Hallowe'en 2019

The science teacher everyone wanted and few got: blowing the eyes out of a pumpkin.

Exploding food? A variety of canned-goods including surströmming fermented fish [poooeee!] heated to bursting point. Don't do this at home - find a forest. Please be safe tonight, don't let your kids do dumb-ass things with fireworks and bonfires.

Platelet donation

It's a thing. I'd never 'eard of it until one of my pharmacy technician PTstudents brought it up in a human physiology lecture a few years ago. I said that I'd find out about it and get back to everyone. It's one of those questions that might be interesting to more people in the room than the student and me [I have a very low threshold for cor that's interesting]. I wish I'd remembered what the answer was because last week another student asked a more focussed form of the same question "Why are people who've been pregnant not allowed to make a platelet donation?". There were at least three people in the room who were aware of the procedeure [and probably not much more: only about 1/1000 adults participate]. I undertook to find out and get back to them . . . and you dear reader.

 As you know, blood consists of plasma, red cells, white cells and platelets. Circulating in the plasma are the clotting factors Factor VIII and Factor IX used to treat haemophilia [which prev], they are proteins, macromolecules, made of amino acids. Also present in the blood of some people is anti-D, an antibody against Rhesus factor; it is used to treat haemolytic disease of the newborn HDN [which prev]. Antibodies are also proteins, macromolecules, made of amino acids. I go on about the macromolecule schtick because my PTs really cannot grasp relative size no matter how much I bang on about it.

Traditional blood donors can give whole blood every 90 days. This blood is usually typed for ABO and Rhesus blood groups and then separated into packed red cells, plasma, platelets and proteins.

Type	Shelf-life	Store Temp	Schedule	Notes
RBC	42 days	4°C	90 days
Plasma	360 days	-20°C	30 days
Platelets	5 days	18°C	30 days	rocker
CryoPPT	360 days	-20°C	30/90 days	FVIII, FIX

These components have different shelf lives and different storage requirements. Platelets must be stored at room temperature in bags on gently rocking shelves and so have the shortest shelf life ~5 days.

There are never enough donors, so "apheresis donation" has been developed to harvest plasma and platelets every 30 days. Donors are given an anti-coagulant (?Warfarin?) and their whole circulatory system is connected to a machine that spins the blood as it comes through, separating the red and white cells, the platelets and the plasma. The cells spin to the bottom of the machine and are returned to sender. The platelets layer themselves halfway down and are directed to one bag, the plasma (54%) is sent to another bag. The clotting factors are later separated from plasma by cycles of freezing and thawing.

Why don’t they want blood from women who have been pregnant or have ever had a blood transfusion? Because they have been exposed to blood from a different person. Sometimes, minute quantities of blood may leak across the placenta from the foetus even early on in pregnancy. Coming up for, and during, delivery there is more active blood-sharing as the placenta loosens up and things down there get squeezed. The mother will develop antibodies to any blood which is different from hers and these antibodies will persist undetectable in the plasma / platelets as they are processed through the apheresis machine. These antibodies may cause problems in the third party in the process – the recipient of the platelets – who will be genetically different yet again from mother and foetus. Like not wanting blood from residents from the UK in the 1980s who may have been exposed to mad cow disease [variant CJD], the Platelet industry is operating under the Precautionary Principle about these potential anti-bodies. Despite crying out for more platelet donors.

They only have Apheresis Clinics in Dublin and Cork and it takes 2 hours. I guess they give you and cup of tea, but better bring a book or a good movie on your phone. Call 01 4322833 (Dublin) or 021 4807429 (Cork) for an appointment.
Sources:
2+ mins on apheresis donation (for plasma / platelets)
4 mins on Blood Component Separation

Stayin' alive

Two days after my colleague died at work despite an hour of CPR, The Beloved was up at an End of Life symposium run annually by The Irish Hospice Foundation. She's been before because we're both quite focussed on the subject being a lot closer to the End now than the Beginning in the 1950s. The key-note speaker was Katharine Mannix, about whose book With the End in Mind: dying, death and wisdom in an age of denial I wrote last year. Mannix looked around the auditorium and asked everyone to guesstimate the rate of survival from a CPR session. Almost everyone in the room was wildly optimistic about this intervention. I straw-polled my class on Friday with the same question and elicited a) a lot of silence and looking at feet [standard response to direct question in class] and b) 50% and 80%. Wrong! It's 10%.

The CDC says that the Bee-Gees can help you pace your push on your neighbour's chest when s/he's dying. They also say that, for cardiac arrest away from hospital, only 10% survive but that your CPR can up the rate 2- to 3-fold. Reuter's report a more realistic definition of a result that matters: 10% for survival to discharge from hospital. With 350,000 'wild' cardiac arrests in the USA each year, people-power CPR results in 350,000 * (30%-10%) = 70,000 incapacitated extra people alive each year occupying 7% of the 940,000 hospital beds in the country. The UK currently has 160,000 hospital beds [down from 240,000 in 2000!]. Henry "Do No Harm" Marsh [prev] says in his new book [Admissions reviewed later] that 7,000 =4% of those beds are occupied by deeply comatose bodies in a persistent vegetative state. Some of the diverted there from "sucessful" CPR. Proportions will surely be about the same wherever you live. They agree with the figures in UK, where someone floated an annual Restart-a-Heart Day. That concept has gone international and happens in mid-October all over Ireland so you've missed your chance for training this year.

A portable defibrillator can be useful for jolting the heart back to life. Word on the street is that, when someone ran for The Institute's defib during the drama last Tuesday, there was nothing in the box. Someone had "borrowed" it. I hope its hanging in an impoverished GAA club somewhere. An AED Automatic External Defibrillator costs about €1200 in Ireland and there is clearly a buoyant market for this kit; with at least 20 competitively priced brands. All competing for a memorable name too: Philips HeartStart shown R. This guide will help you through the marketing to understand what matters in your purchase. Actually that guide is far too wordy and dense. This one is Irish and easier to read and better focussed.

Bones bones bones

Each year, the same lab practicals come round regular like clockwork, or the appearance of the Perseids in August. I think I've finally nailed the count of bones in the human body. It is therefore an entirely appropriate time to hang up my lab-coat and give up my desk for a younger model. When you stop learning you may give up teaching. I've ranted before about how the PubQuiz answer to the count of bones in the human body excludes the 6 micro-bones in the ears which allow us to hear. I have not been correct in this high moral ground. But there are still inconsistencies in how Everyone comes to agree that adult humans have 206 bones. My Cell Biology class this year seems to be a little more engaged in the process than some groups in previous years. They were at least honest to the task because I made them park their smart-phones and think about how many bones they had about their person. It's okay to be wrong, I cried, it's the first step towards knowing. They all had different answers though, which is evidence of honesty, which is evidence that they have thought about it rather than acting as a know-nothing channel for Wikipedia.

