Greg Cochran and I wrote an article together back in early 2021 responding to this extremely stupid article from Lucy van Dorp and Francois Balloux in late 2020. There was an ongoing selective sweep happening at the time and I was concerned that their falsehoods would negatively impact public policy in respect to the alpha Continue reading "RoHO is incapable of accurately detecting increased…
a.k.a I m too lazy to thoroughly investigate COVID origins Edit 4/10/2024: Added a subheading as per Peter s suggestion. As he implies, I m not interested in a deep investigation of COVID origins, just in doing some mathematics review of a couple of Scott his claims. Many thanks to a commenter for pointing out that the Continue reading "How likely is it for COVID to establish itself?"
There s been some discussion around Charles Murray s recent claim that a lot of people would probably try to make their kids smarter with gene editing if it were reasonably cheap. There s been some foolish points, some reasonable ones, but not many with much imagination. So I thought I d point out some possibilities. Hat tip to Continue reading "Possibilities of interest in gene-editing for…
My first post on this blog was about fixation of a new beneficial mutation. I presented Haldane s original 1927 result showing that with some reasonable assumptions, the likelihood that a new mutation with a small selective advantage fixed in the population was approximately . That derivation assumed a Poisson-distributed number of descendants. We ll show some Continue reading "Overdispersion…
One of my perennial concerns in this pandemic has been that the SARS-CoV2 virus would evolve a hypermutability phenotype, mutate rapidly, and become much more difficult to control. I m going to briefly cover 1) why this would be bad 2) why this would be possible and, in a rare bit of optimism 3) why I Continue reading "Watching for SARS-CoV2 hypermutability"
This preproof from Nathan Grubaugh (Yale, PhD in microbiology, 2016), Bill Hanage (Harvard, PhD in epidemiology), and Angela Rasmussen (Columbia, PhD in microbiology, 2009) came across my desk. It s about the spike protein variant that, as Bette Korber at Los Alamos demonstrated, has become the dominant strain of the coronavirus in the last couple of Continue reading "Revisiting viral selection"
I think it s become fairly apparent that effective federal and even state responses to this pandemic are not going to happen in the short term. I had a discussion over at Greg s blog where I pointed out that effective local responses are still perfectly possible in most places. So let s take a brief look about Continue reading "Effective Local Response to SARS-CoV-2"
There s some foolishness going around about this recent preprint from Los Alamos. They ve spotted several mutations in collected SARS2 sequences from around the world that look as though they may be under positive selection. We re going to look into one in particular, a D614G mutation in the spike protein. This mutation looks as though it s increasing Continue reading "Likely selection for D614G…
The state-specific projections from IHME have been widely disseminated and used for federal, state, and hospital planning. For example, here s an interview with one of the UW professors on the project describing how their projections are being used by the feds. They have done yeoman s work in collecting appropriate data, but their actual model has Continue reading "IHME projections are absurdly…
The previous model I built was a toy model: the simplest possible dynamics that would give you a feel for what s going on, and parameter selection that was educated guesswork. There was sufficient interest in it, though, that I decided it would be worth building a more sophisticated and hopefully accurate model. State dynamics and Continue reading "Updated Epidemiological Modeling"