Tuesday, 30 April 2019

unintended consequences

It must be about 25 years ago that I found, in the local library, a planning report for the Swords bypass: a new roadway to expedite traffic between Dublin and Belfast. It was rivetting. Lots of full colour maps showing different land-owner's holdings down to fragments of fields; each annotated with whether they were subject to compulsory purchase. In some cases fields were purchased because they had been exclaved from the farm by the new road and were too small to sell to anyone else. The report included several pages of agonising about a particular badger Meles meles [prev] sett which was to be rolled to oblivion by drainage stone and concrete.

And any new road network's brutal assault across the landscape is not the end of the damage to the local ecology. All those cars tooling up and down to Limerick and Galway have been spitting lead and particulates from their exhaust pipes, wearing out the brake shoes and just leaving additive-laden tyre-rubber on the road surface. As the century turned, some water quality watchdogs said we should worry about this as a source of water pollution. The EPA took up the baton and commissioned Impact Assessment of Highway Drainage on Surface Water Quality 2000-MS-13-M2 Main Report by Bruen, Johnston, Quinn, Desta, Higgins, Bradley & Burns (2006). It is 270 pages of gradients, sumps, gullies, pipe-diameters, kerb heights, polycyclic aromatic hydrocarbons (PAH), French drains, Intensity-Duration-Frequency (IDF) curves, grit-traps and cadmium. Did you know that, in addition to salt NaCl, road salt may contain iron, nickel, lead, zinc, chromium and cyanide? Attempts at remediation of surface run-off can, if poorly designed, hold back contaminants until there is a catastrophic over-flow of toxic crap. Effective drainage can concentrate herbicide, sprayed to control marginal vegetation, and deliver it to a local water-course overwhelming its power of dilution. Those are some of the unintended consequences of piling on a fix for a problem created by people so that they can drive their carbon footprint up the planet's wazoo.

I heard about a rather more feel-good unintended consequence of Motorway infrastructure at the EnvSciCnf two weeks ago. A young scientist, Róisín Normanly from UCD and raised not 10km from Castle Bob, presented her final year research project at that annual National Jamboree for environmental research. It's quite rare to have an undergraduate give a talk at the national forum, and it's competitive: the science must look good to make the cut. What she has done is carry out an audit of the wildlife that can be found in the holding ponds which you see periodically as you zip past on your way to somewhere else. The holding ponds are part of the solution for protecting local watercourses from [toxic] road run-off. Not sooo toxic it seems because Normanly caught 16,000 water beetles and identified them to 62 different species; mostly predatory divers Dytiscidae and crawlers Haliplidae. That's 25% of the total number found in Ireland; 10 of which are red listed. By comparison a series of farm ponds were similarly surveyed.  The farm ponds tallied 14 more beetle species but not so many rarities. That's a nice project with a shedload of data, diligently collected, carefully analysed and presented with aplomb. You might think that she was lucky to land such a project - but as attested by my mother and partner and daughters you make you're own luck. Shaking luck up with hard & focussed work, there's a future for Ireland as a scientific nation FITNa!

This is really important because the relentless economies of modern farming [see yest] have reduced the number of farm ponds in recent years, so available fresh-water aquatic habitat is less than it was 100 years ago. The Road Transport Authority RTA by implementing the EU Water Framework Directive WFD has, as an entirely unexpected bonus, given robust support to ecological diversity. A necklace beaded with open water jewels fenced off from casual human access now extends across the country. The structure and size of these motorway ponds seems quite random. There's an eco-engineering PhD in seeing whether pond design could be optimised to get some of those 10 species off the red list and back to pulling their weight as endless forms most beautiful.
Hats off!

Monday, 29 April 2019


Here [L] is a picture of Polly Higgins talking at TEDxTallinn 2013 about corporate law now; and a future where making money for share-holders is not the legally privileged goal. She's been a fighter for the oppressed since [before] as a teenager she laid out her art teacher to stop him being violent to smaller children. That was the end of her with the Jesuits but she found a more comfortable billet in another place and went on to study at the universities of Aberdeen (BA Cultural History), Utrecht (Dipl Semiology), Glasgow (MA Decorative and Fine Arts). Later, she must have realised that it's damned hard to live on the whiff of aesthetics, so she returned to school at City U. London and the Inns of Court to qualify as a barrister.

I take the view that the history of civilisation since, say, Napoleon has been the curtailment of  the freedom of The Strong to indulge in heedless cruelty against The Weak. It is no longer legal or socially acceptable to . . .
The first law against cruelty to animals the Cruel Treatment of Cattle Act 1822 was sponsored by an Irishman <huzzah!> from Galway, Col Richard "Humanity Dick" Martin who was appalled by the treatment of cattle being herded for slaughter at Smithfield Market. He didn't like cock-fighting, bear-baiting or dog-fights; nor the use of pit-ponies down coal-mines either. But his first prosecution was against Bill Burns a costermonger who was cruel to his donkey [L said donkey as witness for the prosecution 1822]. The British SPCA was founded two years later and a steady widening of the remit of cruelty to animals ensued to include anything bigger than a breadbox with a beating heart that lived in Britain. That's a rather comfortable attitude to breadth of the law's concern. If it's not happening in your town, then anything goes.

It was okay with The Patriarchy if the only people who went out to Africa to shoot lion were my / your cousins Rodney and Willoughby who were crack shots and rather decent old coves: never known to bilk the tailor; could hold their liquor; didn't cheat at cards. The case was altered if the killers were black, once-upon-a-farmers who had picked up an AK-47 in a local conflict and knew a man who knew a man who'd hand over folding money for a rhino horn. So now we have international trade laws that prevent the sale or export of wild animals, or parts of wild animals, dead or alive. If you can square your conscience with the export of live (or dead) sheep while huffing and puffing about the trade in crocodiles or mink coats you may have been educated by the Jesuits. I can't see the difference myself but then I eat meat and my moral compass spins like a top.

And it's not just animals. A tycoon from Singapore was just acquitted in a case of illegally trafficked rosewood logs (Dalbergia maritima) from Madagascar. The SG Court of Appeal went all lawyerly on the words in the Endangered Species (Import and Export) Act to hold that it didn't apply to Mr Wong Wee Keong because the logs were in transit to a final destination rather than imported in to Singapore. It's taken 5 years to get this far and the lawyers are all a bit richer and Mr Wong's bottom line is a bit dented. Who knows what will happen when the shipment reaches its destination in Hong Kong?

Mais revenons a nos Higgins! After qualifying and marrying another lawyer (who went on and up to become a sensible&sensitive judge on the West of England) Ms Higgins had a successful career defending people in court. After a long drawn out case, she looked out of the window and had the epiphany that The Earth herself needed a lawyer.  She packed her black gown and silly wig and assumed the mantle of Gaia's attorney, campaigning to add a 5th leg to the platform from which La Cour pénale internationale aka the International Criminal Court (ICC) utters its judgements. To genocide, war crimes, crimes against humanity and crimes of aggression, Higgins et al. wished to add Ecocide, so that the court could deal with issues beyond man's inhumanity to man.
A lawyer's definition of Ecocide: "loss or damage to, or destruction of ecosystems of a given territory such that peaceful enjoyment by the inhabitants has been or will be severely diminished." Which is worryingly centred on the [human] inhabitants - like the Yanomami in Brazil after the loggers bulldoze a few hundred hectares of tropical rain-forest for a McD's cattel ranch; or the Magyars who lived down-stream from the collapsed Ajka caustic red mud holding pond. It lets you off for mowing your lawn to an inch of its life; lets Ireland off for the list of ecochanges bulleted below.

