Sunday, 31 March 2019


When we was nippers in the 1960s, and living in England, one of the high points of coming to Ireland to visit the rellies was the chance to scoff a Fudge Cream Urney Bar [bottom L] unobtainable in Haslemere or Portsmouth.
That would be: Denthe, Friesland, Gelderland, Groningen, Holland, Overijssel, Utrecht, Zeeland. Duh, I can count: that's eight provinces. Yes, yes, but Drenthe was too poor to pay taxes and so was unrepresented in the States General.  No representation without taxation!

Saturday, 30 March 2019

Oy vey mezuzah

I finished off my very expensive education in graduate school in Boston. I had a desk in the Vole Lab which was down the corridor from Tom Kunz's Bat lab and across it from  Fred Wasserman's Bird Ethology lab. Not all the people with Mitteleuropa surnames were Jewish but some of them were and I learned a bit about Hannukah, lox & bagelsShidduch, and Dreidels. It's kind of interesting when your neighbours have completely different holidays, peculiar food and nail things up on their doorways which aren't horseshoes . . .

. . . that would be a mezuzah מְזוּזָה: a little box or tube which holds a fragment of parchment. The words on the parchment start שְׁמַע יִשְׂרָאֵל יְהוָה אֱלֹהֵינוּ יְהוָה אֶחָֽד׃ Hear O Israel, the lord our god, the lord is one. Which is a straightforward enough statement of faith. Th parchment is called a klaf and must be inscribed by a fully trained religious scribe called a sofer. Ballpoint pen will definitely not do and nor will 80gsm acid-free paper.  The rest of the text is an exhortation to to good and a promise of the god good things which will happen if the proscriptions are followed.  The mezuzah [L] is deliberately shown on a tilt because for some Jews that is part of the protective magic. Many believe that the little object will not only fend off divine wrath but also actual missiles if the neighbours get feisty. Nobody claims any particular mezuzah powers over everyday assailts on the home like junk-mail, dog-shit on the lawn, and hellish loud parties on the student house down the street.

Being a sofer seems a pretty secure gig, what with people moving home, upgrading their mezuzah to this years model, trying to out-mezuzah those Cohens next door. But I'm guessing that even a jealous god would look kindly on folks making home-made mezuzot. There are other Jewish specialists who hold local essential monopoly status a) the shochet שחיטה who slaughters animals in the prescribed way to ensure that the carcasses are kosher b) the mohel מוֹהֵל who does the circumcisions. Don't try these at home folks! Stick to the klaf-scribing if you want to save a bit.

When we lived in England through the 80s, the god-slot on the wireless was Thought for the Day, often read by a genial rabbi called Lionel Blue [shown R in his rabbinicals]. He died a few years ago in the fullness of years much loved by those who'd been braced to face the day by his slightly fey, whimsical, 3 minute morning monologues. In June 1985 I was given his T4tD paperback compendium called Bright Blue. You can get your own copy for £0.01. Our copy surface a couple of weeks ago and I rather like a story I found in there:

A Jewish family moves into a resolutely gentile neighbourhood. Everyone is curious about the new people and when they install the mezuzah someone asks about it. "It's just a box with a roll of paper inside which carries some verses from the bible". The neighbours cannot accept this bizarre explanation and a group of them go by night, unscrew the mezuzah and unroll the scroll. It says: "Help, I'm a prisoner in a mezuzah factory".

Friday, 29 March 2019

On being heard about Water

When I started at The Institute I was told off to teach Water Chemistry to our 4th Year Environmental Scientists.  On other days in those weeks I was teaching Human Physiology, for which my only qualification was that "I have a body". My quals for the 4th Year course were even slighter but I gave myself grinds and learnt a lot about ice, nitrates, BOD, COD, EPA, stone-fly larvae, parametric values, cryptosporidium and the cost of milk. After 4 years of my running water, a real water chemist came in from DCU and I reluctantly handed over the course and all my notes to him.  On Tuesday, he sent out a calling-all-cars e-mail to staff and students asking us to participate in a Focus Group on Water Quality in Ireland. It was organised by Celsius, a think-tank in the DCU Dept Comms.

Meeeeeeeeeeeeeee! I replied. It wasn't that we were offered free-parking and food for giving up yesterday evening from 1800-2130hrs; it wasn't even the €40 One4All shopping voucher; or that we don't have a telly; or that The Beloved was off site that evening. Although what's not to like about getting paid [tax free] minimum wage for for doing something different? The sandwiches were kinda terrible but the tea was hot and I had a great time. Only 8 other people from the four counties CW KK KE & WW, seemed to agree with my cost-benefit analysis. Three of us were professional [water] scientists; there were three students from The Institute; and there were three really interesting interested parties from The Public. It is perhaps instructive that the three students were all New Irish - originally from Congo, Canada and Poland. That's why we should celebrate a more diverse society: they want to contribute, they bring new ways of seeing.

I sat beside a bloke who works for a different branch of the people who organised the Public Consultation on the River Basin Management Plan RBMP which I attended in February.  We had a get-up-and-chat break half-way through the session, and I raised an eyebrow to him to say "This is how they do research in the humanities". Because the opinions of 9 self-selected people is not what we would call data. But actually getting 11 people [+2 facilitators from Celsius] round a table is quite goldiloxian for focusing discussion and letting everyone be heard. They softened us up started us off with a round table "introduce yourself and give us one positive memory of water" - all this being captured on video for later transcription and analysis - I shared my Duncannon dam story . . . because remembering Hugh MacDiarmaid Holding a glass of pure water up in 1974 would be toooo pretentious. From there our Focus Group was led up and down and round the houses: asking us to opinionise on the quality of our own domestic water supply; bottled water; water safety; Ireland's water; water testing; The Man. Each idea was captured by nine post-its on a sheet of flip-chart: the position was data. Are you . . .
not at all confident
quite confident
the sun will rise tomorrow confident
. . . that bottled water is safe. As each positioned post-it carried our name, you could imagine doing some cross-tabulation on the responses by the same folk to different questions. But really, nine punters? Is that even vaguely reproducible? And, as I've asked before about other issuescui bono - who benefits? Who thinks it is worth $40 x 9 + room hire, tea & sandwiches = ~€500 to obtain such wet data?

But I learned some interesting and worrying facts:

  • when a citizen witnessed, recorded and reported a gross raw sewage discharge into the River Slaney nobody was prosecuted and nobody was even really interested [please go away we have work to do
  • that a bottlecapful of glyphosate = Roundup will put 30km of river over its parametric value
  • that a field in S Co Carlow has been under winter wheat for the last 7 consecutive years and has been sprayed with herbicides, fungicides, insecticides, slugicides, pelleted fertiliser . . . 14 times in the last 12 months.
  • that the outfall from  the Glanbia cheese and yoghurt factory in Ballyragget, Co Kilkenny has a BOD [biological oxygen demand] [bloboprev] as great as the City of Cork - I hinted at the cost of milk in my first paragraph.
And I should really read The Garden Awakening by Wexford's Own Mary Reynolds.

