Tuesday, 15 October 2019

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.

Monday, 14 October 2019

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.

Sunday, 13 October 2019

Thirteen October

Few musical links from the last week.

Saturday, 12 October 2019

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?"
"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!

Friday, 11 October 2019

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.  They found 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). 

Thursday, 10 October 2019

Black dog

As I go on [and on and on and on?] I appreciate that my job is only tangentially  about the tasks in the lab manual and the learning outcomes in the curriculum. The things that students will remember is when the script is left on the table and we deal with more immediately current and interesting things which crop up. Like my encounter with a young scientist who is going places, which gave my morale a boost - that was way off the syllabus. I was in good spirits therefore when I left work a little early to pay my respects to the family of a  neighbour, who died over the weekend."No flowers please, donations, if desired, to AWARE." flagged a tragedy, because that charity works in depression and bipolar support.

I think this must be the fourth case of someone making their own exit which has occurred in a 3km radius of our mountain home since we moved there 20 years ago. There is no upside to such events but I feel that repetition helps to de-stigmatise the families involved. If it happens so often, you have to be really certain in your righteousness to be judgemental.  I was chatting to one of my living neighbours, who had signed up to an 8 hours shift marshalling traffic, about what a loss it must be for the family. Even a dark and broody father is still daddy. Neighbour remembered how, at the last such event in the parish, he'd been in the pub with some mates. One of them had suggested that the principle actor was 'selfish' for abandoning his wife and teenage children. A complete stranger turned round and invited him to "Shut the fuck up! You know nothing about the Black Dog. Your pal didn't know he had a family when he pitched out; all he could feel was a world of pain". The raw emotion of that unscripted response put a bit of a damper on the pints.

Last Summer a very old friend of mine  from Dublin killed himself. I had to write to his wife; another old friend of mine, although they were both much younger than me. The only thing I could imagine was to say "damn those neurotransmitters" which had become so unbalanced as to teeter poor Paul off the edge. It's an imbalance like from when your immune system starts to eat your own myelin-sheath [MS] or your pancreas stops producing insulin [Type I diabetes]. But if you can scapegoat something so small, impersonal and essentially beyond our control then it may help unshoulder a portion of the blame which survivors inevitably carry with them forever. It's a bit like Niall Breslin personifying his Black Dog as Jeffrey as a way to establish some distance from the darkness. Another blobbessay on depression.

I was, as always around Irish funerals, touched and impressed by the capacity of the community to come together to navigate the transition from the ordinary daily round abruptly to the grave. And I did note the phenomenal capacity of Irish people to make and consume tea and ham sandwiches. I think we do death well in Ireland.

Wednesday, 9 October 2019

Talking up the sludge

Last Friday at The Institute one of my colleagues in Engineering hosted a mini-symposium on sewage sludge: how to process, de-toxify, transport and process the stuff. The event was sponsored by Veolia the French water, waste and energy conglomerate. Sponsorship meant free food; so I was on it like bird shit on a car bonnet. There was a helluva lot of food but really not many people "It's a bit of a niche interest, processed human shit, isn't it", I suggested to the bloke behind me in the auditorium. After I'd grazed for 40 minutes on goujons and chipolatas while chatting to my room-mates, we went in to the first talk . . . by the Sludge Engineer for Irish Water. She had come up from Cork to talk to the very select audience. Even with people who were in the field, she seemed to have an uphill struggle against the perception of sewage sludge as anything other than a toxic liability.

It sounds like it should be a marketable product: rich in phosphates and nitrates, suitable as a soil bulker and conditioner. At least you should be able to give it away for free. My neighbour-above has been [twice] happy to take tonnes of the stuff from the Veolia waste-water treatment plant WWTP in Kilkenny to spread on his fields. Both times delivery-failures up our steep, unpaved dirt-track access has been a disaster for us: one spill and one stuck trailer this summer. It is indicative of the public relations market in sludge that in the first incident the sludge was free but the farmer paid the haulage. 5 years later Veolia is prepared to pay the haulage as well just to get rid of the stuff.  WWTP currently generate 230,000 squidgy tonnes = 60,000 tds [tonnes dry solid] of sludge a year and there really aren't enough people or businesses to take the stuff so some of it gets diverted to landfill.

Stats. There are 500,000 private septic system across the rural Ireland. 60% [N = 376] of Irish WWTPs deal with the sewage from < 500 people. Only 11 plants treat for more than 100,000 p.e. [person equivalents]. Bring back the night-soil men! If we all shit in a bucket we'd waste a lot less water and be more mindful of cleaning up behind ourselves rather than flushing it all away for Nanny State to deal with.

Sewage sludge has a peculiar, particular and persistent smell. That alone makes people think it is a bit fishy. Then there is accumulating data that, apart from NO3- and PO4+, sludge is loaded with cadmium, nickel, microplastics, anti-microbial resistance AMR compounds, unprocessed pharmaceutical residues and, ominously titled, emerging contaminants. aka unknown horrors. The trouble is that ordinary people are as thick as shit in the use of the flush-toilet: wet-wipes and sanitary towels are the least of it. IF the privatised trash collectors start to charge by weight ANDIF people continue to rebel against paying water charges THEN the WWTPs are going to see pizza-crusts, plastic bags, potato peel and holed socks appear for processing.

One thing that emerged from the seminar is that Irish Water's expert on sludge processing was largely at sea when it came to a deep knowledge of the problems associated with its handling and treatment. In the audience were 3 or 4 representatives from the local authority who were responsible for five pilot sewage processing projects involving reed beds. We were presented with an executive summary for where these plants were set up and how they worked. In the post-talk Q&A an old chap on the other side of the room asked why they were using Phragmites australis the common reed and why it had to be imported from Poland . . . Phragmites only grows for six months in every year; there were at least 30 other reed species which grew year-round in the Irish climate. From the public employees, there was no answer at all, let alone a coherent response to this question. The old chap then asked a supplementary question about the complex set of 'aeration' pipe work in the reed-bed: "You are aware that Phragmites is quite content to grow in seriously anaerobic conditions where it is quite capable to finding enough oxygen from the atmosphere?". Pfffffff collapse of stout government-employee parties. Now I'm sure it's more complicated than that, and Irish Water had shelled out wodges of wonga to their own consultants in the design of their reed-beds; but the optics were terrible.

Sewage sludge really needs a public relations campaign to convince us that it is an asset and not a liability. I didn't have the chance to suggest that all Irish Water employees who are pulling in more than €60,000 a year should be obliged to spread at least 60kg of sewage sludge on their gardens [kg pro-rata for higher salaries] - because it is so good for the roses. It is nearly 30 years since the daughter of UK's Minister of Agriculture refused to eat a BSE contaminated beefburger.