I guess if I offered them €1 for each identified bone, then they'd work harder to get to 206 . . . without working too hard so that they fudge the answer to make it right. I've also included the official answer (from St Wiki of Pedia) of how the agreed N = 206 is arrived at. Compared to my last attempt at this exercise.
Axial = 80 (8+14+7+26+25)

• Cranium N=8: occipital bone, 2 temporal bones, 2 parietal bones, sphenoid bone, ethmoid bone, frontal bone
• Face N=14: 1 vomer, 2 conchae, 2 nasal bones, 2 maxilla, 1 mandible, 2 palatine bones, 2 zygomatic bones, 2 lacrimal bones
• Extras N=7: hyoid, ears: 2 stapes, 2 malleus, 2 incus
• Vertebrae N=26, 7 cervical,12 thoracic, 5 lumbar, 1 sacrum, 1 coccyx
• Ribs+sternum N=25

Appendicular = 126 (10+10+54+52)

• Shoulder and arms N=10: 2 each scapula, clavicle, humerus, ulna, radius
• Pelvis and legs N=10: 2 each innominate, femur, patella, femur, tibia
• Hands N=54: 16 carpals, 38 metacarpals and phalanges (thumb only 2 phalanges)
• Feet N=52: 14 tarsals, 38 metacarpals and phalanges (great toe ditto)

Thus N=206 only works if you decide to say

• fused sacrum = one bone 
• fused coccyx = one bone 
• fused innominates / pelvis = two bones, one left, one right
• fused mandible = one bone
• fused skull = twenty-two bones + two each of malleus incus and stapes rattling around inside the ears = six

Which seems super arbitrary to me. I don't care how many bones there are in your body because it is GDPR personal and also very likely to be different from my tally. So much polymorphism in the lumbar, sacral and coccygeal vertebrae even before fusions start. So many ossicles "sesamoid bones" in the feet and at the base of the thumb which don't count though they are bigger than the distal phalange of the baby toe which does count. That's before we start on cervical ribs, polydactyly, thalidomide and Oscar Pistorius. About 206 but it depends on your definitions will do nicely

But we really must pull each other up on is bold statements like The adult human skeleton is comprised of 206 bones when the person expressing this Certain Knowledge literally doesn't know what they're talking about because they have as much difficulty as me reconciling that number to the inventory.

Sunday sunday 271019

Going up. Last week it was descents.

• Long form essay on scientific replication, fraud and P-hacking [tnx Dau.I the Student].
• It cites Brian Nosek - multibloboprevs]
• ITCC Tree climbing competition in TN. Can you figure out what the rules might be from this clip?
• This help? It's a bit slower
• Voie Petit hand by hand
• Ueli Steck - Swiss speed climber [Full disclosure Steck died in a Himalayan fall in 2017]
• Stair running - it's a thing
• Rocky II
• Pigs in paddocks
• Cheese on Alps
• Singing together
• Fuori dal Coro sing Adiemus by Karl Jenkins

Thrifty Pie

We waste about 1 million tonnes of edible material each year. This shame can be shared about equally 3-ways among producers, retailers and consumers. They call this €700 per household. But another estimate is to say 300,000,000 kg is not eaten by 4,500,000 people: that's over 1kg a week for every manwoman&child. Heck, I've just pitched 4 blue satsumas in the compost in the last two days because they started to turn within 36 hours of purchase. I really don't like to waste food - it's almost a religious thing. I'm not afraid of a touch of Penicillium on the last slice of bread, let alone a white bloom on the surface of cheese. Our EPA supports a rather pious help-site called StopFoodWaste. I find the rule of thumb is to cut off as much of the obvious damage as possible and either eat immediately OR throw the salvage into whatever is cooking on the stove.

• half an apple in the porridge; 
• half a spud chopped into the Bolognese sauce; 
• cabbage, cauliflower, broccoli stalks into the next soup. 
• Never ever peel a potato
• Must stop peeling carrots for grating (I grate a lot of carrots)

Once you've got blooming food up to 100°C it's good for a few more days. Every time I throw anything in the compost, I resolve to review my bargains impulse-buys among the specials at LIDLDI. Mushrooms, even at 80c/kg, aren't going to last forever so I'd better have a plan for them; and the planet.

Despite the insanely low price of chocolate biscuits - about the same/kg as potatoes - I make 1kg of flapjacks at the least excuse:  meetings, funerals, weddings, works-dos, general consumption. They always make an acceptable gift because they are loaded with golden syrup and the oats, which make a third of the weight, fool people into thinking they are healthy. I have successfully made batches for vegans using sunflower oil instead of butter and honey instead of golden syrup, or both.

The other day The Beloved was going to spend the day with her Buddhist pals and asked for the recipe for flapjacks. I wrote butter 8 syrup 6 oats 12 flour 6 sugar 6 cinnamon shake on a scrap of paper. Supplementary question came back about whether vegan coconut oil would substitute for butter. I answered in the affirmative (what could go wrong?) and left the kitchen to chop water and haul wood in the yard. They looked golden brown great after 20 minutes but the slab had no strength and became granola before it could be cut. Turns out that TB went for bust on the coconut front and, as well as the coconut oil for butter substitute, used coconut 'flour' instead of wheat flour. There is a reason why we use wheat flour for bread, pastries, pancakes, biscuits, scones and wallpaper paste: the gluten forms long protein strings which hold the eggs, butter, currants, cherries together. Coconut flour is so much sand by comparison.

What to do with a bagful of coconut-oaty granola? Y' can't throw it out for the birds. I looked in the fridge to see how I might bring it back onto the menu. The answer lay in the prior existence of

• 300g of pastry dough
• 50g of cranberry jam
• 500ml of milk
• enough Bird's cornflour custard powder

. . . which I made into a coconoat cranberry bakewell tart:

which was just as weird as it sounds - and looks. Still I'm training myself up on the what kills not fattens school of catering and over the course of a week ate the whole thing.

The family has Far more nutritious and tasty dishes.

Fabulous cueing again

 . . . not so good out on the road.
Snooker turned out to be a surprising winner for television sport broadcasting. Back in the day on the BBC it was all criccer and rugger and soccer, with the Olympic Games throw in for variety once every four years. Now there is Sky Sports where you can find competitive bungey-jumping and lacrosse. Snooker TV wasn't going to work at all at all in black and white. When the idea was pitched to the BBC mandarins when colour telly started broadcasting, it was sniffed at because snooker involved a lot of smoking, drinking by over-weigh working class men. That was an alien class to the Cambridge educated decision makers at the Beeb. But if you think about it for a minute, it's a winner. Each match lasts about ten minutes, so you can pack as much into programme as the schedule will allow: complete games, replays, highlights, commentary can fill the [half] hour nicely. We don't have a telly at home, but visiting Pat the Salt I'd rather watch snooker than X-factor - it's better paced. It's one of the many games that I learned how to play during my very expensive education.

