviate many of the distressing symptoms of auto-immune diseases and might even promote a bit of healing in the damaged tissue. One of the positive outcomes of 30 years of molecular biological research is that we now have model incorporating some of the key players in the inflammatory response: both what molecules are involved and what cells play a part. As with the nervous system, we reckon that the cellular response is controlled by external molecules = "ligands" which dock and bind with receptors embedded in the cell membrane. "Molecules which are produced by one cell type and act on another cell not in immediate proximity" is a definition of a hormone. But in the context of immunology and inflammation such molecules tend to be called cytokines. Each cytokine will have a particular look&feel and function and will only be effective if it makes contact with a specific receptor. Both cytokines and their receptors are proteins of which we have an inventory of about 100,000 different forms, some quite closely related to each other. Clearly there are two ways to turn inflammation down a notch or two:
  • destroy, disable or interfere with the production of one of the cytokines
  • put a spanner in the cytokine receptor to prevent docking
Stress is also A Good Thing - it is a way of keying up your physiology to deal with a problem - tiger; alpha-male; sudden change in weather; potential mate - but is ultimately damaging if it goes on for too long. Human Physiology, I intone at almost every lecture, is about the checks and balances of homeostasis. Short cartoon, reasonably on the right track. Homeostasis is maintained in the normal run of things by having both pro-inflammatory and anti-inflammatory cytokines and dribbling them out in the correct proportion for the given situation.

One way of nobbling a cytokine is to develop a 'biologic' an antibody against that molecule. I've written before about the absurd unmemorable hard-to-say names for drugs. But there are some clues: if it ends in -mab it is a monoclonal antibody developed by injecting the . . . heck I'm not going to explain this because it's w-a-a-a-a-y outside my competence so I'll hand you off to John Nguyen at Massachusetts College of Pharmacy and Health Sciences - what's a MAb and how are they made.
More etymological clues:
  • omab (original and not the best) = murine monoclonal antibody
  • ximab = chimeric (part human part mouse) monoclonal antibodies like infliximab [prev]
  • zumab = humanized (less mouse more human than ximabs)
  • mumab = fully human monoclonal antibodies are made in human cell lines skipping the mouse protocol. Try saying adalimumab with clarity and authority when explaining its potential to a worried patient.
  • Another John Nguyen gallop through a bunch of specific MAbs, their names pronounced and the uses described
The point about MAbs is that they are extremely specific; they will nobble the target molecule and leave everything else alone. So there are usually fewer side-effects. I've written about infliximab before which targets TNF-α a cytokine that cranks up the inflammatory response when cancerous cells appear.  Its name tumour necrosis factor tells the story: with TNF-α tumours are suppressed without it they grow.  Clearly TNF-α is A Good Thing because cancer is the Black Hat of modern Western medicine . . . except when it runs away with itself and cranks up inflammation when it shouldn't. This is the case for a string of auto-immune diseases including rheumatoid arthritis RA, ankylosing spondylitis, inflammatory bowel disease IBD , psoriasis, and refractory asthma and all these disorders can be treated with anti-TNF therapies.

The trouble is that although the MAb is extremely specific - it will take down TNF-α only - TNF-α is a key work-horse in maintaining homeostasis all around the body. By controlling the level of this cytokine to mitigate the debilitating effects of RA or IBD, the patient no longer has enough of the stuff to do its says-on-the-tin tumour necrosis job and lymphomas are a common side effect under long-term use of infliximab. This robbing Peter to pay Paul is a problem in many aspects of modern medicine and the good doctors spend a lot of time and money juggling the competing forces to get a drug and a dose that is a Goldiloxian just right. Cue not strictly relevant fragment of verse:
I balanced all, brought all to mind,  
The years to come seemed waste of breath,  
A waste of breath the years behind
In balance with this life, this death.

Thursday 15 June 2017

La Joconde

It's someone's birthday today and the triptych above gives a clue as to who deserves a roaring conflagration of 538 candles on her cake. I'm sorry, if there are any youthful readers of The Blob, but this woman has more likes than young-wans Taylor Swift, Adele and  Ariana Grande put together. I have here cast her in a heroic role to show how far her picture can deviate from 'the truth' and still be recognisable. I don't think a satirical pastiche of Ariana Grande as Miss Piggy would work; not least because half the kids who sing along with AG because they know all the words would not recognise a cultural icon of a previous generation - how quickly they forget.

ANNyway, Lisa di Antonmaria Gherardini was born in Firenze on 15th June 1479. She never got to taste Firenze's famous Sou'wester Cake because that's from another time . . . and another place. But the consensus is that she lived a longish and happy life; hence the enigmatic smile. She married, at 15!, a cloth-merchant in Firenze called Francesco di Bartolomeo di Zanobi del Giocondo, was comfortable financially and had six children (one daughter died young) and passed away, in the fullness of her years (for those days! next week I'll be the same age as she died and I'm not quite ready to go yet) in July 1542. Her, now mega-famous, portrait was begun by Leonardo da Vinci in 1503, when she was in her 20s and convincingly matronly and content - if you believe the smile.  The painting is, as everbode kno, now behind bullet-proof glass in the Louvre in Paris. Of the 10 million people who visit the Louvre each year, 80% of them are poured out of tour-buses so that they can tick the been-there-done-that box in their itinerary.  That's 20,000 people a day trooping past and ignoring the amazing treasures that are in other rooms of the old royal palace. The folks back home in Kyoto, after all, think that the Nike of Samothrace is a brand of shoe. Why not listen to Emma Durrant talking about something Louvrelse in her best Dublinese.