Thursday, 28 March 2019

Understanding the World

There's got to be another way - maybe a better way
Way back before Dau.I became a librarian, I wrote a Blob comparing the Dewey Decimal Classification System with the LCC employed by the US Library of Congress. Dublin City, like The Institute, uses the DDC and after decades of academic life, I'm familiar with where I am in that world. Well actually, not so much: as a man should I be in the 570s under Biology or in 301 Sociology and Anthropology? It is instructive to note that there is no DDC section for The Patriarchy, although 306.85 incorporates patriarchal families between extended families and matriarchal families. Why instructive? because Melvil Dewey was an archetype for The Patriarchy and so that concept was the invisible background in which he swanned around. He was a notorious groper of young women: but had the double-standards of his time: Furthermore, a major reason Dewey wanted women to enter the field was because he felt women were ideal for the repetitiveness of library work and "didn't cause trouble." . . . and wouldn't seek promotion too strenuously. Maybe his desire to hire women as librarians could be simplified? Furthermore, a major reason Dewey wanted women to enter the field was because he felt women. [*]

What's interesting boring and disturbing is how easy it is to map the LCC on to the DDC: Like Dewey [Amherst], Putnam [Harvard] and Cutter [Harvard] who invented the LCC were Brahmin Patriarchs and had the same worldview as all the dip-shit Old Etonians who are currently selling the UK down the river to make the fortunes of currency traders - also from Eton. Is that all there is? Is that the only way to view [and classify] the world? And remember that single category classifications are a challenge for librarians: do they file A History of Dublin's Libraries under Irish History [947.5], Local Government [320.8] Local Education [379.1] or Library Systems [025.1]? You can bet that librarians in Geneva or Saskatoon will have a different ideas about where to shelve that book. As a young library assistant, anxious to make information available to all sectors of society, Dau.I is catching some of the frustration about where books should be shelved to maximise their use and, indeed, their utility. Being close enough to the demographic she is particularly concerned about how to expand the horizons of young adults and teens. She refuses to fob them off with Stephanie Meyer's vampire sex and Suzanne Collins' teenage Hunger Games blood-letting; regardless of the decisions made in the cataloguing department, Dau.I wants to intercalate these obvious best-sellers with more challenging fare; and not necessarily fiction.

One of the gripes about DDC and LCC is that they were both conceived in the 19thC before television; molecular biology; decolonialisation; moon landings; Knots Landing; LGBQRSTU+; Twitter or Twerking. In particular, minorities are aggravated to be pushed to the periphery, shoe-horned together and treated as an irrelevance to the Patriarchal Centre. It turns out that there is an alternative cataloguing method called BDC, invented by a Mohawk called Brian Deer [L]. It goes:  Reference Materials; Local History; History; International; Education; Economic Development; Housing and Community Development; Criminal Justice System; Constitution (Canada) and First Nations; Self Government; Rights and Title; Natural Resources; Community Resources; Health; World View; Fine Arts; Languages; Literature. Brian Deer, as the horse's mouth, reckons that is closer to the natural interests of First Nationeers in Canada. Looks peculiar to me, but then I am The Patriarchy, so it would, wouldn't it? Brian Deer died this last January, having made a difference for his people and the world. Any system that shakes us out of our complacency and makes us face, and even embrace, The Other is a good thing.

BDC is employed in the X̱wi7x̱wa library in Vancouver BC, and that serves as a bit of a Mecca for indigenous people who want to find out where they stand, where they came from and what the future holds. Each of those parameters is different from mine but equally wonderful.

Another anti-DDC/LCC system is employed in the Prelinger Library in (you guessed it) San Francisco. Prelinger makes no pretence at universality, although it archives a shit-ton of material: it is rather designed to allow readers to browse through to the unexpected. Here's a long-form article from Harper's via Panix.

You may now re-orient your sofa to watch Wade "TED" Davis [another Canadian] on cultural diversity and ethnographic extinction: And in the end, then, it really comes down to a choice: do we want to live in a monochromatic world of monotony or do we want to embrace a polychromatic world of diversity? Margaret Mead, the great anthropologist, said, before she died, that her greatest fear was that as we drifted towards this blandly amorphous generic world view not only would we see the entire range of the human imagination reduced to a more narrow modality of thought, but that we would wake from a dream one day having forgotten there were even other possibilities.  Wade Davis? [prev on navigation] I'm a total groupie.

[*] old joke: Seven dwarves in the bed feeling Happy; Happy got out and felt Grumpy; Grumpy ran away.

Wednesday, 27 March 2019

Long term storage ATCG

I have an old fashioned steel 4-drawer filing cabinet; indeed we have two. One drawer is brimful of correspondence from the 1980s. Through those years I had a manual typewriter and a supply of carbon paper and hammered out a lot of letters to friends and family; so I have copies of letters sent and the incomming as well. That source of vital daily-grind biographer's information dried up and petered out after 1993. That's about a decade after I [early adopter, me] sent my first trans-Atlantic e-mail - that comms medium was getting widely adopted and letters were only appropriate to my parents. At the same time, I started writing everything on a computer and didn't have carbon paper for the printer. The precipitous fall in the cost of international telephone calls meant that letters were no longer a weekly [or more often] occurrence. Almost all of that electronic to-fro has gone forever as I shifted between ISPs and failed to download the traffic. There is an irony in the fact that my poor biographer is going to be better served from the 70s and 80s than s/he will be for the 90s and 00s. The best medium for lifetime storage is plain old fashioned 19thC ink on paper. It's bulky and sensitive to floods and fire but doesn't require special technology to recover.

There are peculiar streetlights on the post 1993 Dark Ages:
  • In September 2010, m'pal Rissoles Hayes took his family off to Extremadura for a year. I thought he'd be home-sick, so I wrote something in excess of 30 letters - about once a week. Because the postage was the same up to 100g, I filled the envelope with the kind of shite that I later distilled into a 700 word Blob but send in full . . . at least they had fire-lighters in their casa in Spain.
  • Just about the time Chris returned to Wexford, Dau.I left home and country in 2011 and I undertook to write her letters, at least weekly, and send them, in an envelope, with stamps. That project doesn't seem to have lasted as long.
In any case, I have that correspondence for as long as there are USB ports to read my external backup hard-drives. That's a key fact because a lot of 90s correspondence is stored on 3.5in floppy disks [remember them?] which probably could be recovered but only with enormous faff and expense. And, let's face it; nobody is going to write my biography because I have been effectively irrelevant to the relentless progress of history. When MySpace recently lost 50 million files in a server migration fiasco, nobody seemed to mind very much because they've all moved on to other comms platforms. I guess subconsciously, folk accepted that all those songs, all that to-fro, were just ephemera waiting for a strong breeze to flitter it into oblivion.

My correspondent El Asturiano [prev] sent me a tech-geek link about long-term information storage . . . using DNA! I Blobbed about writing English text in a genetic code: in real life the DNA is read in triplet codons which gives 4^3 = 64 permutations: plenty for a 26-letter alphabet. You can have some harmless fun looking for ELVIS in the human genome. Microsoft is behind the cunning plan to convert text to DNA, and recover it when needed. Their prototype pipeline took 21 hours and cost $10,000 to wrote and read "HELLO" but, as I explained recently DNA technology scales up really well; the same technique would cost [in time and money] the same for 5,000 letters as for 5. And DNA being really small scale will pack a helluva lot of information in a very small container. 