I'm very sorry to report that Polly Higgins died on Easter Sunday peacefully after a brief dust-up with terminal cancer in Leckhampton's Sue Ryder Hospice. She was only 50 - a lot done; a lot still to do! She will be buried in Slad Gloucestershire on Friday 3rd May. That's where Laurie Lee [prev] is buried and where m'sister was married. Indeed those two women were friends and allies in the local branch of There's Got To Be Another Way or Holding the Planet or Borrowed From Our Grandchildren. I understand there's going to be a mighty party, awash with organic whiskey, after the funeral, at the Woolpack.

For someone [that would be me] who believes that a very large proportion of the evils in the world stem from there being a) too many people b) too many rapacious millionaires; it is A Good Thing that at least the millionaires and their enterprises can be held accountable for the damage they do in their pursuit of money: either by casual inattention to what's going on around their places of work OR carelessness about the by-products and spoil from their place of work OR by taking so much that what's left is a pale shadow of what was there before the take. All of these sins of omission and commission would qualify as ecocide  if such a concept existed in law - it doesn't . . . but not for want of Polly Higgins trying. In 2011, a bunch of lawyers borrowed the UK Supreme Court in a mock trial of Oil Company Execs over their depredations in the Athabaskan Oil Sands and The Gulf Oil Disaster. If the Ecocide Act was law, then the Oil Sands Suits would have been found guilty but the Gulf Oil fiasco (Louisiana shrimpers notwithstanding) would not.

Finally lest we feel super smug in a nothing to see here way here in Ireland, you should listen to this podcast of Padráig Fogarty of the Irish Wildlife Trust, explaining how we have collectively and completely changed the landscape of Ireland, since the 1970s:
  • Diverse permanent pastures and traditional hay-meadows have been replaced by monoculture deserts of ryegrass Lolium perenne
    • so the fields are still green but like a billiard table not an ecosystem
  • crop rotation has been discarded as old fashioned and unprofitable to be replaced by year after year of nitrate inflated barley or spuds
  • blanket bogs which have been growing and diversifying slowly over hundreds of years have been drained and replaced with monoculture deserts of Sitka spruce Picea sitchensis
  • bogs in general have been cut away into peat briquettes and sent up the chimneys of Ireland 
    • or bagged up and sold in English garden centres as potting soil.
  • uplands with a distinctive flora and fauna have also been replaced with spruce deserts 
    • the trees dry out the soil and shade out all other vegetation, so that when the plantations are clear-felled all the dirt washes down hill into an acidic disaster for the local water-courses.
    • the silt wash and the nitrates driven the pearl mussel Margaritifera margaritifera to the brink of extinction
  • Lazy slow fish-full meandering floody rivers have been dredged and straightened to get rid of excess water as fast as possible
  • Think what beam trawlers do to the sea-bed. We know they are dangerous to the operators. Greenpeace reckons that's in the ha'penny place compared to the holocaust down on the  sea-bed.
As it's Easter 2019 [in Athens and Kiev anyway] let's paraphrase Willie Yeats the Patriarch:
Now and in time to be, 
Wherever green is crying, 
Are changed, changed utterly: 
A desperate spectre is dying.

Sunday, 28 April 2019


Almost drug ourselves through an alphabet of miscellany. X today. X chromosome schematic [R]

Saturday, 27 April 2019

The race is not to the swift

Following on from my rant about the virtues of uncluttered web-design . . .

In 1992, it was a close race as to whether it was faster to communicate with the mainframe in TCD using a 300 bps acoustic coupler [example R] or get on my bike and cycle the intervening 10km. Now the pipes of the internet are fatter but the data that's getting pushed down the pipes is bigger too. My pal Rene's second-hand laptop was acting up when I went to visit last week and I was able to get it started in 'Safe Mode' so that at least they could back-up the data before they sent it in for some remedial doctoring. We were reflecting that a decent functional computer could be bought ready-to-go for about €1,000, which is about the same price that we paid for decent functional computers 30 years ago. Today's model is unimaginably faster and has 100,000x the storage capacity but costs the same.

Here's a sweet story from the early 90s about getting in touch quickly <not>. In 1994, the web was barely commercial and pretty slow but the telephone switch-boards in academic institutions could be slow also. The Regional Technical Colleges [which were rebranded later as Institutes of Technology] were strongly unionised and the union insisted that their chaps needed a proper lunch-break. In the middle of a working day in ~1994, my colleague Ken needed to call Dr Michelle Storrs in Tallaght RTC, so he dialled their switch-board. As the line rang and rang, he thought he'd find out if she had a direct line . . . using the internet. The result of this impromptu research project was the finding that there are a helluva lot of Michelles in Storrs, Connecticut!

Those were the preGoogle days when your enquiries on. say, Altavista would be wholly generic. Asking about dry-cleaners in Dublin would top-load you with hits from Dublin, California and Dublin, New Hampshire, because your geography wasn't embedded in the search and there were far more wired-up businesses in Dublin, America than in Boondocks, Ireland. Now Google guesses better what you probably want . . . but that can have a downside if you're trying to kick over the traces and go on an unNannied search across the universe of knowledge.

Friday, 26 April 2019

Steamboat Bell

Julia Bell [R in her TCD graduating gown] died on 26th April 1979 [40 years ago today!] having clocked her 100th birthday a few months earlier. She was 21 when von Tschermak-Seysenegg [peas Pisum sativum], Correns [hawkweed Hieracium spp.] and de Vries [evening primrose Oenothera lamarckiana] each independently discovered that their cutting edge work in classical genetics had been scooped a generation previously by Gregor Mendel [prev] crossing his peas Pisum sativum and carefully recording the results. Bell was then enrolled in Girton College, Cambridge where women were allowed to attend lectures and sit exams but not get a degree. She aced the Mathematical Tripos exams the following year and started number-crunching some astronomical data on solar parallax.

Between 1904, when Trinity College Dublin first admitted women, and 1907 when that cohort finished their courses and started to graduate, a peculiar window of opportunity for intellectual women opened up in TCD.  Because of a reciprocal agreement with Oxford and Cambridge Universities, women who had qualified at those misogynistic institutions were invited to receive a University of Dublin degree ad eundem gradum [to the same degree]. Certain classes of people can to this day get such a degree [top of page 5] if they can muster €1,101 and appropriate paperwork. In 1904, the polymathic Provost of TCD was Anthony Traill and he pushed to open the door for women to get a proper degree depite their being denied the opportunity in Oxbridge.
Probably anticipating a handful of horse-ridin' Anglo-Irish gells to take up the offer, the college was a bit overwhelmed by more than 700 women, who had passed through Oxford or Cambridge, and were qualified to get dolled up in cap and gown for their conferring in Dublin. They were charged £10 for the privilege and that money was allocated to start building the first off-campus halls of residence (for women) out at Dartry in the suburbs - and a longish tram-ride to keep the sexes apart when they weren't actually in class. This cohort of enterprising, well-connected and smart women were collectively known as the Steamboat Ladies [super documentary on Newstalk FM] because they generally didn't spend more than a couple of nights in Dublin before going back to work on the other side of the water. Julia Bell wasn't the cleverest woman who graduated in this fashion. That feather probably goes to Philippa Fawcett [see L] who sat the Math Tripos in 1890 and scored 13% higher marks than the best qualified man.

