You are wot you eat

Back at the turn of the 21stC I found myself polishing the cutting edge of science. For a chunk of the 1990s I had the office next door to Ken Wolfe, now FRS, who is almost always the smartest bloke in the room; certainly when I am the only other person there. His contributions to science are many [pubcrawler] and varied [human genome and a Nature paper] and go back to his first Nature paper which predated his PhD. In 2000 Science Foundation Ireland SFI was set up with a brief (and a ton of money) to kick-start Irish scientific research. They solicited applications for grants of several millions of IR£s [soon to become €1.27] in biotech and infotech. Ken secured one of five SFI biotech grants to investigate the human and other genomes which were coming on stream. For reasons that I still find hard to fathom I was given a seat in the new lab along with some super-smart young researchers about half Irish and half foreign. I think I was a net contributor but I had an uneasy sense of Imposter Syndrome [it's not only women] for the 3 years I worked there.

Just as I was preparing to leave (retiring again!) Nora Khaldi a new PhD candidate arrived from Provence. She was young and fit and an asset to the nation of geeks with whom she was going to work. The Celtic Tiger was only starting to growl and the SFI salaries were generous [had to be to attract brilliant minds to an intellectual backwater on the edge of Europe]. Someone decided that all work (and we all worked really hard) and no play made dullards of genius and instituted a series of cultural events for the lab. We were each requested-and-required to book something and everyone else agreed to row in with the suggestion. I brought everyone off the see [subtitles! love 'em] a Belgian film Le Roi Danse about Louis XIV and his favorite composer Jean-Baptiste de Lully. I may also claim credit for suggesting The Burial at Thebes Seamus Heaney's brilliant version of Antigone at the Abbey Theatre. I admit that sounds consciously and pretentiously highbrow but The Lads loyally came out for those events. Nora au contraire decided that the best fun was to pile everyone into a Zodiac inflatable boat and roar off at 30 knots in a tooth-crunching cruise to nowhere round Dublin Bay. I for one left a puddle behind on my thwart which wasn't only from the spray. During her PhD Nora knocked off a bunch of seminal papers about genomic evolution in filamentous fungi which have garnered about 1,000 citations which is definitely above average.

After TCD, Nora went to America - everyone who wants credibility in science has to Go America for a spell - and worked at NCSU on mycotoxins. She developed a pipeline SMURF to analyse fungal genomes for their capabilities in producing secondary metabolites. Secondary metabolites are the bits and piece of biochemistry that don't have direct use in energy metabolism and reproduction.  They are often useful in minimising competition and/or deterring predation. Fungal secondary metabolites have, for example, given us the majority of the current available battery of of antibiotics. In due course, Nora returned to The Other University UCD and in short order dreamed up a company Nuritas which mobilised her computational biology skills and her appreciation that genomes produce a rich array of proteins and peptides whose function is not always obvious.

If oral antibiotics can survive the maelstrom of acid destruction that is the human stomach and go onwards, downwards and then around-and-aroundwards to cure a Staph infection in a child's ear, then what about other microbial products? As CSO [Chief Scientic Officer] Nora [L.L] is talking up the benefits of the Nuritas pipeline of discovering new bio-active peptides. Although she is the founder and the brains behind it, they have hired a Chairman from MegaCorp Novartis to steer the good ship Nuritas through the choppy waters of an unforgiving financial world [I bitterly use a nautical metaphor because of the Zodiac ordeal to which I subjected in 2004]. The nascent company had already appointed a CEO [L.R] from MegaCorp Pfizer in 2015 That's a common strategy in tech startups: you may be a mathematical genius and a dab hand at Python but chances are you will do something dopey like forget to add employer's PRSI contribution when you estimate the burn-rate of your wage-bill.  You start to talk about burn-rate when you secure your first €3.2m tranche of Venture Capital.

Nuritas has pipelines in anti-inflammatories [diabetes, heart-disease] and anti-microbials [pathogens] which will finish up as targetted additives in your breakfast smoothie. Here she is again, a) talking up the company but b) for the last tuthree minutes talking up solidarity among women in tech. As a metaphor she points out the women are expected to wear different shoes for every meeting where her male CEO just wears shoes. Going foodiceutical is a canny choice; the development pipeline for novel food products is much shorter, cheaper and less challenged by required FDA trials than the development of new drugs. And the market is calling for novel ways to make people well or better still prevent them from getting sick in the first place. In January this year, Nora Khaldi won  the Woman of the Decade in Business and Leadership award. You need bottle to persevere against a tide of know-it-all nay-sayers. “I was told this was impossible and I decided not to listen" attagurl Nora!  Feckin' Bri'nt!  You can talk like that with Nora because she now talks just like a Dub. You'd think she's been raised entirely on bacon-and-cabbage rather than Salade niçoise and bouillabaisse. There we go again: another bloke laying his truc on an entrepreneur and visionary just because she's a woman. But I'd do exactly the same to my pal Cedric Notredame, another escapee from Le Midi, if he was able to speak Dublinese half as well. He can't: all he can do is imitate a genuine Dub [Des Higgins] imitating a Frenchman [Cedric]: very funny but you have to be there. Because I only have two pair of shoes [one for work and one for funerals], I don't have a leg to stand on in footwear politics.