The Arch Mission Foundation is about to launch 30 million pages of information in a rocket to the Moon. It is stored on a 100g electronic device and will last forever out there while the creators of all that data trash head-office to hot wet oblivion. Doubtless, the next archive Wikipedia project will send the same material stored in GM Bacillus anthracis spores - they last forever.

Tuesday, 26 March 2019

Deaf Aid

Dau.I the Librarian was down for Féile Pádraig. It was good to catch up with her radical tweetiness and be put back in my box on rural driving home from the pub after a pint of two. My case was that on the balance of harms it might be worth weighing the risk of a damaging RTA against social exclusion, depression and suicide among batchelor farmers whose only available social outlet is The Pub. I was imagining a farmer drinking like myself at, say, The Wexford Science Café, where I am not the only one ordering a bottle of alcohol-free Erdinger. Dau.I and her SO advised that abstemiousness of that calibre is quite unlikely - not least because alcohol free beer is a new thing and Old Boys are the last in any society to embrace The New. Another part of her argument was limit creep: whereby if 2 units of alcohol was allowed by licence for those who 'need' to visit a pub to stay sane, then that becomes the new normal and the actual driver average is nearer 4 units on board.

When you're young, you are expected to be righting the world in some way. As part of her work-related CPD [continuous personal development] Dau.I has started formal classes in ISL [Irish Sign Language]. It is obviously good for the Dublin Library Service to have at least some of their counter-staff up to speed with deaf-comms. Perhaps particularly important to have such Capables installed in the Cabra branch which is just down the road from Ireland's Deaf Village - DVI. Accofdingly, once a week, Dau.I gets round a table with other employees of The Corpo and chats in English and ISL with a tutor/facilitator. You have to be considerate and make sure that you look at the person you're addressing and don't mumble. Lip-reading requires clear enunciation just like I find increasingly lacking in my students. Of course, the student body has not become more mumbly but rather my aural acuity is diminishing with age - I R deaf.

The Deaf V includes the Holy Family School for the Deaf: a recent [2016] merger between St. Mary’s School for Deaf Girls and St. Joseph’s School for Deaf Boys. These latter were founded in Cabra in the 1840s when all education was under the control of one or other church. The girls school came first and two Dominican nuns set off for l'école des sourds du Bon Sauveur de Caen to learn best practice from their french counterparts. That's the fundamental, historical inertia, reason why ISL follows the french model rather than the British. Another oddity of historical contingency is that Ireland followed/follows a wide-spread practice of educating boys and girls separately. Ireland is peculiarly hung up about sin and sex like the swinging 60s were focussed on sun and sex. It is hard to imagine how the nuns and brothers imagined that their charges would develop normal respectful loving relationships between the sexes if they never had intercourse [no! ya dink, not that intercourse] with each other.

But hey, here's another oddity: because they developed in isolation, the ISL used by deaf girls departed from that used by the boys on the other side of the wall. That's why we have a Babble of 6,000 langauges across this our blue planet: if you impose barriers between groups of people they develop their own distinctive peculiarities of pronunciation, grammar and vocabulary. For a while, as in the Balkans, they are mutually intelligible but eventually they require dictionaries and interpreters - or indeed signing - to interact. The intriguing idea that women and men in essentially the same community could be speaking different dialects tinkled a distant bell for me. There is one such Nüshu documented in China. This language was used exclusively by women for several centuries, was 'discovered' in the 1980s being used by a diminishing number of elderly ladies, the last of whom died out 20 years later. A brief up-blip on the graph of cultural extinction.

Monday, 25 March 2019

Almighty Dollar

[another cock-up with scheduling published this last night on "3rd March", it's back here for today's post today]
Piece in Wikipedia about the Double Eagle (A gold coin worth $20US) struck for commerce between 1849 and 1907, got me to thinking about the relative value of silver Ag and gold Au. At the same time as the Double Eagle was designed by James B. Longacre, the US mint also launched a shirt-button size gold dollar, here shown more or less actual size:
Same designer 1.62g 1.27cm = half-inch across. This micro coin was appreciated aesthetically "undoubtedly the neatest, tiniest, lightest, coin in this country ... it is too delicate and beautiful to pay out for potatoes, and sauerkraut, and salt pork. Oberon might have paid Puck with it for bringing the blossom which bewitched Titania." but others felt it was too small to be of practical value for shop-keepers and farmers. The Double Eagle was exactly 20x the weight of the gold dollar and both incorporated 10% copper Cu to give the coins a bit more robustness and wearability.
At about the same time the US mints [there were, and are, several across the country] struck a silver dollar which was an inch and a half in diameter and designed by Christian Gobrecht  26.37g 3.8cm ⌀. The silver US dollar was first authorised by the fledgling state during the Revolutionary War (1776-1783) in conscious imitation of the Spanish Thaler which was worth Eight Reals. The Spanish coin was the Talk-like-a-Pirate parrot speak pieces-of-eight only distantly related to Jack Sparrow et al.'s Court of Pieces-of-Eight. In those days, the 8-real coin was a bit heavier than the US dollar but traded at parity in the Caribbean. The Spanish dollars were melted down and reminted as US Dollars with the extra clippings deemed to be seigniorage - essentially profit on the transaction. This is a classic example of Gresham's law - bad money drives out good. Only old and foreign coins were in circulation in the United States as speculators siphoned off full value coins to enrich themselves. I've been on about melting scrap-copper for cash.

The weight of the two 1849 vintage coins allows us to calculate the relative value Ag/Au as 16.3x. In my lifetime
there have only been a few times when the value of gold has been that low: Dec 1967, May 1968, Dec 1979. This week gold is trading at $42 / g and silver at $0.48 /g = ratio of 87x.

What's significant about the year 1849? It's when the California Gold Rush started to flood the economy with gold; but this didn't seem to have any effect on the value of the commodity. The Australian Gold Rushes of the 1850s likewise had no effect on the price. They say there are now 150,000 tonnes of gold above ground of which 60% has been abstracted from the ground in my lifetime. Up to 1849, after 6,000 years of mining the stuff, 10,000 tonnes had been accumulated world wide and about 10 tonnes was being added to the stockpile each year - mainly from the Gold Coast = Ghana and South America. California upped the annual input about 8x to about 80 tonnes average for 1850-1855. That sounds like a boost but was still only 1% of the existing reserves so not really a drug on the market. The New South Wales supplied 25 tonnes in 1852. Beyond those comments is the realm of Economics about which I have no expertise and little interest.

Sunday, 24 March 2019

T for Tennessee

The alphabeT wiTh Trivia conTinues unabaTed unTil afTer easTer

Saturday, 23 March 2019

Reproducing the code

Yesterday, Friday, I got up, tea'd up, spruced up because I was Countryboy Going To Dublin for the 'annual' VIBE symposium. I, wearing my 2014 VIBE organiser hat,  had sent out a call to everyone to remember their name badge, so I had a chance of remembering who they were:
Goodo, looking forward. No registration means no name-badges so could everyone remember to bring one? from their last conference?  Just as a courtesy to confused old buffers and total newbies.
Thanks, Bob
The previous (2016) organiser added a note:
And/or a roll of blank stickers that people can just write their name onto. 
To which the the 2019 organiser replied.
Great; please bring one.
Clearly some people are more invested in the Science than interpersonal signalling. And IMO, a roll of stickers is A Bad Idea because they are not designed to stick to jumpers and it invites useless contributions as shown [R]: Bubba? Who he? Who his boss? Which is his poster? What group is he affiliated with? Should I get concerned when he brings out a banjo?

