Saturday, 24 August 2019

Not drowning but waving

This may save your life.
tl;dr? Drownproofing!
In my researches about the 1966 Heron Bridge disaster, I came across this "just how dopey can young chaps be?" video. Young Ugg looks barely into his teens, knocking away at a roof-supporting pillar with his hands and palaeolithic rocks, until it collapses almost on his heels. He'll probably live to a venerable old age if he can make it through the thoughtless death-wish years from 15-25. In my Heron Road piece I called myself a wannabe engineer but actually, aged 11 or 12, I wanted to be an architect but my family and teachers 'helpfully' pointed out that my handwriting was so crabby that my blueprints would be illegible and I should choose a different vocation. I believed them and, although I taught myself a fine cursive hand a couple of years later, it was too late for me to go head to head with Gehry, Pei, van der Rohe, Rogers, Safdie and Saarinen.

Actually, through much of my childhood, people would say "You can't do that you're too little / stupid / clumsy / illegible" and I would meekly accept their verdict. Somebody had to be the family nebbish, and, for an easy life, that role suited me. As a sub-teen in the Drake Baths in Plymouth, I achieved a minimum Bronze level of proficiency in the water, while my brother and sister sailed through to Silver and Gold medals. I would have liked to match them, but had been critically sapped of determination and was happy enough to swim a length underwater, or two length on the surface and then cease-and-desist. Maybe related to my weakness in the wind [similar]. So I can swim, but I'm not sure how far I'd get if I had to swim to save my life; although I did once save someone else from drowning. Last week, beachcombing alone at Garrarus strand [prev with buoy] on the Waterford Coast, I threw off my clothes and plunged into the sea for the craic, like, but didn't stay in long enough to get fit . . . or even warm.

These damp musings primed me for reading a MeFi blue on Fred Lanoue, a swimming coach at Georgia Tech whose book Drownproofing, A New Technique for Water Safety (Prentice-Hall, 1963) really didn't make waves when it was published 50+ years ago. You can pick up a 2nd-hand copy for about $40. Who can afford that?  But you can get the key information on this single longish Drownproofing page. Lanoue's method works because he counter-intuitively advises survivors to rest with their face in the water and entrain a gentle rhythm of exhaling every 10-12 seconds and bringing your mouth up for an in-breath and returning to rest position. Calmness is key. You can't do anything about hypothermia and sharks, but conserving energy is going to keep you alive for longer. They say drownproofing is similar to dead man's float - but the top video of that technique show a chap who takes no inbreath at all this one neither. US Navy Seals do it sustainably.

One interesting sideline is that Lenoue wrote that 30% of young black males had negative buoyancy and Mike Kearney the Drownproofing page editor quotes that uncritically. Very few white males have negative buoyancy except those that are really obsessed with having a sculptured six-pack. It's the body-fat, lads! A crap-detecting commenter on Mefi called ArbitraryAndCapricious pointed out that, when Lenoue was writing, many young black men were on the edge of starving and that made all the difference to their buoyancy.

Who can not afford to get acquainted with drownproofing? Bearing in mind the RNLI's chilling note that "Half the people who drowned last year didn't intend to get wet", and that about as many people drown each year in Ireland as get oblivioned on Irish roads.  We can finish by quoting in full Stevie Smith's enigmatic existential poem:
Nobody heard him, the dead man,
But still he lay moaning:
I was much further out than you thought
And not waving but drowning.

Poor chap, he always loved larking
And now he’s dead
It must have been too cold for him his heart gave way,
They said. 

Oh, no no no, it was too cold always
(Still the dead one lay moaning)
I was much too far out all my life
And not waving but drowning.

Friday, 23 August 2019

MORE trees are needed

If we want trees to be a solution to our collective carbon footprint, we have to plant 'em, prune 'em and then leave 'em alone for at least 300 years. Planting thousands of hectares with a Sitka spruce Picea sitchensis desert with the intention of harvesting in 30 years is just a money-making scheme; worse in many ways than doing nothing-at-all. We've done our bit, planting up 0.4 ha of our 6.5 ha holding with a mixed woodland: that's about 1,500 trees each for The Beloved and me: or 500 each if we share our smug glow with the people who helped do the planting. We didn't do that in a day! We started in 2007 and spent money and time on the project over the next two winters. Mixed woodland is the best: we planted 10 different species of native Irish trees (mostly
Scot's pine; Pinus sylvestris
Larch; Larix europaeus
Ash; Fraxinus excelsior
Oak: Quercus robur
and there will be other blow-ins on the inventory if we did a careful audit.