One of the current stars is an Australian called Neil Robertson, currently domiciled in Cambridge, UK. He looks reasonably healthy for late-30s and can crack a distant red into tight pocket better than most. In his day he has been World Champion. Not this year however because he missed his qualifying match at the beginning of October. He set off in good time for Barnsley navved by his SatNav and obeying the robot instructions headed West. Fail! Anyone who'd grown up in the UK would know that Barnsley is an old mill town in Yorkshire and from Cambridge you should start up the Great North Road A1. I don't think he made it to Barnsley, Gloucs, pop 209. But by the time he realised his mistake it was too late to turn. He was rueful rather than furious which suggests that he's a good sport.

Fabulous cueing, geography not so good. Sorry Neil!

Lock step and language

I've written about entrainment, the way things can get into a resonance with each other . . . and shake themselves to death, in the case of the Tacoma Narrows Bridge or tall buildings without harmonic mass dampers. But there is also empathic entrainment when you fall into step beside your walking companion without thinking that you are shortening your stride or seeming to trot. I like that because it implies an intrinsic interest in egality and equality, and such things are probably part of the human condition - maybe even of the mammalian condition.

This desire to fit in with the group is also manifest in your conversation; which rarely about substantive matter. More usually it is string of of conventional saws and clichés and echos that make us seem friendlier or at least that we are actually listening to the vapid blather of the other party. It's called phatic discourse, and is mainly used to establish empathy (or a place in the pecking order).

Turns out the blathering on with your pre-verbal child may be imperative for the kid's cognitive development. Most blokes, even doting fathers, are much more interested in getting the wean back to sleep than making goo-goo with the small, incontinent, mysterious creature in the babygro. Here's a BBC summary report, with several links to the primary literature of the science, showing that pre-verbal kids who get less focused verbal interaction with bigger people finish up with narrower language themselves. It's not enough to have the baby in the vicinity while you discuss The Match or the timing-belt of your car with the neighbour across the fence. You've got to get down with the infant and pay attention listen and react. That way the child learns that conversation is about taking turns and, later, that there are several words which mean almost the same thing. We all want our kids to use more than one descriptive adjective - especially if that adjective is fucken.

And for gawd's sake will you please leave the goddamn phone in the other room when you're having quality time with your wean? Research shows that interrupted conversations really inhibit learning new words. You may surmise that it also does bad things for self esteem: the disembodied voice emanating from Dad's black gizmo is more interesting to him than me. But beware: this is when daughters start to twist their fathers round their little fingers: 16 years later the car keys will be required.

De mortuis

. . . nil nisi bonum. I'm not about to slag off one of the administrators who died at his post at The Institute yesterday morning; although we had unfinished business. Word has it that he stood up from his desk, sat heavily back down and died - he was 62. We inhabit a society that finds such abrupt departures unacceptable, so several people who share his office did their best to help him and one of them called the Nurse and an ambulance. We have a Nurse on site during the working day because our community is nearly 10,000 strong and some of them feel not-so-strong periodically. When one of my students slopped concentrated sulphuric acid onto the bed of the fume hood in 2013, and another student rested her fore-arm in the puddle <ouchy!>, it was to the Nurse I sent the injured party with a pal for support if needed.

Yesterday, when the nurse arrived at the double, she started on the SOP [standard operating procedure] for such cases including cardio pulmonary resuscitation CPR. I've done that, or at least the ventilation part of it, with no prior training, back 40+ years ago when I worked as a hospital orderly. It didn't work out in 1978, despite the best resources [well maybe untrained self excluded from 'best resources' in that case] and it happening in a hospital ward. While the Nurse tried manually to force some sort of circulation to the brain, two ambulances arrived, and the paramedics took over. I happened to leave the building at the end of the day with one of the technicians who'd been much closer to the centre than me. I said "Well at least he went quick". He replied "Not really, they went at him, CPR, defibrillator, the works, for an hour. They have to do that . . . until someone tells them to stop". An hour is a long, long time anoxic to retain any sort of quality life if they did get his heart going again. Let's ask some questions:

• Who is it who finally calls it futile and  . . . tells them to stop? 
• Why is that the policy? 
• Is that Institute policy; paramedic policy; Nurse policy?
• Who benefits?
• Is there any sense of informed consent about these procedures from The Principal ?

I think I've made my DNR or even my NFR instructions clear to my family. It's quite okay if they hold my hand [it might be reassuring] or just wring theirs without feeling obliged to Do Something. I have no intention of dying at work, but I will now have a word with my most immediate work-mates to call my family but not call an ambulance. I really cannot abide fuss.

Secondary structure

Part I.
When they started to sequence The Genome Era with baker's yeast Saccharomyces cerevisiae 25+ years ago, I noticed something peculiar about the structure of chr III, the first ever eukaryotic chromosome to be sequenced. It was one of my three [3] big ideas in a life-time of science; and turned out to be probably not true. But it was nevertheless a contribution to the debate which opened up a novel way of thinking about constraints on the sequence of genes and their equivalent proteins. As more chromosomal sequences came on stream, Ken Wolfe, in the office next door, but not yet my boss, also noticed something peculiar about the order of genes. In particular he found evidence of shadowy patterns of duplicated segments. They were "shadowy" because the component genes were a) often only distantly related b) frequently missing. Thus on one chromosome you'd have 12 genes
A - B - C - D - E - J - K - P - Q - R - S - T
and elsewhere you'd find
a - b - e - f - g - h - j - l - m - n - p - q - t

What normal people saw, if they even bothered to think in gene order terms, was that a pair of neighbouring genes A,B were distantly related to another adjacent pair a,b. somewhere else in the genome. And a little further along on the same two chromosomes P,Q were sort of similar to p,q.  . . .  probably a coincidence, nothing to see here. What Ken saw was [hypothesis to test!] that a chunk of the genome had been duplicated, and that most of the duplicated genes had been surplus to requirements and had mutated away to pseudogene, and then to nothing-to-see-here. He was able to see the present pattern through the spectacles of evolutionary time. If you aligned the genes themselves rather than their sequences, then the signal from the pairs was boosted by the similar intervening singletons Ee Jj and Tt:
ABCDE---JK---PQRST
ab--efghj-lmnpq--t
**  *   *    **  *

Ken bounced the idea off Denis Shields, another absurdly smart friend of mine,  and they published Molecular evidence for an ancient duplication of the entire yeast genome in Nature in 1997. That paper documented the existence of 55 duplicated regions incorporating 13% of the total gene complement. That paper included Fig.2. [part shown left] which could claim a prize for the prettiest, most data-rich and informative visual display of quantitative information [Tufte] ever to come out of Ireland. It showed commendable bottle to keep digging in the gene-duplication pit  when 87% of the genome was saying something else entirely.