Fawcett went off to South Africa to train the next generations of math teachers, but Julia Bell was head-hunted by Karl Pearson to beef up the maths in the Galton Eugenics Laboratory in London. She was there for decades, working on the mathematics of [human] inheritance. Her focus moved the field away from the easy cases like Mendel's round and wrinkled peas where experimental crosses were allowable and enormous sample sizes achievable. Human genetics was much more difficult because it relied on pedigree analysis. Pedigree analysis was only useful if there were large families of several generations with reliable diagnosis and excellent record keeping. Haemophilia in the royal families of Europe? That was possible. Hereditary deafness in the Davies family, shepherds and coal-miners up the Rhondda Valley in S. Wales - not so much.

In 1937, Bell collaborated with JBS Haldane [prev] to nail down the genetic linkage between colour-blindness and haemophila, the mutations for which were both known to be carried on the X-chromosome. Because the paper was published in the Proceeding of the Royal Society, the PDF is available albeit in a grey on grey scan that isn't easy for old eyes to read. The data wasn't easy to analyse either and the paper is not for the faint of algebraic heart. At issue is the case of heterozygous women: whether women need two copies of the mutant gene to manifest the disease or if one copy will do. Haemophilia is vanishingly rare in women because a) it is fully recessive = two duff-copies needed b) it requires a haemophiliac father who hasn't bled to death before he was old enough to make babies. This is decades before Factor VIII was available to ameliorate the symptoms of haemophilia. The discussion of the other disease starts with a great Haldanesque tell-it-like-it-is: "On the other hand, colour-blind women whose putative fathers are not colour-blind occur too frequently to be explained by illegitimacy." Which highlights another aspect of dodgy data in human pedigrees [prev on non-paternity] which doesn't happen is properly constituted lab-animal experiments.  I think that analysis was the first description of genetic linkage in humans; and required finding 4 large families through which both disorders ran for several generations.

She is also note-worthy for doing the early studies on the inheritance [PDF here] of what we now know as Fragile X mental retardation but which was for many years know eponymously as Martin-Bell Syndrome: from another big pedigree study [part of which is shown above] in which boys kept popping up with 'mental deficiency', autism, big ears, long face and unfeasibly large testicles. Intercalated in the same extended family are numerous children smart enough to win scholarships. The paper included a lot of peripheral [and judgemental] data <TMI> V 32, said to be very fat, is employed in a fish shop . . .IV 3, a heavily built woman, crippled by arthritis . . . V48 Is unemployable, wet, and dirty </TMI> that would surely not be allowed in today's GDPR-compliant literature. Why Fragile X? Because if you look at the chromosomes of people with the syndrome, you can see a little waist at the end of the long-arm of Chr.X. We now know that this is due to an expansion of a CGG repeat in the FMR1 gene at that location. FMR1 affects the location and abundance of receptors for the neurotransmitter glutamate - ah but that's another story for another time.

After WWII, Victor McKusick, of Johns Hopkins U, started to accumulate and publish everything that was known about genetics in our species; the first edition in 1966 flagged nearly 1,500 conditions.  In 1987, the project went on-line to become OMIM now documenting nearer to 25,000 variations which are heritable. Not all of these are diseases: Kirk Douglas used to feature because his sons have a cleft chin just like their dad; but some post-McKusick functionary has tidied that anecdote out of OMIM entry 119000. OMIM is neverheless a treasure trove of genetical miscellania.

But Julia Bell probably deserves most credit for an infrastructural project that served as the human genetic foundation from which many subsequent forays towards the frontiers of science could be launched. The other great infrastructurialist, McKusick became famous for building on her work a generation later. Bell's gaffer Karl Pearson started compiling The Treasury of Human Inheritance in 1909 and the Galton Lab was still keeping the compendium up to date 50 years later in 1958. The most significant contributor in word count was certainly Julia Bell especially in the areas of ophthalmic and neurological genetics; as exemplified by her work [see above] on the mental and neurological deficits of Fragile-X. There is a good tribute to this period of her life by Peter Harper of Cardiff U. in Human Genetics (2005) v116:422-432 but you may have to go to SciHub to step round the paywall. I allowed myself a snitty comment about extraneous information in Martin & Bell but Bell's work on ToHI is characterised by the breadth of its accumulated, and apparently miscellaneous, data which has allowed subsequent workers to mine her tables for useful information long, long after the patients and their families have passed beyond their ability to contribute a DNA sample.
The Steamboat Julia Belle is an entirely different matter.

Thursday, 25 April 2019

Sustainable newspeak

They say that a camel is a horse designed by a committee. Actually, the quote is attributed to Alec Issigonis one of the great all-in-one-head designers of the 20thC - he created the Morris Mini just in time for it to be the iconic car of the Carnaby Street generation in the 60s.  I was a bit reluctant to fully embrace the EnvSciCnf which The Institute hosted at the beginning of Easter Week - not my gig; won't know anyone; I gave already - but eventually the free lunches and a certain restless curiosity overcame me and I found myself having fun and learning a bit, too.  The theme was Climate Change and some of the talks tried a nod in that direction. Talking to another (and far more competent) silverback we agreed that Climate Change was The Problem for our time. He made the point that cheap oil (to run diggers and drills and mills) had ensured the consumption / destruction of reserves of all the other minerals - tin -- teak -- copper -- !water! -- chromium -- aluminium -- gold - too often in the process of making the metals available catastrophic environmental accidents have occurred. My slightly tangential response was "what are we like? how is that, on a finite planet, the key economic metric is growth?". I asked him if he'd read Richard Douthwaite's The Growth Illusion (1992 publ blurb). He confessed that he'd bought a copy when it came out but only skimmed it looking at the graphs. That was exactly my experience, so we agreed that the main virtue of the book was its title. If you are much younger than me - and almost all the Blob readers are - you may not have heard of the book. That's okay; the subtitle says all you need to take on board: How Economic Growth has Enriched the Few, Impoverished the Many, and Endangered the Planet.