That's sort of pathetic, isn't it? If we wanted to make a difference we'd have Wenceslased in the footsteps of our pal Bill Liao who founded a global tree-hugging charity called We Forest. His enterprise has leveraged the planting of 19 million trees up to the end of 2018 = 2.4million in that year. They have a rather useful FAQ for the science/math of tree-planting to offset our carbon feet. The trees cost between €0.60 and €3.00, and we're looking at an income / throughput of about €2,800,000 on 2018; of which 22% goes on 'livelihoods' which I'm guessing the rest of us would call salaries = a wage bill of €600,000 spread across 43 'heads' who are livelihooding for WeForest. That's less than €15K/yr each which seems very low if you're living near head-office in Brussels and a king's ransom for those nearer the coal-face in Ethiopia and Zambia.

As the contributions of individuals are pathetic compared to NGOs, so NGOs pale into the background compared to Governments, even comparatively poor 3rd world governments like Ethopia's. Prime Minister Abiy Ahmed [sleeves rolled up for work, but tie still round his neck to symbolise the other important responsibilities of the Head of State] has launched a plan [Exec Summ Grauniad] #GreenLegacy for his country to plant 4 billion trees in 2019 - that's about 40 each for the plain people of Ethiopia. Anyway #GreenLegacy was off to a flying start on 29th July when they co-ordinated the planting of +350 million trees on a single day. That beat India's Guinness Book of Record - a mere 50m/day in 2016 - into a cocked hat. Go Ethiops!

On the basis that some plant and some lean on the shovel watching the planting [PM Ahmed is below average "And the women answered one another as they played, and said, Saul hath slain his thousands, and David his ten thousands" 1Sam Ch18v7.] We have data to see who has been punching above their weight on the Ethiopian Tree Planting Stakes. I've snagged populations for each of Ethiopia's provinces from Wikipedia and the tree planting stats from #GreenLegacy, to generate the following table:
Regions
Area
Msq.km
Mpop
Mtrees
Trees
/pers
Addis Ababa (አዲስ አበባ)
0.53
3.4
3.5
1.0
Afar (ዓፋር)
72
1.8
0.4
0.2
Amhara (አማራ)
155
21.1
70.6
3.3
Benishangul-Gumuz
(ቤ/ጉሙዝ)
51
1.1
1.1
1.0
Dire Dawa (ድሬዳዋ)
2
0.5
0.3
0.6
Gambela (ጋምቤላ)
30
0.4
0.5
1.2
Harari (ሐረሪ)
0.33
0.2
0.2
0.7
Oromia (ኦሮምያ)
285
35.5
211.9
6.0
Somali (ሶማሌ)
279
5.7
0.8
0.1
SNPPR (ደቡብ ብ/ብ/ሕ)
106
19.2
51.1
2.7
Tigray (ትግራይ)
41
5.2
9.6
1.8
1,021
94
350
3.7

And the winner is . . . the Plain People of Oromia [6 trees each] which is the largest and most populous administrative region in the country and which includes suburban Addis Ababa. Nevertheless, the diligent Oromians planted more than double the number per head as the lazy-arses in Amhara [3.3 trees each] and Tigray (Project Desa'a and Seret) [1.8 trees each] where WeForest are devoting their main energies. There's not enough evidence to suggest that WeForest is putting a damper on local initiatives. Obviously other factors are at play than available Effectives to plant the trees. The lowest number of trees are in Afar and Somali, which have really low population density, probably because the climate is too brutal for normal Teff agriculture: trees don't grow in deserts. Or it could be that the locals recognise that it would be impossible to protect the baby trees from rapacious goats and donkeys.

Here's a piece-to-mic from the CEO of WeForest about the Ethiopian initiative.


Thursday, 22 August 2019

Where Is Chongqing?

I was recently beating my breast " yew . . 'orrible . . ignorant . . little  . . man" because of  the tiny amount  I knew about Chinese geography. As one person in every six is Chinese, it might be a good idea to beef up our knowledge about that part of the World? Last week, I had a moderate amount of amusement [see 1st link] with 22 youngsters from Southwest University (SWU 西南大学) in Chongqing . . . I have the t-shirt to prove it. We used to call it Chongqing. At the end of their Summer Course, which has cost someone a king's ransom x22, we took them out to dinner at the place where they play traditional Irish music in the evenings. In case conversation flagged, I brought along an outline map of the PRC to see how well the kids knew the internal geography of their country. There's a bit of a meme on youtube and about people from, like, Miami FL who cannot point to Florida on an outline map of the USA. let alone countries where them comm-mune-iss live. Irish know-nothings exist too.