People like me would have taken the gong from Nature and moved on to the next project. Ken kept shaking the tree, looking for, and at, these patterns in the gene order of Saccharomyces cerevisiae. Some more focused [boring, pedestrian, ordinary] scientists started shaking their heads wondering if 'poor Ken' would soon be found crouched in a corner of the senior common room muttering to himself while blocking off imaginary fragments the yeast genome with extravagant hand-gestures. Partly on the back of his Nature paper, he landed one of the first mega +mi££ion grants when SFI Science Foundation Ireland was founded at the very end of the last century. One of the first tasks he set one of the Effectives of his dream-team was to create YGOB the Yeast Gene Order Browser. I remember him trying to explain his vision to Kevin Byrne, the recently recruited Quant who was assigned this task. Kevin could spell DNA but not desoxyribonucleicacid because he was trained as a mathematical astrophysicist . . . but ygob could that boy code! The result of that collaboration was like Fig2 above but with moving parts and incorporating not one but 2 dozen species [see the paper for more details] I always thought it looked like a mighty train marshalling yard for assembling genes into their most functional order:

Like the London Tube Map, the YGOB browser distills from the noise all the relevant data into a clear graphical roadmap with all the evidence (protein sequence, gene sequence, annotation] only a click away. Bri'nt!

With this infrastructural support, Ken then got to know pretty much all the 5,500 genes that kept Saccharomyces cerevisiae ticking: who neighboured whom; which genes contributed to biochemical pathway X; which protein was the receptor for which ligand. It was an extraordinary feat of memory and deep knowledge and a lot more useful than retaining the first 5,500 digits of π. As a teacher when you know everyone in the class you know who's missing. Ken started to notice a few cases of missing data: where every species in YGOB had genes ABCDE but Candida glabrata had only ABC-E [as L]. It turned out that in a number of such cases there was a gene in the expected position but it had evolved so fast that it retained no sequence similarity to any other gene on the planet in the databases. Nevertheless, the turned-up novel protein had the right secondary structure which, coupled with the compelling synteny / genomic location data, made him confident that he could ascribe a function in these peculiar cases. These functional annotations are vital to convert (ATCG)_∞ into making sense of what genes and organisms do. He wrote it up in a (rare nowadays) single author paper for Current Biology: Evolutionary Genomics: Yeasts Accelerate beyond BLAST. A few years later he set one of his students to make a comprehensive search of all the YGOB species looking for similar cases. They were able to annotate a number of other proteins which had fallen through the generic gene-finding sieve when each species was sequenced and annotated. Deep knowledge and a synteny Way of Seeing was able to tidy up a number of peculiaries in the biochemical capabilities of particular species.

I was started down this recent-history rabbit hole because I read a report in Chemistry World about the discovery of a 'missing gene' in Trypanosomes [prev] which are responsible for sleeping sickness one of the most scything neglected tropical diseases. Richard Rachubinski of U Alberta was looking for novel targets to kill the parasites before they could kill their human hosts and was surprisingly unable to find a homologue of PEX3 in the lists of trypanosome proteins. PEX is a family of proteins associated with the development and maintenance of peroxisomes - sub-cellular organelles which are vital for the processing of long chain fatty acids and reactive oxygen species. PEX3 remained elusive until Rachubinski went to a research presentation outside his own field and learned about a bioinformatic tool called HHPred which can infer function based on secondary structure [which is comprised of the intermediate building blocks or structural elements: α-helices; β-sheets; turns; ω-loops] even when the protein sequence is completely different from other members of a gene family.  They are a long way from an effective therapeutic but the first step of identification and annotation has put them on the right path. More shadows firming up into a hard reality!

Similar proteins

Proteins are made of amino acids stuck together in long chains which come curling out of ribosomes in an order dictated ultimately by the DNA in the genes on the chromosomes in the nucleus of every cell which makes new proteins -- which is all cells that
are still alive. I've spent the last 30 years trying to make sense of those sequences: usually comparing them by alignment. Here's part of the sequence of insulin for pigs and humans:
SP|P01315|INS_PIG   PQAGAVELGGGL--GGLQALALEGPPQKRGIVEQCCTSICSLYQLENYCN 108 SP|P01308|INS_HUMAN LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN 110
                     *.* ******   *.** *****  ************************
Notes:
[Each of the 20 amino acids found in proteins has a unique 1-letter code. And a more readable 3-letter code too]
{For the first half of the 20thC, diabetics were injected with insulin extracted from thousands of pig pancreases and it worked just fine.}

You can see that the sequences, and therefore by inference, their 3-D structures, are very similar but with several significant differences: the human version has two extra amino acids GA for starters.  If the final functioning protein is in 3 dimensions, then the linear sequence, as it appears from the ribosomes, or as represented on paper and on screen as above, can be thought of as a 1-D object. In between, biochemists talk about the secondary structure, which is comprised of the intermediate building blocks or structural elements: α-helices; β-sheets; turns; ω-loops.

How similar do protein sequences have to be for us to believe that a) they have a common ancestor and b) they therefore have a similar structure and function? If you line up any pair of sequences, some of the letters will match because there are only 20 amino acids to play with. Like when I align the opening words of the first two paragraphs above:
Proteins are made of aminoacids
You can see that the sequences
3/30 = 10% of the letters appear in the same position in these random unrelated sequences. Molecular evolutionists talk about the twilight zone when ~15-20% of the amino acids are identical between two sequences. More than 20% identity and you can be reasonably confident is assigning similar function and inferring the same 3-dimensional structure. In the twilight zone you really need some independent information to make that call. You might naively think that the random probability is 5% = 1/20 because there are 20 amino acids to play with. But because you're allowed to insert gaps in one sequence [to accommodate the extra GA in the insulin above, for example] and because some amino acids eg LAG and more common than others eg HWC:

the biologically meaningful / statistically significant cut-off (and the Twilight Zone) are pitched higher than 5% at just under 20%. To be continued . . . as gene location becomes the added value independent information to match barely detectable similarities between genes in two different species.

Years ago, in the late 90s, I wrote some code to deconstruct protein sequences as if they had been hydrolysed by 1M NaOH [that's caustic soda to cooks] into a soup of their component amino acids. This might be though of as a protein's 0-dimensional structure. My program also tallied up and counted the frequency of each of the 20 amino acids. Tricking about with a test dataset, I noticed that this string of 20 numbers had quite high predictive value: the AA frequencies of Bacillus subtilis recA could predictably fish out the recA in Escherichia coli etc. I got sufficiently excited about this that I presented it as my contribution to the weekly internal lunchtime research seminar. Ken Wolfe, not yet my boss, but usually the smartest chap in the room, said he'd noticed this several years earlier but hadn't though it worth publishing. My abiding problem as a scientist is that I lack the stamina to get results, even interesting results, down on paper and through the publication process. I am thus glad to be able to publish this executive summary in The Journal of Blob Studies - they will take anything.
  Part II.

20ct19 Osteoporosis Day

If your bone density is top-notch, bear a thought for those whose isn't.

• Lumberjacking
• Bar pinched by awkward settle
• Mighty Oak felled with a two-knob hinge
• Tree-monkeys can go home if this mother can get close to the site
• Descent: 
• The Lhotse Couloir by ski . . . normalising the bat-shit bonkers.
• The Betsiamites River by Kayak
• 8000m without a parachute . . . there is a big net
• Of branches by competent tree-monkey
• Mildly amusing food anecdotes. Like Dau.I's elderflowercordial vs fish-stock mix.
• Thinking man's physics
• Mr Holland's clarinet lesson
• Arlo n Pete sing Presley
• Tao & Pete Viva la quinta /quince brigada
• The Boss Sólo le pido a Dios
• Trek: Picos de Europa
• Cabo Verde? Horácio - Cabeçada
• An everyday story of home-schooling folk in Drenthe, NL. 
• Dau.I escaped from our End-of-Days Farm in September 2011, and Dau.II did a runner in May 2013. We were all so happy eating turnips and wild honey up until then.