The presentations were wide-ranging and all interesting, even those that were whoof totally over my head. Molecular sequence analysis is amazingly ambitious, seeming to keep up the precipitous drop in the cost of generating the primary sequence data. My report of VIBE 2013 noted that analytical throughput increased 4000x-fold in a decade while the co$t per DNA base had fallen by a factor of 10 million in 20 years. In the early 00s, I was tasked with determining if certain classes of genes [those switched on in the cells of the heart, liver and lights] were clustered in the human genome, which had just been released into the public domain. I learned to program in Perl, robbed code from my fellow workers at the genomics, hacked it to do my bidding, learned how to display data graphically using the GD add-in and presented my progress regularly at the lab-meetings. It was a challenge, it was hard work, it was great fun and eventually my mates started robbing my GD code to use for their own projects. A small part of my work-flow was getting a program to work - my first binfo boss used to say "that's just a simple Fortran program, take you ten minutes" which was orders-of-magnitude true: it took maybe 90 minutes. But it took the rest of the day, and sometimes the rest of the week to be confident that the results spat out were true and meaningful. I won't say I was a programming god, but I could do the work even if I still don't feel comfortable with associative arrays.

The first talk on Friday was an over-my-head job: Research and Clinical Applications of Fully Reproducible Containerised Workflow Architecture. Dang, but that could mean anything at all to an old code-kludger like me. Even though I didn't recognise the names of any of the software tools - they having been developed over the last 7 or 8 years since I fell away from the coal-face of science and went back to teaching down the country - I followed with admiration the aspiration. Reproducibility is the key!  It's like using Latin names to talk to Hungarian ornithologists. IF you build a pipeline to integrate a wild variety of disparate but relevant data so that you can develop predictors or therapies or a cure for colon cancer THEN you really need it to be reproducible in Hungary or next year. 

I've been there, and I've been caught with my pants down. Maybe 15 years ago, I was working in St. Vincent's before it became SVUH the University Hospital. The colon cancer people had generated a noisy multivariate dataset and asked me to see if there was any signal there. I had a word with my pal Aedin [prev] before she went all ad Astra and to Harvard on us. She was the local ADE-4 guru and with her help I beat the colon cancer data into submission. I was skeptical about the results I'd generated; not because they were wrong, but because they explained so little of the variation in the data. I sent the analysis up the line, with my skeptical warning, and Team Colon were delighted because TOP2A, a known actor in the development of colon cancer, bobbed to the top of the roiling mess of data, you could see it there, barely visible, awash with statistical noise, but top of the heap of over expressed genes. The project wasn't written up immediately: the bloke who'd done the original analysis finished his rotation, his boss moved to a different hospital and her boss was too busy saving lives. I moved to a different institution too. Four years later, I got a call to redo the analysis because the paper was finally ready for launch and they were checking through their pipeline; and the graphics I'd generated were kinda ugly.

Well it was a freaking nightmare. The computer on which I'd done the original analysis had been left in StVs as obsolete. ADE-4 had been totally re-written, and was reluctant to install on the new computer. I couldn't remember how to get it to work and Aedin was 5,000km away in Harvard rather than up the road in UCD. I knuckled down and did what I was asked but that's when my hair-loss started. TOP2A was still tops, which was a relief, and the paper was published. If it was left to me, it would have been written off  rather than written up - but then my scientific publication record is woeful. Even with the same people and precisely the same data, reproducibility was a hard slog.

The small world connection here is that the presenter of the Containerised Workflow Architecture talk yesterday answers to the same boss as the boss-boss-boss I was serving in 2005 and 2009. In the intervening years, the quality and esp. the quantity of the data has gone up and up. By using containers in your workflow you can let collaborators and rivals replicate your findings and run precisely comparable analyses of their own. The science will be reproducible and we'll be nearer to eliminating colon cancer.  All good until a senior scientist at Friday's VIBE asked - what happens if there is a mistake in your code; will everyone be replicating that error?

Hmmmm! As Osric has it: A hit, a very palpable hit. Later in the day, I was talking to a handful of MSc students who'd come up from Galway for the meeting but missed the first talk. They are a useful mix of biologists and coders and I said that I'd been part of a similar group when their boss had moved from mathematical physics to biological sequence analysis and helped me with my Perl scripting. I hoped they were sharing their expertise and propping each other up. And I gave them an executive summary of the first (Containerised Workflow Architecture) talk of the day which they'd missed and emphasised the critical replicating that error question. Don't do what we used to do, I said, if you are all robbing each other's code there's a good chance that errors will propagate through the lab. If we use computers [and especially fancy pipelines of interconnected software] to find out something new, nifty and important then someone else should rewrite as much of the code as possible from scratch. There are a hundred different ways of computing any reasonably complicated analysis, if you have two independently generated solutions and they agree then your confidence in the result is more than doubled.  Ain't gonna happen though, everyone wants their own apple to polish.

Friday, 22 March 2019

Whoa Excel woes

The thing about software is that it is designed to make things easy - if it well designed. If things are easy to do then they are done often and possibly without sufficient thought. If you had to statistical analysis by hand, you'd make damned sure that you designed the experiment well so that the results of your analysis meant something.
If the statistical analysis is no more than 10 or 15 minutes making mystical passes with Excel then you'd be more inclined to have a punt at the experimental design fully prepared to do it again - properly - if the data turns out to be impossible to analyse. In my teens, I did quite a few statistical computations 'by hand' - working through columns of data calculating the square of each value, the sum of the squared values, the square of the sum of the values etc. All without a calculator because they hadn't been  invented in 1971. If you made an error it would propagate through the table and become a huge distorting wen on the face of the analysis. I must be the youngest person on the planet to use Charlier's Checks for internal consistency in a mighty table set up to calculate the variance of a dataset. Charlier's Checks required additional bookkeeping work, true, but they also gave you a solid confidence in the answer. Now you just lash the numbers into Excel and demand Descriptive Statistics to obtain not only the Variance, but the coefficients of kurtosis and skewness as well [example R]. Ten years later, when calculators were cheap and widely available, I helped construct one of the last hand-cranked commercial spreadsheets before Visicalc and Lotus1-2-3, the progenitors of Excel, swept such activity into the dustbin of history.