The key-note speaker at the EnvSciCnf cited, with approval the Sustainable Development Goals SDG 2030 dreamt up by a UN committee and released to a confused world in 2015:
"The Goals interconnect and in order to leave no one behind, it is important that we achieve each Goal and target by 2030". It's too bloody complicated, ye daft buggers! You can't get behind something you can't get your mouth around. Like Bill Laio's tree-planting venture We Forest which has the mission statement Making Earth Cooler. How cool is that? I could sign up to that as I park all the mixed messages that alienate fellow-travellers from really embracing SDG 2030.
1 Poverty No Poverty
2 Hunger Zero Hunger
3 Health Good Health and Well-being
4 Education Quality Education
5 Gender Gender Equality
6 Water Clean Water and Sanitation
7 Energy Affordable and Clean Energy
8 Work Decent Work and Economic Growth
9 Innovation Industry, Innovation and Infrastructure
10 Inequality Reduced Inequality
11 Cities Sustainable Cities and Communities
12 Consumers Responsible Consumption and Production
13 Climate Climate Action
14 Oceans Life Below Water
15 Forests Life on Land
16 Justice Peace and Justice Strong Institutions
17 Partners Partnerships to achieve the Goal
There are couple of obviously annoying inconsistencies in here. 5 = equality but 10 = inequality. 17 shouldn't be given parity of esteem with the other items because partnerships are required for all the other goals but isn't really a goal in itself. But, obviously given my Douthwaite rant above, my ire is particularly intense for 8 = Work and Economic Growth. Aaarghh not the goddamned growth, that's what has fucked the planet to give us all hula-hoops and pop-tarts while removing passenger pigeons, quaggas, Tamanian wolves, and Steller's sea cow.  I'm trying to think of a mnemonic to help me nail all the goals, but not too hard because the list is so poorly constructed that it won't go anywhere or, more importantly bring anyone there.

Wednesday, 24 April 2019

Fall on your sword, please

Years ago ?2005? during the Celtic Tiger, I applied for a part-time (2 hr / week)  job at The Institute where I now work. After the interview, I was offered the job and after some dithering I accepted. That was the middle of November, so there were 9 weeks to finalise the pay-and-conditions, before I started teaching in January. My interactions with HR were exasperating, so much so that I terminated one phone call with "I can't bring myself to speak to you any more without starting to shout, so it is better if we conduct further dialogue by e-mail - brrrrrrrrr". The details were complicated so I won't bore you with them here but I will say that when the contract finally arrived in the mail, it was a contract for another post with another name at the top. While I was still smarting, I ranted about this sorry interlude with my friend Nick [whom we've met before] who used to be a senior HR manager for a merchant bank in London. With Socratic rhetoric, Nick asked "If you were the hottest property in HR, would you be working for a sleepy under-funded Institute of higher education in the Irish Midlands?" To which the answer must be "No".

Science Foundation Ireland is, apart from the EU, the main source of funds for scientific research in Ireland. They have several schemes and calls and several application deadlines each year. Because we are, finally, in the 21stC, the submissions are all electronic and the website refuses to accept any submissions after the deadline. All automatic, no people involved, so you can't slip an application under the door after the official deadline. In the 00s, I helped my gaffer put many grant applications together and I always found it stressful because I don't do deadlines well. In ~2004 here was a call from the Department of Agriculture's Food Institutional Research Measure FIRM [whc we've laughed at before]. We decided to apply; but the process stalled on the back burner [as we spent the last of the old money doing science] until about two weeks before the deadline . . . when we started to populate the various parts of the Application. The science; the budget; the payroll; the Deliverables; a Gantt chart with all the Workpackages WPs; a PERT diagram to show the dependencies; the scientific summary; the lay summary; the bibliography; the UncleTomCobblology. The deadline was 5pm on Friday. I only worked at the office on Thursdays and I put in a long day, sucking a pencil and writing chunks of text to fill each of the boxes on the form. The arrangement was that when the final draft was approved, the Technician would print it all out and hand-deliver it to DoAg in town. On the Friday, the Gaffer and I were both working from home putting final touches to the application. At lunchtime, I packed it in and went offline & offsite for the afternoon. It was before ubiquitous smartphones so you could escape in this way. I returned in the evening to a succession of increasingly frantic e-mails from the Technician asking for the final final copy for printing and delivery.

It was sitting in the outbox of The Gaffer's computer but not Sent. In 2004, we were still Ould Ireland. At 0900hrs on Monday, the Gaffer phones up the contact in the DoAg. He says (I paraphrase) "Sure we aren't going to start looking at the applications until after lunch; if you can get your application in by about 10am, that will be grand". Which was both endearingly laid-back and infuriatingly complacent and prone to corruption at the same time. The key back then was the post-mark on the envelope. My other boss at the time discovered that, if you took your package out to the central sorting office on the Naas Road before Midnight, then it would be date-stamped within the deadline. That won seven after-office hours for recalculation and polishing.

SFI had a deadline at Noon on the last Friday of March. The Institute is less sleepy than it was in 2005 and several of the more ambitious young lecturers decided to apply for funds. No more than any corporation with proper governance, The Suits of The Institute insists that, while the scientists write the science, the final sign-off must come from The Suits. Well the process failed that Friday. The scientists sent their final drafts off up the hierarchy but failed to get the expected acknowledgement. The Suits or their robot proxies had failed to forward the application to the SFI!  When they were apprised of the deficit after lunch, they tried to submit (late) but SFI server made that rigidly robotically impossible. A telephone call to SFI was met with a firm, almost incredulous, borderline contemptuous, No! That's the bargain we've struck with 21stC Ireland: transparent; incorruptible; inflexible; monolithic; professional; unimaginative; fair.

Anyone going to  lose their job over that blunder?? Either the Suit who should have signed off the applications but failed to do so OR the fellow who designed the mail-bouncer that allowed the relevant Suit to be playing golf on Friday afternoon?
Hint: the HR people who, in 2005, cheese-pared my salary and treated me and my lifetime's experience with contempt are still drawing a salary, still being doctrinaire, confrontational and unimaginative; and presumably still occasionally sending out the wrong contract to potential employees.

Tuesday, 23 April 2019

Dead to rights

A few years ago the media had a field day over the revelation that illegitimate babies, who had the misfortune to die under the care of nuns running mother-and-baby homes, were disposed of in concrete tanks in the grounds of the institution. Mother-and-baby homes were the places to which young women, pregnant outside of wedlock, fled to deliver their babies away from the prying eyes and judgemental attitudes of the neighbours. Illegitimacy was a terrible stigma in the Ireland of the last century. After The Boy was born without a wedding in 1975, we took him along to the Dublin City Registrar to have his birth officially recorded and pick up a birth certificate. The functionaries behind the desk refused to acknowledge that the child had a father whose name could 'legitimately' be entered into the 4th column of the certificate [see Yvonne Barr's birth-cert for how 'legitimate' looks]. After a long time trying to argue with The Patriarchy about natural justice and "Behold the Man"; we caved in and had my name entered in the 7th 'Witness' column with (father) in brackets.

20 years later we were registering the births of Dau.I and Dau.II who had been born at home in a drafty old farmhouse out near Dublin Airport. To the nearest whole number, in any random month, nobody gets born in Fingal County because home-birth are really rare in Ireland and 99% of mothers in Fingal county get into one of the Dublin maternity hospitals in time to be registered as [city] Dubs. In 1995, the registrar had plenty of time to chat and we related the trauma of registering The Boy in the 1970s. Recent legislation allowed for birth certs from the Dark Ages to be retrospectively altered to reflect the biological truth that all children have two parents whether married or not. It was waaaay too late for that, for us. But that gives some flavour of how the children of unmarried mothers were othered and de-personalised by society back then. By society; not just by the, now demonised, nuns: that's too easy a snow-job.