This last week: Margaret Attwood shares Booker prize with Bernadine Evaristo. Attwood for her sequel to The Handmaid's Tale. Now that THT has been televised / serialised, it gives women a uniform to ironically protest their rights. Irony is effective because it enrages the strong.

Dunmore Chronicles

My Grandfather was harbourmaster of Dunmore East in Co Waterford from the foundation of the [Free] State until he retired in 1947. That year my own father, his son, turned 30. Insofar as the younger man had a home, I guess it was Dunmore until he married in 1950. The woman he married, my aged mother, has recently turned in her cards as a self-catering, autonomous 99 y.o. and signed heraself into A Home about 5km from the village where she lived since 1983. It took a medical crisis and a trip to hospital than made everyone realise how exhausting it had been to cook and clean for herself being registered blind and increasingly wobbly. Dau.II and I did a Thelma and Louise a couple of weeks ago to help tidy up the house for sale.  We turned up a little framed photograph with broken glass in a desk drawer and I brought it away for rescue and restoration:

The little cutey is my father, aged 10ish in ?1927? He is sitting on the quayside in Dunmore not looking the least bit proprietal because his father was The Gaffer. It reminds me of The Boyhood of Raleigh, without the ruffs:

And less you think that my Old Man was a passive poser for pictures, I also came across this seascape:

That was painted by my father in the Summer of 1939, just before the Scheiße trifft den Fan with WWII. The good ship D3 in the forescape is one of a class modified from a design by famous naval architect Uffa Fox and built by my grandfather, I guess with help from his son when the latter wasn't at school in Co Down or Dartmouth or sailing the main. I've always been a little in awe of my grandfather, who knew me aged 2 but not vice versa, because he died the following year in 1957. He lived a riotously adventurous life and definitely could sew on a button. On the striking coincidence front, I had just returned from England when the man who occupied my father's bed in his capacity as son of the subsequent harbourmaster of Dunmore East sent me this clipping from The Munster Express 12 Jan 1940:

The principal in that obituary is the great-grandmother of The Beloved and Mr Patk Baldwin-Cardiff is Pat the Salt's father. When The Beloved and I met in 1973, we were a long way from our roots in East Waterford. Indeed it was weeks before we realised that there was any kind of connexion.

Legitimate death by assault

Patrick Day [L looking happy] is in the news because he's dead. Here's the wikipedia exec summary: Patrick Day suffered a traumatic brain injury after being knocked out by Charles Conwell in a USBA super welterweight title bout on October 12, 2019, and died four days later. Boxing announcer Michael Buffer described Day as a "wonderful young man" and that "everyone in the boxing community is crushed". WBC president Mauricio Sulaiman said boxing had lost a "brave, kind and wonderful friend". Charles Conwell, the boxer who caused Day’s brain injury, wrote an open letter on Instagram to him expressing his sorrow and regret.

This may remind you of The Onion's ironic take on gun-control in the USA ‘No Way To Prevent This,’ Says Only Nation Where This Regularly Happens. Which story they have published multiple times after another mass-shooting. Eddie Hearn, who makes a living matching youg men to batter each other for money, wept during his comments on Day's death "You can say 'it's boxing' but it is so hard to justify." How about saying "it's assault with a couple of deadly fists what do you expect", would that help you clarify your ethical position, Mr Hearn?

I was a child boxer. After lunch on Wednesday as eight year olds we used to flail at each other in a temporary ring set up in one of the class-rooms. But the physics of it says that small damage can be done with little fists in big padded gloves; and the past [1962] is a different country. Back then  it would have been unthinkable for little girls to have a go at each other in that way; the moral corruption of society is such that Katie Taylor can now serve as a role model for young women. The case is altered when fit young adult men and women at the peak of their physical strength batter each other until one falls down . . . and someone makes money on it. Shocking is what it is. Should be unacceptable in a civilised society. And, as you know, CSE Contact Sport Encephalopathy is not limited to boxing.

We all got guts

Wexford Science Café WSC met, as ever, on the 3rd Tuesday [15th] of October 2019 in the Sky&Ground. It was me, again [*], talking about the gut and its darkling denizens. This has been of spectator's interest to me for at least a decade and is more recently surfacing into public discourse both scientific and popular-press. Needless to say, a lot of unsubstantiated nonsense is uttered in the latter medium. The field is at the stage now where a lot of data is accumulating that changes in the gut microbiota are associated with irritable bowel syndrome IBS; inflammatory bowel disease [worse!] IBD: Crohn's Disease CD, ulcerative colitis UC; peptic ulcer [Helicobacter prev]; obesity; diabetes. No surprises there; although it is not obvious what is the cause and what the effect of these co-occurences. What might be more surprising are the psychobiotic associations between the gut flora and . . . anxiety, autism, chronic fatigue, dementia, depression, Parkinson's. And note that your gut flora goes on a journey from cradle to dotage with different classes of microbes rising and falling in a reasonably predictable manner as we age.

Sources: nobody expects you, dear reader, to get down and dirty with the scientific literature. Each paper will normally present only one study indicating that bacterial strain X is associated with condition Y in either mice or humans, occasionally both. If you take the materials and methods on trust [and you shouldn't!], you can get the key factlet from the PubMed abstract. Or you can read Giulia Enders book: Gut: The Inside Story of Our Body's Most Underrated Organ; [originally Darm mit Charme. Alles über ein unterschätztes Organ] which I reviewed a tuthree weeks ago. I was all set to present an ExecSummary of that book when one of the WexSciCaf lurkers pointed me at The Psychobiotic Revolution by Anderson, Cryan and Dinan. Scott Anderson is a US-based science journalist, while John Cryan and Ted Dinan are academics from UCC in the Independent Republic of Cork.

In the airy arm-wavy world of popular science books you have to polish your crap-detector before you invest time and money in 'facts' therein presented. Here, I'll share some of the interesting intel which I gleaned from my reading.

The money is in probiotics but you and I don't want to spend our hard-earned dollars on products of dubious efficacy and doubtful quality control. Dinan & Cryan cite one study where the contents of 13 probiotic supplements were compared to what it said on the tin. Only 4/13 had a table of contents than actually matched the contents. Probiotics are food supplements and have a far lower administrative and licencing bar to leap than drugs which are classified as medicine. But the thrify should follow the prebiotics route: these are the dietary changes that can encourage the growth of good bacteria: try ginger, garlic, carrots, apples for starters. Actually, keep it simple and follow Michael Pollan [multiprev]: Eat food; not too much; mostly plants. Un-food is anything that comes in a packet with more than 6 indredients.