But enough of blokes, in science or otherwise:

here's a lot more Women in Science

There and back again

The Hobbit or there and back again is the title of a road trip by the eponymous hobbit and a LOT of dwarfs called Boing, Going and Doing, Bash and Clash, Winky, Tinky, Ditsy, Lala and Poo . . . I forget the details. I seem to remember they came back with a lot of treasure; maybe they found a lotto ticket along the way? Yesterday The Beloved and I went on a similar epic journey to the top of Solsbury Hill with a team of short people; Gdau.I aka Hawkeye; Gdau.I's pal Daisy aka Dog-girl; Gdau.II aka The Ballast; The Blob aka Pathfinder Worm-eater; the Beloved aka Freeman Jim.  I'm not sure how I got demoted from the wily and dependable navigator to some sort of mole. The main thing I got from the journey was a sheep tick Ixodes ricinus [prev] which Hawkeye was canny enough to spot before it got embedded in my arm and thus could be easily pinched off.

Solsbury Hill is 600m due North and about 140m higher than where the Gdaus live, so we thought we were quite heroic to make it to the top with an enormous hamper of food, drinks, parasols and picnic rugs. Our sense of epic achievement deflated pffffffff quite a bit when a dozen preschoolers topped the summit with their trainers / minders / teachers. Turned out that the parasol - which I had thought was a wildly extravagant, and not very Scott-of-the-Antarctic, indulgence - was a handy melanoma-preventer because when we emerged from the scrubby trees the Sun was broiling. Almost exactly 40 years ago Peter Gabriel had a life-changing experience while climbing Solsbury Hill and wrote a song about it. He heard an eagle; we just heard a very angry sparrowhawk Accipiter nisus casting up and down the hedgerow as we walked down towards civilisation. Well I (crap at ornithology) thought it was a sparrowhawk. Gdau.I (beginner ornithologist) stoutly maintains it was golden, and so more likely a kestrel Falco tinnunculus.

The previous day, Gdau.I and I had gone for another walk to her school through the fields [ref: To School Through the Fields: An Irish Country Childhood by Alice Taylor is available for 0.01c]. England is covered in a network of Public Footpaths access to which is zealously defended by ramblers and dog-walkers. These folks maintain that, since time immemorial, the plain people of England have had The Right to walk across other people's land to get to church or to work or to take the dog, or the grand-daughter,  for a walk.  And a very edible walk we had too. Along a mere 1500 m [and back again] through woods and along field edges we found: early black-berries Rubus spp.; fat filberts / cobs / hazel-nuts Corylus avellana not yet ripe; small juicy yellow plums Prunus domestica; several varieties of apple Malum pumila and blackthorn Prunus spinosa bushes covered in sloes. Of course, the sloes aren't going to be ready to eat [or more likely add to a bottle of cheap gin] until they have been bletted by the first frost. Throw in some young dandelion Taraxacum leaves and unopened leaf buds from hawthorn Crategus monogyna and you can breakfast heartily, including greens, on the way to school. Children are no longer generally allowed to walk to school by themselves anymore in case they get scooped up and eaten by a marauding band of orcs. Which is a shame really. And it doesn't have to be like that - even in cities.

Pixellation

We're hanging out in Bath formerly Aquae Sulis. You want to be careful of getting run-over by culture in Olde Worlde towns like Bath - or struck by the selfie-sticks of a bus-load of Japanese tourists following the guide with the red-and-white umbrella aloft. The waters are something else in the line of sulphur and give pause to ever complaining about residual chlorine in the tap water: try a glass if you're in town; it's a unique experience. We walked into town between heavy rain-showers on Saturday morning to catch some museums with the Gdaus. The Victoria Art Gallery VAG is one of the nicest and least pretentious late 19thC civic museums in the whole world. Minor art works, by artists of whom you've heard, cover the walls and the oak floor-boards creak as you walk reverentially through the galleries. I have a good friend who raised two children in the Museum of Fine Arts MFA in Boston when there was no entry fee and you could take the kids in for 20 minutes or whatever period for which they had patience. The VAG is like that for Gdau.I: increasingly familiar and friendly and a quiet haven from the beeps and crashes of devices.