The mother&baby spotlight has now (April 2019) moved on to Bessborough mother-and-baby home in Cork and St. Finbarr's Hospital up the road. The fifth interim report on these matters has found that more than 900 infants were allowed to die in Bessborough or whisked up the road in extremis to die in St Finbarr's. Of these, 836 babies are currently unaccounted for: logged in but not logged out - no death certificate; no known burial place. Because a hospital was involved in this sorry tale, it made me think that many of those babies (or parts of them) might be still around - pickled in a glass jar in a pathology lab . . . not necessarily in Ireland

Q: Why would he think that?
A: Ahem - because of the Madden Report [the actual 150pp report], maybe?
In 2005, Dr Deirdre Madden was appointed by the then MinHealth Mary Harney to look into 'organ retention' from babies: perfectly legitimate, catholic, two-married-parents, dead babies. Ireland has one of the best records in obstetrics abd gynaecology . . . if you define success as 'mother and baby alive'. Less wonderful if you insist on 'mother and baby well' or 'mother and baby entirely happy' with their experience in the maternity unit. There are still a lot of induced labours, C-sections, professionals who don't say hello; episiotomies. Neonatal death is so rare that doctors are required to do a post-mortem on pretty much all children who die in hospital. Post-mortem will very likely involve an autopsy where the liver-and-lights of the child are exposed for inspection and possibly sampled for histological or biochemical tests. Everyone accepts that as necessary; but everyone assumed that the bit and pieces were respectfully returned to the body after examination. In 1999, it was revealed that many of the out-going tiny tragic white coffins were leaving Crumlin Children's Hospital with short measure. If the pathologist thought that the failed liver would serve some useful purpose in teaching or research he would just keep it. It was a breakdown or failure of communications between doctors and the bereaved Mr and Mrs Murphy. To quote Madden:
Another reason given for the non-disclosure is that doctors had a different perspective in relation to organs and did not equate organs with the body as a whole. Doctors generally did not see the organs as having any emotional significance once the child was dead – ensuring that the body be released for burial within the timeframe sought by the family was more significant, in their view, than all the organs being replaced in the body for burial. Doctors were trained to pay less attention to the emotional and symbolic aspects of organs, and to concentrate on the functional or medical aspects.
I'm with the doctors on this one, as I wrote in 2015 in my last rantovestigation on ethics and blood-samples. But it's not really relevant what I think; the doctors and pathologists really need to acknowledge that being quite casual about dead bodies is not normal. "Normal" being that which is asserted, believed or acted upon by the majority of people.

Monday, 22 April 2019


When I was at the Business Expo 2019 on a pen and post-it gathering expedition, I was lapelled by a seller when I paused near Blacknight solutions an Irish web-hosting and support service. I boasted mentioned that I'd set up a web-server and written my first web-pages in 1994 . . . possibly before she was born. In those early web days, before Dreamweaver, you had to write the HTML by hand in a text-editor. Because the <paininthetits> tags </paininthetits> were awkward to write, and unforgiving of typos, my markup was very simple. The signal [text and diagrams and links] to noise [necessary HTML to split paras] was about 90% words vs 10% <tags>, so it was very efficient even it it looked a bit clunky.

Now the ratio is worse than reversed. Here on Blogspot a recent 775 word posting requires 120,000 bytes of bandwidth to be read in Ballyhaunis or Bangalore.
What Total Text Ratio
Words 10,500 775 7%
Chars 120,000 4450 3%
This problem magnifies if you have fat graphics, or widgets, or ads, or demography-capturing software installed. Why is this a problem? Because 10% [and rising] of the world's electricity is being consumed by internet servers and every extra superfluous redundant fat electron on some dipshit website requires another hydro-electric power station in the Rockies. The other side of the coin is the quixotic pursuit of rural fibre-to-the-farm broadband in Ireland. Why does Bob Bó, living up the remote bohereen in Co Carlow, need broadband? Because it takes 25Mb of HTML nonsense for him to access the Co-op website to order 10 sacks of Ewe and Lamb Muesli [mmmm good].

I tried to explain this to the Young Marketeer from Blacknight but I could see her eyes glaze over with here's-another-batshit-crazy-old-bloke frustration. Because she was convinced she had it all covered:
Blacknight's server is on the right with their huge bandwidth connexion to the Rest of the World. Their client is the Provider on the left. Blacknight want to design a really swish sexy clickable website for their client: all the client needs to do is provide Blacknight with some copy [mission statement; phone numbers; picture of the CEO; dreamy background of green fields and munching dairy cows [4096 x 2048 pixels = 4Mb] . . . and a loada money, of course. Their server serves the data out and the orders come surging in . . .

Except that Bob Bó, not to mention Bhavesh Bangalore, needs to find 10 minutes between milking the cows and breakfast to download the Home Page, let alone get down to the order form. For my money, ISPs and web-hosters could play their part in the band-width crisis. Like we could all play our part in the carbon wars - if we could hold back from consuming energy [wear a sweater inside in winter; don't drive to the shop twice a day; let the kids walk to school] then we wouldn't need another power-station. If clickers need to upload a huge JPG or a fat javascript before they can get down to business, then the designer is at fault. All those megabytes on Dropbox and Friendface - they count carbon too.

Sunday, 21 April 2019


A parable of compassion for Easter 2019
Thursday two weeks past I gave the last two lectures in my Human Physiology course for the 2018-2019 year. I threw in a couple of bonus slides to help them handle a couple of wholly predictable questions on the exams in May. Which may have been largely wasted because only 8/18th of the class turned up. You may be sure that the students who needed most help were the most likely to be absent. That week I also gave and marked wrap-up Excel quizzes for my three remedial maths classes. My weakest link scored 38% on the Excel, having failed to answer 2/5 of the questions; but I inched him over the line because he tries hard but has been easily distracted from class in his first year away from home. A good friend of mine flunked his first year exams in Law at TCD but passed the September re-sits and went on to a stellar career of torts and litigation and retired on his money before the age of 50. There is a good chance the WeakestLink will settle down too.

I learned such constructive charity in school during my very expensive education in the 1960s. Back then if you had a lapse of discipline or learning you were put on a Satis Card. Actually, you were required to make your own Satis Card as a time-table with blank boxes for all the lessons for a week. At the end of each lesson, you had to present the card to the teacher who would either scribble his initials (implying satis) or write the much dreaded N.S. = non satis = not [good] enough in Latin. At the end to the week the card had to be presented to Chris Evers, the central authority, for scrutiny and, if necessary, punishment. I was often On Satis because I was drifty, easily distracted and rarely did the necessary prep and home work - especially in Latin and Music.

One week, eleven year old me neglected to get his Latin box signed. That omission, in and of itself, was enough to attract a N.S. which probably meant, at the very least, another week on The Card. I decided that the best way forward would be to forge Mr Latin's initials in his characteristic red ball-point pen. I used completely the wrong shade of red and the tangled loops of random lines bore zero relationship to the teacher's signature. At the end of the week, I presented my card to Mr Evers with a mixture of dread and fatalism. I knew that it was far worse [cad, bounder, bad-hat] to be indicted for forgery than caught with a blank on the card. The Boss looked at me, I looked at his shoes, time paused . . . and then he screwed up the card and binned it. He must have realised that nothing positive could come from an inquisition, let alone further punishment. Or perhaps he was in a hurry to nip down to the village for a pint and didn't want to delay his social life with a lecture to scatter-brain me. His inaction was notably successful if it was designed to win the heart and mind of one of the young chaps for whom he was responsible.

