The Herd

The Wexford Science Café is still lumbering along after three years of monthly meetings. Somehow, the mantle of Convener and Master of the Rolls fell upon my shoulders and I haven't been able, like St Martin, to find a beggar with whom to share it. There are 40+ people on The Rolls but, even with a following wind, no more than 10 people ever turn up and nobody, ever, volunteers to think of a topic and prepare 5 minutes of material to launch discussion. At my pleading, the suggestion materialised that we have a go at vaccination, but the suggester wasn't able to make an appearance that day. I was okay with that because I had a mass of material loaded up on The Blob about the ethics, epidemiology and economics EEE of Gardasil the controversial vaccine against Human Papilloma Virus HPV and by extension against cervical cancer. Here are those links H - P - V - Splashback. I clagged them altogether into a 5,000 word briefing document and sent that out to The Roll as preparatory homework.  But then, dang-and-blast-it, on the night I was caught up on the farm waiting for someone to come and take two bales of last year's haylage. I got three other unavoidably delayed apologies and nobody claimed to have turned up so I suspect that we can do Vaccination for the April meeting and nobody will complain.

One of the compelling reasons for choking back your anxiety about side-effects and getting your healthy, well-fed, warm-housed, walking, middle-class child vaccinated is the idea about Herd Immunity. If enough susceptible people become unable to propagate the pathogenic virus because they have been vaccinated then the virus doesn't propagate through the population. This means that the poor, the dispossessed, the very young and the immuno-compromised don't get exposed to that virus and so do not die, . . .or survive deaf, blind, brain-damaged or heart-damaged. Go on Rich Reader, take one for the team in a community spirited way: you have nothing to lose but your firstborn.

In the back of my 'mind' I've always know that the epidemiology of vaccination is different for each pathogen. Some diseases are really difficult to catch (Leprosy) while others propagate easily (chicken
pox). Then I came across this really handy document written by Patrick Honner a New York high-school teacher and jobbing quant. It explains the maths of herd immunity. You should read it.

The point Honner makes is that we'll all be fine if each infected person transmits the lurgy to one other person: that's linear growth. If each one infects 2 other people, you have exponential growth because those two pass it to 4 those four to 8 and after 10 rounds of replication you have 1024 people down sick - a kilobug you might call it. If we can interrupt or slow down the propagation to one-a-time after ten rounds only 10 people have been affected. There are two aspects of the life-cycle of the pathogen that are relevant 1) how easy it is to catch and b) how long is the infectious period.  These can be conflated into a single statistic the 'basic reproductive ratio' R₀ which varies for each disease. Measles [tiny case shown R above] is usually reported as top of the list:

Measles	Airborne	15
Diphtheria	Saliva	7
Smallpox	Cough	6
Polio	Fecal-oral	6
Rubella	Cough	6
Mumps	Cough	5
HIV/AIDS	Sex	3
Pertussis	Cough	5
SARS	Cough	3
1918Flu	Cough	2
Ebola	Bodily fluids	2

Honner goes on to explain the very simple math to convert these R₀ figures to a Herd Immunity Threshold HIT which is the % of the population that needs to be vaccinated to knock a given disease on the head. The HIT is inversely proportional to the R₀ and equals about 90% for measles but only 50% for pandemic 'flu. One problem is that measles is communicable for 4 days before first symptoms appear, so it's roared through Miss Kehoe's First Class before anyone knows it's in town. That's one reason why the HSE really pushes out the flu vaccination programme each Winter because you don't need to get everyone on board to achieve significant results for the population 50% will do and that's achievable. It is also the reason the WHO was able to bring Ebola under control at all at all. A ripping through the kids disease like measles requires extra-ordinary levels of compliance to achieve the HIT. Back in the 1950s and 1960s with polio, leg-braces and iron-lungs really fresh in parents' minds, several Western countries were able to achieve those necessary compliance numbers or close to them. Not any more. Parents tend to be young adults who in the core of their being think that they and their loved ones are immortal, so they don't buy into actively preventing infectious diseases. They don't buy into preparing for a long number of years after retirement either - but that's another story.
If you're a teacher this worksheet may be useful.

Power fosters political inertia

Five years ago, I cited a couple of short pieces by/ about/ with Michael "Exposé" Lewis. Check this one about the transition from Obama to the Trump administration. What strikes me, in the reprise, is the superficial quality of the discourse. There are three fat-salaried people on the other side of the CBS News-desk and they want a wrap on a key element of political and government dysfunction in three minutes.

A couple of months back, my old grad school pal P ordered me to read The Premonition: A Pandemic Story [NPR] by Michael Lewis. I'm an institutionalised bloke; can obey orders, so I put in train its translation from a shelf in Dalkey, South Dublin to a bin in Tramore Co Waterford awaiting my collection. Viva the national electronic library service! Lewis is an accomplished and successful non-fiction author, with an agent, a publisher, editors and friends-who-read. It is no surprise therefore that The Premonition reads easy: weaving several parallel, same-time, threads into a coherent warm blanket of understanding. Part of the skill is deciding which of the stories is the hook and which can be left to later chapters. Indeed, I'm sure that leaving researched and written characters on the cutting room floor is another part of the process. Must be a little galling to be interviewed at length and not get name-checked in the published book.

Because it is A pandemic story rather than the Official History of SARS-CoV2, Lewis has chosen to centre the tale on the Three Covideers shown above 

• Joe DeRisi, a super-smart, tech-savvy, open-handed, molecular biologist, epidemiologist and genome sequencer from UCSF
  
• Charity Dean, a no-nonsense, buck-stops-here California Public Health physician
  
• Carter Mecher, a smartest-bloke-in-the-room medical data-slinger and medical historian from the Veterans Administration
  

These are the people who were right, knew they were right early on and tried to overcome the inertia, terror and vested interests of people, institutions and corporations who were doing just nicely in a warm bath of status quo. In the interests of balance, Lewis finds people on the Other Side - whose actions, or more generally inaction, hyped up the impact of the pandemic. First among these Bad Hats is the CDC, which Lewis characterizes as a political tool, utterly risk-averse and mired in red-tape. Thus, even if it was clear what policy would save most lives or alleviate the pinch-points in response protocols, it was institutionally impossible to find a CDC Effective with sufficient authority to implement a change that was a clear public good. Close reading of the history of the pandemic may conclude that it was impossible for the CDC to implement any change, like ever. Lewis says. "And it's removed the brave ones. The brave ones have all got their heads chopped off. So it's sort of institutionalized a cowardice that we're going to need to face up to so that this business of punishing people who are doing their damnedest to try to save us from ourselves has got to stop."

As well as a poke at John Ioannidis, the fallen angel of epidemiology, Lewis also singles out Sonia Angell, Charity Dean's boss at California Public Health as the main impediment preventing Dr Dean from being brave . . . and stomping SARS-CoV2 into oblivion with, like, public health measures. PHMs are actions which inhibit individual freedom so as to protect "society" or its more vulnerable members. This idea puts its finger on the pulse of politics over the last 40 years: since Margaret Thatcher announced "There is no such thing as Society". In this worldview you and I have no obligation to the dispossessed, the future or the planet. Dean, DeRisi and Mecher and their team were sure that only by early intervention and draconian curtailment of individual rights could the virus be brought to heel. Angell, along with the POTUS, many senior political appointees and public representatives, didn't see a virus with a death-rate of 1.5% as something to get the economy [and, yes, Society too] all bent out of shape about. I don't doubt that your mind is made up on these matters - as well as, half-alphabetically, antigen tests, boosters, China, D-vitamin, entry requirements, hydroxychloroquine, Ivermectin, Johns Hopkins, kids-as-carriers, long-covid, masks . . .

If you are a covid-interventionist, then you'll probably enjoy The Premonition.