Well I didn't use the map for that purpose because a much better idea presented itself. I asked the young chap, who was scoffing sirloin beside me, why he chose Chongqing, of all the places in the world, for college . . . and where did he come from? His explanation was hard to follow, so I whipped out the map and asked him to put a dot for his home place. The young woman opposite (from Yunnan right on the border with Vietnam) did likewise and then I sent the map round the table for data. This came back:
The rules of Central Tendency suggest that the cluster of red dots more or less in the centre of the scatter is the most likely location of the Alma Mater and that turned out to be true. Chongqing City is in the middle of one of 4 "Municipalities" (the others are Beijing, Tianjin and Shanghai) which has an area equal (within 2%) of the island of Ireland; but with 30+million people on board: about 5x more than Ireland N+S. That sounds stuffed but the population density is about the same as Belgium's and much less than England's, so there must be plenty of green space, farms, and parks. Knowing where your students come from can be useful in designing recruitment drives.

The Chongqing 22 came with one of their professors who launched into the map to explain which provinces were where. She was spectacularly wrong in pretty much every attempt: locating Tibet where Xinjiang is and mixing Hainan and Formosa/Taiwan the two largest off-shore islands claimed by the PRC. While we're down South, I've indicated where Hong Kong HK is located at the mouth of the Pearl River. My asserted that the city of Canton was just up river from Hong Kong and Macau was met with incredulity. But I was right, although everyone calls it Guangzhou 广州 nowadays. The province of which Guangzhou is the capital is Guangdong [Canton geddit?] and they speak Cantonese. Cantonese vs Mandarin is about the same as German vs English or Spanish vs Portuguese. The amazing thing is that they write with the same characters, so the characters are pronounced differently but read the same. That has been a major unifying force in the region, even when the area presently called PRC was a patchwork of warlorderies and corrupt governments.

And the fact that Chongqing, clearly one of the smaller territorial divisions of the Republic is the same size as Ireland gives you some sense of just how Big China is. The scale-bar on the map should help also. It's about 2x bigger than the whole EU, and about the same as the USA.

Wednesday, 21 August 2019

Bobbie goes to Hollywood

Optional soundtrack - FG2H The Power of Love
We are signed up to Blackstairs Farming Futures BFF, and I have undertaken to log all the evidence of human impact on the environment that will be here in 200 years time. "the environment" here being the 200 hectares which we own in common with 18-20 other neighbours. It's fun because I get to name the artifacts which I find. The more obvious artifacts like the Sitka spruce Picea sitchensis plantation, or the sheep-proof fence that separates it from the commonage; or the sheep themselves? None of them are likely, let alone guaranteed to be there, then. But the stones, split by judicious and musical hammers and wedges? The rocks remain [Horslips] [Maxwell]. I show [L] the most obvious example [it's the parallel lines of wedge-holes, silly] of a project to craft a lintel or doorstep from a granite boulder. For whatever reason the mason stopped his own gallop one minute and cried "Feck it! this is going nowhere" and started work on a more promising rock. It is a snap-shot in heritage time quite as vibrant and informative about human activity as Stonehenge or the pyramids if a trifle more humble.

BFF is a pilot study to help imagine and then create a more productive future for Ireland's upland habitats: there's got to be more to it than burning the heather, running some sheep and planting out more spruce deserts. Can we, with a deft twist of a limiting factor in the environment [Iron; Foxes Vulpes vulpes; Pasteurella haemolytica; blocked drains; impenetrable forests of gorse Ulex europaeus] change the whole landscape like The Man Who Planted Trees? Yesterday, eleven of our commoners rented a minibus and directed it to a Teagasc showcase in Hollywood, County Wicklow. We The Eleven sat in the Hollywood Community Hall for an hour being talked at by ecologists and agrifunctionaries. |Then we were bussed up towards the hills to a commonage called Granamore [view below] to see how ten farmers with mountain rights can get round a table and then round a trough of sheep dip and talk out a sustainable future for their lives and livelihoods . . . and give access to hikers and orienteerers and kite-flyers. They told us a little about the practicalities of road-mending; river-fording; draining; controlled burning and a bit of tree-planting.

One qualified statement got me thinking. They showed a poster of sustainable stocking rates (in ewe-equivalents / hectare) for
upland grassland 1.5-5 ee/ha;
dry heath 1-1.5 ee/ha;
wet heath 0.75-1.0 ee/ha;
blanket-bog <0.75 ee/ha.
Those rates are different for the different habitats but all those habitats are represented on Granamore Common . . . and here are no fences. How to keep most of the sheep out of the blanket bog and more on the few patches of good, palatable, nutritious grassland? One cunning plan that has had some success is to lug a 20kg bucket of mineral lick [essentially candy for cows and sheep] to the areas covered in deergrass Trichophorum cespitosum or matgrass Nardus stricta as a honeypot. While there the sheep will eat some matgrass [though it's a bit bleh to normal sheep], trample some deergrass and give better grass elsewhere a chance to grow after, say, a controlled conflagration. All that is predicated on the fact that farming hill sheep is a really unproductive way to earn cash for children's shoes and cornflakes. Farmers will be better off spending time taking sheep to the mart; working in the mart; shearing, ploughing, mowing and baling for their neighbours; working for Teagasc or as a teacher.