There has been a bit of interest recently in the few cases of auto-brewery syndrome. This occurs when a colony of bakers' yeast Saccharomyces cerevisiae, against the odds and its normal environment, sets up shop in some person's intestine. There it scarfs up any passing sugar and anaerobically converts it to ethanol and carbon dioxide. The CO₂ causes a certain increase in fartiness but the alcohol crosses the intestinal epithelium and starts to intoxicate. I don't think you'd have a leg to stand on [you'd be legless, arf arf] in court if you got arrested for driving under the influence.

Now before I forget, I'll note some of the major players in the gut flora: some good and some bad; all just tryimng to make a living. There may be 1,000 different species of microbe donw in the dark, but 99% of them fit into 4 different Phyla [major groups of bacteria]

• Actinobacteria
• Bifidobacterium longum, B. breve; B. dentium [richer in infant guts]
• Proprionobacterium shermanii [bubbles in Emmenthal]
• Firmicutes
• Clostridium difficile, C. botulinum [botox]
• Bacillus cereus [re-heated rice poisoning]
• Lactobacillus spp. LABs good guys
• Bacteroidetes
• Bacteroides thetaiotaomicron [prev]; B. fragilis; B. plebeus [freq in Japan]
• Prevotella
• Proteobacteria
• alpha: Rickettsia prowazekii; Brucella abortus [prev Alice Evans]
• beta: Neisseria gonorrhoeae, [the clap] N. meningitidis [meningitis]
• gamma: Escherichia coli and other enterics incl Salmonella; Pseudomonas aerogenosa
• epsilon: Campylobacter jejuni [food poisoning] Helicobacter pylori [ulcers]

[*] Footnote: Wexford Science Café is still trundling along - but seemingly only if  I continue to push and heave t'bugger up hill. It just doesn't seem to be gathering momentum although further adherents occasionally appear. As with a lot of such voluntary things, 90% of the work is done by 10% of the people. As a max of ten people turn up on a good day, the 10% is Me. When the call for next month's speaker is issued, everyone looks at their feet. And nobody seems willing to take on the minute adminstrative burden of calling the faithful to prayer once a month [Over the Summer, I e-asked this question direct of several of our most frequent attenders, only some of whom bothered to reply and all of whom were too busy]

Dirty protest

Dirty Protest will be an evocative phrase for anyone who can remember the 1970s & 80s in Ireland. If you don't remember, or didn't study late 20thC Irish history in school, you'll have to Google "Long Kesh" "Blanket Protest" "Dirty Protest" and "Hunger Strike"; maybe also "Laurence McKeown" who survived? I was reminded of this by the phrase "instead of slicing through it the knife-edge simply melted upon contact, leaving streaks of fecal matter" in a scientific report from Kent State U, Anthropology Dept Experimental replication shows knives manufactured from frozen human feces do not work. Whaa'? Why would you want to do an experiment that starts with adopting diet rich in fat and protein, and harvesting what's left after a passage through a human bowel?  Because of a widely repeated story by ethno-anthropologist by Wade Davis [of whom I am a quite shameless groupie multibloboprevs] by an Inuit informant whose grandfather had escaped the prospect of government internment by using a frozen-shit knife  to kill and butcher a dog and using the carcass as an improvised sled.

It would be hard for Davis not to take this personally as he is the sole living, broadcasting witness to the grandson's tale and is on record as believing it as fact rather than a tall tale to bamboozle the educated Westerner. It's like a colleague of mine suggesting, at the twice yearly faculty meeting, that final year student research projects involving computational molecular evolution aka bioinformatics should be marked out of 50% because they doing aren't real science . . . and then asking me not to take it as a personal attack despite me being the only person to offer and supervise such projects.

Davis responded to the critical experiment with a peculiarly pedantic essay in Nautilus (the science magazine that "combines the sciences, culture and philosophy into a single story"). As far as I gather, Davis thinks:

• there are more important things to research when the Inuit's whole world is melting under their feet
• dog butchery is significantly different from the pig butchery carried out by the Kent State team
• with a side-swipe at Western society in general and Ethical Approval Boards in particular which accepts killing pigs for food [or insulin] but gets daintily precious about treating dogs in the same way.
• shit-knives last longer and sharper when the ambient temperature is -50°C rather than whipping them out of a freezer and hacking away on the lab bench next door.

Perhaps it would have been better to maintain a magisterial silence about the failure to replicate the Inuit experience. Not least because his response has given the story a lot more sled a là Steisand Effect. Did someone mention replication? That's a key tenet of science because the singular of data is anecdote. Only one shit-knife was made in Ken State it didn't work so good. If you started the process with 10 different bowels, including some inside native Inuit who always eat blubber and meat, maybe the case would be altered. But let's not forget to credit the Inuit for being handy and thrifty with the limited resources available to them: they've lived in the Arctic for thousands of years where/when most of us wouldn't last 1,000 minutes.

Source: Metafilter were the comments point to a Japanese experimentalist who makes knives out of ice, tin foil, rice and other unlikely products.

Did somebody mention Insulin and Banting & Best? Check out this essay about the miraculous power to cure diabetes from B&B's break-through <heart warming>.

Pláinéad amháin

One Planet [ta-daaa L]! There is no spare, no back-up. We've been fucking it over for the last 200 years since the Brits, and then everyone else, started digging coal out of the ground and converting it to carbon dioxide to make individual entrepreneurs spectacularly rich and supplying people with things they didn't realise they needed: gravy-boats; knives, forks and spoons for everyone in the family . . . and guests (no need to bring your own spoon); cast-iron, wrought-iron then steel bridges; skyscrapers; concrete bridges and roadways; billions of nails, safety-pins, screws. Later on it was hula-hoops; cuff-links; one-use water bottles; paper tissues; "disposable" diapers designed to last forever in land-fill.

In any society, even in Bhutan, someone rises to the top: by accident of birth; by election in representative democracy; by bloody coup; by promotion from apparatchik to chairman of the praesidium of the supreme soviet Президиум Верховного Совета. Those people are Leaders but, In Ireland at least, we no longer expect them to lead; for many years we know that our government will be craven in the face of adversity, incapable of doing anything bloody, bold or resolute in a crisis. We have a choice of two centre-right main parties which blame each other for the unpretty pass we have come to and an pathetic in thinking beyond the next election - where they will have to please everyone to win enough seats to get re-elected. Thus Paschal "Craven" Donohoe, the Finance Minister, having failed to put any increase on the carbon tax for budget 2019 last year has now put an additional €6/tonne on fuel . . . deferred till May next year for home heating oil. 6€/tonne is less than 2c/lt for unleaded and diesel. It's a token because far too many voters love their cars far too much to be offended by a painful increase in their fuel taxes. One of the points of taxation is to change behaviour to better serve the community - it's not only about raising revenue, Paschal.