Skull Valley Sheep vale

Ancient Roman citizens used to leave the party with an ave atque vale = hail and farewell. By contrast, Roman gladiators used to begin there party with Ave, Imperator, morituri te salutant = hail emperor, those about to die salute you. 6,000 sheep from Utah started off St Patrick's Day 1968 with little thought that without vale farewell they were morituri about to die . . . but they were. About 2/3 of them dying [R for sample] from inanition and internal haemorrhage, the rest shot in the head by their human minders when it was clear they weren't going to get up.  It is exactly 50 years ago, that a phone call was made to the US Army Dugway Proving Ground, alerting them to the fact of wide-spread sheep death in Skull Valley about 30 miles NE of their Top Secret chemical and biological warfare CBW playground [warning sign below L] on the edge of the desert a couple of hours outside Salt Lake City.

hmmmm? well it turned out that, on the 13th of March that year, there had been 3 separate experiments at Dugway on the distribution of what we now call weapons of mass destruction WMD, in particular a nerve agent called VX. VX is a denser, more viscous, relative of Sarin which has been used with such abandon in Syria.  Both VX and Sarin (and the Новичо́к Novichok stuff which took out Серге́й Ви́кторович Скрипаль and Юлия Сергеевич Скрипал in Salisbury a couple of weeks ago) are anti-cholinesterases. Cholinesterase is an enzyme [most biologics ending -ase are enzymes] is which breaks down the neurotransmitter acetylcholine ACh after it has been used by motor neurons to stimulate the muscles. Anti-cholinesterases stop the enzyme working, so the ACh continues to call for muscle contraction and you die all locked up in the agonising spasms of tetanic paralysis. Botox kills you with flabby paralysis because it prevents the release of ACh from the motor neuron.

Team Dugway seem to have done a controlled experiment by trying out three different methods of dispersal: they fired an artillery shell; they burned 600 lt in an open-air pit; they loaded a fighter-plane with two tanksful and sprayed it out over the countryside.  In all cases, they cut the lethal load with a red dye of similar density to make easier the post hoc detection. I wrote about using Serratia marcescens as a marker in another friendly-fire incident for CBW dispersal over San Francisco in 1950.  A low-ranking officer on the Army's PR team mistakenly released a confidential report to the press and public opinion quickly gelled into the certainty that the [poor] sheep had been killed in a carelessly conducted experiment by the US military. It became A Mighty Wind that blew fresh air through the establishment and changed government policy on CBW and probably directly saved thousands of Vietnamese people and their livestock from a fate worse than probably involving death. That loonngg essay A Mighty Wind is by Dr Steve J Allen of the right-wing independent investigative think-tank Capital Research Center. In a previous life Allen was a researcher for 1990s Speaker of the House Newt Gingrich [R, Georgia], but we won't hold that against his views on the Skull Valley Incident; which I find to be informed and informative about the history, chemistry, biology, ecology, epidemiology, politics, and press coverage of those times.

The 3 internally inconsistent issues that interest me are:

• that the physics of dispersal and dilution of VX - which is lethal at small-small concentrations [LD50 about 10mg / person or about 10x more toxic than Sarin] but not so small that a single molecule homeopathically diluted by the wind can kill several thousand sheep - don't seem to be consonant with the supposed action-at-a-distance. 
• the symptoms in the dying sheep - no difficulty breathing but internal haemorrhage - are definitely not consonant with VX poisoning: anti-cholinesterases exhaust the muscles which power the lungs because the neurotransmitter acetylcholine is left permanently ON stimulating them.
• only sheep Ovis aries seem to have been affected by the VX; not the jack-rabbits Lepus californicus; marmots, Marmota flaviventris; beavers, Castor canadensis; ground squirrels, Urocitellus mollis; Coyote, Canis latrans; Raccoon, Procyon lotor; nor Mule deer, Odocoileus hemionus. 

Here's what I think from my sofa, 50 years after the event. The US military had been lobbing toxins about the range in Utah for the best part of 20 years and 17 March 1968 was the first time that a lot of farm-stock had beencome ill in the vicinity. That's in the vicinity in the uniquely American way of people who will think nothing of driving 80km to have dinner or take in a movie. The 6,000 sheep died in two tranches 50km and 110km distant from the flight-path of the spraying jet-fighter, and 4 days after the last run of tests at Dugway. I suggest that flight and fatality were coincidental and that the sheep succumbed to a sheep-specific enterohaemorrhagic bacterial infection. That pathogen having been spread through both flocks of sheep, by exchange of stock in the days before in the attack became obvious. The farming corporations who owned the sheep got compensation from the Feds at about twice the market value of the stock. So they had a vested interest in allowing the press to put the blame on the military. The military, maybe paradoxically, in the realpolitik of the cold war liked the idea that their potency was in the public domain and hopefully putting the frighteners on the Soviets. As evidence of the credibility of my pathogenic insult explanation, remember that half the saiga antelopes Saiga tatarica of Central Asia died of Pasteurellosis in May 2015.

lá fhéile pádraig

Yes we have no bananas

Uniformity is a grand thing altogether in manufacturing if all the screws, chips, widgets and switches in a gizmo are identical THEN you can have economies of scale, Henry Ford [prevorecent] famously said of his Model T " you can have any car, of any colour you like, so long as it's black". He brought the production line to a peak of perfection by insisting that the parts were generic. Perfect for the share-holders, less so for the poor folks who installed the same two bolts in the same position on every car that passed the soul-deadened eyes.  The quality control in the automotive industry is such that you can go to a breakers yard for a second-hand door if you happened to have dinged your motor: it will fit perfectly. Tree-huggers like me are rather skeptical when this drive for identity is carried into the realm of biology, especially in food. There is something wrong in presenting for sale 6 identical carrots or apples in a neat plastic tray.

My aged father-in-law Pat the Salt likes a banana Musa acuminata x balbisiana in the morning.  Can't fault him on that - slow release, low [51] glycaemic index, loadsa potassium, conveniently packaged. A few months ago, one if his other carers suggested that presenting The Banana with his morning coffee would help everyone get ahead with the day - breakfast could come later (the banana doesn't count). I've  taken this advice on board. But two Mondays ago because of a cock-up with the commisseriat there were no bananas. While he was getting dressed I nipped up to the supermarket to replenish supplies and I was delighted to see 10 singleton bananas bagged up and reduced to €1 . . . WIN! The next week, I went up at the same time and secured the same bargain and last week again. Clearly one of the morning tasks for the fruit and veg department is to gather up all the loose bananas from the weekend feeding-frenzy and sell them off quickly. If Pat is eating 7 bananas a week and I'm buying in 10, then there will soon be an embarras de richesse in the larder, so last time I brought the surplus away to make banana bread: yum!

Unless you live in Honduras you will have been struck by how boring bananas can be. There is no place for pretentious gits posturing about the hint of strawberry or the mouth-feel. All the bananas you have ever eaten are genetically identical of a cultivar called Cavendish. Up until WWII, a different variety Gros Michel was king. But ' Panama disease' a novel fungal pathogen Fusarium oxysporum ripped through the banana plantations about that time and shook Dole, Geest, Fyffes and Chiquita's shareholders to the core. The great banana moguls responded by replacing Gros Michel with another seedless, but crucially F. oxysporum-resistant, strain. Cavendish didn't taste so good but that sort of consumer resistance was reduced to nothing by an aggressive advertising campaign: "These are not the droid you are looking for; these are bananas, they taste delicious." There is an interesting article in Wired setting out this stall: good on the epidemiology, more arm-waving on human [=consumer] psychology.

One of the points made about the vulnerability of bananas is that the cultivars are seedless and propagated by cloning. But this is the same with potatoes - they make flowers and set seed (like tomato seeds) but are propagated by distributing genetically identical tubers in sacks for planting out - in Ireland by tradition on St Patrick's Day when there is a holiday. When I worked in Wageningen on potato blight in the Summer of 1976, my boss had just returned from a field trip to Peru and Bolivia where he'd been haunting the local markets buying up purple, knobbly, diminutive tubers with the intention of incorporating them in a breeding programme for blight-resistant spuds. The banana people could do that too but it would have to be accompanied by a marketing campaign convincing me-the-consumer that variety is the spice of life. Sometime about 1971, when I was still in high-school we went on a field-trip to the local plant-breeding station which specialised in developing new varieties of apple. One of my pals asked the chief breeder what the latest apple tasted like. It was as if they hadn't even considered the issue! Even back then it was all about packability, transport and disease-resistance. So long as it was reasonably wet inside, consumers would buy.

Another reason given for why bananas are particularly at risk is that they are planted in vast monocultures too close together so that a fungal pathogen can spread like wild-fire once it has drifted into the locality from some gap-year student's back-pack. This is why the Irish potato was so quickly annihilated by the late blight Phytophthora infestans in 1845 and many many subsequent years. But a monoculture is not required for Armageddon. As we have seen with black ash Fraxinus nigra and English elm Ulmus minor, the next susceptible individual doesn't have to be next door it merely needs to be within the dispersal range of the fungus or its insect vector.

The Wired article does proceed inductively from the case for bananas to look askance at the depauperate nature of our food variety. Far too much wheat and potatoes, far too few local seeds, nuts and greens and that's ignoring entirely the worryingly narrow diet of beef- and dairy-cattle feeding on tonnes of corn Zea mays and soya Glycine max and us eating the result as hamburger. Our food security depends on us eating much more rocket Eruca sativa, rabbit Oryctolagus cuniculus and radish Raphanus sativus. Quite apart from that making life more interesting.

