(Note – this is a copy of a post I stuck on my shiny newish blog which, so far, consists solely of gibberings about Covid and vaccines! I need to expand my focus… Posting this here as it has an evolutionary flavour. Looking forward to arguing about Natural Selection for the tenth time!).
I have discussed Geert vanden Bossche’s debatable theories before. Briefly, he argues that mass vaccination in a pandemic ‘selects’ for mutants that escape the immunity conferred by the vaccine, and this threat is reason enough to just stop. He ignores selection for escape of what is loosely, but erroneously, termed ‘natural immunity’, and the enormous health and social costs attaching to the sledgehammering of this nut. Unfortunately for his theories, all variants so far have arisen in poorly vaccinated settings.
Now, Bret Weinstein – who claims to be an evolutionary biologist, yet – attempts, in his podcast and substack, ‘On Driving SARS-CoV-2 Extinct’, to rescue vanden Bossche from the dumpster and brush the banana skins from his shoulders.
Here’s an excerpt – ‘Rounding the earth’ is the work of one Mathew Crawford:
(I am aware that a properly-conducted review would include links to sources. In my defence, I can’t bear to! Do your research.)
Now, this is pretty desperate stuff. Rather than recognise the possibility that there are other causes for increase of a variant besides vaccine, it is enough that a vaccine has been used, on however small a number, within a few hundred miles of the epicentre!
Selection requires a differential in output. If one variant produces exactly the same number of secondary cases (on average) than another in the same environment – if they possess the same R value, in epidemiological terms – there is no opportunity for selection. It cannot increase relative to the other (by selection) without a differential it can affect: to get into more bodies it must have the greater R.
The role of vaccine effectiveness
Now, this selective advantage can only happen even in principle if the efficacy of the vaccine against infection (VE(i)) is greater than zero. Efficacy in ideal conditions represents the differential between a vaccinated and an unvaccinated group of the same size and composition, where no-one knows which group they are in. In real world use, the term ‘effectiveness’ is used instead of ‘efficacy’. In the real world, people know if they are vaccinated or not, affecting behaviour, and it also becomes more difficult to equalise groups with respect to other differentials such as age, comorbidity, socioeconomic factors and so on. Because of this – news though this will be to countless amateur internet data analysts – you cannot naively count cases in the two groups, and claim this accurately captures VE.
So, an accurately determined VE(i) gives the percentage differential in case count between treated and untreated groups of equivalent composition. 100% effectiveness means no cases in the vaccinated group, 0% means an identical (or a statistically insignificant differential in) case count. Intermediate values give the percentage reduction – eg 40% VE means 6 cases in the vaccinated for every 10 in unvaccinated: a 40% reduction. From this and the above, then, it is clear that VE 0 cannot generate vaccine escape – there is no possibility of getting into more bodies if the vaccine is completely ineffective; there is no selective pressure if it doesn’t work.
But the relationship is not simply dichotomous. The strength of selection in the vaccinated, minimal when VE is zero and maximal when 100%, must therefore vary continuously between those extremes. The phrase “does not stop you catching it or passing it on”, regurgitated monotonously online and whenever anyone sticks a microphone in front of a sceptic, means only that VE(i) is less than 100% – whereas the intent of most regurgitators is to suggest VE(i) is therefore zero, and there are exactly as many cases in a vaccinated as an unvaccinated group.
It is true that VE(i) is steadily going down, due to waning, antigenic drift and the generalised immune escape of variants. Many even claim (based on shoddy VE-hacking by those amateur analysts referenced above) that VE(i) is negative for omicron.That being so would mean that omicron, at least, is not the variant vanden Bossche is looking for.
For how can it select for immune escape if it confers no immunity?
We can extend this argument backwards. Each variant going forwards has successively diminished VE(i) – and, as the ‘does not stop’-ers continually remind us, immunity wanes anyway. Therefore, Vanden Bosschian Selection must have been getting steadily weaker as a force, if it ever existed. But because Crawford has managed to locate a handful of vaccinees in the vicinity of each step, he gives them the same assumed selective force as ‘wild-type’. I’d bet a pound to a peanut that Crawford and Weinstein have been pushing the implicit-0% “does not stop” narrative throughout 2021 (God forbid anyone should have a reason outside themselves to get jabbed!). And yet, a classic have-cake-eat-cake scenario, they also argue as if selective power were maximal throughout the series. No waning, no antigenic drift.
It is interesting to see how doggedly people have been pursuing the absolutist “does-not-stop” line, and they seem almost relieved that omicron and waning have come along to retrospectively justify the falsehood they have been pushing throughout 2021. “It’s going down” is a tacit admission that it was once up, no? But you’d have struggled to find a sceptic able to concede that in mid 2021. To concede it would kick one of the legs out from under their no-vax-‘cos-I’m-OK stance. Yet the graphs they gleefully point to now show clearly that, when they were vigorously arguing against there being any protective effect whatsoever, there quite clearly was.
Sure it wanes. But you don’t start off waned. Anyone commencing a course now will not have to worry about waning for a good while. Regarding waning as a justification for not getting jabbed is akin to regarding a motor vehicle’s Certificate of Roadworthiness as unnecessary, since it will expire next year. On the other hand, anyone who had the disease in early 2020 may have little protection left; renewal may be appropriate.
The role of frequency
Ignorance of diminishing VE is not even the main thing wrong with Crawford’s analysis. If we assume, for argument’s sake, that a variant can gain a copy specifically by infecting a vaccinated person, and these are rare, how is this supposed to translate into widespread transmission? The individuals in these trials were jabbed then went back to their communities, spread out; little pinpricks in the broader ground of unvaccinated individuals. Our variant gets an extra copy from infecting such a vaccinee, but it may have a long wait to find another. Remember that it only gets an advantage in vaccinees, in this example. The rest of the time, it wanders round the unvaccinated in direct competition for bodies with its ancestor, against whom it has no advantage. So this restrictive scenario isn’t going to work.
OK, you say, let’s give it an advantage in the rest of the population too. Perhaps it can evade innate immunity, or evade the immunity of the previously infected. Indeed it might, and does. But now, we have abandoned vaccination as a unique cause of selective advantage altogether. If we create a selective advantage outside of vaccinees, that could easily be a prime driver itself – especially if there are far more such individuals. It doesn’t speak well of Weinstein’s grasp of evolutionary biology that he failed to notice this effect of the rarity of the advantageous circumstance on the strength of selection.
This is what we see in practice. The variants thrown up so far do not differentially ‘prefer’ vaccinees. They are simply hyper-infectious, and evade innate, infection-acquired and vaccine-induced immunity with not much discrimination. Such discrimination as does exist appears to give greater advantage, if anything, to escape of infection-acquired immunity. This is the opposite of what is needed; people can’t argue that ‘natural immunity generates fewer cases’ at the same time as arguing ‘vaccines select more strongly’.
The role of mutation
Mutations do not necessarily arise where they find their advantage. They are a function of number of replications – the more infections there are, the more opportunity for mutation. Once arisen, mutations are metaphorically chucked against the wall to see if any stick. Outside of hosts that provide an advantage (in terms of additional bodies entered), they can only drift. Once they hit the right kind of host, they get a boost, and if there are a lot of such hosts, they get a lot of such boosts. This can be enough to drive out and replace the ancestral type, where ‘the right kind of host’ is common. But consider: if there were a way of reducing the number of replications, that would reduce the number of mutations. Do we have such a way? Well, yes. Vaccination. Sure it’s not perfect. Sure it wanes. But it will help limit the problem. If people who spent last year arguing against the protective effect had instead embraced it, we might be in a better position now Even 20% effectiveness against infection is protective – 8 cases per 10 unvaccinated, instead of 10. That’s two individuals not passing it on who otherwise would have. And because, unlike additive parameters like hospitalisation and death, the effect compounds, the benefit goes beyond one generation. With an R of 2, after 1 interval we have 16 instead of 20. After 2 we have 32 vs 40. After 3, 64 vs 80, and so on. And of course, the presence of other vaccinees in the population reduces that R anyway. Every little helps.
Hi Allan
Is there a possibility of a TL;DR. I confess I’m not quite sure if I’ve totally grasped the points you are making. Is it vaccine good, not getting it bad?
Anecdote alert!
Our little village has a rash of new cases. One guy, Matthieu, who has just tested positive has resisted getting vaccinated. He’s a nice guy in his forties so I hope he doesn’t get really ill but…
what an idiot!
TL;DR. would be: people buying into Geert Vanden Bossche’s vaccine escape variants scare are clueless.
Mathew Crawford is a particularly entertaining example — he and Steve Kirsch have never met a covid conspiracy theory they didn’t love — Ivermectin and HCQ work, dammit!
The idea that the observation that {each variant arose in a geography where vaccines were being trialed} supports GvB’s escape variant evolution argument is hilarious. The math doesn’t work. Also the “no gain of function mutations were observed before they started trialing vaccines” is factually incorrect: we’ve discussed D614G on these very pages.
DNA_Jock,
Thanks for the info and links. A clean sweep, a trifecta, of names I did not know! I need to get out more! I see Dr (in veterinary medicine) Vanden Bossche has responded to criticisms by his fellow Belgian academics who smeared him thusly:
The curriculum vitae of Mr. Vanden Bossche (annex) does not indicate any significant or assessable academic, biotechnological or pharmaceutical scientific contribution in the field of human medicine, vaccines, immunology, virology, or public health. The almost total absence of recent publications (< 5 years) listed in PubMed attests to this. These two parameters are sufficient to invalidate his status as an expert. Informed scientists in immunology, virology or vaccines, instantly detect the scientific ineptitude of his written or filmed statements, strewn with untruths, disseminated exclusively on social media or the web pages of his organization, and obviously not benefiting from any critical peer review.
It’s that stopping vaccination based on bogus evolutionary arguments bad!
1) If vaccines select for resistance (kinda true, but not the whole story), then diminishing vaccine efficacy reduces the strength of that selection. You can’t keep saying every new mutant proves the point, if the strength is diminishing all the while. There’s progressively reduced payoff for resisting, but vanden Bosschians act as if it is constantly high.
2) If vaccinees are at a low frequency, such as in a trial, they don’t offer a strong selective environment – there are too few instances to make significant gains, and any gains made are diluted by lack of any advantage outside of vaccinees.
Also, a bit in the middle, a grumble about absolutism regarding protection. People who say ‘does not stop you getting it’ in an absolutist sense – if they effectively argue VE is zero – are either displaying a complete inability to grasp nuance, or being misleading (that’s a false dichotomy of course, ironically!).
The true irony is when people try to argue both the 0% and the 100% cases simultaneously – vaccine has no effect on transmission, but at the same time selects for vaccine escape as if it did.
Sorry, my tl;dr now needs a tl;dr!
Alan Fox,
Laurence Fox (actor, famous dad and uncle, now carving a career as rightwing knobhead). He posted a picture posing in a t shirt: “No vaccine needed, I have an immune system”.
I know… 🙄
People had a field day photoshopping. Then, with perfect comic timing, announced barely a day later that he had Covid … and was dosing himself with ivermectin (bought on holiday in Mexico, oddly since he thinks it’s just a cold), quercetin and nasal flushing. None of which he really needs, ‘cos… 🤣
He looks like shit. I never looked that bad with a cold. He will undoubtedly survive, an n=1 dataset for the power of ivermectin and good old pluck.
This article is a reasonable introduction, along with the links to the analysis by Nirenberg and by Iannelli. It appears that vanden Bossche has scrubbed his LinkedIn profile…
I happened to see that picture and yeah, that was some cold!
Thanks, Allan and Jock, in the light of your interventions, the OP now makes more sense to me.
And the McGill Uni Office for Science and Scoiety ideas intrigue me. I have subscribed to their newsletter.
And Laurence Fox (no relation) is certainly a bit of a twat. I suppose someone has to be.
Meatloaf, singer, orange idiot supporter and outspoken anti-vaxxer died last week from covid. His asshole family wanted to hide the cause of his death, instead of coming out and saying, hey, don’t let this happen to you. Wtf.
Other than being sort of fat, he didn’t appear to have a whole lot of other co-morbidities. I think he becomes the most famous person to die from this so far.
But some will say it doesn’t really count, because, well he was sort of fat.
I’ve been in a bit of a crusade here in local forums against antivaxx disinformation these past few months. Unfortunately, the mantra that vaccines don’t protect against infection has been peddled by some pro-vaccine talking heads as well. I’m guessing their intentions were good. They probably were trying to convey the message that we should not get too overconfident after being vaccinated and that we should still do our social distancing and wear our masks.
I’m not sure if they were misled, or it was a patronizing white lie, but the damage is done.
Also many people think herd immunity is almost metaphysically impossible with SARS-Cov-2 at this point. What do you guys think about that? Could the virus plateau at some point and stop producing variants at such a high rate so that a new vaccine, one that is highly effective against infection, might push that R0 (or was it Re)) bellow 1 for long enough?
Allan, your blog link doesn’t work for me. I think you might have posted the link to your control panel in blogger.com. I believe the actual link should look something like this https://allanmillerblog.blogspot.com/, with your user name followed by “blogspot.com”
Same here (the link leads me to my old abandoned blog) . Also, the graph in your post just shows as a large grey rectangle with “IMG” in.
dazz,
Thanks, will take a look.
Corneel,
Cheers for that. That happens in Blogger on preview, but resolves itself on publish, I just kinda assumed that would happen here too.
dazz,
Yes, that ‘does not stop’ thing is my #1 pet hate. It’s the implicit ‘at all’ that bugs me – some people really do struggle with nuance, others are just dishonest. Also confusion between transmission (little effect once caught) and infection (less chance of being caught in the 1st place).
Yeah, there’s a whole bunch of crap going on round comorbities too, as if they were at death’s door and Covid just tipped ’em over the edge. Or, they didn’t die ‘of’ Covid, but of their comorbidity, which for many comorbidities is nonsense. Also, Covid death is often pretty distinctive …
A lot of minimising percentages too, eliminating human suffering by rounding up. 99.999% of kids survive. That’s still 700 don’t, in the US.
dazz,
Pre-vaccine, I used to be reasonably optimistic about herd immunity. After all (I reasoned) every other pandemic finished, why not this one? I also felt it very unlikely we’d get a vaccine as quickly as we did, so infection had to do the job till then. It still must happen sometime. But R for omicron is so high it takes a mallet to HI calculations (which are themselves a bit too homogenised for real populations). 70% might have done for alpha, but not enough now.
It will settle down eventually. The problem at the moment is that mass infection is a mutant-generator, and selector. If we could get everyone on board with vaccines, and got smarter against variants, we’d be a lot better off.
So true. I wouldn’t really call it “struggling with nuance” for someone who cannot grok the idea that {vaccine|masking|distancing|avoiding indoor parties} all reduce, but do not eliminate, risk. These people seem incapable of multiplication.
Does the vaccine reduce the risk of “infection”? Well, that A) depends on your definition of “infection” and B) doesn’t really matter since, as you note, it’s transmission that matters (along with morbidity and mortality, where the data is overwhelming)…
One telling thing is the number of times I come across the same supposed “fact” that arises from a failure to understand; this whole “co-morbidities” shtick is a case in point.
“For COVID-19 deaths there were, on average, 4.0 co-morbidities listed.”
Yeah, and the top listed “co-morbidities” were (in order) pneumonia, respiratory failure, hypertension, diabetes, cardiac arrest, and ARDS.
So diabetes is seen in 15% of US COVID deaths (of course it’s present in 11.3% of the population, so the Hazard Ratio isn’t even that big…) and hypertension is reported in 18% of COVID deaths, lower than its prevalence in the general population [!!].
More to the point, I can say with some confidence that all COVID deaths involved some pneumonia, respiratory distress, and eventually, cardiac arrest. Those aren’t really co-morbidities…
DNA_Jock,
I might disagree with your B). Once caught, onward transmission is little different between the vaccinated and unvaccinated (as, another of my pet hates, ‘even Fauci said’, or ‘even CDC said’). Those Fauci/CDCisms are misinterpreted as ‘no effect on case load’. There’s some reduction of SAR due to faster shedding and (presumably) lower viral loads, but the result is relatively small . But VE(infection) is significantly impacted, and is the real driver of lower case rates among a population with a significant proportion of vaccinated people, and hence the protective effect that the “it only affects me” brigade are determined to reject.
All VEs contingent on infection are really composite, and the 1st step always must involve a term for VE(i). That feeds into the next filter – eg hospitalisation.If VE(h) is 90%, that could be the resultant of
VE(i) of 80% and VE(h given i) of 50%,
or
VE(i)=0 and VE(h given i)=90%
or some other permutation, obviously.
Which leads to an interesting conundrum. If VE(i) is going down, as it seems to be, but overall composite VE(h) is staying steadier, would that mean the protective effect of vaccine against serious effects – VE (h given i) – was going up?
UK government report reveals that British children, 10 to 14 years old, up to 52 times more likely to die after getting a COVID shot
https://www.lifesitenews.com/news/children-in-britain-up-to-52-times-more-likely-to-die-following-a-covid-shot-report-finds/
Can people better at stats help me correct this article?
Thanks Allans!
J-Mac,
https://en.m.wikipedia.org/wiki/LifeSiteNews
Seems this organisation has already been banned from social media sites for spreading misinformation on Covid.
I suggest, if J-Mac wants to support a claim that vaccination is killing children, that he start with the raw data supplied by ONS. There’s no doubt the ONS has a deserved reputation for reliability and integrity.
J-Mac,
It’s on Life Site News. That is all you need to know, O Sealioning One.
Alan Fox,
Yep. Although the Contrarian World is currently ejaculating over some published UKHSA data. There is a significant denominator problem, referenced in the data notes but completely ignored by the disseminators. The result is that it appears that vaccinated people are twice as likely to be a case. But it ain’t so.
I opened J macs site, saw two of the articles and thought, my God, people actually read this shit. And Jewish lizard people rule the world and want to eat your babies. True story.
Allan Miller,
But, given his medical expertise, J-Mac should have no problem spotting the issue. I don’t see why he would need our help correcting something this obviously wrong.
DNA_Jock,
I did have a quick look, but couldn’t work up the enthusiasm to begin to be bothered to make head or tail of it. I did notice no confidence intervals, bit of an issue with such small numbers.
What’s amusing is that your opinions are as outlandish and absurd to many of us as that site is to you. You are the living embodiment of that sort of nonsense with regard to your opinions about evolution. You are that site!
Just about everyone who has made a prediction about the course of the pandemic has been burned. Including me, of course.
When omicron are along, and many people said it was less deadly, I suspected it was less deadly because 90 percent of everyone has either been vaccinated or has had the bug.
Now we have a shitload of people who’ve done both.
It sorta kinda makes sense that a virus that specializes in the upper respiratory tract would be more contagious. And by coincidence, slower to infect and damage the lungs. Provided the immune system jumped in before it spread to the lungs.
Despite the poopooing above, obesity is the factor most associated with landing in the hospital. After age. I’d like to know if median population age and incidence of obesity account for a lot of the difference between countries in per capita deaths.
I read there is no necessary link between infectiousness and mildness, but I’m wondering if the route taken by omicron links infectiousness and delay in infecting lungs. Which gives the immune system a bit of extra time.
The milder symptoms might be an advantage to the virus in spreading, because there’s less warning.
petrushka,
It is possible. The issue on mildness is that the virus only has to keep people alive till they stop shedding. After that, there’s no advantage (nor disadvantage) to keeping them alive. It’s reallly our immune response that kills us.
Staying higher in the airways might reduce the opportunities to get into the bloodstream and become a vascular disease. But it’s still not clear (to me) if omicron is ‘genuinely’ milder, or is being made so by immunity.
Also: even if a milder course on average, there are signs it can damage components of both innate and adaptive immunity.
It’s looking like, when you adjust for immunity, it’s a little milder than delta but comparable to the earlier variants. From “Challenges in Inferring Intrinsic Severity of the SARS-CoV-2 Omicron Variant”:
But that’s only looking at hospitalization and death rates; there’s no guarantee that other damage is proportional.
Indeed. That article also mentions,
I was thinking that spending more time in the upper respiratory system might mean more opportunity to spread, more time before the immune system gets involved, longer life for the host. And milder disease allows the host to continue socializing.
I’m just thinking there could be natural contingencies selecting for mildness. Just as spreading before symptoms benefits the virus. The ideal virus would produce no symptoms. Indeed, we are loaded with microbes that produce no disease.
petrushka,
This is a good point, that would seem the most natural conclusion of natural selection, if such a concept really existed. Viruses would be neutral or even beneficial, then they could spread like crazy.
If natural selection was a real concept. Maybe in an alternative universe.
Concept.
I don’t think that word means what you think it means.
Then I don’t think means means what you think it means.
I wonder how many neutral or beneficial viruses have been identified over the past 100 years. I guess it would have to be a lot.
There is of course the tiny problem of assuming control over the cellular machinery of the host and lysing its cells, without harming it. But yes, commensal viruses exist. Warts come to mind.
Gee, it almost sounds like you are talking about how difficult it would be to have a random mutation to a DNA code that doesn’t destroy it.
But that’s probably just a caricature anyway.
Then you misunderstand. SARS-CoV-2 has already acquired numerous mutations to its genome that have not destroyed it. Take a look at the Nextstrain site to get a taste of the tremendous diversity that has already accumulated since the virus was introduced into the human population 2 years ago. RNA viruses are prime examples of evolution in action.
No, I was merely trying to say that given the parasitic nature of viruses it is not surprising that many will not become neutral to their host.
Think Phoodoo prefers the concept of a All Knowing designer ,for some unknown reasons , creating the virus which has killed millions of folks . Then changing it again to evade vaccines to eliminate some more.
Sharks exist , sharks are not the beneficial to swimmers , therefore natural selection does not exist .
phoodoo was just repeating the old creationist argument that modern genomes tend to be intolerant of new mutations and therefore are unlikely to have evolved by their accumulation. I have just not seen that argument used before on a virus for which by a massive world wide sequencing effort we have demonstrated in real time that this is actually what happens.
Just out of curiosity, are there beneficial viruses, to us or to bacteria or whatever?
I wonder, given the opportunity and rate of virus mutation, if there haven’t been a great many “strains” that failed utterly, lasting at most only a few generations. My intuition is that the large majority of mutations are, as with everything else, either neutral or harmful to the virus. Fire enough billions of times, though, and now and then you hit the bullseye.
It ‘s quite rare, but I am aware of at least one example in insects.
Corneel,
That is amazing.
Corneel,
I was thinking of examples where a lysogenic infection by one phage confers immunity to closely related phages, but that’s a rather narrow and dubious benefit. HaDNV-1 is waaay cooler.
For the hard core anthropocentrists here, there’s always the various oncolytic viruses…
The “vaccines” are very effective that ‘s why you need a booster every 3-6 months…
Who could argue with that shittific argument?
I agree that the mutations that SARS CoV2 has “acquired’ leads to only one conclusion: another lab leak, unless, of course you are ready to abandon your evolutionary faith???
It will come to that. I guarantee it. Are you ready??? lol