On Tuesday 8th October, I was down in the next county, at the second annual plenary session of the PPN [Public Participation Network]. I don't only go to these things for the cocktail sausages afterwards; I'm also there for the cocktail party chatter and networking. One of the consequences of getting old is that I no longer hide in the t'ilets but wade in to talk to randomers to see what they do - heck, you never know how they might be interesting or useful or both. The theme of the meeting was Sustainable Communities and the PPN praesidium had arranged two separate speakers and a panel to discuss the subject. The first talk was about Bee Aware and the All Ireland Pollination Plan. It was astonishing to me that someone can have a job as liaison for this vital aspect of the future of farming [no bees; no apples, no oranges, no almonds] and be quite shameless about knowing no science. Quite apart from the fact that the All Ireland Pollination Plan is barely aspirational, let alone articulated and implemented. The second talk was about Sustainable Energy Communities. When we came back to Ireland 30 years ago The Beloved worked in fuel poverty, sustainable energy and domestic energy efficiency. Nearly 1 million homes have been built in the Republic since then, with a barely perceptible nod towards insulation or fuel efficiency: just fire up the boiler, lads! Retro-fitting is so much more expensive. At least the speaker was competent and on top of his data, even if the story was so distressingly short-sighted.

We were left with a panel discussion, the most useful part of which was a "speed-dating" session where each invited panellist was invited to name one thing that would make a difference to our planet in these "interesting" times.

• Damn single use water bottles: make them illegal, or tax them up the wazzo so that their 'convenience'becomes painful
• press windfall, part bug-eaten?, apples into juice
• make ponds for invertebrates
• damn wet-wipes: make them illegal, or tax them up the wazzo so that their 'convenience' becomes painful
• Insulate, insulate, insulate
• LED lights have a smaller footprint
• luv your daisies Bellis perennis; mow the lawn less often; feed the bees (all same thing)
• Greener cleaning products
• smokeless fuels
• take your canvas bags

You can see that some people are incapable of focussing on one big thing. cf Fox and Hedgehog. My friend and neighbour Mary White, who secured the last seat in the constituency for the Green Party in the 2007 general election, affirmed that in minority politics you can only hope to achieve one thing while in office. As a county councillor she sponsored a bye-law making recreational quad-bikes illegal on the uplands of the county. I guess she reckoned that the balance between pain and political gain among her fellow councillors would allow her that much of her green agenda. If she pitched higher she might get nothing.

Forensic plate pouring

At almost the last minute, I got to teach one lab section of Yr3 Food & Fermentation Microbiology. That was because a couple of last minute registrations pushed the numbers in the year just over the magic number of 36 (= 18 x 2;  18 being the health & safety limit to the number of bodies in the room. I think that, if surplus hadn't appeared, I would have had nothing to do on Thursday afternoons and had short hours for my last year teaching at The Institute; that would have been okay also!

I've had two weeks with these 12 students, about half of whom I had for QM [remedial math] 2 years ago. As in recent years, I'm going to appoint each pair in rotation to the rank of Autoclave Liaison Officer ALO. At least some of our students will be confident and comfortable with this potentially lethal scalding instrument when they move into their final year. They also need to be confident, comfortable and reliable when pouring Petri dishes if they want a career at the microbiology end of biology.  reliable here means: can you pour 20 plates from 500ml of agar so that they are all the same weight / depth? You only get to be able to do that by deliberate practice and it's important to get some feedback on how you're progressing towards the goal. Accordingly, last Friday while putting away the previous day's plates for use next week, I recorded the weight of each one.

Each pair of students had poured a wildly different number of plates: in general those who had poured light plates got more out them out of the bottle. That's not necessarily a good thing: the empty plates cost about €1/dozen so it's better to pour fewer plates so long as you have enough. Also thin plates dry out and blow away more readily, so don't last as long waiting to be used. Again, the shelf life needs to be enough - either one week or two weeks usually. Fat / thick plates otoh aren't getting as many functional plates from each run through the autoclave. In the table [L] I've recorded
1) the number of each type of Petri dish
2) the weight of just the plastic - count x 13.15g
3) the total weight of all the plates less the plastic
4) the average weight of each filled plate
5) the standard deviation of each batch
I've highlighted the lowest Standard Deviation [in the 3rd data column] because those boys were clearly in the zone when they were pouring - each plate the same as the last. But they still have things to learn. Expecting to pour 20 plates, they had labelled 20 empties before pouring because they poured a little mean, they only used 401g of their half litre of agar. That's enough to make 4 or 5 extra plates from the batch. But the lazy arses decided not to label the extra plates; preferring to throw away the surplus agar. If we have enough starch agar plates for the class next week, that was a good call. If not then someone will have to go sort in their investigations at the frontier of science. In the interests of nerdnik completeness here is the analysis of variance which shows clearly that there is a significant difference in the average weight of Petri dishes poured last Thursday - tsk on the quality control, lads.

Vela catches a flash of change

Marion Island is named for Marc-Joseph Marion du Fresne, the French explorer and cartographer - and nothing to do with the DuFresne lenses you find in lighthouses because those are Fresnel "no relation" lenses. The boy named Sue thang apppears to be less of a problem with the French than it is with Johnny Cash. But enough of this free-association. Marion Island, half way between South Africa and Antarctica, appeared over my horizon because of a mysterious <ba-DUM> double flash that was picked up nearby by a US satellite called Vela 5B or OPS 6911 on 22nd September 1979. These icosahedral satellites were launched in pairs [Vela5A and 5B shown R prior to launch with an engineer's bottom for scale] as part of a project to detect and monitor nuclear explosions in space or the atmosphere in contravention of the 1963 Partial Test Ban Treaty (PTBT) signed by USA and USSR. The double-flash was, supposedly uniquely, characteristic of a nuclear blast with a 1ms pulse of light followed by a longer brighter pulse as the initial opaque shockwave dissipates and allows the fireball to shine through. The Vela signal was complemented by some hydro-acoustic data from the Naval Research Laboratory NRL which was capable of picking up all sorts of anomalous underwater soundwaves. The Vela Project had a long line of positive controls as well, when their satellites had correctly identified 41 known nuclear explosions.

The current consensus is that this was an early exercise of nuclear power by Israel, probably with the collaboration or connivance of the Republic of South Apartheid RSA. President Carter's diary for Feb. 27, 1980: “We have a growing belief among our scientists that the Israelis did indeed conduct a nuclear test explosion in the ocean near the southern end of Africa.” indicates that it was the then consensus as well. But admission that Israel had become a rogue nuclear state was extremely inconvenient politically and an "independent" body of high powered US physicists, concocted a scarcely credible collision of possible natural phenomena to explain the Vela flashes. Indeed subsequent advances in science have exposed the explanation as physically impossible rather than scarcely credible.

The Vela incident thus did lasting damage to the political credibility of US policy in its fatal attraction for the state of Israel. It also did transitory damage to the scientific credibility of US technocrats who were seen to be capable to squaring any circle of deceit to suit their paymasters. It was badly done, Emma, badly done . . . badly done.

Thirteen October

Few musical links from the last week.

