Watching paint dry

Last Friday I was doing a double-skype with Dau.I in Dublin and Dau.II in Cork. It was amazing, not from the content but the process because I can remember how inconvenient and expensive long-distance phone-calls were when I was student in Trinity College Dublin TCD in the 1970s. In 1974 I'd go out into the storm, with a fistful of coins, after 6pm when rates were cheaper, to find a traffic-quiet phone kiosk. I'd ask the operator to make a connexion to Fyfield 352 - no, not the Fyfield in Wiltshire; the one in Essex. It would take the operator some time to find a route zig-zagging across Wales and England until the phone rang in my parent's home. After a particularly efficient connexion the operator told me the coding that had been successful [Holyhead 54 - Chester 72 - Birmingham 458 - Bishop's Stortford 8] and recommended that I tell the next operator. To 1970s me, free video-conference calls would have been science fiction fitting Arthur C. Clark's Third Law "Any sufficiently advanced technology is indistinguishable from magic."

Dau.I was telling us about her adventures at the coal-face of culture in the Capital. She and a pal had tried to go to the Dead Zoo to pat the Quagga but it was closed, so they'd drifted into TCD to see the giant Irish deer in their Zoological Museum. That was about to close, so the pair went down to the Physics Department where Dau.I had attended an evening course in astronomy when she was a teenager. I got moderately excited and asked if she'd seen the TCD replication [replication very important in science!] of the World's longest running experiment. On the phonio I was out in my timing by about 80 years tsk! but I was right in the principle that bitumen/pitch is a liquid with a boggling-high coefficient of viscosity.  In 2014, the TCD pitch-drop experiment yielded an observed data-point because the web-cam had been invented since the experiment started in 1944.

In that video capture, the Irish had stolen a march on the really longest running experiment - a pitch-drop device started in 1927 in U Queensland [Look L for suspense!]. By a wonderful coincidence, the morning after I had told The Girls about a local pitch drop experiment, the Australian venture hit Metafilter. It is news-worthy because the Ozzies are gearing up for the delivery of the ninth drop after 86 years of run-time. Ten years between events sounds long but 'tis nothing compared to Transits of Venus.The pitch was heated and poured in 1927 but allowed 3 years to cool and settle - "running" started in 1930. You can register and sign in here. If you are logged in when the bedside alarm-clock registers the tremor of a falling drop, then you'll be inducted into the Dweeb Hall of Fame or made a co-author on the Nature paper or both.  This webcam image capture is as old as the WWW. A Cona coffee pot was fitted up with a web-cam in the Trojan Room in Cambridge U in the early 1990s so that the boffins would never make a fruitless trip down the corridor for caffeine. It went on the Web on 22 Nov 1993. I can remember checking up on the coffee-pot from Dublin in 1994 when I was setting up one of the earliest Irish web-servers. It was a metaphor for the absurdity and futility of much of the content on the later WWW including the trivia of twitter. You can forment a riot and topple an oppressive regime by effectively mobilising twitter, sure. But you can also flood the servers with pictures of your breakfast toast. Reminder before you post: 10% of the World's electricity is consumed by servers . . . a single picture of the toast will serve - a video of the butter melting is maybe OTT, hmmm?

Viscosity effects? Try something intermediate between pitch and ethanol. Destin Sandlin at Smarter Every Day looks at the patterns made by falling honey and looks at the equations of fluid dynamics - <whoop whoop algebra alert> but also explains that there are areas of the problem which are currently beyond the reach of science. Nobody knows why the the falling honey flips from coils to chaos but you can easily observe when it happens with a shampoo bottle in the show. Neat! Here Destin launches his SED channel with a noisier explanation of the difference between detonation and deflagration than my wordier and more killing essay of 4 years ago

Young Mason younger Dixon

Did you ever wonder what happened to Mason and Dixon [Line] before they became famous?  It's a bit like Oscar Levant's quip "I'm so old I knew Doris Day before she was a virgin". [that's a misquote].