We caught the first few hours of a Summer show called Here Be Dragons which is a gallery full of original artwork dragons from kid's cartoon books. That's nice, especially if you are up-to-date with the latest dragons which are trending in children's literature. I may be over-empathising with my 6-year-old self but I can't imagine many children having the patience to look at loads of pictures of dragons without looking for a bench on which to sack-out-exhausted. I reckon you-the-adult have to give the weans some structure. Me, I'd concentrate on the evolution of dragons, some of which are far more credible than others. All the descriptions suggest that they are some sort of reptile and all land-dwelling vertebrates are tetrapods. Even if, as adults they have lost some of those four limbs. Thus for me dragons with four legs AND a pair of wings are a) unlikely and b) almost certainly descended from a common ancestor. If you were hot-housing your kid to be Director of The Museum of Comparative Zoology in Harvard, you could help them design a check-list of attributes and use these data to construct a phylogenetic tree of relationships among Gruffalo, Smaug, and Haku.

Another brilliant idea was to mobilise a day's worth of kids and their Dads in the Lego Dragon community art-push. Anyone younger than me is familiar with Lego: I was part of the first generation of Lego-builders when the little plastic bricks came to  the UK in 1960ish. There were red bricks and white bricks. The Lego Dragon project was create a paint-by-numbers, highly pixellated, picture of a dragon out of buckets of 1x1 lego bricks in 32 different colours. The whole picture was broken up into 16x16 blocks which were distributed to punters along with a map of that section specifying which colour went where. Your task should you choose to accept it was to fill a base-tile with the coloured bricks according to this recipe and turn that in to Dragon Central.  Each completed tile was then stuck in the appropriate on the wall. There wasn't room for a third pair of hands tricking about with minute Lego-bricks so I set myself the task of of picking up, colour-sorting and returning to base bricks from the floor and abandonned on tables round the room.

 

The Boy and Gdau.I went at a rather boring (mostly black and dark blue) infrastructural square [L indicated by maker]. At least she stuck to her last like a good cobbler. The room was mostly populated with isolated fathers doggedly finishing up while their sons ran noisily around the room like . . . well, boys. The whole picture consisted of 16 x 12 of the 16x16 blocks or 256 x 196 = 50,000 pixels, You just need a couple of hundred people to contribute 25 minutes of their time et voila dragon!
Well it turns out that making Lego-mosaic pictures is A Thing.  Like all Lego stuff it is expensive.

Verdict: good idea, please copy for 

other art-work; not necessarily dragons.

Snow White inside

I'd like to think that one of the running themes in The Blob is that there is no such thing as little utility in black and white thinking. Der Reichskanzler was kind to children; there is some value to a belief in god; not everything the other side says is utter nonsense. On Sean Moncrieff's Newstalk FM radio program, he noted that the twitter-storm went on for 36 hours after they had a piece on the unborn (both sides going at it hammer and tongs) while a feature on homelessness among Irish 'born children' elicited only 5 comments.  But those issues are metaphorical black and white, although quite edgy. When it comes to actual black and white animals, the firm ground on allocation and definition is hard to find.

An old logic puzzle hinges on the fact that all swans are large white long-necked ducks [family Anatidae] which allows us to assert that any a) large b) white c) long-necked d) duck is a swan and failure at any of the enumerated criteria makes the thing you're considering a non-swan . . . until you go to Australia and encounter Cygnus atratus [R]. Naseem Taleb wrote The Black Swan as an investigation of certainty and our failure to correctly process information from outlier events - "unknown unknowns" like 9/11 and the inexplicable Harry Potterism of Google - to help us deal with the future. Taleb's book has plums in it but there is also a lot of duff to chew through [critical Guardian Review] and Taleb himself can sound simultaneously know-it-all and woolly, which doesn't help illuminate the plums. Black and White animals? Should make Blobbistas think pandas [no not those pandas] or rhinos or ice-floes and polar bears.

Bears, you say? Well I was reading about the unfortunate irony that the bear on the California State Flag [L] is extinct; less than 75 years after the Gold rush of 1848, the last grizzly bear Ursus arctos californicus in California was shot and killed in Tulare County in 1922.  Note that the California Grizzly is a subspecies of the Brown Bear Ursus arctos which, as a species,

 is a long way from being extinct but the key conservation-biology question remains: whom should we save if we are to retain the greatest possible genetic and ecological variation. Because variation is the stuff of evolution and we know not when a Black Swan event will put the survival of the species at risk. But when that event occurs, genetic variability is the best hedge against an uncertain future. We now have molecular tools to gather the genetic data to help conservationists make these hard decisions - El Blobbo has covered such studies for: fairy penguins - rhinos - giraffes - elephants - wildebeest - Tasmanian devils - whales.