Corona Corona

Damn and blast it; Corona is owning centre stage in my life. Not least because I danced with a man who danced with a girl who danced with the Prince of Wales: which mean that I sat next to someone in the pub for 90 minutes on Tuesday. The previous Thursday an early CoVid-19 case was identified on the very floor on which she works in Dublin. The math in the links below indicate that the true numbers of contagious (even if asymptomatic) people is about 10x the official figures. Last night the official count was 129 which is more likely 1,300. So here we go with my One Stop Shop for Corona
Virus 2020.

• Corona codona: My pal Bobbos academic analysis to point the finger at bats as the CoVid-19 natural host.
• Hints of LockDown at Ireland Inc.
• 3blue1brown on Covid-19 exponential growth
• Preparing for the end of the world - a fortnight of self-isolation
• Crap-detecting: sales of the beer [R] are not [Snopes] affected by the virus going viral.
• This just in: the horse's mouth on Covid-19. Globalisation spreads the disease (air-travel) but it has also made drugs and medical devices vulnerable to supply-chain glitches: from economics, weather, social instability etc. Too many eggs are in too few baskets a long way from you and me if we need, say, an egg or two.
• good news is that kids are low risk for Covid-19
• not so good news their middle-aged parents are at risk (not just the grannies)
• Michael Osterholm (the horse) credentials the whole Joe Rogan interview is findable but 100 minutes.
• Covid-19: reasons for lock-down; impact of failing to do this: triage, death, disruption; with charts and graphs
• Stats graphs timeline of CoVid-19 developments in Ireland [Wikipedia]
• Putting Covid-19 in perspective: it's going to be worse than Swine 'flu but better than Spanish 'flu
• Hats off to Jurgen Klopp who knows he knows nothing about epidemiology
• The end of the world as we know it: toilet-roll wars
• Suggested reading for 14 days at home On the Beach by Nevil Shute: an invisible deadly killer sweeping round the world (after nuclear holocaust) and what folks do while waiting for the end

Learning academic writing

Each year at The Institute - ir's coming up to five years in January - I've been supervising final year research projects: sometimes a handful, sometimes a dozen, one year 16! The kids have a choice of doing this task in the lab "all wet" or with me using computers "dry" to reveal the pattern and process of evolution. The 'Binfos' are a mixed bunch - some, like me, known to be inept at the lab bench; some slackers looking for an untaxing option; and every year tuthree who are really the best students we have - curious, motivated, self-starting and independent. I love 'em all! Not least because of the mix - getting our least academic students to fulfill their potential and a little bit more is just as rewarding as having an adult discussion about the evolution of 'flu viruses or the epidemiology of  Huntington's Disease. Whatever the level, these are all original research projects - finding out something about the world that nobody else on the planet knows. That's a pretty rewarding challenge for someone who has just got the vote.  How do we know that nobody has been there before? Each student is requested and required to carry out a review of the scientific literature on some part of the natural world. Sometimes, especially with our rocket scientists, I will be bullied into 'supervising' a project which is driving the student. Otherwise, I'm allowed to let my butterfly mind flit over the meadows of knowledge looking for a pretty flower to investigate. It must also be admitted that I'm not above whoring out my Effectives to answer questions posed by colleagues and collaborators. That can work out really well, and at least one student has parlayed that relationship into a Master's degree elsewhere.

It's nearly the end of term and by 1700hrs Friday 8th, all our students, wet and dry, had to submit a first draft of their Lit Review. I then had a really interesting half-week's work reading, critiquing and returning them. This year the reviews were all serious pieces of scientific research, neatly capturing a variety of different topics. Even the essays submitted with a "this is crap, but I'm drawing a line under it here" warning were on-message, coherent, unwaffly and full of interesting stuff. So I've learned a lot, and we should all be collectively proud. In a number of cases, the LR has thrown up potential avenues for research that I had not thought of.

I won't pretend that all the work was written in perfect grammatical English: we have two Polirish this year and they are quite mean with their definite and indefinite articles. And don't get me started on the apostrophes scattered like confetti at a wedding. But this is really the first substantive [5000 words] piece of academic writing they've ever submitted. Accordingly I've had to explain some of the basics of communication.

They read, they write, I read, I come across a strange word. Now I had an expensive education, some of it involving Latin, so I can often make sense of long words. But sometimes I'm totally foxed so I Google it up and find a definition there. That's not really good enough. The Lit Review should aspire to being self contained, so I push the students to include a Glossary.

Glossary - should include all the words that only appear in your report, which you wouldn't expect your bff or another Binfo to know; because you're the only person on Campus who has read what you've read. In some cases, that will be an essential addition for the readability and utility of the report. Remember that the report goes off to an external examiner who is a generalist. S/he may not be able to spell Blast, let alone Huanglongbing or Sporolactobacillus. The glossary also serves as a memory aid: that three letter acronym TLA which you defined some place earlier in the report; I've forgotten what it means. All those should be in the Glossary.

They read, they write, I read, I come across a strange idea which I'd like to follow up. If it's come from the literature, there should be a citation embedded in the text which will kick forward to a list of references.

References.- Everyone should use referencing software like Endnote Mendeley or Zotero to match the citations to the references because it is part of the training. But the result has to be fit-for-purpose which is to allow the reader to follow up one of the statements to the source. In the old days of print this required: Authors, initials, (year), Title, Journal, Vol, pages. Back in 1977 I could write Smith AB 1975 NAR 213: 410-417 in my notebook and hunt out the relevant volume in the library. The students of The Institute are submitting a hard copy, so all this info shd be included for that reason. In the modern world of epub and full text, for any biomedical paper, it is handy to include the Pubmed ID like PMID: 8441625 because I can easily get to the source then. Referencing software operates on a GiGo [garbage in garbage out] principal and some of the kids have driven the software so that itmangles the author name or the citation, or doesn't include page numbers - it is part of the learning experience to sort this out.

As our reading gets so cluttered with hypertext links, I like the idea of being forced to think that a written essay is a mode of communication. To reflect on what must be done to ensure than your reader is not misled and is empowered to follow your thoughts forward into the unknown.

Multitasking Me

The first week in the new job was, as always there, a bit chaotic, so I had to cancel/postpone a few lab classes and I lost one class entirely as we were looking at different editions of the timetable. But the students so far are all engaged, or well-mannered or happy or all three .  So I been teaching Lovelock and CFCs; epidemiology; the human nervous system; introductory e-mail; confidence intervals a la ExCel; density, dextro-rotation, viscosity to determine [conc] of sugar solutions.  I've got a desk, a telephone, a parkplatz, an _excellent_ colour laser printer, unlimited pens/post-its. I borrowed my first two library books, found the staff canteen and the t'ilets.  I haven't worked so hard for 20 years and I've spent the whole weekend prepping 2 hours on the ozone layer.  I know I'm going to learn a LOT in the next few months.

Covid Comms

We've been running the Wexford Science Café WSC for nearly 6 years now. The idea was that STEM-folks in the Sunny South East would have the equivalent of a Book Club, a Choir, or a Men's Shed - a place to gather with like-minded adults to chat about about science. For those who have made the effort - it can be all to easy to stay indoors on the 3rd Tuesday of February if it's dark with a whippy wind and the roads are a litter of fallen branches - it has been rewarding. Then again, there are more people who came once only than those who stayed to learn the handshake and the secret sign. We've covered a few bases because the community is diverse in its interests and expertise:  Air-quality and asthma; Allometry; Back-garden astronomy; Bacteria in food; Cider; Compost toilets; Diabetes & Alzheimers; Diets; Erwin Schrodinger; Galena; Generic meds; Gravity waves; Greenland ice melt; Gut Microbiome;  March for Science; Neuroscience of torture; Oroville dam; Pheromones; Radon; Science book-swap; Soil microbiome; Stephen J Gould’s spandrels; Thomas Kuhn’s paradigms; Toxicity from botox to beer; Urination once again; Water quality; Wolbachia and tropical diseases; Zombies;

The theme or topic for each night is part of the attraction but the networking and the sense of belonging is at least equal in importance. Last year [2019] we tag-teamed with the Wexford Science Festival WSF which had been launched with some razz-ma-tazz the previous [2018] year. That was a success because their publicity machine was better funded than ours and we swept a handful of new STEM faces into our orbit. Our mutual admiration and common ground made us promise to do the same again in 2020. Then Coronarama swept out of Wuhan [L market-watch] as a pestilence and a great disruptor of all social events; perhaps especially those which habitually met in a pub!

Well, whatevs, we are meeting tonight for a discussion about Coronarama. Far too many people pretend to know everything about: Corona Viruses; SARS-CoV-2 itself; Covid-19; epidemiology; statistics; zoonoses; masks; mink! long-covid; asymptomatic covid; my dead neighbour; PCR testing; R-numbers; vaccines; the Economy; care homes; Sweden and intubation. But when the usual suspects are wheeled out for a sound-byte by the media there is far too much hubris and not enough humility. I am working on a hypothesis that the usual suspects are overwhelmingly male . . . because they are so goddamn certain; which means that whatever news requires a response can be explained and finished with in 200 words or 90 seconds whichever is shorter. Accordingly tonight we are digging with the pink foot and hoping for a more measured discussion about how scientists communicate their findings and how they could do better in explaining things to Jo Public. The gig is hosted by podcaster Dr Megan Hanlon and Cliona O'Farrelly, the Chair of Comparative Immunology at TCD.

Megan's channel is called Unravelling Science, where she is currently on a podcast jag interviewing successful scientists about where they came from, where their inspiration came from, what they do and what can they say to encourage early-stage scientists that it is worth the candle. I like the interview genre very much, it conveys the Passion for Science in a way that any number of dry, passive voice, peer-reviewed formal scientific papers manifestly fail to do. The irony is that the only thing which counts in scientific progress [= promotion] is peer-reviewed papers while the only thing that will recruit the next generation is the passion and engagement of mentors and teachers. Strength along these two unrelated axes rarely meets in one person.

Y'all come along down; you need not leave your sofa but you do have to book one of the 100 seats in the virtual Wexford Science Café. Looking forward!

More than 3-D

When we bought the farm 25 years ago, we paid no attention to the fact that we were to be on the edge of an SAC. We also paid no attention to the fact that, in the auction, we'd actually bought a chunk of this Special Area of Conservation dry heath that characterizes the vegetation of the red hill which gives its name to our postal address. Our share of the 24th part of the commonage came with the house. Pro rata we own more acres of hill than we have in our 6.47 hectares of in-bye fields which surround the house.

Those upland acres turned out to be an asset when The Beloved started farming from the kitchen table by applying for grants to do the right thing by current government agricultural policy but also by our druthers. REPS [Rural Environmental Protection Scheme] GLAS [Green Low-Carbon Agri-Environment Scheme but also green in Irish] and AEOS [Agri-Environment Options Scheme] followed each other as a succession of application forms. The consequent cheques paid for 500m of hedgerow, 12 acres of traditional hay meadow, a mini orchard, innumerable if currently uninhabited bee-boxes, bird-boxes and bat-boxes [trio L], and regular piles of gorse Ulex europaeus brash for small creatures to hide in. The gorse woody stems make excellent quick firing for the wood-burning stove.

The dry heath of the Blackstairs, and other uplands along the NW fringe of Europe is worth preserving because it gives elbow room to a unique assemblage of plant species and their associated vertebrate, invertebrate and microbiological hangers-on. If the heath goes through inattention, over-grazing, under-grazing or carting away in 40t trucks to access the lithium or andalusite mineral below then a handful of species and an irretrievable ecosystem will go extinct. And extinction, as we now know, is forever. The brief of the National Parks and Wildlife Service is, partly through designating SACs, to preserve Nature from the depredations of commercial expediency or ignorant collectors or quad-bikers.

But wait! Dry Heath is as much the work of human hands as it is fruit of the earth. If it wasn't for first clearing trees and the annual round of grazing by sheep, let alone occasionally burning the heather, there would be no dry heath. It is a stage in the process of succession from bog to forest artificially maintained by farmers trying to extract a living from that unprepossessing resource. All those cheques from Min Agric took account of the 7.89 ha we owned [in common] on the hill. But until recently it was an alien place: I spent far more hours beachcombing the Waterford Coast than walking through wet-bracken. A couple of years ago (and proper order), The Man announced that if we were going to claim a subsidy for farming the hill we'd have to put some sheep up there as evidence. The last 3 years, accordingly, I've spent many happy hours fossicking about the hill looking for sheep but finding moths, flowers, stone work and myself.

After a summer mapping the territory and paying attention I concluded that our uplands were more than a 3-dimensional pimple on the World. A proper appreciation of its existence and its "value" required attention from multiple disciplines including historians, archaeologists, botanists, hill-walkers, agronomists, economists, bird-watchers, poets and . . . farmers. It was, indeed, A Holistic Landscape.

That essay is the opposite of the way governments and the education system works. There it is a territorial war: science professes to know nothing about The Arts Block. Historians and art critics are baffled by science.  Even within biology geneticists and immunologists operate as if the other discipline exists over there; which is a disastrous stance for dealing with the epidemiology of a pandemic. The Departments of Welfare, Justice and Health fight each other during the budget negotiations and are Resolute in shuffling off responsibility for drug-addicts, the homeless and the mentally ill onto the other departments. Jakers, we need some joined up thinking! Damme! I came here to talk about a notable bridge builder and I've consumed 700 words on the Intro . . . come back here tomorrow for Pontifex Maximus?

Clear crumblies off the road

I caught a snippet on the wireless where they interviewed Desmond O’Neill, Director of the National Office for Traffic Medicine. Yes, there is such a thing. It's hard to work out how big the quango is because a) O'Neill has day-jobs as TCD's Professor of Medical Gerontology AND Consultant in Geriatric and Stroke Medicine at Tallaght Hospital and b) the NOTM is under the umbrella of the RCPI Royal College of Physicians in Ireland.

Aside-o-rant: What is it with all the Royals, already? Royal College of Surgeons, RCPI, Royal Dublin Society. and whole raft of organisations where the great and the good hobnob together. Do we not live in a Republic?

What are we talking about here? Let us consider the NOTM's definition: The term “traffic medicine” evolved to embrace all the disciplines, techniques, and methods aimed at reducing the harm traffic crashes inflict on human beings. This includes medical and surgical care provided to crash victims, improving vehicle crashworthiness, developing better safety belts and brakes, designing safer roads and traffic control systems, training and educating drivers, research into the biomechanics and epidemiology of traffic crashes, and developing and enforcing traffic safety policies. The best-known element of traffic medicine is the need for medical certification showing fitness to drive.

Aha! That's why the Office is headed up by a Geriatric specialist. They have just launched new 7th Edition October 2018 guidelines so that doctors are well informed when they certify that their patient Bridie O'Crumble is fit to drive. The guidelines are issued by the RSA = Road Safety Authority = Údarás Um Shábháilteacht Ar Bhóithre. My late lamented mother-in-law got the cert from her GP whenever she asked for it despite getting through a quite remarkable number of wing-mirrors in her declining years. I'm sure Bridie similarly gets a pass because the doctor would rather please her client than please the unknown parents of the child who will be killed when Bridie has a senior moment while driving. Will the new guidelines help get some rational decision-making into the process of certification? I don't think so because the 'guidelines' are 126 pages long! I cannot imagine what the full report looks like - it must fill the boot of Bridie's doctor's car. I also cannot imagine a busy GP reading through such a mass of information when they haven't time to read their copy of The Lancet and the BMJ. Certification is not only about oldies; here are the chapter headings.:

• Neurological disorders incl epilepsy and seizures
• Cardiovascular disorders  
• Diabetes Mellitus  
• Psychiatric disorders
• Alcohol & Drugs misuse and dependence  
• Visual Disorders 
• Renal disorders
• Respiratory and sleep disorders incl. Obstructive Sleep Apnoea Syndrome OSAS
• Miscellaneous 

That has the ring of sense, my father was late onset diabetic and a bit of a boy-racer. Our greatest fear was not that he would fall into a diabetic coma at the wheel and write himself off; but that he'd fall asleep at the wheel and plough into a line of kids waiting for the school-bus. That is a real and present danger for diabetics but OSAS seems a bit odd in this context. Sleep apnoea is a condition where the soft pallet at the back of the mouth collapses during sleep and stops air making it to the lungs; this causes a micro-wake which opens up the gullet; sleep returns; apnoea follows; repeat until frazzled or death ensues. If you're asleep enough to experience apnoea you surely shouldn't be driving! On that face of it, including OSAS in the list of driving contra-indications seems nutty. But the disturbance of normal night-time sleep leads to daytime tiredness and that has the potential to cause fatalities.

I'm sure that there are GPs across the country who wish they had time to read through these guidelines because the compromises to safe driving are so many and varied. What's required is for one of the GPs to read the whole document and write an executive summary that can capture the most likely events / conditions that will have the greatest adverse effect and lay them out as bullet points on a single side of A4. That might be fit for purpose.

Buoys

Amazing what you can learn from the TV - or from DVD boxed sets because we don't have a TV in the house.  We were lent a box of boxed-sets of Numb3rs a few years ago, and enjoyed it at least partly because of the touch of scienciness.  The conceit of the series is that one brother is an FBI dude and the other is an academic mathematician who helps out with fluid dynamics, epidemiology, topology, engineering, cryptology and whatever-you're-adding-yourself.  The difference between science and scienciness is that, in the former, the insights don't come so thick and fast, the expertise is a little more focused and it takes a lot longer to wrap it all up. I still think it's better than, say, Desperate Housewives or Mad Men because in among the tidy plots and soap-opera development of personal relationships you can learn something that might be useful outside of The Box.  I've forgotten all the clever mathy details but now know that, and this was news to me at the time, many nautical Americans tie up their boats to "boo-ees", while all my life I've been rhyming buoys with toys or indeed boys.

A friend of mine went on business to Boston a few years ago and arranged to stay the following weekend with friends whom he hadn’t seen since college.  After breakfast on Sunday they suggested that taking the kids to one of the sandy beaches of the North Shore might be a nice way to fill the morning. He agreed with enthusiasm thinking that a few gusts of fresh sea air would clear his head both of a busy week and last night’s drink.  When they arrived at the coast he, along with every member of the family, was presented with a large black plastic bag from the trunk of the car to fill with tide-line rubbish.  The hangover was making him a little cross-eyed because he forgot his usual impeccable manners and indignantly refused to spend even a small part of his hard won leisure cleaning up the detritus of strangers.

I can see his point.  Even five bags of trash transferred from foreshore to landfill is insignificant compared to the quantity of plastic that is reputedly being trundled slowly round the ocean by the North Atlantic Gyre.  Furthermore much of the brightly-colored stuff you see on the beach seems to need rubber gloves to handle.

On the other hand, there’s lots of good stuff to be found on the foreshore if you’re not squeamish about picking it up. I salvaged a cabin door from the rocks beside Dun Laoghaire’s East Pier in 1976 and re-purposed it as a garden table. In the 1980s, I picked four or five serviceable wooden fish-boxes out of the storm-wrack.  After cleaning all the sand out, and soaking in bleach over-night to reduce the pong, they were just the right size to shelve four rows of standard-sized paperbacks.  Shortly after that, much to my regret, fish-boxes were suddenly all made of plastic, which are useless as book-shelves ; but they make excellent  tomato planters – the drain-holes are integral to the design of both functions.  In more recent years, I’ve salvaged hundreds of fathoms <a word to remember on Talk Like a Pirate Day> of rope.  This is often found clotted with fish-nets, driftwood, buoys, seaweed, seagulls.  It is sensible, therefore, to go down to the sea with a good sharp knife, so that you can trim off the perfectly foul and untangle the rest.  To salvage a lifetime’s supply of clothes-line by solving a puzzle is restful and challenging: better than sudoku because it’s three-dimensional!  The fish-net itself is usually so knotted as to be not worth the trouble but I have some fine sections in the garden which the beans to climb up each summer and I’m ever hopeful to find enough to make a hammock.
How green would that be?  Swinging gently in a summer breeze, teasing out an increasingly long line of recycled cordage, saved from the sea (where it was a mere hazard to shipping) to be re-incarnated as a swing for the children.

And the buoys?  I have an ever-growing collection.  They are now hanging, like multi-coloured grapes, as an artistic installation in the garden.  What else can I call it but  “Fruits de Mer”?

Which gives me an opportunity to share an appalling if apposite and personal joke:
Q. What do you call a man with no arms and no legs in the sea?
A. Bob!  (eeee how we larfed)

The Lady of the Lead

My girls Dau.I and Dau.II never went to school and have now left home and are productive tax-paying members of society. We got a fair bit of lip, and also unspoken brow-furrowing about how they had burned their boats for college.  I find this quite tiresome, so it's always nice to hear about people who were home-educated and did well by the usual criteria of wealth and status rather than things that matter like kindness and good humour.  Alice Hamilton didn't go to school and finished up as the first woman to obtain a faculty position at Harvard. Like Gerty Cori, she also got herself a stamp [L].  She was raised, with an extensive brood of sisters and a brother on the estate of her grandfather, a self-made magnate from Scotland, outside of Fort Wayne, Indiana.  Her parents had peculiar ideas about what education was about: they had no time for 'nonsense' like arithmetic and American history, but really valued theology, literature and language, in about that order. As each girl turned seventeen, she was sent off to 'finish' at Miss Porter’s School in Farmington, CT, where according to Alice some of the teaching was "the world's worst"; but I guess they learned how to curtsey neatly and knew which knife to use with the peas.

Her mother had instilled a strong sense of social justice by conspicuously disapproving of such societal norms as lynching black men, child labour and police brutality.  So it was not completely out of character when Alice announced that she wanted to be a doctor to help poor people in the slums of the grossly unequal society that was the USA in the early 1890s. To this end, she cobbled together an education in biology, physics, chemistry and anatomy and enrolled in Medical School at U. Michigan. That was a good fit and she found that her bleeding-heart ideas of helping the poor took better focus in the idea of doing clinical and laboratory science to help the poor.  She did a year of postgraduate research with Simon "Shigella flexneri" Flexner, one of the giants of 19thC microbiology, at Johns Hopkins U in Baltimore. Then she went on a tour of Germany with her sister Edith: brushing up their languages, doing the galleries and . . . auditing university classes in pathology and microbiology.

On her return stateside she landed a job teaching pathology at Northwestern U in Chicago at the same time as finding a billet in 1897 at Hull House; an extraordinary experiment in living where middle class people lived cheek-by-jowl with the dirt-poor and attempted to bridge some of the gaps between their unequal lives. Such "settlement houses" were loosely modelled on Toynbee Hall in East London. A few years later she was invited by the Governor of Illinois to serve on a committee of physicians investigating industrial sickness in the lead, paint and munitions industries. Work-place sickness was a consequence of industrialists itemising 'labour' as an expendable and seemingly bottomless resource: there was always some fresh chap off the boat from Europe who would work under any conditions to get a foothold on the ladder of the American dream. Health&Safety was a) expensive and b) hadn't been invented yet.

Alice Hamilton took to this with application and rigorous standards and she had a nose for finding breaches of the emerging standards for safety in the workplace, particularly about the effects of lead poisoning.  White lead 2PbCO₃·Pb(OH)₂ is a particularly opaque, white pigment widely used in paint that is also highly toxic [L data from the Report of the Commission for Occupational Diseases]. Unfortunately, lead paint tastes sweet, especially to children who have calcium deficiency. Like the Lady of the Lamp, Florence Nightingale, Hamilton was not adverse to gathering boxes of data in a process she called "shoe-leather epidemiology" and then analysing it to make clear where the problems were.  It was the compelling nature of these data that started. s l o w l y, the process of legislating at state and federal level for a better work-place for the workers on the shop-floor.  By recognising the characteristic symptoms after decades of observation, she turned up cases of lead-poisoning where nobody was awake enough to realise that lead was being used in some process in their factory.  She spoke out against leaded-petrol, for example, as early as 1925 but it was still for sale in Ireland 70 years later.

Sometimes it was evil and callous industrial robber-barons who were wearing out and discarding their work-force but often enough managers and owners were good men trying to turn an honest profit who failed to realise just how toxic their work-places were. I think Alice Hamilton must have had an extraordinary mix of empathy and assertiveness to face down and shame the men behaving badly whom she met every day in the course of her investigations. Exploring the Dangerous Trades was the title she chose for her autobiography. That's what it says on the paint tin, that's what Alice Hamilton spend her whole adult life doing. She was born on this day 27th February 1869, before DDT, PCB, TNT, CFC, BPA, added new levels of 'excitement' to industrial and environmental chemistry. She lived on and on through two world wars and unbelievable changes before finally pegging out in 1970 at the age of 101.  A lot of poor people, not only in America, owe their greatly extended lives to her.

Under the influence

</bollix Alert> 04Jun20: The paper which triggered this post has been flagged EOC by the Lancet. EOC Expression of Concern is a not-quite[-yet-]retraction. The Grauniad has investigated the company which supplied the data on which the original study was based. Also check out commentary on Metafilter. </bollix alert>
A former talk-show host and current Head of State says:

I think people should [take hydroxychloroquine], if it were me, 

in fact, I might do it anyway. I may take it ... I have to ask 

my doctors about that. But I may take it. 

Bob the Scientist says:

You're about twice as likely to die in hospital of covid-19 

if your doctors give you hydroxychloroquine than if they don't.

Who to believe? It's important because you can't do all the research yourself: not enough time, not enough data, not enough savvy, not enough tool-kit. Your knee-jerk reactions = gut-instincts don't work <be honest> for your bets on The Grand National, so they defo won't work when you're choosing treatments for your mother-in-ICU. That's why informed consent is often a polite charade as the medics-in-charge frame the questions / options in such a way as to elicit the answer the Doc believes is best for the patient. Put your cynic back in its box if  "best for the hospital's bottom line" edges forward in your mind.

There is a class of people out there whose main qualification for being an Influencer is that they have a work ethic, a gabby mouth, an attractive personality and have been lucky. Like myself, jacksepticeye, a nice, funny BIFFO from Ballycumber posts every day. Over the last 8 years he has accumulated 12,000,000,000 views of his youtube channel. He's got a degree in Music Technology and Production from LIT.  Now you might turn to Jack for insight into Animal Crossing but maybe pensions, art history or epidemiology not so much?

The cult of personality is mostly harmless so long as everyone respects the guidelines of non-overlapping magisteria: Beyond what we can all read in Time magazine, I know nothing about meditation; the Dalai Lama and Thich Nhat Hahn know nothing about science. The other two lads have considerably more influence but you'd be better off talking to me about data, evidence, and statistical analysis . . . and I won't gab on [much] about Ahimsa, Bodhisattva, or Chakras . . . promise. Sometimes you can be fooled: Linus Pauling was a colossal biological scientist with a string of Firsts and a Nobel Prize to his credit. But he was [whoa evidence!] just wrong in barracking everyone around him about a clearly biomedical issue like the cancer-curing capacity of vitamin C.

All kinds of people, with all kinds of random qualifications get to be President of their Country. Proper order: you wouldn't want to office to be held only by lawyers, publicans or pensioned politicians. Heck, I wouldn't want all presidents to be competent in science, or even numerate. Quiz time: who, before they became Pres, was a professional teacher; tailor; soldier; sailor; comedian; peanut farmer; poet.  It's real nice when your head of state has a few enthusiasms; it indicates work-life balance. The UK Head of State with the corgis and horses; her grandfather with his stamp collection; the Dalai Lama can fix your watch; Churchill was a nifty brick-layer. But you hope that these small obsessions don't edge too much into policy or public pronouncements. FDR kept both his polio and his adulterous bonking under covers. At the top I quoted the POTUS early on in the pandemic suggesting that hydroxychloroquine was a potential cure for covid-19. He doubled down on this affirmation later by saying that, if it did no good at least it could do no harm and later still telling the world that he was taking the stuff as a prophylactic.

Hydroxychloroquine HCQ and its relative chloroquine CQ, are anti-malarial meds which have been around in that capacity for 65 years. More recently they have seen some success in treating inflammatory and autoimmune diseases, including lupus and rheumatoid arthritis. Earlier this year, somebody noticed that people already on these drugs seemed to fare better when they presented to hospital with Covid-19 symptoms. In desperate times, when all other therapies have failed to work, some doctors will try anything rather than allow people to die quietly . . . even if that something is not FDA approved; even if there is no solid evidence supporting its efficacy; even if it's something they read on the internet or heard mentioned in a news cast from Bergamo. In January, I cited a case of Olanzapine being prescribed for senile dementia despite it being likely to precipitate a stroke. Trump is not the only person who is pushing HCQ as a cure for covid-19; doctors all over the World are giving it a go presumably after a well-framed informed consent conversation.

Well Stop It! Stop it Now!

A very recent paper in The Lancet by 4 MDs (Mandeep R Mehra [Boston], Sapan S Desai [Chicago], Frank Ruschitzka [Zurish], Amit N Patel [Salt Lake City]) has accumulated a lot of data and shown that hydroxychloroquine HCQ and chloroquine CQ with or with Macrolide antibiotics MAB are positively harmful.  Let's look at the numbers. They started by trawling the published literature to identify any controlled experiments of these drugs in a Covid-19 setting. That 'registry' got to include nearly 100,000 patients from 671 hospitals across all 6 continents. My summary tables count

• the number of people in 5 categories 1) The controls = no [H]CQ treatment 2) HCQ on its own 3) HCQ with MAB 4) CQ on its own 5) CQ with MAB
• the % in each category who didn't make it
• the % in each category who experienced (potentially damaging / fatal) ventricular cardiac arrhythmias "heart flutter"
• one man's ventricular tachycardia caused the deaths 14 people in Oklahoma 18 years ago today <cw: bridge collapse>
• the excess of dead people in each of the "treatment" categories

If you are in hospital with covid-19 you are neither asymptomatic nor mild-to-moderate, you are ill with a potentially fatal infection. 11% of the people in the study didn't make it. That's more than 10,000 coffins. But the point of the study is in the last table. ~1,785 people are dead because they were actively and consciously given a treatment which we [now] know to have significant adverse side-effects. More than 1,000 of them are US citizens. Insofar as anyone pays attention to pronouncements by the head of state in formal press briefings [and what's the point otherwise?] then Donald Trump has used his influence to off people whose life liberty and the pursuit of happiness he swore to defend.

Refuge

Catechism time!
Q. What kills black babies in sub-Saharan Africa? 
A. It is the unholy trinity of tuberculosis [TB], infectious diarrhoea and malaria. 
Actually TB should get first prize because that is caused by a single species of bacteria Mycobacterium tuberculosis, while the others are portmanteau diseases.  Infectious diarrhoea, for example, is caused by a huge range of bacteria, including Escherichia coli and apicomplexans [a class of single celled organisms with defined nuclei] like Cryptosporidium.  I'm never sure whether they include Vibrio cholerae in the I.D. statistics or treat cholera as a separate way of draining people of their vital fluids.  Malaria also is caused by a grab-bag of different apicomplexans but all in the genus Plasmodium.

It is important to recognise the difference among these Plasmodium species because they occur in different habitats, are very different in the severity of their symptoms, and are amenable or not to different therapeutics.  I've had occasion before to emphasise the correct identification of similar species, but it is only conservationists who really care which species of vulture or elephant we are talking about.  Being wrong about the species of Plasmodium can kill you or the small child under your care. Malaria's epidemiology is complicated by the fact that there are other essential players in the game - mosquitoes of the genus Anopheles which carry the Plasmodium from person to person and spread the disease.

The scale of the problem is enormous: malaria infects about 200 million people worldwide and kills much more than half-a-million each year. Most of the deaths are among children and that is a tragedy for each family but the loss of work days, the frightening-off of tourists and the costs of medication is draining $20 billion out of the African economy each year.  Controlling malaria could provide the energy to put Africa back on its feet but we have to box clever and think of the most efficient and cost-effective way to intervene because we of the West would rather buy a new iPhone than send $100 to Oxfam or the Gates Foundation. Solutions have included drugs, mosquito nets and DDT. There is something appealing in the idea of swatting the fly that is carrying the parasite before it can bite anyone else - those solutions don't please the shareholders of Big Pharma but they can work really well if carried out systematically - we don't have malaria in Europe any more.

One of the interesting aspects of swatting theory is that Anopheles needs to have water in which to lay its eggs and that water needs to exist for at least eight days which is the adult-to-adult life-cycle for these mosquitoes. In Europe, draining swamps was singularly effective in breaking the cycle. One of the long-standing mysteries is what happens in the dry season when there is no standing water;  how and where do the mosquitoes hunker down to burst out in epidemic disaster as soon as the rains return and provide the puddles in which the mosquitoes breed. Nobody knows where the mosquitoes go when they are not breeding and sucking blood.  If we could track them to their lair and kill them there it would be mighty.  There are two theories - aestivation and migration.  Aestivation is when the mosquitoes find somewhere quiet to hang out locally - although nobody really knows where that is; while the migration has to happen over distances of 100s of km because google-maps shows that the nearest water is that far away from villages in the Sahel where malaria is endemic in the wet season. As neither scenario looks likely there have been some ding-dong word-wars between aestivists and migrationists.

In the Christmas issue of Nature last year there was a News and Views to interpret a research paper that addressed the controversy by gathering lots data. Both those are behind the Nature pay-wall - sorry. Dao et al. stayed in a village in Mali for 5 years and collected mosquitoes - more than 50,000 of them and tracked their abundance through the whole year.  What was interesting is that they showed that "Anopheles gambiae" is really three species which are impossible to differentiate by looking at. One of these species Anopheles colluzzi could be found all through the dry-season and showed fluctuations in abundance of 10x to 100x even during these times. The real Anopheles gambiae which they now call sensu strictu or s.s. cannot be found locally and shows a peak of activity that lags behind Anopheles colluzzi when the mosquito season hots up after the rains. It now looks likely that A. gambiae is migrating incredible distances while A. colluzzi is hiding out in a local refuge.  The third species Anopheles arabiensis is not so abundant but behaves partly like A. gambiae s.s and partly like A. colluzzi.  So both sides were right but about different things and you could have wished that, instead of blaggarding each other in print and at conferences they could have devoted their energy to solving the problem.

Now wash your hands

As I mentioned Dau.II came home for the week-end.  For the last several weeks she has been working (very hard) in a new restaurant in Cork called Burritos and Blues. You should check it out - the food on the menu is Mexican and tasty and doesn't seem outrageously expensive given that you get a balanced meal wrapped up in a tortilla the size of a baby's leg.  If the staff is especially charming and helpful by all means leave a big tip.  The hierarchy is very flat in this business: everyone wades in and does what's necessary - prep, cook, serve, clean, or cash.  The gaffer clearly has a good business head but it seems that paperwork and bureaucracy wrecks his head.  So when the Food Safety Authority (FSAI) offered a day-long seminar on hygiene and good practice, he sent two of his recent hires to represent the business and take notes. I had some informative chat this w/e about the issues of Food Safety in the retail sector.

The first thing I found interesting was the observation that servers in Sandwich Bars and similar outlets all wearing ludicrous, often outsized, polythene gloves while they pile up your sambo.  It didn't use to be like that.  A couple of decades ago when I was working in Dublin there was a shop on Fenian St, D2 that sold a sandwich the size of a sailor's leg (forget your delicate baby's leg sized burritos of nowadays) for £1.25.  The staff there were quick and sassy and efficient and piled handfuls of lettuce, tomatoes and coleslaw in on top of whatever you'd paid for (ham & swiss for me, please).  No gloves, no worries. Dau.II was saying that the gloves are so big and klutzy on her delicate hands that she's likely to cut off the plastic finger tips and leave them in the burrito along with the meat. No folks: it hasn't happened yet! The FSAI which knows whereof it speaks (science, microbiology, epidemiology data etc.) and The Public which knows bugger-all about microbial biology are in disagreement on gloves.  Sean Public wants the chaps behind the counter to wear them from an ill-informed and rather insulting fastidiousness about whether the serving hands have been washed.  FSAI prefers that servers don't wear gloves because doing so discourages the washing of hands that is key to avoiding cross-contamination.  Their take on gloves is nicely non-proscriptive but clearly against gloves. 

I'm much more confident about the efficacy of the FSAI after reading this.  A lot of food hygiene is a series of shibboleths whose reason is not properly articulated. If people knew why they should wash their hands then they'd scrub under the nails rather than rinse under a tap and dry on a probably contaminated towel.  About the same time I was eating a sailor's leg, The Beloved was commuting back and forth to Birmingham for work.  The Bean an B&B she stayed with mentioned one morning that the UK health&safety people were about to issue a diktat forbidding the drying of dishes with tea-towels; they recommended rinsing and air-drying on a dish-rack. All that has been replace by dish-washing machines now, but you take my point.

I learned one thing (perhaps the only reasonably certain thing?) from nearly ten years researching the relationships between the microbe Campylobacter jejuni and the immune system of its alternative hosts: chicken (Gallus gallus) and us (Homo sapiens):

Don't wash your chicken before you cook it!

Chickens - all chickens even/especially? the free-range, organic chaps - carry Campylobacter up their wazzoo.  It is part, maybe an essential part, of the intestinal flora of those birds and causes no symptoms of illness.  Au contraire, when we ingest a few of these bacteria the result is very likely to be a giving at both ends before the night is out.  The best practice therefore is to take your chicken carefully out of any packaging and get it into the oven directly and then now wash you hands please.  If you do the 'natural thing' and give the ould bird a rinse under the kitchen tap then you create a fine aerosol of air-borne Campy quite apart from splashing the lettuce you've left on the counter-top next to the sink.

New Rule: you're much safer if the girls behind the counter don't wear gloves when handling your lunch.

Undulant zoonosis

I've started my final year research project students off on their 20 week sojourn at the frontiers of science - discovering things that nobody else knows. This year my numbers are down to nine but numbers are down across the board, so it's not (entirely) all about me. I fielded a question from the immunology-of-tuberculosis chap who is currently reading like mad about his chosen field. "If Mycobacterium tuberculosis which causes bloody sputum and a lingering <coff> <coff> death in people and Mycobacterium bovis, which does ditto damage in cattle, are 99% identical? Why do they have different names?" That's a damn good question which I've been asking people for the last 15 years and hasn't yet gotten a satisfactory answer. The same day I had that question I came across a very similar situation from 100 years ago, which concerns one of those extraordinary women who, in far less equal and inclusive society that we have today, carved out a niche in the cliff of science and made ground-breaking discoveries from that vantage point.

I speak of Alice Evans [L] who earned her B.S. from Cornell in 1909 and an M.S. from U. Wisconsin at Madison the following year. Bear in mind that, despite being an adult and highly educated, she wasn't entitled to vote in those distant times. She had the opportunity to carry on for a PhD, they begged her to do a PhD but she just couldn't afford any more education and instead secured a federal job working for The Bureau of Animal Industry (Dairy Division); initially in Wisconsin and latterly in Washington DC. One of the problems which she worked on  was the causative agent of undulant fever or Malta fever which some suspected came from goat's milk. This was years before DNA-based diagnostic tests were invented; indeed 40 years before the structure of DNA was revealed by Crick and Watson. The main identification tool was the microscope, coupled with Gram Staining which had been around since the 1880s. The shape of bacteria, which you could observe, was treated a key diagnostic feature; which turned out to be largely irrelevant for categorisation. A good example of streetlight science.

David Bruce, a world-roaming Scot, who discovered the causes of African sleeping sickness - Trypanosoma brucei - was also working on Malta fever which he observed as spherical and so assigned to the genus Micrococcus. Meanwhile Bernhard Bang in Denmark had isolated a rod-shaped microbe strongly associated with an outbreak of spontaneous abortion in cattle which he binned to Bacillus, which much later came to be known as Brucella abortus [R very short rods especially immediately after cell division]. Alice Evans looked at numerous cultures of both 'species' grown under a wide variety of conditions and basically couldn't tell them apart. Interestingly she observed them as both spherical and rod-shaped morphs depending on the growth conditions. Her paper laying out the results was published in 1918 and met with near universal skepticism. Evans was correct nevertheless, despite being a woman and not having a doctorate.

Almost immediately afterwards, everyone around her was engaged in the epidemic of Spanish Flu which killed 20 million people worldwide in the months after the Armistice. Alice Evans herself felt crook at work one day, realised she had probably contracted the disease, went home and took to her bed for a month. No 'flu vaccines back then, you just had to tough it out. One problem was that nobody could reliably identify the causative agent. The gamma-proteobacteria Haemophilus influenzae was so frequently isolated from 'flu patients that it was a strong suspect, but a red herring because, as we now know, Influenza is caused by a virus. That is another example of how the most obvious feature in the landscape turns out to be irrelevant. Maybe it's not too tendentious to find a moral or a metaphor for the current obsession, which the best of us are trying to shake loose, with gender and skin colour as the defining criteria for worth, talent, intelligence, ability to throw a baseball, or run a business.

Evans' interest in brucellosis was not satisfied with identifying the cause, so she shifted her duff to the Hygienic Laboratory across town. Her new place The Division of Pathology and Bacteriology later evolved into the NIH. And I'm getting much of this information from an autobiographical memoir, by Alice Evans typed up, in 1963 when the author was 82 years old, on a really crappy manual typewriter and now captured as PDF by the NIH Office of History. Her researches into the epidemiology of brucellosis started a long long trek to eliminating it from both cattle and people. The disease was eradicated in Malta as recently as 2005. Shamefully it took until 2009 for the same declaration to apply in Ireland. Her evidence, culled from the literature and from her own researches that brucellosis was frequently transmitted from cattle to people was rigorously opposed by The Patriarchy of the day in which the dairy industry was in cahoots with some of the Big Boys of Bacteriology. This was especially true of Dr Theobald Smith, a Professor at Harvard and the Rockefeller Institute and a pioneer in tick-borne diseases [whc prev], Salmonella infections and anaphylactic shock. He spent about ten years of his life in steadfast denial of Evans' evidence and making it his business to snipe at her work behind her back. When eventually the overwhelming tide of fact put a stop to his gallop, he never found the grace within himself to apologise or admit that he had been wrong. It mattered because brucellosis was hard to diagnose accurately and was therefore quietly but relentlessly knocking $100 million a year off the value of the beef and dairy industry while Smith maintained stoutly that there was nothing to see here.

One of the studies Evans carried out would absolutely fail the informed consent ethics rules today. Evans and here team got access to 500 blood samples submitted to the Hygienic Laboratory for a Wassermann test (for syphilis). They tested these samples for Brucella and found about 3% positive; implying that this potentially dangerous bacteria was much more widespread than previously believed. You can't nowadays just use somebody's blood because it is sitting in a freezer in the basement of your place of work.

Perhaps inevitably, despite astute and rigorous precautions, Alice Evans eventually unwittingly took one for the team by getting infected with Brucella. It persisted as a chronic infection undulating between her feeling reasonably fit with feeling like death warmed up. It was many years before she was diagnosed and the suspicion of malingering or neurasthenia aka chronic fatigue syndrome was finally scotched.

To bring this Blob full circle, Alice Evans' memoir also recounts how Robert Koch, early paragon of microbiology, was largely responsible for asserting that the two strains of Mycobacterium were quite different species and the bovine strain just couldn't infect humans. He was wrong. The proof of the pudding turned out to be in the drinking and human tuberculosis was given a severe knock when  authorities started to clean up the dairy industry and/or insisted that milk must be pasteurised.

More Women in Science

HPV collateral damage

Last week in September was multi-post week on blood, Rhesus, anti-D and hepatitis C I - II - III - IV. This week we're onto another controversial health intervention. Human Papilloma Virus HPV, anti-HPV and cancer. I - II.
The analysis so far of the profit and loss of HPV immunisation has not yet taken account of the collateral damage. The girls who have experienced adverse effects shortly after getting their HPV shots. I've deleted the shortly because the time-line for association can be months down the line.The news last week was about the uptake of the [free] vaccine falling from 87% in 2013 to 70% last year. This is probably on foot of media coverage of the adverse effects giving parents the same wobblies as we experienced about MMR in 1976. Some of the parents of these affected girls have gotten together to raise awareness, compare notes and get redress for the tragedy that has devastated their homes and families. Their organisation has got itself a shocking name "Reactions and Effects of Gardasil Resulting in Extreme Trauma" REGRET and a website.  Like your approach to literature from National Immunisation Office and Merck, you need to put on your skeptical hat when assessing the information put out by REGRET. William Campbell claims that they are wilfully misreading the evidence to agree with their own certainty.

We've had a case of willful mis-reading of the evidence aka cooking the lab-books over vaccination before. In 1998, Dr Andrew Wakefield published a report on an association between MMR vaccination and autism which was widely, even jubilantly, reported by the common press.  It was subsequently found that Wakefield had faked / massaged /sexed-up his data to push the association into statistical significance. The paper was subsequently retracted. That retraction wasn't news and so only appeared, if at all, on page 5 in small print. The hullabaloo seeded Joe Public's mind with the idea and the anti-vax movement really started to rock-and-roll. That could be bad from two angles:

• reducing the number of measles-vaccinated children will increase the susceptible herd, and a measles outbreak becomes more likely to propagate. Measles is no fun even if you don't end up blind, convulsed or dead.  Dau.I contracted mumps [after vaccination] when she attended a middle class Summer School in DCU where a large enough proportion of the teens had not been vaccinated.
• by fingering the wrong culprit we go off the boil in trying to find the true cause of the epidemic in autism . . . first off, of course, we have to establish whether there is, or has been, such an epidemic rather than it's just that doctors are now recognising, diagnosing and reporting more cases.

The Gardasil information page put out by the FDA after consultation with the CDC lists all the adverse events that have come to them through  Vaccine Adverse Event Reporting System VAERS. It reads like the time-worn advice never to browse a medical encyclopedia: "local injection site reactions, syncope, dizziness, and nausea, headaches, hypersensitivity reactions, such as rashes, hives, itching, anaphylaxis, Guillain-Barré syndrome (GBS), transverse myelitis, motor neuron disease, venous thromboembolic events (VTEs), pancreatitis, autoimmune disorders, pregnancy, and death". Surely the outcome 'pregnancy' after a course of injections is based on confusion about what got poked into where? The position of Dr Corcoran and the HSE is that we have not seen a spike in incidence for any of these events. If there is something generally wrong with Gardasil or Cervarix, and 30,000 young girls get exposed to it every year for several years, you'd have to see the effects. But neither in USA, with 100x the population, nor in Ireland have we seen more moodiness, lethargy, painful wrists, rashes or whatever you're having yourself  in the teenage girl cohort.

The thing is that puberty is a time of change. The hormonal tsunami, the spots, the tuftiness down there; exposure to a larger and more diverse / diseasy population in secondary school; the difficulties of creating a separate identity from your parents; the expense of adopting an identical identity to your peer group. Just look at the hormone aspect: estrogen does a lot more than make breasts develop [in Alan Turing for example]. We only have a few hormones and a few hormone receptors [part of the 100,000 strong complement of proteins we make on a daily basis] and an immensely complex [100 trillion cells!] organism, so all the actors have many parts to play. Why just last night I read in IFLS a piece associating The Pill [=hormones] with Depression [or at least anti-depressants]. And, if the epidemiology of osteoporosis tells us anything, then estrogen has something to do with maintaining bone-density. Not everyone is able to regulate the flood of new hormones equally well and the difference can manifest in peculiar ways. There is likely a genetic component, so if your older sister gets horrendous period pains, you may have to brace yourself for similar. There are 10,000 Irish cases of chronic fatigue syndrome, for example, but it's no more common now than it was before-Gardasil; except in the sense that the population is larger because the economy is picking up and a) the diaspora are drifting home b) couples are trying for a family.

It seems like REGRET have mustered about 400 families with teenage girls who a) had the Gardasil b) had various crappy outcomes. It is not beyond the bounds of possibility that some of these girls have a peculiar / particular genetic make-up for which HPV acts as a trigger. Like a taste of Campylobacter jejuni, from a dodgy chicken nugget, develops, in a tiny fraction of cases, into Guillain-Barré syndrome. You should re-read that piece because it reviews the association between the Pandemrix 'flu-jab and nacrolepsy. The data there look pretty convincing that you're about 15x more likely to experience narcolepsy if you have the jab than if you don't BUT in neither case is that condition at all common. Some of the REGRET cases would have happened anyway but it is also unlikely that none of them are due to being insulted with proteins derived from HPV. You the parent have got to assess the balance between these two extremes. That will be difficult if you think, along with most people as the Minister of Finance announces the 2017 Budget, that a billion is about twice as big as a million.

If we had achieved the socialist paradise proclaimed by St Padraig of Pearse in 1916 then we would be "cherishing all the children of the nation equally". But that fine aspiration never made it into the Constitution. We have become instead a nation ruled by the adversarial system of the courts. IF you want help with raising children who are too much for any family to cope with; or you want a level playing field to minimise the difficulties which your child experiences THEN you have to prove culpable negligence on somebody's part. Look at the anti-D cohort of women, they had to fight their elected representative and the apparatus of the state to get the acknowledgment and support they deserved.

Is it worth investing a couple of million €€€s in a retrospective study of the genetic make up of the REGRET 400?  Probably not, because the sample [each a tragedy is acknowledged] is too small to achieve an unequivocal result. Too small? = too noisy: the some vs none argument two paras above suggests that many of the girls will have a different cause for their troubles and of those which are genuinely HPV-sensitive, each could be due to a raddle of different genetic / biochemical causes. The only useful outcome would be pharmacogenetic. That's the idea of tailored medicine: drugs only given to those who will respond.  It's unlikely that there will ever be a black&white pre-HPV-jab test that will say: you really shouldn't have this treatment; it will be less risky for you to dice with cervical cancer later.

If you have a teenage daughter [or son, they help spread HPV16 because it takes two to tango], you should put aside the suspicion that Big Pharma is driven by profit; that government cares less about the welfare and future of citizens than getting elected next time round; that your kidder will be among the 98% won't get cervical cancer and you'll be dead before she does . . . and sign the consent form.