Chris "Drummer" Stewart [Driving Over Lemons is wonderful] retired young to Andalucia to potter and write. He earned an honest crust as a sheep-shearer and got to know his neighbours. Several of them were shepherds who were active on the hills more or less all the time. I always thought that the shepherd and his mastiff's primary task with sheep was to prevent predation; and to stop them wandering into the next village for vino tinto y tapas. Wrong! especially now that we have decimated all the top predators. The shepherd can, by her presence, gently shift the flock wholesale from areas-to-be-protected to areas-where-they-are-a-grazing-asset. Even a chap can serve this purpose: load up his smartphone with credit and let him off up there being useful.

Tuesday, 20 August 2019

Is the mouse a good model?

A few years ago I was embarrassed to admit that I'd never heard of the 4th biggest city in China. [Ans: Tianjin 天津市 - it is near Beijing in the NE of the People's  Republic]. The 3rd biggest city in PRC, after Shanghai and Beijing is Chongqing 重庆市. Now I had heard of Chungking because it was the Capital in Exile in WWII after the Japanese sacked Nanking and occupied Beijing and much of the N of the country. Note the last character 市 is the same for both cities: it means city! Our ignorance of China is immense: the population of Chongqing alone exceeds that of the island of Ireland: could we take the trouble to find out more?

That opportunity was provided last week at the end of a 3 week Summer Programme at The Institute for students of Southwest University (SWU 西南大学) in Chongqing. I was 'volunteered' for 6 contact hours to play some computational-biology games.  They paid me, but not enough to create a whole new course, so I modified part of a comparative immunology module I developed a few years ago. The question I put to the students was
"Is the mouse a good model organism for developing 
a novel therapeutic against such-a-disease".  

One pharmaceutical research avenue which has been fruitful is the development of monoclonal antibodies specific for key molecules in immunological / inflammatrory response pathways. Monoclonal antibodies MABs are amazingly specific in seeking out rogue actors which get over-excited in  a particular disease. What I know about normal human physiology, after teaching it for 7 years, is that the whole system is a set of checks and balances; disease is when this delicate, multiply redundant, complex of interactions goes AWOL. MABs are given dork-dopey names , mostly ending in -mab so that Google-savvy patients don't be bothering their doctors to try the latest me-too drug they read about in Hello magazine.

The standard protocol for a new drug prospect is to build on our increasing knowldge about the molecular fundamentals of a disease and ask . . . if we could put a damper on MAPK then it wouldn't be able to gee-up STAT3 and the whole over-heated system would cool off. MegaPharm is only interested in drugs that will make them a load of money, but they have to ensure that a) they do indeed work in the way intended and b) they are safe to use: that their side-effects are not too damaging. The usual thing is to try out the prototype drugs on a couple of hundred lab mice Mus musculus, and then do some statistics to see whether the idea might be a runner.  If none of the mice get the screaming abdabs [technical term] and enough of them get better, then it's time for the first human trial.

In 2014, I wrote about the most famous case where that next step went horribly wrong with a test of TGN1412 which seemed in mice to counteract the effects of CD28. It was a salutary reminder that mice and men are similar, yes, but also different. Nobody died in that first human trial but several of the human guinea-pigs were badly roughed over and won't ever properly recover.

That gave me the bones of a hypothesis to test with the boys and girls from Chongqing. Let them compare a list of drug targets to see how similar those molecules were in Mus musculus and Homo sapiens. TGN1412 was to be a treatment for Rheumatoid Arthritis. My correspondent G who is pain-wracked by RA has been taken off Infliximab because her condition is no longer responsive to having her TNFα tricked about; so she would welcome a novel therapy to help her get out of bed in the morning. But TGN1412 and multiple organ failure is a bridge too far even for her.