I'm reading Andrea Wulf's 2012 book Chasing Venus The Race to Measure the Heavens which cashed in on the most recent transit of Venus 5/6 June 2012. I picked if up remaindered for €2.50 in June 2017 and almost didn't. There are so many books which set out to explain something at the interface between science and history and they are not all of equal quality. If it's remaindered it's probably for good reason, I reasoned. I was wrong, I got stuck in and read the first 100 pages without coming up for air, It was favorably reviewed in The Guardian by Nicholas Lezard who expresses his ennui - yawn! - about transits of Venus when our generation had the chance to see two. Because he wasn't properly primed about how exciting the transits of 1761 and 1769 had been and how they had given science and the public understanding of science a huge boost. And it turns out that I secured a copy of one of the few 5 year old books that is not available on Amazon for £0.01.

Johannes "Ellipse Orbit" Kepler had calculated the orbit of Venus from numerous observations of its position against the fixed stars at specific points of Earth-time. For those of us who are not astronomers with 20/20 hindsight, it seems a colossal feat of the imagination and trigonometry to be able to do this. In 1627, Kepler predicted that Venus would traverse the face of the Sun in 1631 and have a near-miss in 1639. He died in 1630 without being able to verify his prediction. Two British observers Jeremiah Horrocks in Preston and William Crabtree in Manchester were able to refine Kepler's calculations to be convinced that there would be another transit in 1639. Lucky with the weather, they were, on 4th December 1639, able to project the image of the planet against the Sun's disc through a telescope and onto a sheet of paper. Winter in N England has a very short day, the weather is usually crappy and it was only possible for Horrocks to make an estimate of a) the relative size of Venus and the Sun and a guesstimate of how long the transit was. His calculations of the Earth-Sun distance were out by about 50% which is pretty good given the constraints and lack of any precedent.

Those 18thC transits of Venus in 1761 & 1769 became a huge raree show because careful observation and quite complex calculations based on the timing of the transit in multiple locations allows competent people to work out exactly how far we are from the Sun. Competent people who were also ambitious, adventurous and well-connected could hope to make their names and a small fortune from being at the right, distant, place at the right time. The transit [R composite image from the 2012 event] takes about six hours and it is a bit of an ask to have cloud-free observation conditions for such a long period.

In 1716 Edmond "Comet" Halley wrote a paper predicting the 1761 and 1769 transits were a) going to happen and b) would be really useful for measuring the scale of the solar system. That's rather a long lag time between this call to arms and the events at point and indeed Halley died 20 years before  the first one. The measurements are only really useful if they are carried out from widely separate parts of the world and getting 'foreign' was a mighty logistical problem in the days before steam-ships let alone bookings with Air France. The astronomical collective came within an ace of literally and figuratively missing the boat and it fell to Joseph-Nicolas DeLisle to serve as the catalyst to get some Effectives in place.  The British Royal Society and the French Académie des sciences led the charge and were, remarkably, in contact despite the fact that their political masters were 1756-1763 engaged in the Seven Years War = Guerre de Sept Ans = [in USA] the French & Indian War which could qualify as the First World War. Thus in addition to the hazards of weather in the day, the risks of storms on the way there was the possibility of being killed or captured in a naval action.

Charles Mason, aged 31 in 1761, was the assistant to the Astronomer Royal in Greenwich. He was contracted for £200 to sail Sumatra to make southern observations of the 1761 transit. This was abut 4x his meagre salary for being the gopher at Greenwich.  He took with him an even younger surveyor and amateur astronomer called Jeremiah Dixon who was a neighbour of a Fellow of the Royal Society. Dixon also accepted £200 to sail to the far side of the world for an ephemeral chance at making astronomical history. It was as important to know where your were making the observations from as it was to measure the length of time of the transit; so they made a good team. But 4 days after leaving Plymouth their ship was attacked by a larger French frigate and badly mauled. Putting back to Plymouth for major repairs Mason and Dixon seem to have temporarily lost the bottle for adventure and sent a series of truculent letters to their employers at the Royal Society refusing to go to Sumatra. Eventually they were shown their contract and told that they didn't have any choice in the matter. And there was no time to lose; indeed they were now too late to make Sumatra in time for the 6 hour window of opportunity. Accordingly they broke their contract again by electing to stop-off in Cape Town to  make observations from there - despite the fact that the first part of the transit would, from South Africa be invisible because the Sun would not have risen. Fortune favored the bold (and stroppy) and Mason and Dixon obtained the best set of data from the Southern hemisphere! Their success outshone their previous tantrums and they won a surveying contract in 1763 which makes their names far more recognisable today than any of the other astronomers involved in the events of 1761. That contract was to survey and mark the boundary between Pennsylvania and Maryland which is now immortalised as the Mason-Dixon Line - sing Dixie!

Here Andrea Wulf and CBS sets out the transit stall.  Here's the maths for how timing the transit allows an estimate of 1AU the distance from Earth to Sun. Matt Parker explains (with ExCel!) why the transits come in pairs separated by 8 years every 100+ years.

Amblyomma unamericanus

I pulled a tick off The Beloved's back last week when she came home from gardening in the long grass. It was almost certainly an example of Ixodes ricinus the European sheep tick because that is the commonest long-grass sit-and-wait predatory tick in Ireland.  I've written about these annoying arachnids before: counting their legs, enumerating the diseases which ticks carry, advising on the best way to remove t'buggers. And I've elaborated on the spread of Lyme disease across Europe as the ranges of Borrelia burgdorferi, Ixodes ricinus and Homo sapiens overlap: for Lyme disease it takes all three to tango.

But wait, isn't Lyme disease named for a town in Connecticut? I know there are humans in that state, but isn't I. ricinus a European tick? Yes, but the role of the third horse in the deadly troika is taken up in North America by Ixodes scapularis or in the West by Ixodes pacificus. You can see from the map that Lyme disease is confined to E, SE and S Central states . . . and to Wisconsin and parts of Minnesota and the Upper peninsula of Michigan. I'll guess that this North-Central island of infectivity has been created by importing dairy cows to the cheese states.  You'll notice that the map includes a third species called Amblyomma americanus the lone star tick which has been in the news stateside these last tuthree years because it appears to be the cause of a new and distinctly unamerican medical condition called mammalian meat allergy MMA.  Midwesterners should also note that the overlap-map is a couple of years out of date and now A. americanus may be found in Ohio, Indiana, Illinois and Iowa which used to comprise the blue tick-free band just S of the great lakes. What caused the break-out? Nobody knows but the obvious money is on climate change despite the fact that this phenomenon is also highly unamerican.

MMA, which puts even red-blooded Americans off their hamburgers and steaks, appears to be due to the immune system over-extending its brief from killing pathogens to attacking food. The key molecular player is the disaccharide galactose-alpha-1,3-galactose hereinafter and everywhere known as alpha-gal. This is a common component of the cell membranes of most mammals, except peculiarly primates, so could well be recognised as non-self by an over-active immune system. They haven't yet tracked down why A. americanus triggers the cross-reaction. Suggestions include remains of a previous mammalian blood meal about the mouth-parts; something in the tick saliva that looks like alpha-gal; some as yet unknown microbe carried by the tick.  Whatever the mechanism, the association between MMA and a tick bite from A. americanus is epidemiologically quite clear. And from years of experience with fighting Lyme Disease and Rocky Mountain Spotted Fever it is also clear how you can avoid the zoonoses: sit on the couch eating potato chips and watching other folks exercise on the TV is one strategy; wearing long pants and giving yourself a check-over when you come home, is another. Come to think about it checking each other all over for ticks after every time you go outdoors could be a way to cement a partnership in an I'll show you mine, if you show me yours sort of way.

My new interest in ticks was triggered by an article in Wired on MMA and alpha-gal which also brings in the connection between tick-bite and the blurf of side-effects from the anti-cancer medication cetuximab (which must be a chimeric monoclonal antibody). Finding these connexions requires alertness and a wide-ranging curiosity and deserve a hats-off from the rest of us.

You might also reflect here on the fuzzy boundaries of immunological self vs non-self. Clearly food isn't normally treated as non-self, so the study of MMA may give us clues about the discriminatory powers of the immune system. The cross-over between allergens should remind you of Campylobacter chickennuggeti triggering Guillain-Barré syndrome.