The portrait, although commissioned by the Giocondo family, was whisked away by da Vinci who continued to work on it for another ten years in Italy and France and I don't think it ever got to hang in the Giocondo's hallway. Accordingly, knowledge of its provenance was lost and speculation grew legs.  Many famous women were seriously suggested as being the model: Isabella d'Aragona,Cecilia Gallerani, Costanza d'Avalos, Isabella d'Este, Pacifica Brandano, Isabela Gualanda, Caterina Sforza. There is even supposition that the actual sitter was Leonardo himself in his pre-beard days, or his impish assistant Salái. The latter claim is vigorously disputed by the suits at the Louvre.
In 2005, Armin Schlechter, a scholar blowing dust off the antient folios in the archives of Heidelberg U discovered a marginal note in a copy of Cicero's Letters written in 1503 by Agostino Vespucci. Seeing the painter Appeles referred to by Cicero, Vespucci wrote in ink "Apelles pictor. Ita Leonardus Vincius facit in omnibus suis picturis, ut enim caput Lise del Giocondo et Anne matris virginis. Videbimus, quid faciet de aula magni consilii, de qua re convenit iam cum vexillifero. 1503 octobris" [Translation]. Scribble scribble Mr Vespucci tsk! That sort of thing may well remind you of  the most famous marginalia Hanc marginis exiguitas non caperet written by Fermat and serving as a challenge to Mathematicians for the next 350 years. Incidentally Agostino was cousin and contemporary of Amerigo Vespucci whose name was attached to the New World over much stronger claims by other explorers.

Wednesday 14 June 2017

Mental load

As you know, if you've been here before, I surf a corner of the blogosphere which starts at 8-10 jumping off points and then goes off down any rabbit-holes that there present. Even these same-wavelength places have quite long fallow periods where there is nothing that captures my imagination - heck, that might be me in one of my downers. Then there will be a flurry of stuff that calls [yoo-hoo, you!] to be followed up.  If we still had children at foot, or I was a proper farmer, or I rejigged my course notes every year at The Institute, then I wouldn't have time for butterfly hops about other men's flowers.  Then again, I didn't start bloggin' myself until I was furiously busy at a new job and only a week ahead of my students.  I wouldn't say something like "If you want something done, ask a busy person to do it." that was Lucille Ball, I just lived it.  aNNyway, one of those jump-stations is Metafilter aka The Blue and the other day I saw a piece about role-filling in heterosexual relationships; that in turn was citing an original source. That source is interesting because it helps builds my knowledge of contemporary colloquial French because the author Emma is a thirty-something cartoonist who writes in French Faillait demander but gets her stuff translated into English You Should've asked when it goes viral. Her bailiwick is "Politique, trucs pour réfléchir et intermèdes ludiques"; which is whatever is floating her boat this week.

When I worked in the zoo in Rotterdam in the late 1970s, we all mucked [literally a lot of the time] in together but joked [*] that some of the daily tasks were vrouwenplicht - women's duty - while others were for The Men. As the latest addition to the team, I did all the [vrouwenplicht!] cleaning and polishing of the front panes of all the aquariums as soon as i started work and before Jan Publiek was allowed in to grub them up with their poky, pointy finger prints.
*you could make such jokes in those days without
fear of being called up by an Offense Tribunal.

Emma's position is that, although modern chaps fondly believe [ahhh bless, 'em] that they carry half the sky around the house -
  • they change diapers nowadays, 
  • can wash dishes or or at least load the dish-washer
  • can clean a toilet and mop the bathroom floor
  • cook up a storm for eight on the weekend - esp if barbecue involved
  • as well as the [bizarrely: who makes these decisions?] manly stuff
    • take out the trash
    • mow the lawn
    • wash the car
    • fix light-fittings
in fact all the mental heavy lifting is carried out by women.  The extensive commentary on Metafilter seems to agree.

We live in changing times! My father never changed a diaper in his life. I could and did; both in the 1970s with The Boy and in the 1990s with Dau.I and Dau.II. I could also sew on a button, turn up a trouser-cuff, cook, bake flapjacks, wash dishes and saucepans and clean a bath. But I remember, when Dau.I was about 8 weeks old, I was tasked to look after her for several hours while The Beloved went to a business meeting in town. At the end of the afternoon, the child was clean, fed and uninjured BUT diaper bin hadn't been emptied; there were dishes in the sink; the laundry was one wash behind schedule; the bed was unmade; and I had no idea whether there was sufficient tea, sugar or eggs in the house. I sent a You Should've asked link to the family and got two responses.
  • One from The Boy pointing out that the French do less housework than any other civilised country.  Skeptix alert: that is published in a British newspaper; an average of 16hrs/wk in France compared to 19hrs/wk in UK and you may be sure that stacks of ménages français do more [and less] than the UK average - the data distribution is going to be heavy on the variation and low of the average.
  • One from The Boy's partner: "SO not true in our house!"
That tells me that, in one family [so anecdote not data!], over three generations, The Man is stepping up to the plate and not just stepping up with a plate waiting for it to be filled.