We need that molecular data because brown bears are bigger than a bread-box and quite variable as to size and colour and so there has been a tendency to pronounce that specimens deserve their own sub-species because of a trivial difference in size, or habitat or feeding or colour.  This is partly due to ambition - getting to name a [sub-]species ensures your immortal fame while acknowledging your specimen as essentially-the-same-as is much less exciting. WWF has to hope that taxonomic lumpers eventually win over splitters: it's cheaper that way, because then they don't need to save two morphs.  You want to be a bit careful on defining things by skin/fur colour: a rat, black as my hat, ran across our yard the other day but I knew it couldn't be Rattus rattus, the black or ship [plague] rat, but rather a melanic form of Rattus norvegicus which has been so successfully invasive on the Shiants, the Scillies and Ile Bouvet.

Mais revenons nous a nos ours. There is the Black Bear Ursus americanus, for example, which is a good, reproductively isolated from Ursus arctos, species. The last common ancestor lived 5 mya, about the same separation as between us Homo sapiens and chimps Pan troglodytes according to molecular clocks. And there are melanic forms of the 'brown' bear just like there are blondies, red-heads [prev], dark-brown and sandy-coats. Grizzly refers to the grey de-pigmented tips to the hair shaft which give a distinguished pepper-and-salt look. At the other end of the spectrum is the polar bear Ursus maritimus which are definitely white but not so definitely a good species! It turns out that one of the 90 named subspecies of brown bears Ursus arctos sitkensis is endemic to the ABC islands in the Alaskan panhandle. ABC for  Admiralty, Baranof and Chichagof Islands, the largest northerly lumps of the Alexander Archipelago from which the city of Sitka faces out across the broad Pacific Ocean.  When they looked at the DNA of these beasts it turns out that they have distinctly polar-bear chunks of their genome.  It is now suggested that a population of polar bears was stranded by retreating ice on the ABC islands at the end of the last ice age. In absence of available male polar bears, some females acceded to the attentions of roving brown bears from the mainland and delivered healthy offspring. We know it was that way round because the ABC brown bear (a single individual, as far as I can make out) is most polar-like (6.5%) on the X chromosome than in the rest of the genome (1%).  Those healthy offspring grew up and started to look for potential mates in their turn and found only brown bears and so the polar-bear contribution has been stochastically diluted over the last 10,000 years. It's a bit like, if you send your saliva off to 23andme, they will analyse the DNA and tell you that  at least one of your ancestors had a romantic interlude with a Neanderthal. There will be no detectable difference on the heaviness of your brow-ridge but the DNA will bear a distinctive other-species signature. The algorithm can quantify the amount of miscegenation.

So there's hope for polar bears as the ice caps shrink and their habitat gets destroyed and they have to swim further than the cubs feel comfortable about. They have been there before and survived for some time in a brown-field site. Good news for seals?

Island Index

Sun Misc 230717

A tuthree of longforms

• How doctors die . . . with No Code medallions /tattoos conspicuously visible when they turn up in the emergency room, so they won't have their ribs cracked by CPR.
• How journalists get scooped via Mefi. They get scooped like scientists do - heck, they invented the term
• All you'll ever need to know about irrigation.
• Vox on UBI uconditional/universal basic income. Articulate folk from Left and Right are advocating UBI so that it becomes a Rorschach test, a canvas onto which people of various bents can project their hopes and dreams . . . and unevidenced prejudice about who the poor are and how they get that way.

Shorter stuff

• Vaccine rap: propaganda to save kids' lives
• The language of high finance
• Lucy Kellaway of the Financial Times on mixed metababble doublespeak
• Antidote: Warren Buffet talks normal
• Sailing
• Comanche 30m long crosses Atlantic in a wet working week
• A tour of the minimalist high-tech boat
• View from the boat flying-fish get tonked above and below
• Food and cooking
• Trad soy sauce
• Bas de Groot milk sommelier – it’s all in the terroir
• War and cheese: the production of Russian parmesan
• Getting it: cockle harvest with Belgian horses
• Sing of the week:
• Zorbing by Stornoway
• Fuel up ditto

We're primates

No No, only some of us are Archbishops but we are all great apes (rather than fallen angels).  I can say that safely because almost all my current readers (according to the Blogspot statistics) are French, or at least have French IP addresses, and only a minority are Merkins. I'd be quite confident that the latter are from the minority Evolutionista party rather than from the man-is-built-from-Eve's-rib-Genesis majority.  But there's no future in he-said-she-said on our ape ancestry, we need evidence. For me a compelling datum is the remarkable similarity between the genomes of humans, chimps and gorillas.  But other scientists have their baggage in a different toolkit and a group from St Andrew's U in Scotland is following up the commonality of non-verbal communication among the great apes. There is a strong tradition in such ventures for starters see Chuck Darwin's The Expression of the Emotions in Man and Animals [prev].