Olde folk fair deal news

Preamble [skip if tl;dr]
I've had occasion to question the relentless spread of three-letter acronyms TLAs in biochemistry and astrophysics. There probably aren't enough TLAs ( 26 * 26 * 26 = ~17500) to go round especially if you have no expectations for the utility of ZXZ and QFQ. ZQZ is of course <slaps forehead> the IATA code for Zhangjiakou Ningyuan Airport. Haven't heard of Zhangjiakou? For shame! it is home to more people than the Republic of Ireland. I've been caught out <duh!> woeful ignorant about the basic political geography of China before. Anyway, when we run out of TLAs we can gear up to the half million FLIGs - four letter initial groups. No fun unless these acronyms are self-referential. I mention this because a couple of new health related FLIGs have been in the news this week - HIQA and NTPF. Not really news I guess because I've slagged the Health Information and Quality Authority (HIQA) (Irish: An t-Údarás um Fhaisnéis agus Cáilíocht Sláinte would that be UFACS?) in the past for taking a year to report on the cause of a single iatrogenic death. I compared that with the Penney Report which laid out the causes of the 1957 Windscale nuclear meltdown on the Prime Minister's desk 16 days after the adverse event. The other FLIG is NTPF National Treatment Purchase Fund.

Meat
There is a new report from Age Action, the charity and advocacy group for older people, about the 'extras' which are added to the bill in nursing homes across the country.  My view of the nursing home business tends towards that of predatory publishers in science. How difficult can it be, an entrepreneur will say - you charge each occupied bed in excess of €1000/week;  pay the cleaners, orderlies, receptionists and cooks at the minimum wage = €350/week and the degree-qualified staff a little more. On dit que you need 2.4 carers per caree which suggests a 'profit' of €160 per person per week = €8,000/yr . . . say 50 beds = €400,000 gross.  If you're running the thing as a business, then you'll have an accountant looking for ways to pare down the overheads in any way that doesn't involve sacking the accountant.  €1,000/wk is for bed, board and laundry. Possibly a lot of laundry because the old tend to be a bit leaky. That is rather to the point because apparently some elders are being charged extra for incontinence pads whereas you might expect that to go with the territory.

A few years ago, the Government implemented a Fair Deal scheme which was a first attempt at getting a balance between the state being responsible for the care of the elderly and infirm and people being responsible for themselves and their aged parents. The realpolitik of it says that The State has a vested interest in having people die shortly after their 65th birthday while the family may well see further utility in the retired. We're off to England later this month to have a week's qual-time with the grandchildren, for example.  The Fair Deal scheme says that, if you have assets, you are expected to contribute 80% of your income and 7.5% of your assets each year towards the cost of your nursing home. If your assets are property you can take out a Nursing Home Loan and pay the 7.5% after your death. The scheme is obviously not for the super-rich who can afford to pay whatever private nursing homes charge. The compassionate purpose of FD is that an old citizen in need of care should not have their choice curtailled because they are poor - we don't want the bring back the Workhouse.

The extras more generally include such things as social events, newspapers, GP visits, chiropody and can run to €100/wk - even when you don't avail of them. As a commentator on the wireless pointed out there is a difference between choosing not to go to Friday bingo because you're feeling crook or you're quarrelling with That Sadie Murphy and not going because you're blind. The problem is that Fair Deal is a contract with the government for a minimum service and that (ignore my simplistic accounting above) is a tad above break-even; the extras are what allows the proprietor to send his kids to fee-paying schools. The logistics require that some bundling of the costs is allowed otherwise you'll have people claiming they only ate half their peas and asking for a discount. It's probably kinder and more inclusive if you don't have any extras at all. By legislation or compassion we need to decide what needs to be provided to achieve a certain minimum QALY <woot another FLIG!> [prev] for everyone involved. That must be more than bed, food and laundry or we'll have a shameful Romanian orphanage scenario. CareChoice in Dungarvan Co Waterford has drinks and pig's feet every Friday afternoon: which is clearly good for morale. They found in the Relief of Belsen that lipstick and respect were better than food for survivorship. The thing about a nursing home is that it is Home but one from which you often cannot escape. In a just society everyone should expect to be cared for with respect, compassion and competence in their declining years but they shouldn't also expect to be able to leave a farm of land to their children.

And we'll leave aside the disconnect between it being unethical to allow your dog or sheep to 'suffer' and unethical also to off your aged and respected grandfather under any circumstances. I could also make an argument that inheritance perpetuates, even exaggerates, inequality of opportunity and what's left when you die should be shared more widely than your immediate descendants.  You have, after all, been supported in your declining years by your postman, your neighbours, the corner-shop and the HSE.  Few people leave a bequest to Pat the Post.

• Glorious - chap tribs and edutains [her eyes on stalks!] his granny on her 100th bday. A beguiling mix of quiet and personal and gross participatory consumerism. Heck-n-jimminy if you can't get a tat or a strippogram at 100, when can you?

Reading forwards

I wrote recently about publishing the results of my PhD thesis research. That paper in the Journal of Biogeography was a second attempt to get my stuff into print: an earlier draft had been rejected by a slightly more prestigious and definitely more main-stream population genetics journal. Many previous papers had been published showing that gene frequencies of domestic cats differed among different populations, but my paper was the second that was a sort of meta-analysis comparing the results from several different earlier studies. It was rejected for two reasons 1) serious population genetics research was then carried out on Drosophila fruit-flies and mice not on domestic cats 2) A key part of my analysis used a 1973 paper by Lewontin and Krakauer to show that one could detect natural selection in the populations. I was happy to cite that paper because Richard Lewontin [bloboprev] was a giant of population genetics and the L&K analysis was so clearly expressed and convincingly argued. Their contention was that if you have a bunch of populations cross-tabulated against a bunch of genetic traits you can carry out an analysis of variance. If one of the traits has more variance than the others, a likely explanation is that differential selection is driving the gene frequencies for that trait apart. It was neat, I had the data, I was computer literate so could apply the LK test and so I did.

In his interview Eugene Garfield developed the idea of citation consciousness. It is the requirement that, if you are going to cite an earlier paper, you have to ensure that it is still valid: by using Garfield's citation tools to work forward from that key paper to see who else has cited it and to what effect. I, publishing my thesis in 1983, had conspicuously failed to carry out this necessary validation task. It turned out that in the months after Lewontin and Krakauer published, there was a shit-storm of criticism from Masatoshi Nei, Alan Robertson [BIG cheeses in the field] and other savvy population geneticists who haven't made it into Wikipedia yet. Nei & Co rubbished the L&K paper, exposing its false assumptions, tendentious findings and specious reasoning. I was totally unaware of this slag-fest because I was living in a bubble. The referees for the journal where I submitted my first attempt were up to speed with the literature of theoretical population genetics 1973-1983, saw that I wasn't and that cast a wider doubt upon my competence: consequence? reject!

Later on, I moved away from bigger-than-a-breadbox population genetics and into biological sequence analysis, that was a more recent field and there were no 10 year-old papers for me not to know about. Apart from that my boss was ambitious, and really on the button and wasn't going to allow me to be vague about the literature or anything else.

It was embarrassing to be caught with my trousers round my ankles and I think I blamed my thesis committee for not putting me right when I came to defend my thesis. That was quite unfairly shifting the burden of responsibility: when you get a PhD you are - finally - an adult. You can't blame Mammy anymore for deficiencies in your scientific practice. I could have decided then that I was unable to carry out the basic tasks of science and gone off to be a carpenter. I'm glad I didn't, and I think I've been a net contributor to the task of making sense of the World.