• Satie, Eric. I find his stuff super-restfulzzzzzzzzz
• Gnossiennes 1,2,3
• Trois gymnopedies
• Sara Bareilles et al: Once upon another time.
• Brave
• First Aid Kit - un hommage to Emmylou Harris
• FAK - The Lion's Roar
• Katie Melua - Fields Of Gold
• I will be there
• If you were a sailboat
• Horse-racing wrongs bloboprev now MeFi commentary
• Lateral. A quiz for Internet "celeb" nerds led by Tom Scott.
• Primes, spirals, Dirichlet (1837). Beautiful explanation of the distribution of primes by 3blue1brown . . . just zzzzz off when it gets too much - I did.
• More narrow-gauge trains than you can shake a stick at.

Go West young man

"Go West, young man . . . and grow up with the country." is usually attributed to newspaper editor and later presidential candidate Horace Greeley. He felt that by making a difficult, and adventurous, choice, a young chap could do the state some service but also do himself a power of good. Every year since I began teaching Yr3 Food and Fermentation Microbiology aka F&F3C, the student body has been leavened by les  français a handful of whom come to The Institute under the Erasmus Scheme [prev]. Erasmus is a flagship of EU social engineering: subsidising the cost of taking young people out of their comfort zone [and away from The Mammy] to mix with others in the EU melting pot and learn new ways of thinking, eating and conversing.  Actually, I don't care which way young people go, so long as it is over the horizon and not just on holiday.

My academic colleagues shake their heads <tsk tsk> and wonder why none  (to the nearest whole number in an average year) of our students avail of the opportunity. I don't say out loud, but I suspect it's partly because none of those <tsk tsk>ers do that sort of thing themselves and so don't really have a European network of colleagues to tap for the placement of our brightest and best. It depends on how you ask the question [ne nonne num]
"Surely you want an expenses paid trip to Spain; all the chorizo you can eat; and ready access to the films of Pedro Almodovar on the telly?"
vs
"You know that they make tea with warm water?"

I was in my one hour a week supervising lab practicals last Tuesday and one of the students, who had never been in one of my previous class groups, asked if I had any contacts in Europe or ideas about how he could position himself outside of Ireland after he graduated next May. With a quickening pulse, I asked him what field floated his boat because he hadn't signed up to do one of my computer-based projects. Turns out that he was one of two lads who had spent Summer 2019 in Dijon (where the mustard comes from) in Burgundy. So he and his pal will have completed their 12 week work placement before they sit their final exams. "My" chap had spent his time doing chemical analysis in a Kombucha lab, taking samples from the brew and measuring the phenolics, the tannins, the colour and the acidity in each batch. He'd written a long formal report for his french supervisor, albeit in English: his french is much better now than before his departure from Ireland but not yet really up to writing a report in french science-speak.

Kombucha should now be familiar to all my tree-huggin', Birkenstock-wearin', woowah-believin' readers. It is a SCOBY ferment from sweetened tea (green black white separately or together) but can also be made from fruit-juice. SCOBY? an acronym - Symbiotic Culture Of Bacteria and Yeast - where the yeast is probably not brewer/baker's Saccharomyces cerevisiae and the bacteria is some sort of Lactic Acid Bacteria LAB. There is a market for the stuff if you can make it in sufficient quantities and with reliable quality control.  But as we agreed, making it is the least part of the process if you intend to retire on your money before you're 50. What makes the difference between a hobby and a fortune is branding, advertising, and distribution. I suggested that he might start building the management team for his enterprise Killeshin Kombucha by flirting with students taking the Digital Marketing course in the School of Business. I've already sown the seeds for Killeshin Soy "soy sauce with a hint of guinness", ギネスのヒント醤油 which will carry off prizes for best in class at the Tokyo Food Festival in 2029.

The two francophone biologists have been recruited by our International Office to tell their bubbly and productive story to the current cohort of 3rd Years. No better men!

No Neck

With a very expensive education, some surprising things clash up against each other in my head. So surprising indeed, that occasionally I cannot follow myself when I read some earlier pieces in The Blob's back-catalogue. Last month, I tasked my students in Yr1 Quantitative Methods for "Group Work and Presentation". This required them to pick a topic, do some collaborative research, summarise it on half a dozen powerpoint slides and present that in a 10 minute talk. One group from the Brewers, Distillers & Fermenters class had chosen to do chorizo but there was some discussion about the pronunciation. I explained <TMI TMI!> that they had a choice: choritho or choriso. The latter being easier for Irish eyes and ears, Andalusians and all their South American descendants.  The former being preferred in the rest of Spain because their king Carloth Thinco had a lithp. He had a lisp, possibly because of the peculiar and distinctive architecture of his Habsburg jaw. That recognisable face was cemented into the dynasty because they would marry each other. Vice is nice but incest is best - the game the whole family can play.</TMI TMI>  Our Brewers decided to follow Andalusia rather than Madrid.

Don't get away with the idea that inbreeding is only long ago and far away. A certain amount of endogamy is expected if you live in a village without cars or buses; or in a wider community [Hutterites, Ashkenazim] where conventions limit the available partners. My Pal Johnnie, who grew up a Protestant in Tuam Co Galway, was faced with a choice of three potential opposite sex partners from his church; none of whom was less than 40 years old. When I knew him 25 years ago, he had turned sufficiently that he was dating a very nice Catholicker girl from Sligo whom he's met in Dublin.

An extensive [exec summ] and exhaustive [full paper] study of the 456,414 genomes from the UK BioBank has been carried out by a group from U. Queensland, Brisbane, AU. They analysed the status of each of 300,000 genetic variants SNPs in both copies [maternal and paternal] of these these peoples DNA.  Theyfound that the genomes of 125 of them or "1 in 3,652" people born in the United Kingdom between 1938 and 1967 show extreme inbreeding, indicating couplings between full siblings, a parent and a child, a grandparent and a grandchild, all of which are specifically forbidden by the Church of England's Table of Kindred and Affinity. Most SNP variants have two possibilities from the choice of four nucleotides A T C G. If a string of SNPs in a particular part of a maternally inherited chromosome

A - G - G - G - C - T - T - A -T - C - C - T - C - A - T

is also found in the equivalent part of Dad's teaspoonful

A - G - G - G - C - T - T - A -T - C - C - T - C - A - T

it could have happened by chance (there are only 4 possibilities at each place after all to the odds are about 4^15 = 1bn-to-1) but, as the duplication extends, this explanation becomes increasingly unlikely.  They found that this ratio of 1/3500 is about the same rate of reports to the police of incest (11,200 cases in a population if 55 million). Acknowledging that reported cases of incest are likely only a fraction of actual cases of incest (everyone knows incest is frowned upon by polite society, so the perps aren't going to bruit it abroad?) it suggests to me that motherfuckers use condoms. I never thought I'd have occasion to utter that phrase! It turns out (I'm sure you knew this already, but I live a very sheltered life) there is a brand of condom called Motherfucker Rubbers.

In a sense this is like a genetic disease and its occurrence has about the same prevalence as Duchenne Muscular Dystrophy DMD (1:3500 live births); haemophilia (1:10,000); cystic fibrosis CF (1:2,000 in Ireland, less elsewhere).