We're in England{spending time with | minding | bonding with} Gdau.I who uses words to achieve her aims "Dado said we're allowed to watch Peppa Pig for the whole of Saturday morning" and Gdau.II who is pre-verbal.  Her older sister claims that she knows purple and yellow but that is more responding correctly to "Say yellow" rather than "what colour is elemental sulphur?" or "what dye-colour can you abstract from Murex gastropods?". There is a hypothesis that this verbal deficit is physiological and larynx-developmental rather than cognitive. Same argument has been applied to Koko and Washoe and other languaging great apes. If you make the assumption that a pre-verbal child knows nothing you can make communication frustratingly difficult. Like the does he take sugar? syndrome when dealing with Stephen Hawking and other physically handicapped adults.  Well, help is at hand [literally] if you're prepared to embrace Sing & Sign and learn a reduced instruction set with your toddler [see R]. You're not going to discuss meaning in the works of Wittgenstein but at least you'll be able avoid pissing off the child so it throws a tantrum when the grandparents [very high standards there] are visiting.

On the journey across country from the ferry we tuned into BBC Radio 4 and caught a piece on the Great Ape Dictionary. Cue joke:
Two apes in the bath.
One goes "Ah ah ah ooo ooo ach ACH ACH"
There other says "If the water's too hot, mate, you can run some cold in"

The Boy can run that joke in French from his time surfing in Biarritz.  The French Connexion is actually important because that link invites you to participate in a test to see if humans can correctly [multiple choice] interpret ape gestures captured on video. If the only responders are graduate students from Scotland there will be bias. Mostly they'll be thinking "that gorilla really needs a pint o' heavy".  Because the language of gesture is not universal among humans. If you try la barbe in Ireland, folk will think you're making the universal sign of choking and wrap you in a Heimlich embrace.  Well I've helped push the frontiers of science by participating in the St. Andrew's Experiment . . .  and I haven't done as well as Jane Goodall! Indeed I suspect that, if I had to hang out in the Gombe Reserve with some chimpanzees and asked one  of them for a share of termites I'll get soundly rogered by the alpha male. Nevertheless, I scored 12/20 which (with 4 choices in the MCQ = 5/20 ) is much better than random!

The one chimp gesture that I felt most confident about was when an infant chimp raised its arms in the hope that someone would pick her up . . . because I had, minutes before, acceded to a similar demand from Gdau.II. It's like those reflexes - Babinski [prev], Moro, etc. - which small-small human infants have but which fade as they grow up. I don't know enough about the field of non-verbal comms to know if they have Trevor Lloyd arguments about whether the gestures are random with cultural accretion of meaning or if they are more deeply embedded in the genome of behaviour. aNNyway: you are encouraged to help the St.Andrew's Experiment.

Mappy links

I recently asserted that I love maps, 'tis true and here are the links to prove it.
Scandinanvian triple-point land-deal;
Indiana standard time in flux
Hilarious twinning of Ukrainian Oblasts with Irish Counties
Ditto Belarus and Ulster
PrairyErth
Oola Oval
Baarle
I thought it would be time to cull some more from the interweb:

• One of many investigations of topological distortion on the London Underground map.
• Senator Al Franken (Minnesota Democratic–Farmer–Labor Party DFL) does his draw-the-United-States from memory party trick.
• Explanation of  numerous anomalies along the borders between those states. A bit galloppy but well informed. Several of these The Blob, being boring and derviative, has also blobovered:
• Point Roberts
• Ellis Island
• The Prime Meridian: fascinating [as Tom Scott often is] journey from Greenwich and George Airy in 1830 to SatNav, GPs and Johns Hopkins in 1973 to plate tectonics in 3 minutes flat spheroid.

And now for something completely diff: documentaries about Art

• It's Edward Hopper's birthday 22 July 1882.  Wim Wenders and Brian O’Doherty talk about his life and works.
• While we're about 20thC US art, let's check out Michael Palin’s Wyeth’s World: