an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

Archive for the ‘viruses’ Category

Reading matters 8

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Outbreaks and epidemics, by Meera Senthilingam, journalist, editor and public health researcher, specialising in global health and infectious disease.

  • content hints – Dr Liu Jianlun, index case, ancient viruses, smallpox, ancient Egypt, eradication v elimination, hookworm, yaws, polio types 1,2 and 3, malaria, measles, Guinea worm, Edward Jenner, cowpox, eradication programme 1967, WHO, Donald Henderson, SARS, Zika and microcephaly, Ebola, mosquitoes, MERS-CoV, Crimean-Congo Haemorrhagic fever, Rift Valley fever, Yellow fever, more mosquitoes, breeding grounds, Aedes aegypti, Lassa fever, tuberculosis, syphilis, gonorrhoea, chlamydia, MSF, International Red Cross, dengue fever, staphylococcus aureus, bacterial meningitis, rabies, zoonoses, vectors, vaccine hesitancy, seasonal influenza, types A (H1N1), B, C and D, asymptomatic spread, antibiotic resistance, failed infrastructure, effects on poverty, affected by poverty, Dr Jan Semenza, effects of globalisation, investment, learning, co-operation…

Written by stewart henderson

August 9, 2020 at 11:45 pm

2019-nCoV: where does it come from?

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whether or not they led to 2019-nCoV in humans, leave pangolins alone

As mentioned previously, there are lots of coronaviruses. The four most commonly found in humans have these memorable names: 229E, NL63, OC43 and HKU1. These are humanly-borne viruses that seem to be more interested in increasing spread than increasing pathogenicity. We seem to have developed enough of an immunity from these common coronaviruses for them not to be a major problem. It’s perhaps the new strains that jump from bats to humans via an intermediate species – civets in the case of SARS, dromedary camels (probably) in the case of MERS – that are most likely to be pathogenic. Researchers are on the hunt for the intermediate carrier in the case of 2019-nCoV. Snakes were first suggested, but this has now been dismissed. The most recent candidate has been the pangolin, after research from the South China Agricultural University on the genome sequences of pangolin viruses found them to be 99 percent identical to those in coronavirus patients, but this is unpublished, unverified data at present.

Civets, pangolins? These are just some of the more or less exotic wild animals that some Chinese people like to consume or use for ‘medicinal’ purposes. Traditional Chinese medicine, aka medicine that doesn’t work, has a lot to answer for. Health experts are now recommending that the Chinese government clamp down on this practice. The presence of these creatures in open Chinese markets is disturbing. A prohibition was apparently put in place by the Chinese government just last month, a matter of shutting the stable door, but how well this will be enforced is a question.

Civet – harmless purveyor of SARS, and forget the coffee hype

Over the past 24 hours I’ve been coughing up a storm, and I’m due to work tomorrow. Medications are reducing the inflammation, and I note that wearing a common or garden surgical mask, which we see everywhere now, will not help. To quote from Live Science:

Coronaviruses can be transmitted between humans through respiratory droplets that infected people expel when they breathe, cough or sneeze. A typical surgical mask cannot block out the viral particles contained in these droplets, but simple measures — such as washing your hands, disinfecting frequently touched surfaces and objects, and avoiding touching your face, eyes and mouth — can greatly lower your risk of infection.

Of course I don’t have such a virus, and there are no known cases of it in Australia, though at least five Australians on a cruise ship off Japan have been confirmed as having contracted it. But as to surgical masks, the point is that viruses are much smaller than bacteria (on average about 1000 times smaller). They’re not cells, with their full complement of DNA, but strands of nucleic acid (DNA or RNA) encased within protein. They’re parasitic on hosts, unlike bacteria, and they’re generally pathogenic – we don’t have ‘good’ viruses as we have good bacteria. They can live outside of hosts for a limited period of time – hence the need for hand-washing and general cleanliness. Viruses in general may take a variety of shapes and sizes, ranging from the recently-identified DNA-based pandoraviruses at 1000 or so nanometres (1 micrometer) down to 20 nanometres or less. As to coronaviruses in particular (the largest of the RNA viruses) their structure and their ‘spike proteins’ will be glanced at in the next post.


Written by stewart henderson

February 9, 2020 at 12:27 pm

coronavirus – a journey begins

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this is an electron micrograph of 2019-nCoV – ref JOHN NICHOLLS, LEO POON AND MALIK PEIRIS/THE UNIVERSITY OF HONG KONG. The cell is infected with the virus (the little black dots), which migrates to the cell surface and is released

Lots of information and disinformation around the recent outbreak of coronavirus, and my own occasional workplace, a college that teaches academic English to overseas, predominantly Chinese students, is naturally affected by the precautionary procedures and the possibly OTT concern.

This is a new strain of coronavirus, first detected late in 2019. It hasn’t been given a specific name, as far as I’m aware (apart from 2019-nCoV,  which I doubt will catch on) so lay people tend to think this is the one and only coronavirus, since most have never heard the term before. These viruses are zoonotic, transmitted between animals, from bats to humans. My interest is most personal, because when I read that the signs are ‘respiratory symptoms, fever, cough, shortness of breath and breathing difficulties’, I recognise my life over the past several years. I wouldn’t go as far as to say I have a fever, but all the other signs are just features of my life I’ve become inured to over time. I’m reluctant to even talk to people lest my voice catch in my throat and I have to give myself up to hideous throat-clearing, which I do scores of times a day. I’m also afraid to get too close as I assume my breath smells like rotten meat. I should probably wear a face mask at all times (hard to get one for love or money at this point). My condition has been diagnosed as bronchiectasis, possibly contracted in childhood, but I’m fairly sure it was exacerbated by a very severe bout of gastro-enteritis in the late eighties, which left me bed-ridden for several days, too weak to even get to the toilet. When I eventually recovered enough to drag myself to the doctor, she arranged for me to go to the hospital next door for blood tests. It was unspoken but obvious to me she thought I might have AIDS, which I knew was impossible given my non-existent sex life and drug habits. It seems to me, but I might be wrong, that my life of coughing, sniffling and raucus throat-clearing took off from that time.

All this by way of explaining why these types of illness catch my attention. WHO advice is for people to, inter alia, wash hands regularly, cook meat and eggs thoroughly, and keep clear of coughy-wheezy-sneezy people like me. 

Coronaviruses are RNA viruses with a long genome, longer than any other RNA virus. According to Sciencealert they’re so called because of the crown-shaped set of sugar-proteins ‘that projects from the envelope surrounding the particle’. This one is causing perhaps a larger panic than is warranted, when you compare its fatalities (and the numbers should be treated with skepticism at this stage) with those associated with regular flu season. Of course, the difference is that this coronavirus is largely unknown, in comparison to seasonal flu, and fear and wariness of the unknown is something naturally ‘programmed’ into us by evolution.  

There’s an awful lot to be said about this topic, biochemically, so I’ll write a number of posts about it. It’s not only of great interest to me personally, but of course it fits with my recent writings on DNA and its relations, including RNA of course, and to a lesser extent epigenetics. I’m becoming increasingly fascinated by biochemistry so it should be an enjoyable, informative journey – for me at least.


Cases of the new coronavirus hint at the disease’s severity, symptoms and spread

Updated: Your most urgent questions about the new coronavirus

Written by stewart henderson

February 8, 2020 at 10:57 am

Posted in coronavirus, health, RNA, viruses

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some thoughts on regression to the mean and what causes what

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Regression effects are ubiquitous, and so are misguided causal stories to explain them. Daniel Kahneman

Canto: So here’s an interesting thought, which in some ways is linked to the placebo effect and our attributing recovery from an illness to something we ate, drank or did, rather than to the silent and diligent work of our immune system. You know about the regression to the mean concept?

Jacinta: Of course. It’s a statistical phenomenon that we tend not to account for, because we’re always looking for or imagining causal effects when they don’t exist.

Canto: Well, they do exist but we attribute the wrong causal effects – we don’t account for ‘bad luck’, for example, which of course is caused, usually by factors we can’t easily uncover, so for convenience we give it that name. For example, a golfer might be said to have had an unlucky day with the putter because we observe that she she went incredibly close to dropping a number of difficult long putts, but none of them went in, so she made five over par instead of even. Of course every one of those failed putts was caused – one because her aim wasn’t quite true, another due to a tuft of grass, another because of a last moment gust of wind and so on… 

Jacinta: And some of those causes might be deemed unlucky, because on a less windy day, or with a better maintained green, those putts might’ve gone in.

Canto: Okay okay, there is such a thing as luck. But luck, I mean real luck, like the effect of a sudden gust of wind that nobody could’ve factored in, tends to even itself out, which is part of regression to the mean. But let me get back to illness. Take an everyday illness, like a cold, a mouth ulcer (which I suffered from recently)…

Jacinta: Or a bout of food poisoning, which I suffered from recently…

Canto: Yes, something from which we tend to recover after a few days. So the pattern of the illness goes something like this – Day 1, we’re fine. Day 2, we feel a bit off-colour. Day 3 we definitely feel much worse. Day 4, much the same. Day 5, starting to feel better. Day 6, definitely a lot better. Day 7, we’re fine. So it follows a nice little bit of a sine wave – two peaks and a trough – as shown above. 

Jacinta: So you’re saying that getting back up to the peak again is regression to the mean?

Canto: Well, sort of, but you’re getting ahead of me. Maybe it isn’t precisely, because a mean is the midpoint in a fluctuation between two extremes. Sort of. Anyway, let me explain. When you’re ill, you can choose to ride it out, or you can go to a doctor, or take some sort of medication, or some concoction recommended by a friend, or a reflexologist, whatever. But here’s the thing. You’re not likely to go to the doctor/acupuncturist/magus on day 2, when you’re just starting to feel queasy, you’re much more likely to go when you’re at the bottom of the trough, and then you’ll attribute your recovery to whatever treatment you’ve received, when it’s really more about regression to the mean. Sort of.

Jacinta: Hmmm. I agree that we’re unlikely to rush to the doctor or even the medicine cabinet when we’re just feeling a bit queasy, but that’s probably because experience tells us we’ll feel better soon – that maybe we’re already at the bottom of a little trough. But when we start going into a deeper trough, naturally we start getting worried – maybe it’s pneumonia, or tuberculosis…

Canto: Or diphtheria, malaria, typhoid, cholera, bubonic plague, acute myeloid leukaemia….

Jacinta: Don’t mock, I’ve had all of those. But it’s interesting to think of illness and wellness in this wave form. I’m not sure if it works as regression to the mean. Because wellness is just, well, feeling well. Feeling ‘normal’ or okay. We don’t tend to feel super-well – do we?

Canto: You mean you don’t believe in biorhythms? So you think the line pattern would be like, a straight horizontal one with a few little and big troughs here and there, and then finally off the cliff and straight down to death?

Jacinta: Well, no, isn’t it a slow decline into second childhood and mere oblivion – sans teeth, sans eyes, sans taste, sans everything?

Canto: Haha well not so much with modern medicine – though my hearing’s starting to go. But one of them-there invisible implants should fix that, at a price. But you’re probably right – what we call wellness at sixty is a lot different from the wellness we felt at twenty, but we’re probably lucky we can’t feel our way back to that twenty-something feeling. But getting back to the case of the person who applies a treatment and then gets better, there are, I suppose, three scenarios. The treatment caused the improvement, the treatment had no effect (the person improved for other reasons – such as our super-amazing immune system), or the treatment actually had a detrimental effect, but the person got better anyway, probably due to our wondrous immune system.

Jacinta: So that’s where the placebo idea comes in. And our tendency to over-determine for causality. You mention something like a cold, which is generally a viral infection, and mostly rhinoviral. The symptoms, like a runny nose and a sore throat, are actually caused by a mixture of the virus itself and the immune system fighting it, but mostly the latter….

Canto: Yeah, is that about antigens, or antibodies, I always get confused…

Jacinta: Well, it’s very very complicated, with T cells, immunoglobulin and whatnot, but essentially antigens are the baddies which trigger an antibody response, so antibodies are the goodies. So, if someone has a cold then unless they know their immune system is compromised in some way, the best thing is to let their immune system do its job, which might cause a few days’ discomfort, like extra phlegm production as the system, the antibodies or whatever, attempts to expel the invaders.

Canto: Yes, but the immune system is invisible to us, and is vastly under-estimated by many people, who tend to like to see something, like a big bright red pill, or a reflexology foot massage, or a bunch of needles needling their chi energy points, or unblocking their chakras…

Jacinta: Can they see their chakras?

Canto: No, but the magus can, with his various chakra-probing methods, and aural and oratorical senses developed over a lifetime – that’s why he’s a magus, dummy.

Jacinta: Yeah, and I’m sure we can all feel when our chakras are unblocked. It’s sort of like body plumbing.

Canto: So, getting back to reality, there is definitely something like this regression to the mean, to our own individual ‘normal’, but maybe ever-declining physical and mental state, that our wonderful immune system helps us to maintain, a system we rely on more than we realise….

Jacinta: Yes, but you know, it’s good that we don’t realise it so much, because think of all the acupuncturists, Alexander technicians, anthroposophicalists, antipharmaceuticalists, aromatherapists, auriculotherapists and ayurvedicists whose jobs might be on the line – and that’s just the A’s! Then we have the baineotherapist, the bead therapists and the bowen therapists, not to mention the chakra scalpel weaponmasters… can you imagine all those folk not being able to make a living?

Canto: Okay, that’s enough. It truly is a sad thing to think upon, but never fear, your horror scenario will never eventuate, my faith in human nature tells me….