The kids from Chongqing were invited to choose one molecule from a list that had been used as a target for a named monoclonal antibody. Starting with Infliximab and ending with TGN1412:
They were then requested-and-required to use the Blast server at NCBI to find the homologous [equivalent] gene in mouse and see just how similar they were. I show above the target-list and, in the last column, the answer for the class. The specific hypothesis under test was that CD28, the TGN1412 target, would be noticably more different mouse-vs-human. And the answer is . . . No!  I emphasised that nothing like this analysis had ever been carried out before since science began in the 17thC: the kids from Chongqing were pushing the Frontier of Science.
Here's some more detail on IL13 one of the crappier comparisons. At 59% identical, you might think that IL13 is missing in mouse and P20109 is something else entirely. But a reciprocal best hit analysis shows that the two sequences are indeed orthologous and probably have the same structure and function in both species.
IL13 Mouse P20109 Query vs Human P35225 Sbjct
Expect 2e-40 Identities 76/130(59%) Positives 93/130(71%) Gaps 8/130(6%)
Query  6  TAVLALACLGGLAAPGPVPRSVSLPLTLKELIEELSNITQDQ-TPLCNGSMVWSVDLAAG 64
          T V+AL CLGG A+PGPVP S +L    +ELIEEL NITQ+Q  PLCNGSMVWS++L AG
Sbjct  20 TTVIALTCLGGFASPGPVPPSTAL----RELIEELVNITQNQKAPLCNGSMVWSINLTAG 75

Query  65 GFCVALDSLTNISNCNAIYRTQRILHGLCNRK-APTTVSSL--PDTKIEVAHFITKLLSY 121
           +C AL+SL N+S C+AI +TQR+L G C  K +    SSL   DTKIEVA F+  LL +
Sbjct  76 MYCAALESLINVSGCSAIEKTQRMLSGFCPHKVSAGQFSSLHVRDTKIEVAQFVKDLLLH 135

Query 122 TKQLFRHGPF 131
           K+LFR G F
Sbjct 136 LKKLFREGRF 145
The fundamental problem is more complex than 22 undergraduates from China can solve in 90 minutes; but we probably knew that. I still think it's an empowering exercise.

Monday, 19 August 2019

Might have been

<Guest Blog Alert> [never done this before]
I wrote recently about my exercise-induced arse-ma; which put the kibosh on my prospects with the loneliness of the long-distance runner. It struck a nerve with my correspondent [recent] G who wrote about her own lack of wind so eloquently that I'm posting it here (with her permission):

Exercise-induced asthma - the bane of my life and only recently diagnosed by an occupational therapist of all people. When I was 15 and gasping for air after a couple of minutes on the trampoline double and triple somersaulting, my PE teacher used to make cracks about me giving up the cigarettes (a few years before I took them up). This made a huge impression on me in terms of unfairness and amazingly one of these incidents was memorialised in a poem by a schoolfriend forty years later. 

When playing hockey, if a game was very defensive and as a left back I had to be on the move continuously then I'd see things like the far corner of the hockey pitch lift up and roll itself towards me. Charles Bonnet Syndrome [prev] or purely oxygen deprivation? When I told the PE teacher, she suggested for the first time that I give up smoking - at 12, in a convent - FFS! She had to be on drugs to think that! 100 yards sprint was no bother to me, the fastest in the school, till I'd finished it... but the three rounds of the hockey pitch after dinner every day, that the couchiest potatoes in school found easy, never happened for me. I could never finish one round... a long and short side and I'd hit my wall with no running through it. Courtney Dauwalter is a better woman than me.

Five years ago, before the chance discussion with the OT, I was determined to take a crack at running in the dark instead of standing on sidelines and started running, using a Couch to 5K app. By the time I'd repeated six weeks of Week 1 without any visible difference in my fitness, I muttered curses and let the weather get the better of me and ceased my running endeavours. It has been a constant wonderment to me how one of my friends can get out there and do 5K cold from the couch without wanting to die during or after it. 

How did a woman fresh out of a four year PE teacher training course in Thomond College which presumably contained both sports physiology and psychology modules fail to see that the most active sporty girl in the entire school wasn't a smoker but had a real health problem? She never put together that, while I excelled at all sports, that basketball, netball, tennis: any sport requiring stamina were washouts for me after very promising oxygen-loaded starts. 

What could have been! Such tiny things to mould a character and change a life. The Blob sometimes hits a nerve [ouch].
G's nearly on her pension now but, in her youth, people who knew the field talked up her potential as an Olympic gymnast. But that dream would have required getting many ducks in a row, and for network and exteernal support, G hadn't even a feather, let alone one full duck.
“Strange friend,” I said, “here is no cause to mourn.” 
 “None,” said that other, “save the undone years, 
 The hopelessness . . . Strange Meeting Wilfred Owen

Sunday, 18 August 2019

Catchup ketchup 18Aug19

As The Blob gradually fills out the last remote corners of my universe, new stuff is likely to recall a bloboprev.