A number of epidemiologists and virologists did not expect to see significant adaptive evolution for increased transmission in covid-19, and continue to argue against that hypothesis. Vincent Racaniello, well-known virologist, takes this position. So does David Dowd, an infectious disease epidemiologist at Johns Hopkins.
They think that chance can drive a new variant with no transmission advantage to high frequency, even when there are many cases ( tens of thousands or more) . The B.1.1.7 variant went from ~1% to a big majority of cases in England.
I’ve just run some sims ( with the sort of transmission dispersion observed in cov-19). R (fitness) = 1, in both cases. I propagate 100 times in each run. Variant A starts out with 5,000 cases, B with 2000. How often did B catch up with A? 6 out of 100 runs.
How often did B catch up with A when A started out with 50,000 cases and B with 20,000 cases? zero, out of 100 runs.
Start out with 2000 B and 50,000 A, same fitness: how often did B catch up? zero out of 100 runs.
Start out with 2000 B ( with a fitness of 1.05) and 50,000 A with a fitness of 1: How often did B catch up? 100 out of 100 runs.
The top curve shows the relative frequency of B.1.1.7 as a function of time in Denmark. Dowd can look at that and believe it is a random fluctuation. Wow.
West Hunter 
Recall that the Astrologer Royal, proponent of a lousy model badly programmed, holds a PhD in theoretical physics.
He’s done fairly well.
His code was a trashfire, and if he got this one right; his record of past predictions (remember the 150m who died of avian flu in 2005?) ought to give one pause.
Modern physicists ain’t Enrico Fermi. My generation (Ferguson’s) was decidedly mediocre, and the one which came after is functionally retarded. I have a Ph.D. in physics and I would have a real hard time finding a reason to hire one.
In the matter of predicting epidemics he has a record to be shame-faced about. In the matter of getting promotions, research grants, and whatnot he’s obviously played the game well.
No wonder people are becoming more cynical about science.
Nope.
Nope what? Do you mean that people are getting more cynical about science for the wrong reasons? Or do people tell fibs when pollsters ask them about scientists and pretend they still hold them in high esteem?
His record isn’t bad.
“A number of epidemiologists and virologists did not expect to see significant adaptive evolution for increased transmission in covid-19, ..”
Why not? Was it pure wishful thinking or is there some sort of semi-plausible argument for this expectation?
it’s apparently conventional wisdom within the field. It’s much closer to true for an old virus that’s been in humans for a long time.
Hmm.. what other reasons? They’re not taught any theory: generally the case in biology, medicine, genetics. A friend that does know theory ran into someone in ag genetics that was surprised: she expected nobody outside of ag genetics to know any evolutionary/popgen theory.
Speaking of, I was told of grad students in genetics that were reading my book for a light dose of pop gen, with quals coming up. I think there’s one equation in the whole book.
They don’t know much math.
Hmm, what else? dumb?
One more thing: there are plenty of past examples of adaptive changes in epidemics. But these guys don’t know much about history, as well not knowing much about biology.
Moreover, this virus has reached far higher copy number ( infe3cted way more people) than flash-in-the-pan pathogens like SARS-I or Ebola. More chances to mutate: Fisherian acceleration.
These posts always take me back to Dr. Harpending’s post, “Eebers and robbers.” Personally, I expect this to only get worse, since today’s grad students are not being selected for the right traits (such as a healthy knowledge of eeb).
A Random Walk was a fun book
As more than one writer has pointed out, “we are doomed.”
No.
Biology is the science people go into when when they like science, but are bad at math. Perhaps some remedial math in intro bio? Maybe some quantitative evolution when they learn the basics of evolution and ecology? Nothing crazy, just comparing, say 1e^x with ce^1.05*x. Ask them if there is any positive number c such that the second equation will not grow larger than the first (there is not), and when c=0.01, how long does the second population take to overcome the first?
Maybe take the math out of it. Teach them the mechanistic basis for evolution: differences in phenotype lead to differences in number of offspring, over time, selection on random variation crafts things that look as if they were designed. You may laugh, but I know a whole lot of people who laugh at stupid creationists, but do know what evolution by natural selection is – they just know it as some magic words. Even most biologists do not think hard about evolution. In their defense, the upper middle class zeitgeist does not encourage people to think evolution is both true and always happening. Think hard about heredity and evolution, and one might start wondering about the wisdom of putting all the smart girls on the 0.5 TFR track. One might think individuals and populations varied. Just those two will get one excommunicated from the Church of the College Educated.
I think the second path, with case studies of viruses. Give clear descriptions how peoples’ immune system act as selectors on viral populations. SARS-CoV-2, to pick a random example, will make a great case study. Biology majors tend to be fairly good with words – give ‘em stories about evolution.
As to the comment above mine. What’s the chance that the country can have a soft, pleasant course correction? I see very little sign that the political establishment can bend on diversity, immigration, eliminating the SAT. Given that the country is becoming dumber fast – the lower IQ immigrants’ kids are beginning to work their way up in age, and are a growing fraction of workforce.
The Democrats believe a ton things that are counterfactual. The Republicans also mostly believe false things, though different false things. On top of that, Republicans always lose. Just take immigration alone. The permanent lowering of America’s average intelligence compared to, say, 1965 is permanent. We are dumber than we have ever been. It can get worse, but almost certainly cannot get better. The educational establishment has turned on testing. How will we get smart people into the right spots in society? The top whatever fraction of intelligence do not ‘look like America’. They especially do not look like the new America that has come about to keep the capitalists’ and landlords’ investments ever-growing.
You say we are not doomed, but how?
Your generalization about biologists is far too extreme. Some people go into biology because they become fascinated with a particular taxon, in my case reptiles and amphibians because of the aesthetic quality of an encounter with a vivid garter snake in a brook when I was 15. As to training, I went to a middling graduate program in the 1960’s in which there was an excellent course in ecological genetics, and that was in the early days of the rigorizing of evolutionary biology. Evolutionary science is now a highly quantitative field. The flawed expectations regarding SARS-2 evolution came from people whose propensity to shoot their mouth off for public attention was greater than their propensity to think carefully.
Among virologists, the consensus. People that write textbooks. Now they’re mystified, those that aren’t denying the facts in front of them.
The Republicans are the Washington Generals to the Democrats Harlem Globe Trotters. They get paid by the same masters who dictate the outcomes of the games. Those on the right lose because what they want is against what the elites want and our elites are incredibly short sighted, greedy and narcissistic.
Not sure if it was the same variant, but they wouldn’t have killed 17 million minks (0.2% of the number of chickens the US kills each year) if they didn’t think variants were a problem.