The Talent

There is a great moment in Shakespeare in Love [watch! that's an order] where Art triumphs over Cash.
Hugh Fennyman: Now listen to me, you dregs, actors are ten a penny and I, Hugh Fennyman, hold your nuts in my hand.
>!RUMPUS!<
Hugh Fennyman: Uh, one moment, sir.
Ned Alleyn: Who are you? 
Hugh Fennyman: I'm, uh... I'm the money.
Ned Alleyn: Then you may remain so long as you remain silent.
It should be made compulsory watching buy [sic] all who affect to support the Arts. All those who have a comfortable desk in the Arts Council or make decisions on behalf of some millionaire bond-trader who is 'giving back'. The metaphor "actors are ten a penny" sums this attitude up just perfick. Because it's just not true. True talent is fabulously, worryingly, rare. And far too often it dies, like Keats, in a garret. Well, erm, actually, of course, it was the TB that did for Keats. Having talent is not always consonant with having infinite bottle and you can hardly blame youngsters if they give up, or back-burner, their Essential Self to get a job that pays some money - because eating can be fun too.

Yesterday was Small Press Day 2017 in Forbidden Planet in Dublin. I am amazed and delighted that two dozen 'creators' turned up to showcase their work - there is hope for the world if that many examples of The Talent are walking the streets of Ireland today . . . and some of them may even have warm homes and dry beds in which to sleep tonight. I only know about the event because I've known one of the participants, Clare Foley, since before she could tie her own shoe-laces, and Dau.I and Dau.II told me that their BFF was launching her latest oeuvre Frozen Waste [L] [reviewed] yesterday. This recent interview gives some insight into the process of creativity and inspiration. I got hold of a copy of her illustrated version of Honoré de Balzac's La Grande Bretêche which Foley had released plate by hard-won plate on Tumblr before getting a very short run printed. Whatever it was that inspired a young woman to spend months drawing and lettering panels to represent a minority interest short story from a different country, it was not to make a million bucks. That seems to be the empty and unsatisfying 'ambition' of too many unhappy people in these benighted times. I won't make a million bucks either by selling my 1st Edition when Foley goes all Harry Potter on us . . . I'll only make £40,000 for making that modest contribution to the support of a young artist at the beginning of her career. As I said at the top of this piece it's not about the money.  It is, as Neil Gaiman says, about Make Good Art.  Any art! I've tribbed W¡ld a bunch of young-and-amazing, and like Foley home-educated, musicians before.

And I've written before about paying every adult a Basic Income so that each one can get on with making something of themselves rather sacrificing their talent on the altars of Mammon.

Fishy tales 090717

I have done a bit of fishing although rarely as an adult. I lack the patience to sit on the bank of a river waiting for the bob to bob and get sea-sick in small boats unless it is flat calm. My father knew how to fish with flies and tried to teach us to cast flies across the lawn into a washing-up bowl full of water. That was never going to induce a passion for fly-fishing! I've cited Robert Redford's lovely fishing film A River Runs Through It. But I'll share some short fishy films for those who, like me, have the attention span of a gnat.

• A family legend vindicated through research: Mrs Salmon, the director's granny, was invited to the opening of a Welsh oceanarium because of her name and met lots of people called Haddock, Codde, [prevs] Crabbe, Herring [prev], Jelly. Just lovely.
• Tarpon season
• Herring fishery Dunmore East [prev]
• Sing it! Shoals of herring
• Fly fishing is a joke: because it makes you smile but it's hard to analyse why.
• Along the Way: Boys bonding up and down Canadian Rivers
• Seven with one blow - mackerel fishing off Donegal rocks
• Fishing Miami storm-drains for peacock bass Cichla spp. and large mouth bass Micropterus salmoides - move over crocodiles in NYC sewers.
• Cambodia: traditional hole-trapping for misc fish
• Hundreds of tuna getting poled aboard  - Greenpeace approved!
• becomes sashimi
• I know (I'm a biologist!) that sperm whales Physeter macrocephalus are not fish but they will fizz up as they ferment
• It's not just men
• 7 year old bears fishing salmon
• 7 year old girls fishing trout
• Grown-up woman ditto
• Silver Carp Hypophthalmichthys molitrix is a worrying US invasive species of Asian Carp. 
• Rednecks take 'em out with a variety of primitive weapons.
• The fish fight back >!whup whup!< Tnx Russ!
• Going all technical:
• Using a cannon to launch your bait to sea
• Or, of course, you can deliver a small load seaward by drone
• Magnet-fishing is a thing. These amateur videos are usually far too long and the sound quality is crap but I find them a bit addictive.