My career as a forger didn't really take off until I left school and started work.

Saturday, 20 April 2019


Y'll need some background music to this, what better than a compendium of Turlough O'Carolan Toirdhealbhach Ó Cearbhalláin (1670-1738) Sí bheag, sí mhór - Planxty IrwinEleanor Plunkett - Farewell to Music.

Almost the last talk at the EnvSciCnf this week came from the Geological Survey of Ireland GSI, one of Ireland's most productive government quangos. It was a report on the 400 examples of 'groundwater flooding'. This is when water comes blurfing out of the ground instead of either falling from the sky or travelling by beck rill stream and river through on its way to the sea. They only occur if the underlying rock is super soluble limestone karst: the water dissolves the calcium carbonate CaCO3 so that it becomes a complex network of sub-surface fissures. Given several thousand years, the fissures grow into interconnected tunnels and caves like Mitchelstown. Limestone cave-systems are thus always connected with and by water: as my pal Roy found in his near-death experience in Sleet's Gill. Groundwater flooding is when, hours or days after a good spill of rain, the underground network fills up and spills out of the top to flood the landscape. In Ireland these temporary lakes are called turloughs and they look like this:
Joan Campanyà <trigger Catalonia> of the GSI is The Effective in project GWFlood tasked to map the turloughs in space and time, so that all the stake-holders have a good idea about when and where and how deep water will appear. We have a pretty good idea of the location of all the [N=400] places where a turlough has ever appeared, but some of these locations are up a rough bohereen in Co. Roscommon and [so] there is no continuous record of their ups and downs and disappearance. There are two main techniques
  • Put a sufficiently tall pillar in the lowest part of the local landscape. Incorporate an electronic dip-stick in the bottom and a radio-telemetry beamer on the top and an hourly report of water-level can be captured in GSI head office.
  • Satellite  mapping with LiDAR [prev] and SAR - synthetic aperture radar.
This before and after picture-pair caused an audible WTF?gasp at the conference - to which I contributed. In a dry summer, the landscape is covered in grass and quietly chomping cattle belching us all into oblivion with their methane-laden burps. In a typical winter windsurfers can scud across the choppy waves. Rahasane turlough in Galway is 2500 ha in extent. My post-talk question was "how often must you change the batteries?" A: never nowadays because each post has a solar charger. Nevertheless setting up 400 wet-depth poles doesn't scale up from the N=20 pilot study. This is where SAR kicks in with its ability to detect back-scatter;
SAR-sat directs a radar beam to earth as it passes over the landscape. IF it strikes flat water THEN radar-waves bounce off and awaaaay [the angle of incidence is equal to the angle of reflection] ELSIF the beam strikes something bumpy [trees in pic above, but also rocks, hillside, undulations] THEN some of the waves are returned to be picked up by a detector on the satellite. Joan and co. have cross-referenced the terrestrial depth-post data with the satellite data and found a good enough match; so that's probably where they are going forward. For me this is a really nice mix of 19thC mapping & surveying with 21stC satellite magic. On the top of our hill in the Blackstairs is a rainfall monitor owned by Met Eireann: a copper funnel with a precise diameter over a collecting churn. One of the teenage girls in the last cottage up our bohereen was contracted by Met Eireann to yomp up the hill on a regular basis and measure the accumulated water since the last tally and throw it away so the churn was zeroed for the next slop of data. That is romantic but not efficient.

Why does it matter? Continuous data streaming of depth and area from groundwater flooding can help planners to determine where NOT to allow building to address Ireland's housing crisis. Because GW flooding involves landscape with no surface escape path for the flood-water, turloughs tend to hang around for a long time. Several families were unable to drive to-fro their homes for weeks after the "100-year floods" of Jan 2015. With climate change, you can bet your sweet bippy that 1000 year floods are now 100 year floods and 100 year floods will come more frequently. Cross-referencing the rainfall data with the flood-rise data allows a much wider demographic to plan their lives so that the car is on the right side of the turlough as if spreads across the bohereen . . . and go and buy a dinghy next time ALDI has one on Special.

Friday, 19 April 2019

Exploit the water [again]

Free the water Part I.
Last Friday I was wandering about in Dublin waiting to have my toothy extracted at 1330hrs. As a navy brat, trained to expect lunch at 1pm ± 2 minutes, I got predictably hank marvin as I stepped of the DART to walk into deepest suburbia where the orthodontist has her practice. I had a sandwich to hand [forward planning, me] but had been planning to eat if after the event. I needed something to drink and popped into a convenient Tesco for a 500ml bottle of water. Well what a shower of bad bargains:
  • €0.85 Tipperary  500ml
  • €0.95 Ballygowan 500ml
  • €1.09Volvic  500ml . . . up to
  • €3.29 London Essence Orange And Elderflower Tonic Water !!
€3.29? I could have drunk my tears of frustration! But then, bizarrely to a sheltered chap such as myself, it turned out that you could get twice as much water for a fraction of the price:
  • €0.35 Tesco Sparkling Water Apple And Raspberry 1 Litre
  • €1.59 Ballygowan Sports Still Water 1 Litre
  • €1.59 Tesco Ironing Water Spring Petals 1 Litre
  • €1.69 Tesco Prune Juice Water 1 Litre
  • €2.09 San Pellegrino Sparkling Water 1 Litre
That Tesco Ironing Water Spring Petals sounds pretty good, must go down well in Scotland as an alternative to Irn Bru. But I plunked for The Apple and Raspberry [35c and all] and it was okay; served its wash-down pupose anyway.

I get, as you see, rather exercised about the productification of water. The whole point of having Irish Water [and its predecessors] was to produce clean clear potable water from every tap in the country. More or less coincident with the final delivery of this dream - boiled water notices are no longer normal in Roscommon - is the widespread belief that Chateau Tap is unfit for human consumption. Almost certainly carried forward by the omnipresent marketing of minute quantities of water for fantastical prices. What, you can't afford bottled water? Ye'll never marry my son, y'trollop.

Bad as marketing something quite normal for inflated prices is, at least it is honest capitalosm. There is another crowd who are selling the stuff that falls from the sky but braying an ecoplanet message with their mark-up. They are called Ecofil and I first encountered them as a Youtube ad. Then I checked out their webpage. They provide water fountains [I think] Putting an Elkay ezH2O Bottle Filler in your school will provide:
  • Ready access to drinking water and hydration.
  • Elimination of Plastic bottles in the environment
  • Filtration of Lead, chlorine and other impurities.
Here's the thing, in our house these benefits come fitted as standard - it's called the kitchen tap. The other element of gall is that, for €8+vat, Ecofil will sell you (and everyone in your school) bottles made from Green Polyethylene, a renewable raw material derived from sugar cane ethanol. During their growth cycle, the raw materials used to produce Green Polyethylene absorb and repair CO2 in the atmosphere, reducing greenhouse gases and it’s carbon footprint. That statement, apart from being apo'strophe-, Capitalisation- and subscript2- challenged, is forty shades of bollix . . . even if "for free" Ecofil will print your school logo on each bottle. That's still a t€nn€r for a plastic bottle before you put any water in it. I just got a free bottle when I bought 35c-worth of fizzy water, I'll use that until I drop it under a bus by accident. Economies of scale there are: if you buy 500 (!) of their logo-encrusted fashion accessories aka "our New Bio-degradable sports bottles", Ecofil will throw in a "free" bottle-filler worth €2,000. In no realistic natural situation will polyethylene degrade within the life-time of the children for whom these bottles are purchased.

But that's a good thing! One way of solving the world's runaway carbon footprint is to make lots of things out of polyethylene [86% carbon by weight], use them as long as you can and then pop 'em into nice big anaerobic landfills. It will be like recreating the Carboniferous coal-measures all over again.

Thursday, 18 April 2019

Illusory transparency

Nobody thinks nepotism is a good idea - except the benefitting nephew. You hope and expect that the best qualified candidate gets the job; that only the competent students pass the exam; that the marks in some sense are a predictor of ability. In all the examiners meetings I have attended, the objective truth of the marks has been tempered by common sense (=prejudice and expectation). I can't remember a case when a student was done down unfairly rather than raised up without justification: but my neighbour John described one from Durham U thirty years ago.

In 1st and 2nd year college it doesn't matter what mark the student gets; so long as they achieve a certain minimal standard in the learning outcome department. Of course it can give some students a bit of a boost to morale if they do unexpectedly well, and that is no bad thing. At the end of their course in science, most students will carry out an independent research project. In The Institute, about 25% of the hours allocated to our final year students are devoted to project work and the marks are are equivalent; so the mark matters. A few years ago someone distributed a marking scheme with the implication that everyone would follow it to ensure equity, transparency and an audit trail in case of a dispute:
  • 50% Written report:
    • Presentation
    • Methods
    • Results
    • Understanding of topic
    • References
  • 30% Performance in Lab
    • Planning and organisation
    • Dedication and initiative
  • 10% Literature Review
  • 10% Public presentation
This damned form really didn't work for me. Like marking weekly lab reports our of 10, nobody is going to get 10/10 or 0/10 for understanding of topic, so the marks tend to normalise at about 65%. Then I found myself sub-consciously deciding on the final mark and massaging the incremental figures so they added up to The Sense of the Meeting. Nevertheless, each year I dutifully filled in a form for each student and sent it in to the Project Liaison Officer. A while ago, this feller, about my age, told me that he never bothered with the official form: "This chap is a solid II.2" he'd think and plunk 55% confidently in the mark book. Could do worse by the students. Each project is double marked but only the supervisor was present for 30% Performance in Lab, so that section is only marked once. If you care enough, you can probably bully the other marker to more of less match your assessment.

I'm reflecting on this [again] because I was asked to mark student presentations at this week's environmental science colloquium meeting using these criteria:
  • Slides 30%
  • Presentations 30%
  • Time keeping 10% deduct 2 marks for every 30 seconds over
  • Questions
  • Science 20%
  • Total 100%
I found my fellow session-marker at the previous coffee break and asked him if he was any sort of  obsessive about the goddamn form. Asked this passive aggressive leading-question way is quite "have you stopped beating your wife?" but the answer was No. In any case we only had one student who was eligible for a [monetary] prize, so after the session we put our heads together and agreed that the talk was pretty good for an early-stage scientist but not stellar. He gave 'them' [pronoun alert] 65% [solid II.1] and I had 'them' at 62%, so it looked less like a stitch up. We then herded unto a quiet room with the other judges where the data for all the talks for all the students had been gathered into a spread-sheet [displayed transparently on the white wall]. The out-going chair of the organising committee announced that Student Z [91%] had won the big prize. Another poor sap had scored 89.5 and got nothing in the Harry Potter Winner Takes All society we live in. The marks of two candidates for the prize for tree-hugging were tied at 87. The out-going chair and the in-coming chair announced that the prize was awarded to the bloke . . . "the fact that the other contender was a final year undergraduate was irrelevant" and the fact that she had XX chromosomes of course didn't enter into the equation. As it happened I'd attended the session where these two talks were given, and I agreed with that assessment - the bloke by a nose. But I would think that because I am The Patriarchy with an unconscious bias for XY up-and-comings. What aggravated me was the charade of making grown people filling in forms to an obsessive level of detail and then throwing them all in the bin when there was a difficult case.

With 20:20 l'esprit d'escalier I would have split the goddamned prize and given half to Mr Harry and half to Miss Potter  . . . partly because we can therefore ♬cue Katie Melua♬. Well, it's not my gig or my community and I won't be going to next year's meeting, so I don't really have locus standi on the high moral ground here.

Wednesday, 17 April 2019

Holistic accounting

For every Irish person living in this Our Bold Republic there are 1,999 other people on the planet - Inuits, Italians, Indians, Indonesians. That 1:2000 ratio makes the accounting fairly straightforward when trying to fairly divide up the pain we will all have to endure to reduce the global carbon footprint to sustainable levels. We don't need to take more than our fair share of hair-shirt. Well actually, compared to Inuits and Indonesians, we really should recognise that we've consumed far more than them and so could give up proportionately more - ice-cream, the second car, that trip to Majorca, that electric sandwich toaster, that U2 concert in 1997, all the €30 restaurant meals, deliveroo, the subsidised education, a two three flush toilet[s] - to stop the ice-caps melting.

I'm thinking thus because this week The Institute is hosting the national environmental science "colloquium" [as they rather pretentiously call their annual talk-fest and knees-up]. It's the welly-brigade's equivalent of the nerd-fest that I organised in 2014. The theme of this year's meeting was 'Climate Change' and many of the speakers tried to give their research presentations a CC gloss. This was a bit of an ask if the talk presented a count of aquatic invertebrates identified in the gut of another, more rapacious, aquatic invertebrate. But in other cases, the organisers had secured a talk from senior experts working directly on quantifying the amount of carbon produced by [species | countries | ecosystems] or developing policy on how to slow down our voracious consumption. One of the good aspects of a general eco-conference is that you get exposed to a wide variety of subjects and approaches. Some times those rather random juxtapositions can generate new-think on the basis that two half-ideas [even half-baked] is a whole idea.

For the last generation it has been a truism, accepted by the whole Irish agribusiness sector, that the very best that you can do for your cattle-farming bottom line is to plant a mono-culture of perennial ryegrass Lolium perenne, lurry of the nitrates, and feed the grass to the cows - direct or as hay / silage. More nitrate = more tonnes of dry-matter / hectare which means more muscle or more milk and therefore more money. Teagasc, the agri-advisory service, has graphs and analysis backing up these equations. One of the talks yesterday was from a young chap who seemed to be saying that planting a pasture with 6 carefully thought out species - notably including clover Trifolium repens to fix the nitrogen naturally [it falls from the sky stupid] - could have an equivalent productivity to Lolium only + double nitrates. That was rather iconoclastic but he had data. hmmmmm half-idea.

Both of the carbon drives climate change big-wigs independently waved their hands rather imperiously to say " . . . IF we ignore the agricultural contribution THEN carbon footprint is generated thus:
  • 48% heating poorly insulated homes and offices in poorly chosen [the whole temperate region north of 50° lat] locations.
  • 32% transport - driving between these two places 5 days a week and flying to more exotic locales every month
  • 20% energy to make the shite which we have been convinced that we need or desire
At the end of the second such talk I raised my hand and asked "That's all very well but, for me the udder in the room is the agri-contribution which you have waved aside (because methane doesn't last as long in the atmosphere as CO2) what about if we all stopped eating butter and burgers . . . starting with meat-free Monday?" [whc prev]. I did get a coherent answer to that question but it requires more numerical analysis than I can muster right now.

Twenty minutes later I was scarfing up the tea and iced-dainties which delegates think they deserve at conferences and said hello to another old bloke carefully filling his plate like he hadn't had any lunch. I more efficiently skipped the plate and was eating straight from the tray. Turned out that he works with the fellow whose one-dimensional view I had just publicly criticised, so I apologised for being a bit full of myown gas. He knew rather a lot about dairy-farming and subsidies and we agreed that there was more to agricultural grants than making more butter and cheese as cheaply as possible so it could be exported to England. As well as the butter, the grants allowed thousands of people to have fulfilling lives on family farms embedded in a unique and enduring community. Without the subsidies, the whole family would have to up-stakes and head for the city where they would finish up living in a shed in a favela on the outskirts of Dublin - there is insufficient housing stock to shelter the present population of the city without adding 130,000 families from Irish farms all of which depend upon Brussels to avoid going bust.

I asked him if he'd seen the poster presentation by the young-feller who had multi-species pastures. He had . . . and I was suddenly able to articulate the thought [primed by my earlier half idea] that feeding cows a variety of species might affect the microbiome of their rumens . . . quite apart from being a low-nitrate solution to increased biomass. What if a grass&forbs mix could be found that would make uncomfortable the methanogens down in the dark. Imagine a rumen that could still deliver energy from cellulose but without burping up a load of methane - which is >25% more potent a greenhouse gas than CO2 . . .  and that win-win could be achieved simply by modifying the diet. The microbiome is coming into focus, from obscurity, for a wide range of problems which cannot be solved with traditional medicine. This might be another example. We generate a fantastical amount of excess carbon in this country, we are obliged by treaty, by law and by common sense to reduce this adverse CO2ntribution to a sustainable future: we can't allow agriculture to be scored only by its potential to earn export income.

The wider issue is the danger and uselessness of reductionist thinking in science [recent-rant] . . . and in politics. We have a persistent and shameful trolley crisis in the Irish health system. Hundreds of sick people are parked on makeshift beds each day in corners and corridors of Irish hospitals. They are waiting for a bed in a ward. Upstairs the aged Mrs Doohickey, in for observation after her latest trip&fall, wants to go home, the ward-sister wants her bed but it's not going to happen because Mrs D can no longer look after herself at home - she needs a couple of hours help each day to get out of bed, and get breakfast. That help comes from the Dept Social Welfare whose minister has been unable to wrestle the money for sufficient home-help from the common purse . . . because the Minister of Health has corralled another €billion from the budget. IF MiniWelf and MiniHelf would talk to each other rather than fighting their respective corners at the cabinet table THEN Mrs.D. would be sleeping in her own bed tonight and one trolley would be empty in the trolley-shed.

Tuesday, 16 April 2019

Fruiting bodies are many

P, my New England correspondent and copy-supplier,  alerted me to the passing of John Tyler Bonner [a younger edition seen R] earlier this year: Bonner was still writing in 2013! I had assumed him long dead. And that assumption is reasonable given that he was born 12 May 1920. Bonner is science-famous for his work on slime-molds like Dictyostelium dicoideum which, when the good times roll, exist as single cell amoebae sliding around scarfing up bacteria for dinner. When the going gets tough, these individual life-forms gather together into a multicellular slug which makes its best progress to a hopefully more habitable clime.
If /when the migrating aggregate reaches the Promised Land, the previously identical-looking cells differentiate to fulfill several different tasks. Some of them form the foundation and some form the body of an fragile looking teetering stalk with a spherical bollupe atop [Bonner movie]. It is only the cells at the top of the tree that form reproductive spores which make up the entirety of the next generation of amoebae . . . sliding around scarfing up bacteria for dinner. And so life continues.

For Bonner this simplest, transitory, form of multicellularity was key to understanding how we [ants, birds, crabs, dogs, eels, flies, goats, humans] scrabbled ourselves together to have a larger, more cooperative existence. He spent many years doing careful observations to work out a) how the amoebae came together b) how they stuck together c) who would finish up at the top of the fruiting body. It found out that the coming together was driven by a chemical attractant which was given off by amoebae near the centre of the cathering slug and detected by passing amoebae. Because he was Harvard trained, he called the mystery molecule acrasin after Acrasia, a witch in Edmund Spenser's Fairie Queene who attracted men and turned them into beasts. The fact that slimes molds are members of the Acrasiales is only icing on the waggish clever cake.

Bonner is more widely know for a fat dozen of books making key concepts in evolution and development accessible to numbskulls like me. Not actually me, however, because I could not recall reading any of his books or indeed even knowing of Bonner's existence until after his death. I went as far as checking out his book Why Size Matters From Bacteria to Blue Whales from Wexford Library. It's a pretty good general introduction to the constraints and advantages of being a particular size. Bonner has summarized his musings into Five Rules of Size
  1. Strength varies with size
  2. Diffusion surfaces get more crinkly with size
    • Crypts and villi of your gut
    • inflorescence of your lungs
    • heat shedding elephant ears
  3. Cellular complexity, division of labour and specialisation increases with size
  4. Metabolic rate changes with size. Metabolic rate dictates
    • generation time
    • longevity
    • locomotor speed
  5. Abundance decreases with size: more Prochlorococcus than Porpoises
In one of his books, Bonner develops the idea that fish continue to grow in size after sexual maturity. As a keen fisherman, he recognises that this is A Good Thing - he can always hope to land a monster. On a cruise in the Hebrides, with a fellow scientist and angler, his boat pulls into a remote harbour where the fishing boats are watched over from the end of the quay by a statue of Christ. As they pause to wonder at this article of faith, a local man sidles up to them and says "We call it 'the one that got away'".

All mammals, for example have capillaries 10μm in diameter because they need to winkle between cells on average 10μm across. If they were wider they wouldn't fit, if they were narrower they couldn't allow red blood cells to squeeze through the gap to deliver their load of oxygen. And of course the proteins that carry the oxygen haemoglobins are the same size in mice and whales.  JBS Haldane wrote a famous essay called On Being the Right Size which skims over some of the detailed calculations which Bonner graphed in his book. Haldane's essay has the advantage of being shorter and available. Then again so is the PDF of Bonner's 2006 essay for Natural History Matters of Size from which I have snagged this neat [and not obvious to all thinking people except in hindsight?] graph of one length vs another length: