On occupational hazards

(First posted over at the day job.)

On Christmas Day I received an email. It was addressed to my 7-year-old son, and it told him that his coronavirus test was positive.

There were mixed emotions. I was amused at the thought of this strange Christmas present. I was also relieved – ever since his school had closed a day early the previous week because a teacher had tested positive we’d been living with uncertainty. Although a little scary, the knowledge we now had was reassuring.

There was some consternation, of course. When I had swabbed him 4 days previously, I’d kneeled down with my face very close to his open mouth as I tried to tickle his recalcitrant tonsils. Was I now infected? My wife?

I was also curious about his symptoms. He’d said he couldn’t taste his toothpaste, and seemed to be less hungry than usual. That was why I’d decided to order the test that weekend. But apart from those very minor symptoms there was nothing to suggest he’d been ill.

Before Christmas I’d met a friend who had COVID back in March, and was still suffering, 8 months later. Another friend who is a consultant at the local hospital spent 5 days in bed over New Year, not being able to taste anything. Yet my 77-year-old mum, who had to go into hospital for a broken hip, tested positive on discharge and hasn’t had any symptoms.

And when we got my wife tested after the Christmas weekend, it came back negative. She and I both felt a little ‘funny’ about three days after our last London Underground journey in March, so I’m wondering if we’ve been exposed but been fortunate enough to have only very mild symptoms.

Unsurprisingly, there have been genome-wide association studies looking at disease severity. See for example this preprint, ‘Genetic mechanisms of critical illness in Covid-19’. These authors from the University of Edinburgh found at least three genetic loci that seem to be associated with severe disease, including one that encodes antiviral restriction enzyme activators and another in the interferon receptor gene IFNAR2.

While I would very much like to see if I could get the entire family tested for those loci, there is also an association between occupation and mortality. The type of job you do predicts how likely you are to die from COVID.

According to the Office of National Statistics (ONS), men in elementary occupations (such as labourers and other ‘unskilled’ professions) are twice as likely to die from COVID as working-age men in the general population.

Men in caring, leisure and other service occupations are only just behind this group, while management and professional occupations fare a lot better. Women aren’t as likely to die from COVID as men, but the trends by occupation are similar.

Now, the ONS didn’t adjust for factors such as ethnicity, place of residence or socioeconomic status beyond occupation, so you can’t claim conclusively that differences in levels of occupational exposure to the virus cause different rates of death. But what’s fascinating is that when you look at ‘teaching and educational professionals’, the rates for both sexes are almost half what they are in the population at large.

Teachers get exposed to many different viruses. Any parent of primary school-age children can attest to the cycle of coughs and sniffles that coincides with the new school year. Yet in my experience, teachers are rarely sick, implying that teachers have somehow evolved an immune response that defends them against the onslaught of hundreds of highly mobile fomites every September, while failing to initiate cataclysmic interferon cascades. Perhaps there’s some sort of natural selection going on whereby only those people with perfectly balanced immune systems can make it as teachers.

Anyway, looking deeper into the ONS data at individual teaching occupations, it turns out that a mortality rate can only be calculated reliably for secondary education teachers. And in that subset, the rate is not statistically significantly different from the wider population. Which logically means that the low mortality rate is being driven by tertiary and primary school teachers.

But I’m wondering if we’re not missing an opportunity here to simultaneously maintain some semblance of organized education, relieve the pressure on stressed parents of primary school-aged children, and contribute to the vaccine relief effort.

Imagine: armies of primary school children on extended day trips across the country, carrying little backpacks stuffed with vaccine vials and syringes. Their suitably trained teachers with their invincible immune systems walking door-to-door to deliver vaccinations. The children could learn about the area they’re in and take Maths and English lessons on the fly – and just as importantly, they’re out of their houses and with their friends.

And the vaccine gets delivered to every street in the land.

Worth a shot, no?

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On fraud, redux

One of the worst things about the pandemic is that it reminded me that once upon a time I was really rather good at RT-PCR. And that reminded me of when I spent 8 months in Sydney trying to replicate a result that was, essentially, made up.

A brief exchange on the Twitter with Henry Gee of this parish made me think that the story, which I have told once elsewhere, probably bears repeating.

But more of that in a moment.

Another story that bears repeating, and indeed updating, is that of the … person … who came to work for us at the med comms agency back in 2017. I first told this story at Occam’s Corner at the Grauniad, and so you don’t have to give them any clicks you can read it here.

This … person … joined the writing team, and a bit like me was an ex-labrat who had jumped ship. That, I hope, is where the similarity ends.

I was assigned to mentor the new hire and inculcate him in the Ways of the Agency. So within the first couple of days I invited him to an informal chat.

After the usual pleasantries I asked him why he’d left science. I got a plausible answer: he’d got to the stage where he was spending so much time writing grants and papers that he had no time to do bench work, and so decided to make a clean break. Apparently he was writing all the lab’s papers and grant proposals, and was good at it, so a career in medical communications seemed to be a natural step.

Fair enough.

But the next week I came to review his first piece of writing, and had to take a step back.

Reader, it was utter dreck.

After the first paragraph—which I’d pretty much totally rewritten—and a cursory glance through the rest of the document I gave up. Instead of commenting further I instead sent a friendly email saying maybe I hadn’t been clear about what we were trying to achieve here, and here’s some tips for creating a newsletter that people might have a chance of wanting to read.

I got a very terse reply saying, in effect, “Yes, yes, I know all this.” So I left him to it.

The second draft wasn’t any better though, and then my boss told me he’d resigned because his partner was “relocating overseas and he wants to join them”.

Well, that’s fair enough, I guess, except a couple of days later, halfway through his notice period, he simply didn’t turn up to the office. And that was that.

Except, the following week we discovered that he had previously worked for a short time at another agency in London. And had left there in similarly mysterious circumstances.

It was then we found his name in the newspapers, on Retraction Watch, and in a few other places.

According to the reports, he had falsified and published data on a number of occasions over several years, both as postdoc and as principal investigator. An inquiry at his home university had upheld allegations of misconduct, and he had been fired from his position.

After telling this story at the Corner, I was contacted by a couple of people who had recognized the description of the behaviour, and knew who I was talking about.

One of my correspondents told me that they’d do an experiment, and then this person would take the results and “send the data to Ireland for processing.” They didn’t know any better, and of course it turns out that this was code for making shit up.

I’d like to get “send to Ireland for processing” in the lexicon.

The email testimony backed up what we’d discovered, and painted a picture of a thoroughly unpleasant, arrogant and sociopathic character. To which I might add, ‘shit writer’ and ‘unschoolable’.

So back to Sydney.

What happened was that I had been tasked with replicating the result of an experiment performed by our collaborators over the road, because it was fairly central to showing what our new protein actually did. We thought it was a splicing factor, and our group had identified candidate RNA binding sequences, but we didn’t know which genes or set of transcripts it was acting on.

So by doing RT-PCR on messenger RNA derived from cells that either had or did not have our protein I should have been able identify splicing patterns that could tell us what our protein was doing.

Technically, I was soon able to prove that I could do the experiment, with appropriate positive and negative controls. But there was no way I was able to reproduce the figure that our collaborators had published. In fact, the more I thought about it, the more I wondered how—if their theory was correct—this particular pattern could have arisen. Biologically it just did not make sense. The more I understood the system, the less I understood their result.

And then we had a joint lab meeting to share results and generally plan the next stage of our collaboration. I’d moved onto other lines of enquiry, but I showed a few of my gels at the meeting, more to vent my frustration than anything else.

It was then that one of their senior postdocs said, “Oh yes, we had to do it about fourteen times before we got the result we wanted.”

Back in the safety of our own lab there was a brief discussion about what we could do about this—sending to Ireland for processing not being an option—but there was a certain nervousness about pissing off the collaborator.

It’s too late now, and I’m still not sure we know exactly what the protein does (although it appears to be involved in glioma, which could be exciting). Could I have done anything different?

Would it have made a difference?

You tell me.

Posted in ethics, Ill-considered rants, Lab ratting, Me, War stories | Tagged , , , , , , , , , | 3 Comments

Sounds of the suburbs

I’m sitting outside our apartment at Podere Castellaccia, the evening sun still quite high as the maestrale warms the porch.

Our apartment is Grecale, the colder, northeast wind. Castellaccia is a fattoria and azienda vinicola; their olive oil is superb and at 5 Euro a bottle from the cellar door, why would you drink sangiovese from anywhere else?

Alfonzo’s father, Sinibalda, founded the establishment, and now Alfonzo’s daughter Barbara runs the agriturismo business (with a little tax help from the Italian government). Alfonzo speaks no English but we converse nonetheless, and he gives Joshua tractor rides around the farm. I only remember Sinibalda’s name because it is memorialized on the grappa riserva, a bottle of which I bring home each time we visit—along with all the oil and wine we think we can fit in our 23 kg each of checked baggage.

Wine, in my book, is a minor miracle. Fermented fruit happens by chance and there are all sorts of wonderful drinks you can make at home, using apples or elder flowers or dandelions or anything else growing in English hedgerows, but wine, proper wine is on a level beyond. Little wonder that Jesus chose it for his first (recorded) public demonstration, at the wedding in Cana.

Speaking of miracles, we’re actually here in Italy.

Back in May, things were looking a bit dicey. For the first time in our lives we’d been organized and booked the flights stupidly early, back in January or February; and then there was Covid. BA canceled our outbound booking, but not the return—and Jenny called them up and got us switched to the early Pisa flight instead. And we waited for 2 long, long months until finally we were on the way to Heathrow at oh dark hundred.

The early start meant we were able to visit Lucca for lunch, and still reach Grosseto with time enough for essential groceries, and a swim in the pool.

We love this place. We always talk about going to other places, but every 2 or 3 years we find ourselves asking if Barbara has room this year, and booking a flight and hiring a car. There are beaches 20 minutes away, a crystal clear mountain stream with trout as big as your arm and their fry that come nibble your toes an hour’s drive north, the pool, the weather… and I may already have mentioned the oil and the wine.

Last night I was able to show Joshua comet Neowise, and he’s written about it in his diary today. He also found a nocturnal toad, and we listened to il pipistrello thanks to our ‘Batseeker’.

But what this post is really about is assiolo, or assiuolo as he’s known locally, or Scops Owl in less romantic tongues.

At his largest, assiuolo is no larger than a blackbird, according to Italian Wikipedia. What’s distinctive is his call, “djü” or”chiù”; again, in our less romantic language we say ‘boop’. Every night we hear him from the pine trees, regular as clockwork after half nine, more often than not answered by his lady singing back, half a tone higher.

Assiuolo is Tuscany to us, and we are very happy, very blessed indeed to be here.

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Clampdown

Hey Mike. Mike? Mike.

Mike, can you hear me? Cannn youu hearrrr meee.

Yes, I can hear you, but I don’t think you can hear me. No I’m not on mute. Have you got your sound up? Better? Good. No, don’t worry. We’ve all done it.

I think Janice has just jo—ah. Janice. I can—I can hear—dammit—I can hear myself.

Try

Your

Headphones.

Let me try it now.

Yes, that’s better.

Cool. And here’s Ralph and Sally. We’re just waiting for Theresa. Ralph. Your video is futzing. Does anyone else see it? No, it’s just you. Janice and Mike and Sally are just fine. Try—all right, we’ll wait for you—OW. Who’s causing the feedback?

Will everyone—SALLY. It’s no good. Mute your laptop and dial in on the phone. Yeah, we get that sometimes. Don’t worry about it.

Okay, so, I’ve just had an email from Theresa. Her previous call is overrunning. We’re stuck without her though because we need her decision from the internal team meeting. Yeah I wondered that, but she says she doesn’t want to put it in an email. I’m going to have to drop off in another 20 minutes though, so if she’s not done I’ll have to leave it with you, Sally.

Yeah, I had a lovely time off, thanks. Don’t really know where the time went. We had planned to go visit my father-in-law in Colorado, but obviously all the flights were cancelled and he’s like eighty-six or something so would have been too risky anyway.

Did some gardening, fixed a few things up. Tried to stop the foxes getting in. I wanted to do some writing, get into the loft and finish the model off with Joshua, that sort of thing, but the weather was so nice we just hung out in the garden. Yeah, very fortunate.

Hey Ralph. It’s not brilliant but it’s better than it was. Try rebooting your modem when you get a chance.

The model? A scale model of London City Airport. Well, the runway at least. It’s about fifteen feet long.

In the loft. I got into a habit of buying Joshua those little die cast aeroplanes from all the trips I was doing, and decided he needed somewhere to keep them. He loves it, even if it isn’t finished yet.

They’re doing great! Percy seemed to be a bit poorly a couple of weeks ago, but she’s laid an egg every day for eight days on the run now, so I guess she’s fine. We’ve been letting them out for hours at a time when we’re in the garden, they’re very happy. Lots of eggs—fortunate we got them before all this kicked off. Complete coincidence, yeah. We’d been talking about keeping hens for ages, and got them beginning of February. Very lucky, yes.

Hahah. No you can’t.

Man, I know. My legs are killing me. I’ve got muscle pains where I didn’t know there were muscles. Oh, a guy called Joe Wicks. He does these PE lessons every morning, live-streamed on YouTube. Ostensibly for the children out of school but I think lots of parents do them too. Millions of views daily.

You think so? End of May earliest, I’d have thought. Heh, I was reading something by this guy I know on twitter, he’s a VP at a big pharma—no, UK; GlaxoAstraSmithklineBeechamZeneca or whatever it’s called now—and he’s hoping, get this, he’s hoping open plan offices slash hot-desking will be made illegal. I’ll dig the link out after this call.

Seriously, I’m with him. Open plan offices are bad enough but this hot-desking lark? I hate it. Especially after being able to work from home for a month now! I want a little cubicle with my own stuff where I can just sit down and focus. I wrote about this before. And all that horseshit about serendipitous interactions or being close to the people you’re working with so you can talk to them? It’s bollocks.

Hm, sounds like Theresa isn’t going to make it. And I’m going to have to go to the doc’s in a minute.

Haha, like where would I have caught it? Yeah, nothing serious. I was playing hide and seek with Joshua and leapt over a bush that had a fencing spike in it. Got to go back and get the stitches out.

Didn’t hurt that much, to be honest. At least, not until the medic started poking it to see if the local anaesthetic had kicked in yet. It was “Nope, nope; a little pressure, nope, OUCH. Positive control?”

Well, that’s what I was worried about. I rang the minor injuries unit up, they said fine, come in. There was someone masked up on the door, quizzed me about any fever or cough, and nobody else in the waiting room. But the receptionist… so there’s like barbed wire and watchtowers and minefield signs all around her desk, stay six feet away, all that stuff, and she’s wearing a face mask, right? But she’s speaking very quietly, behind the mask, six feet away, and I’m leaning forward feeling a right div ‘cos I have to ask her to repeat everything.

Medic was lovely though. Had a nice chat about her career in IT before becoming a paramedic, her time in Australia, trying to keep the kids sane during the lockdown.

Seriously though, I don’t know what the fuss is all about. I was walking out of the unit about an hour after it happened, six stitches and a steristrip better off. Saw one other patient.

OK, I’ve got to go. Sally, can you align with Theresa please and reschedule if we do need to talk through it?

You’re the best. Catch you guys tomorrow.

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If music be the food of love, rock on

One of the problems of having so many websites is knowing which particular wibble goes to which one.

And generating enough content to keep them fed, of course.

Confessions has been neglected of late—not because I want to, or am uninspired, but because it’s difficult to find subjects that are ‘safe’, considering the day job. Especially seeing as the HR person at work stalks me on Twitter.

Something I’ve been meaning to do for a long time; in fact, ever since I came across the word; is create a website about my exploits in the culinary arena. I’ve been saving straight recipes at the BioLOG, but I finally got around to not just registering the domain name but actually putting content there.

Magirism is defined as the art and science of cooking, and I can’t think of a better description of what I do the kitchen. And so Magirisim.org is intentionally descriptive rather than prescriptive, and it’s mostly about the stories.

Please enjoy—and especially the cider.

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The Twelfth of Never

I may have mentioned once or twice the collaborative webstory that germinated a decade ago and half a world away (quite [lab-]literally).

In fact, I’ve just found on my Mac a file from December 2006, with some notes on how to finish the story—written around the time I was recovering from pneumonia. In Australia.

Anyway. Without further ado, A Momentary Lapse of Reason is now being serialized at LabLit, land of the free, the brave, and the scientist in fiction! /inc sound.fanfare

Go read it. Please.

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My blue heaven

Bluebells in a wood

Wordsworth lost it when he saw fields of daffodils. I wonder what he thought of bluebells.

It’s been a busy 2 weeks—a long-awaited holiday from work, with my birthday in the middle. Staycations around here always end up with a list of things I haven’t done, often seemingly longer than the to-do created at the beginning. Back to work tomorrow, and it’s tempting to slip into a maudlin haze of regret and self-flagellation.

But this afternoon we took a trip out to some nearby woods with their eye-aching green and blue carpets, and the memory of what brought me back to these shores 10 years ago.

I found peace again.

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Alice’s Restaurant Massacree

I fell a bit behind with the shopping lists, which is a shame because I really wanted to show you this one before Christmas.

It’s a full-blown pre-Christmas shop. Right at the top we’ve got mistletoe and greenery—both queried though: maybe she (definitely a ‘she’) wasn’t sure if Waitrose would have them, or maybe there was already another trip planned.

There’s an interesting mix of precision here: carrots, leeks, clementines … but four bananas, two each of limes and lemons; haddock … but a general ‘dinner.

Two crème fraiche (again; with diacritics), but a small cream. 

How many baguettes? A misfiled pastry (together with the foil this makes me think she shops by aisle, although I happen to know that the cream is not near the bread, so not entirely sure what’s going on there. Perhaps it’s by recipe rather than aisle?).

Questions remain. What sort of wine? Why is panko underlined? Did she decide on tonic, or soda? Which paper?

And the pièce de résistance, right down at the bottom, in the middle of the page, set aside from everything else on the page, underlined …

TURKEY!

I feel there’s a metaphor in here, somewhere.

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Twelve days of Christmas

So that was Christmas. And what I did was a little project that you might have missed: a photo for every day of Christmas, from the first to the twelfth. No commentary or explanation, just the photo, and the day as a title.

Each photograph had something to do with our family Christmas, and hopefully will remind us of some of the fun things we got up to.

While each photograph might not have been from the actual day it was posted, it was taken within a few days.

They’re all on Instagram, no tags or anything (so really difficult to find or link together, not entirely by lack of design), but they are our first 12 pictures on the account.

Enjoy.

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There are worse things I could do


Hastily snapped this, as we went into the shop. But to be clear, the mystery shopper wanted the same number of fillets as en croute. Perhaps they were having coeliacs around?

An engineer’s or a computer programmer’s brain behind this list, I fancy. Or perhaps ex-military. Eggs, large*. Vanish, small. Tea, milk two sugars. I’m assuming the tin (large; cut) is bread. Purée, accent (approval).

I’m hesitant to forgive the ‘water’ though. Come on. This is England, and plastic is overrated. Won’t somebody please think of the oceans.

*But a strange inconsistency—I would have expected ‘Eggs, large, 6’.

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