Excel is designed for businesses rather than science ans seems unduly driven by time and date. If you are a teeny bit careless the number 12 will become 12th Jan 1900 while 19,892 will be treated as my birthday 17th June 1954. Excel has a number of such helpful features which, if you're not careful,  will leave you with a red face if nit in tears. There was a paper in Genome Biology a couple of years ago by Ziemann, Eren and El-Osta, which exposed a widespread casualness about data-in-excel. Molecular biology and genome analysis are now capable of generating terabytes of data for half-nothing in money and time. Scientific papers would be unreadable if all the data were put in tables; if not unreadable, then at least many many pages long. The rules of engagement dictate that the raw data has to be made available, so that rivals, reviewers or referees can critically evaluate it. The data is, accordingly installed in Supplementary Tables somewhere on The Cloud. Z.E.E. wrote a bot which trawled through these Excel tables associated with a number of reputable Journals and looked for damn-foolishness, sloppy copy-editting, and culpable negligence. They found a great deal of errors like where the gene Septin2 aka Sept2 had been helpfully translated as 02-Sep or March1 [Membrane-Associated Ring Finger (C3HC4) 1, E3 Ubiquitin Protein Ligase] became 03-10-2006 because Excel decided these names looked like dates. More to point, none of the authors or editors of these tables had ever checked them through, let alone corrected the errors. Just by following this line of reasoning, they found errors in about 20 % of all the Suppl Tables they ran through their wringer. Do you have less confidence in the findings of the associated peer-reviewed papers if the data has such obvious feet-of-clay?

I found this paper through a link in MeFi pointing at a group calling itself The European Spreadsheet Risks Interest Group - EuSpRIG - (“yewsprig”) for short. They have compiled a long list of errors compounded by the casual use of Excel, which they call horror stories. Whatever about a few 'typos' in the supplementary tables [which clearly nobody has read] of some specialised genome analysis papers, the horror stories have consequence: loss of money, loss of credibility, loss of reputation and loss of jobs. It's the kind of trusting-the-software stupidity that had the HSE flagging patients as less than dead in 2017.

I was reading these horror stories with a mix of nerdiness, incredulity and complacence actually not me with the complacent. I never believed what I caused to be generated by writing software: I checked all the calculations by hand many times before I accepted the output. I did my best to push through some edgy data to see how robust my programs were. Just before leaving work and going home to surf the blogosphere looking for nerdnik copy, I had calculated the final marks and breakdown for the continuous assessment CA part of my human physiology course. As it is a small class and as I couldn't work out how to send this compendium through Blackboard, I emailed each student the relevant line from my summary Excel spreadsheet. It was a bit of a rush, so I didn't double-check the numbers - partly because the sky wasn't going to fall if I got things wrong. Indeed, part of the reason for sending out the marks was to solicit complaints and queries. I might have forgotten to credit a sick-note, for example. When I next checked my mail there was indeed a query/complaint that the individual marks from Oct, Dec, Jan & Feb were not consistent with the recently compiled executive summary. Ooops! There is a peculiar legacy issue with student names at The Institute. Some early kludge software had choked on apostrophes as Not Alphabetic so email aliases now come as O Reilly, O Donovan, O Beirne. But one of my students is not properly registered so I have her as O'Donovan. Excel sorts O Leary before O'Donovan and in a frenzy of cutting and pasting between Excel sheets I had managed to transpose O Leary's marks with O Donovan's. Only a Pink Face over this because it doesn't really matter but it is a lesson to be vigilant in future.

Thursday, 21 March 2019

sleep early and often

The Wexford Science Café meets on the third Tuesday of every month . . . except when it doesn't. It has been lurching running for more than 4 years now and we've covered:
Stephen J Gould’s spandrels; Galena; Thomas Kuhn’s paradigms; Organic soil microbiome; Composting toilets; Water quality; Bacteria in food prep; Urination once again; Toxicity from botox to beer; Air-quality and asthma; Gravity waves; Neuroscience of torture; Greenland ice melt; Cider making; Zombies; Wolbachia and tropical diseases; Radon; Diabetes & Alzheimers; Marketing generic meds; Oroville dam crisis; March for Science; Allometry; Science book-swap; Erwin Schrodinger; Pheromones; Back-garden astronomy. 
All interesting and showing the reach of science and the collective interests of the WSC participants. I am quite religious about turning up even if it means driving nearly a hour from home to get there: It is one of the few social engagements I have outside of work and nuclear family so is important for my mental health.

Last Tuesday we heard that getting a good night's sleep is also vital for your mental health. One of our reg'lar participants in the WSC Happy Family is Mr Pill the Pharmacist, who has recently become a Daaaad and two years into the gig is still laboring under a sleep deficit as the wean frequently neglects to snooze the night through. If he was a Kiwi, he'd have an instructional video. What the child's father has noticed is that he can be unaccountably ratty at work - amazed at the stupidity of his customers; furious when things go wrong; narky with his colleagues. Then he put two and two together to realise that his anger descended when he'd endured a really wretched night.  He also floated a hypothesis, as yet unquantified, that most of the kids who present a script for ADHD medication are no way ADHD: they are just sleep deprived. When a family comes to the doctor's surgery with €60 and a troublesome restless teenager, it is impossible for everyone if they come out with only a suggestion that a good night's sleep is required . . . and why not lock up the youngster's phone before bedtime? They'd rather dose the trouble away . . . and then get really indignant when Young Jimmy scores a few Es at the weekend.

The hook on which our discussions about sleep were hoist was the book by Matthew Walker, British author of Why We Sleep and Prof of Neuroscience at UC Berkeley. It is Walker's contention that sleep hygiene is at the root of many woes: mental and physical health; success at work; success "ín bed"; that car crash; that slice of chocolate cake. The book was a surprise runaway best-seller in 2017, so must have rung a few bells (or jangled a few chains) with the reading public. Which is a rather diminished cohort because book-reading is soooo yesterday and pushed to the back of the closet as everyone embraces screens. I've written about the negative impact of the [blue] light used to make screens work. Dau.II pointed out that device content is designed to be seductive if not  addictive. What are we like? The evidence of the damaging effects of sleep deprivation is piling up while we're swiping just one more tweet long after after midnight.

The sleepy discussion at WSC led on the work of Annie Curtis and her Clock Lab, now at RCSI in Dublin. She is finding that disruptions to another cycle can have serious health consequences. Lots of things go round and round and up and down for us on a daily basis - core body temperature; sleep-wake; the bowels. Curtis has put together large datasets [like half a million middle-aged Brits] showing that other aspects of well-being and equanimity fluctuate on an annual basis. You're more likely to have a fatal heart-attack in the Winter; surrogate cardio markers also tip up as the days get shorter: we get fatter and our blood-pressure goes up significantly, for starters. And another large cohort study showed that clinical depression descends on many women in Winter. The underlying basis of these adverse events is the molecular clock which is ticking in us all: cranking up the immune system at certain times of the year (perhaps because that's when the pathogens are abroad??) with unexpected side-effects in other systems of the body. Those epidemiological studies are paralleled by lab-based studies in which the undulating concentration key molecular immune markers are tracked across time. What's not to love about someone who can use a quote from Wm. Shagsper as the title of one of her papers.
“Sleep that knits up the raveled sleave of care,
The death of each day's life, sore labor's bath,
Balm of hurt minds, great nature's second course,
Chief nourisher in life's feast.”
Night-caps off!
More Women in Science.

Wednesday, 20 March 2019

Iditarod goes Idatadog

We spent St Patrick's weekend at home; and, although Mohammed stayed away, 50 years of strong smart women sat down to Sunday dinner up the mountain: The Beloved in the Matriarch's chair, Dau.I and her SO, Dau.II, Dau.II's odd-mother, o-m's daughter. I won't bore you with the ages but the range was 50+ years. The youngest person present is beginning to run and the adult women present were full of cogent advice and encouragement. Someone cited Chris McDougall's Born to Run [bloboprev] because in the elite ultramarathon world, women are at least as good as the men. If you can run 100km, then your chromosome count [and consequent testosterone titre] is no handicap. I can run 100m, uphill if necessary, but I cannot speak at the end of it and I have neither the wind, nor the bottle, to run 1km let alone 100km. otoh, I did walk 700km in 1989 and 800km in 2004, so I have [blistered] skin in the game. Me I'd cite Feet in the Clouds: a tale of fell running and obsession by Richard Askwith as a source of inspiration for young runners.

My preferred charity is the RNLI because a) it does good but b) it allows people to be their very best = heroic. Running also allows people to be their best selves: against self; in competition but also in compassion and kindness. Marathons and a fortiori ultramarathons really sort the sheep from the goats. I've recently become a bit of a sofa-groupie for dog-sled racing like the Iditarod Race which is not a direct commemoration of the famous diphtheria antitoxin delivery to Nome, Alaska in 1925. The race happens every year since 1973 and takes at least 8 days to cover 1500 km through a winter wilderness by a sled and dog-team. This year the third person across the line was Jessie Rover. Susan Butcher won rhe race outright four times in the last century, while Libby Reynolds was first home to Nome in 1985. That was a dreadful weather year and Reynolds took 18 days to cover the course. This year a lot of attention has been on rookie Blair Braverman who finished 36th and six whole days behind the winners. While she was mushing on through the blizzards, her fan-base were raising $000$ of dollars  #uglydogs to support Alaskan schools. Commentary at MeFi.

BB was one of 17 (about a third) female entrants in 2019, including Jessie Royer. It has got to be harder graft to finish 36th after such an extended and calorie sapping journey than in the top three.. Anyway, our youngest visitor over the weekend is mad-about-the-dogs having acquired a puppy  a few weeks ago to walk and clean up after. It occurs to me that if Jamaica can field bobsled teams, both men and women, Ireland can surely furnish an entrant to the Iditarod in about 10 years time.

[You can stop reading right now unless you are fully nerded up]
Scoping out the results of this years gig, I noticed that one of the variables was Dogs In with numbers from N = 6 to N = 13. Hmmmm, I pondered, is the number of  Dogs In correlated with the time taken and/or is there an optimal number of dogs for getting over the line in the quickest time? That required cut&pasting the data from the results page in Excel and plotting Dogs In vs the time in seconds.
[Time in seconds = days*86,400 + hours*3600 + minutes*60 + seconds].
There are about 700,000 seconds in 8 days.
This picture is a special class of scatter-plot called a dot-plot where the range of values for each count of dogs is graphically displayed. This shows [me] that the range of race-times for a particular number of dogs is greater than any difference in the average time among dog-numbers. The display is far more important, and provides better insight into the distribution of the data than any ANOVA [analysis of variance] the standard statistical test for such data. The intuitive feel that here within group variance trumps mean values is actually borne out by the ANOVA. It takes about 1 million seconds or 11 and a half days to run the race regardless of the number of Dogs In. I'm not sure exactly what Dogs In signifies: are substitutions allowed during the race the way soccer players are ordered off the pitch by the coach and replaced by a player less puffed or less limpy?  Regardless of the details, I'll be using these data in Quant.Meths next year at The Institute to show the value of dot-plots.

Tuesday, 19 March 2019


The other day, one of my project students was looking more competent than me [red face] in the tools of his/our trade. In too much of a hurry, I thought that Proboscia was essentially the same as Proboscidea. When I slowwwwwed down I twigged that one Proboscia is about 50μm on length while elephants are about about 100,000x longer trunk-to-tail. What a difference a '' makes! The accident tinkled a distant bell that there were pairs of species which really did have the same name but were completely different.

A recent explanation of the rules and regs for the naming of parts in biology is The use and limits of scientific names in biological informatics by David Remsen Zookeys. 2016; (550): 207–223.  It's something that requires a certain amount of precision to prevent misunderstanding. If you want to communicate some measurements blue-tit [the bird in the picture] wings to your colleagues in Hungary then using a universal [dead] language prevents ambiguity: Cyanistes caeruleus is the only thing it could be I would be skeptical about using the Google - Magyar translate to kék cinege. Not a big problem in this example because the bird appears on both the EN and HU versions of wikipedia. But what about something more obscure: the White-bellied rice-rat Oryzomys albiventer isn't in hu.wikipedia.

One of the rules about taxonomy is naming priority. 25 years ago, I had a heart-in-boots moment on that front. We'd just published a sequence analysis paper on Aspergillus nidulans. and I thought I'd check the database to see if there were any new A. nidulans sequences which I could add to our tiny dataset. When I asked, ACNUC (the then cutting edge database interrogation software) came back with No Sequences Found. It was like arriving at the 13th Floor by elevator in an episode of The Twilight Zone. As Aspergillus nidulans is a widely studied standard genetic organism like lab mouse Mus musculus and Drosophila melanogaster, it wasn't just me who was hopping mad disconcerted. The naming people at GenBank had been following priority rules to rename the species as Emericella nidulans. Luckily they were pragmatists rather than pedants and, at the next full release of GenBank three months later, all my Aspergillus sequences were back on line.

The key element of nomenclature is to be unambiguous. If things are different they get different names. Careful analysis [bloboprev] of the biology and biogeography of giraffes Giraffa giraffa made experts believe that there were really 9 different species of long-necks in Africa and they all needed a separate species name. The names of animals are decided / approved by ICZN; a different body to the ICN namers of plants fungi and algae.
Partly from the inertia of the system; partly because the two entities are unambiguous different there are an least half a dozen hemihomonyms: species which have the same official Linnaean monnicker. Here [L] is a nice pair, both Agathis montana: LL is a braconid wasp widely distributed across Eurasia from Korea to UK. LR is a long-lived conifer from New Caledonia in the far east.  It is critically endangered from a perfect storm of bark-beetles delivering fungal disease, feral pigs, and habitat destruction from climate change and logging. That extinction will nicely tidy up the taxonomic conundrum, no? Here are the other hemihomonymous pairs acknowledged by wikipedia:
venomous fish
another fish
That's only the top of the iceberg, however, Алексей Шипунов from Russia has compiled a mighty database of hemihomonyms - including 12 examples where a Genus is triplicated in bacteria, plants and animals:  Catenococcus  Gordonia  Kingella  Lawsonia  Leptonema  Microcyclus  Moorella  Morganella  Rhodococcus  Rothia  Spirulina  Stenocybe.

Because these worthy taxonomy-mavens are aware of illiteracy, dyslexia and Latinophobia among those who need to know the Names of Life, there is another class of wrong-wrong-almost-right called parahomonyms which are at best discouraged if not absolutely verboten.  Thus Astrostemma Benth. 1880 has been rejected in favour of Absolmia Kuntze; because it was too much like Asterostemma Decne. 1838 another genus of plants in the same family. To crowd confusion on ambiguity Asterostemma depressa is a fossil mammal from Argentina.

A couple of years ago I was laying out a very similar problem with the naming of drugs: where errors are more likely to kills people than mistakes

Monday, 18 March 2019


Kosher is a set of dietary laws which Jewish people take with a pinch of salt. Actually rather a lot of salt because cuts of meat are often ladled with the stuff to draw out the last traces of visible blood. I've worried about whether rabbits are kosher - they are not kosher because they chew the poo rather than chew the cud to max out the nutritional value of what they eat. Camels are not kosher on the other side of the definition - they indeed chew the cud but the hoof is not split.  Whaaa'? Looks pretty goddamned split to me [R]. Note to self: do not google "camel toe".

On the fish front, the definition is also two-fold: if the cr'ature has both scales and fins it is good to eat. Weirdly if it has scales then it is assumed to have fins. This excludes eels, sturgeon (and caviar), catfish, sword-fish . . . and of course a whole rattle of not-fish like shrimp, lobster, crab, mussels, scallops, whales and octopus. I think that one of the delights of kosher for Jews is that it encourages pedantic arguments about whether a kosher fish found in the belly of not-kosher fish is kosher - it is.

The Lord wasn't able to give a neat paired attributes {scale&fins | cud&hooves} definition of permitted birds. Instead the Torah lists -in Hebrew, natch  - 24 forbidden birds - none of which had the unambiguous Linnaean Latin binomer. And even if they had a clear label, would an averagely educated Jewish housekeeper recognise Otus scops or שעיר, שעיר מצו or Zwergohreule if it jumped up and bit him? That's rather inclusive: there being 10,000 different species of bird, only 2 dozen of which are suspect. Ambiguity and identity problems were only a challenge to the scholars of the yeshiva: nothing better than poring over an old manuscript to read the opinions of a long-dead scholastic rabbi from Lvov. The Torah is the word of god (equivalent to the Christian Olde Testament) the subsequent notes, criticism, arguments and counter arguments form the Mishnah, Gemara and Talmud.

If the forbidden birds have anything in common, it might be that they are hawks, eagles, owls and other raptors: birds that eat other vertebrates. The scholars of the Mishnah came to agree on three other 'helpful' criteria
  • having an extra toe
  • having a crop [a muscular pocket for grinding seeds etc.before the contents osdelivered to the stomach - some birds swallow small stones to help the grist-mill]
  • having a gizzard that can be peeled
all these characteristics are shared by chickens. You have to suspect that the scholars were stacking the discriminant function so that, whatever got spat out as not kosher, chicken soup and schmalz was allowable.
That diligent scholarship in the medieval ghettos of Lviv [priv] and Warsawa to determine what a good jew can eat without damageto the immortal soul has been recently emulated on Tumblr.  Here is a list of the (alas all too few = 77/800+) Pokemon which are kosher. Like with the Mishnah dealing with real animals, with clear rules most of the decisions are easy. It is the edge-cases which challenge the scholar; the grey areas; the equivocal; the noisy; the things that are not internally consistent w.r.t. to the rules of the kosher game:
  • Stantler: kosher, in my opinion. the split hooves are only visible from some angles and in some sprites. Consult your local Rabbi. 
  • Psyduck and Golduck: perhaps controversial, but i am going directly AGAINST the Kashrut Laws in Pokémon guide by declaring these two kosher. yes, they’re water types, and could be arguably treated like fish, but look at them; they’re ducks 
  • Cherubi and Cherrim are kosher. if you make them into wine, a Rabbi must be present. 
  • Skiddo and Gogoat are doubly kosher, as both legitimate goats with split hooves AND plants.
The names mean nothing to me; the SOs of Dau.I and Dau.II both know how to spell ポケットモンスター though.

Sunday, 17 March 2019

sh sh sh Sherborne

Sax six *** sox sux

Saturday, 16 March 2019

Suspense threshold low

I grew up watching Richard Greene as Robin Hood . . . from behind the sofa. It was far too frighty-me to watch on the telly while sitting normally. My excuse now, is that I was only 6 years old when the BBC stopped making episodes; of which several are available on youtube. That series is the archetype for such harmless nonsense as Men in Tights. But watching the telly from behind the sofa more or less set my clock with a low threshold for vicarious violence and, especially, for suspense. Getting to be an adult is to acquire a certain amount of autonomy - can choose what to watch without consulting siblings.

I walked out of Straw Dogs in 1974 even though I'd paid money to the UCD Film Society to watch it and I was quite a fan of Dustin Hoffman. It wasn't so much the rural English thuggery and viciousness as the expectation of RET&V in the very near future. I had, for example, sat through Peckinpah's The Wild Bunch despite its balletic bloodiness. The Beloved walked with me, so that was a bit of a mistake-date. Or maybe not, we probably went somewhere else and gazed into each other's eyes and talked about poetry. I'm not stupid, and I can read, so now I'm generally able to avoid getting into under-seat-puddle situations.

At the end of last month, I walked out of Dogman [trailer = summary] which was the Feb 2019 choice at the Blackstairs Film Society. I have a standing request in with the BFS organising committee to have more fluffy films: a gentle rom-com is what I'd call entertainment. Of course, having subtitles is desirable / essential - so a French rom-com from the 1970s would be ideal . . . but it ain't gonna happen. The committee have limited choice through Access Cinema and quite different tastes to mine. Dogman is about a dog-groomer living in a relentlessly bleak Italian sea-side town where affluent tourists have been replaced by graffiti and petty crime. Call me judgemental but dog-groomer is on my list of utterly useless ways to make a living - somewhere between telephone-sanitizer and currency-trader. The film started to go pear-shaped when the fellow's dog refused its kibble and started eating yer man's pasta - from the fork and then from the bowl [R from trailer]. We have been inured to the pornography of violence but most of the audience were audible in their disgust at these antics. The dog-groomer takes up with an enormous psychopathic petty criminal and, shortly after the dog-bowl incident the psychopath tries a bit of mindless violence. More seepiness ensues with barely-clad young women at a night-club . . . and I made my exit as quietly as possible.  No point in laying my values / sensitivities on other people.

If you want a better film about low-lifes you could shed the final N and watch Dogma written and directed by Kevin Smith. I enjoyed that.

Friday, 15 March 2019


Come on, Bob; where's yo bin livin'? Under a stone? With your interest in Braille - Irish Sign Language which is very different from British Sign Language - American Sign Language - Ogham - Morse - Kanji - Unicode . . . surely you should have picked up on Makaton [words and sentence in which above] before this.

I'm in Makatonland because the oldest son of John and Sally Bercow [he's Speaker of the UK House of Commons; she is a celebrity in her own right] was diagnosed [early] with autism. He got an early identification and therefore appropriate intervention partly because he had two articulate, well-connected parents; but also partly because they all lived in Westminster which has allocated some resources to those issues. Without early intervention a youngster who is without language is fritzed for school and social life and work. Makaton came up because Sally B. included it in a list of things she embraced to do the best by her boy. He's doing fine now, thanks, he's in regular school, has tolerant friends, forgiving siblings and hopeful parents. He could have finished up clutching a blanket and rocking himself in a corner of a bleak institution. Autism is generally not high on the list of priorities for governments in allocating social / health resources. Heart transplants, yes; dairy farmer subsidies, yes; auditing educational attainments, yes; ministerial car, yes;; but council houses, nah; mental health, nah; sex education, nah; drink education, nah.

My pal Lulu worked for years in the catering trade and late in life landed a job as a care assistant in the National Rehabilitation Hospital NRH in Dun Laoghaire, Co Dublin. There were young men there who had come off motor-cycles at speed; had been patched up in A&E; and then discharged. Their physical and, especially, neurological deficits could be immeasurably improved by early and intensive intervention. While the damage was fresh it was possible to restore function, or by-pass lesions, or develop sustainable work-arounds. With each passing day, the fluidity decreased, systems hardened into sub-optimal troughs and it became increasingly impossible to achieve any substantial improvement. There is only one NRH in the state containing a finite number of beds but there is a mountain of rehabilitation need. The [terrible] solution is to eke out the resources 'fairly' so that nobody gets the full whack of treatment that will give them the best chance of a fulfilling and productive life after their disaster. Huge waiting time means that any treatment people get is too little, too late.

Thursday, 14 March 2019


It is Pi day [for month-first in dates Yankee-dogs] = 3.14. At one minute before my 1400hrs Microbiology class it will be 3.14 1:59p I've got the nerd-shirt too [R] . . . and now for something rather different:

I am fond of intoning that Science is A way of knowing. Because I know that a lot of things that matter can't be measured; while many things that can be measured don't matter. Indeed the current obsession with measuring a record keeping can have a net negative effect on productivity. I left work last night (at 1704hrs) with our chief technician, for example, but she had to clock out with her work ID card as she left the building. Not me, I'm an officer teaching staff and my union wouldn't wear it! But our time is measured (in contact hours) in a number of mean-spirited, bean-counting ways that shout lack of trust from the management. The consequence of these impositions? A wide-spread reciprocation in kind: clock-watching; hour counting; least effort; minimal commitment; never stay beyond 1700hrs; never volunteer for extra duties; short-change the students on feed-back, marking, mentoring. I don't know of anyone who pilfers spoons from the staff canteen, but I could understand where they were coming from.

Science's way of knowing is to measure stuff and assemble evidence to make sense of the world. The spirit of the times is that only STEM is productive for the economy; none of those Arts-Block degrees are actually going to create jobs or swell the government coffers . . . so they're useless. This week is Research Week and there was a speed-dating session for researchers from the Two Institutes in the regions that the govt is trying to force into an arranged marriage. Shamefully they asked the contributors to prepare a 10 minute presentation and then, overwhelmed by subscribers, cut the time down to a rigidly chaired 5 minutes. Rigid chairing is generally A Good Thing: stops the class bore from droning on and on. But 5 minutes is rather disrespectful of any research that isn't wholly superficial. Ho hum, maybe the twitter soundbyte, low-attention-span, generation is now the new normal. And, I'm afraid to say that several of these fishing for interesting collaborators talks would have been unengaging if they'd gone on for another 30 seconds.

But one researcher shilling for someone to talk to; and maybe collaborate with, was interested in caring, how to, in the best possible way. Her interest started in her mother's head when the older lady suffered a disabling stoke  . . . and the speaker became her mother's primary carer . . . between the initial trigger in 2005 and the old lady's death in 2012. That's seven years of increasing dependence and closeness that was by this account pretty intense, generally exhausting and mostly positive. Less reliably positive was the couple's interaction with other people, protocols and institutions. A couple of years after her mother's death, Our Carer encountered an acquaintance whose mother was demented and wondered "how would our experiences compare?". From that question a research project was born

  • find a way to reliably capture the experience of patients and their carers
  • assess what adverse and positive events had greatest impact on the well being and QALYs [prev] of the patient and the equanimity of the carer
  • calculate what changes in professional practice would cost the least to have the most postive impact on the experience of 'receivers of service'
  • implement these changes until the money runs out
  • assess whether the changes do actually enhance the well-being and QALY-longevity of patients on their final run.
Hard to reliably measure happiness and well-being; and QALYs are in a sense an assault on the lived experience of sick people. But being a bit fuzzy doesn't mean that these "outcomes and deliverables" are not worth striving towards.

Wednesday, 13 March 2019

Hello I'm Bob

At last! VIBE is about to land in UCD. We, the VIBE community, have been expecting the big bird to land there in 2017 and 2018 because they undertook to bat her down in 2016. When I organised the 2014 meeting, there was, and is, only me to carry it forward. My head of department insisted that I form a committee to help with the logistics but tbh the schedule of committee meetings imposed another, largely unproductive, layer of things that I had to organise. And The Institute contributed bugger-all except the use of a vacation-empty lecture theatre: didn't even stump up a round of tea-and-coffee without I pay for it . . . and I made the flapjacks myself. I suspect the UCD cyclical no-VIBE no-VIBE vibe was/is because there are three Professors of Bioinformatics or Molecular Evolution all with international, not to say stellar, reputations. Organizing a mere international meeting is a low priority and so falls between [three] chairs.

Whatever; I am looking forward to Being There on Friday 22nd March because these are the people I've been teaching; collaborating with; employed by, for the last 30 years. It is a racing certainty that I'll be the oldest person there but I'm not expecting to be recognised. That's because my academic career has been earth-bound rather than stellar but also because of the rapid turn-over of Effectives in any scientific field. There will be Young Turks who were in short pants at the last VIBE meeting in 2016 who are now at the top of their game putting the final gloss on their PhD thesis. They will never know as much about their research field as when they write The End on the last page of that PhD thesis and take it off the the printer. I imagine that, with at least three research groups [to match the three Profs], there is critical mass and synergy in UCD so every there knows everyone else. But let's hope the hosts are not too cliquey and inward-looking: us boondock binfos need to feel welcome.

👁 kneed a name badge on my left tit [there is a sign language joke] with Bob Scientist  in large print and The Institute in slightly smaller font underneath. To the nearest whole number nobody else will think to perform this courtesy for other delegates. You need to be able to casually scope out to whom you are talking: you had a really interesting talk with them 3 years ago; but who in heck are they? Last meeting I went to [nit VIBE], name badges were supplied on an A6 card (with the programme on reverse) on a lanyard to dangle just above everyone's toolbox [same joke] - not the best way to promote neutral social information gathering if you have to stare are folks' groin to work out who they are.. I certainly don't expect people to know my name and I intend to quiz the youngsters closely about their research presentations. That being the appropriate role for a olde codger Senior Scientist.

I got into rant mode here [not sorry] because of a clever not to say life-saving improvement in non-verbal comms in operating theatres. This simple hack was invented by anaesthetist Dr Rob Hackett - put your name and role  Rob anaesthetist in large letters on the front of your surgical scrubs cap! That way you know how to unambiguoisly address the other people in the room - none of whose faces you can see properly. That might make the difference between getting a clamp on in time or just-too-late-sorry. This may remind you of the courtesy of wearing a Hello MY Name Is name badge - and introducing yourself to patients - before carrying out a medical procedure on the patient's body.