California subsidies for dairy cows’ biogas are a lose-lose, campaigners say Guardian (resilc). This reads like an obvious joke except it’s not…
A Lonely Universe Inference (Anthony L)
Webb Space Telescope Successfully Sees Its First Glimmer of Light Gizmodo (Kevin W)
NASA Details Its Plan for the End of the International Space Station in 2031 Universe Today. Furzy: “More privatization.”
A highly virulent variant of HIV-1 circulating in the Netherlands Science (martha r) and New HIV strain found in the Netherlands: Highly infectious variant makes people ill twice as quick Daily Mail (Kevin W). GM, based on the Science paper:
You will see that it [the variant] increased in frequency in the 1990s — the plot is weirdly done, but it looks like it was the dominant strain for a while, then went down in the 2010s
Of course after the 1990s you had much more powerful ART combinations, so everything has been suppressed and thus a bit distorted in terms of relative frequencies
The paper is notable because it is an example of a highly lethal virus (doesn’t get worse than 100%) becoming even worse.
Also, notice that this strain had 300 amino acid mutations. The whole genome is <10 kbp, so that's almost 10% of it mutated. And it's still HIV and very fit too. Now HIV is particularly notorious for its plasticity, but that shows you how much space for things to evolve there actually is when it comes to viruses. Especially if the mutation rate is really high, as it is in HIV. So throwing something like Molnupiravir at SARS-CoV-2 while allowing astronomical numbers of replication events to occur in the human population is a really really bad idea. Who knows what previously hard to reach sections of the fitness landscape we are going to unlock by making many mutations at a time with that drug? Omicron shows something like that too -- those mutations at S371, S373, and S375 baffled everyone. That region is very highly conserved in sarbecoviruses, you would have never guessed from the phylogenetic analysis that you will get a cluster of mutations there (and there is one more in BA.2). So this wasn't even a case of it exploring the usual plasticity in the largely unconstrained areas of RBD, it went into a completely unexpected direction.
Thomas Nagel · What is rude? Midgley, Murdoch, Anscombe, Foot London Review of Books (Anthony L)
Does Quantum Mechanics Reveal That Life Is But a Dream? Scientific American (Anthony L). My dreams are way better than reality so I hope so.
Here it is by age group, since they started sitreps. You basically can't even see the previous waves now. This really illustrates just how radically different this wave has been, both pic.twitter.com/4zWGEjekAd
— Brett Favaro (@LetsFishSmarter) February 4, 2022
The hospitalization rates for babies are *extremely* high.
— Gabriel Hébert-Mild™ ⓥ (@Gab_H_R) February 3, 2022
Um, and ~50% of total population boosted….but Israel started boosting early, and GM estimates that boosting efficacy v. Omicron is pretty kaput after 10 weeks.
What the hell is happening in Israel? pic.twitter.com/rvDnd1jNf2
— Python WebDev and Muckraking – Pureblood ? (@marvin_nz) February 3, 2022
I don’t understand why Leonardi is so cautious. Scientist GM said early on (as part of a cadre of scientists who talk among themselves about Covid studies and data) that Covid was expected to cause T-cell derangement and exhaustion for some, perhaps many, and I’ve been regularly giving readers the Cliff Notes version of that line of thought. But if nothing else (recall Leonardi is a T-cell expert), this confirms that we are not crazy. And our big concern is not “depleted T-cells = less robust Covid defenses,” it’s “depleted T-cells = weaker defenses against cancer” (you are growing cancers all the time but T-cells run around and normally stomp on them before they go too far):
A fact then a bit of speculation as my contribution:
fact: Naive T cells are a correlate of protection independent of age (but it correlates)
Speculation: As sars cov 2 infections greatly deplete Naive T cells, there may be a point where decompensation occurs (less protection)
— Anthony J Leonardi, PhD, MS (@fitterhappierAJ) February 4, 2022
More bad news on immune system damage by Covid
COVID-19 causes a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells.https://t.co/WCCj9TIoBl pic.twitter.com/oDynHMREFc
— Yaneer Bar-Yam (@yaneerbaryam) February 4, 2022
— Anthony Costello (@globalhlthtwit) February 2, 2022
My latest article in the Globe and Mail focuses on how Omicron will provide little immunity, leading to a crisis of repeated infection unless we change our behaviour. "It’s a delusion to think mass spread of Omicron will end the pandemic" https://t.co/xRTYoqNBzf ?
— Blake Murdoch (@BlakeMMurdoch) January 31, 2022
Short summary — we are not getting a Omicron-specific booster, but another WT.
“Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing antibody titers against D614G were 4760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (pre-boost), respectively, and 320 and 110 for Omicron. Two weeks after boost, titers against D614G and Omicron increased to 5360 and 2980, respectively, for mRNA-1273 and 2670 and 1930 for mRNA-Omicron.”
So another WT boosters gives you higher titers than an Omicron booster, including against Omicron itself.
Expect this to be spun as good news (“WT vaccines still work, no need for an update”) but it’s actually really terrible.
I wrote about this quite a few times previously regarding B.1.351/Beta — when they immunized naive mice with WT or Beta spikes, or a mixture of the two, they got much higher titers for WT in the 50-50 mix, and 20-30% higher titers against WT even with the Beta booster.
So it was not an OAS [original antigenic sin] effect, but something about the spike itself.
And with Omicron we saw from several studies now how those infected develop low antibody titers against Omicron.
So it increasingly looks like the Omicron spike is just not very immunogenic.
Which is not good news at all — the WT booster wanes in 6-9 months as it was, titers against Omicron will wane even faster, and we are back to another wave even if Omicron remains the dominant variant.
Meanwhile it could accumulate backbone mutations that will make it no longer “mild.”
P.S. This will lock in mass infection for the foreseeable future (until we get intranasal vaccines, if we ever get that).
We know that even three doses of WT Moderna don’t do all that much to stop infection, and based on these results, three doses of WT Moderna will be what we are left with (with perhaps additional doses further down the line, and hopefully Novavax does indeed achieve better somewhat better results, but it will not be a game changer).
And we see the situation in Israel now.
The virus has decisively won the first round of the fight with the vaccines, the white flag on our side has been raised…
CDC turns to poop surveillance for future COVID monitoring ars technica. Kevin W:”Not a repost of a 2020 article.”
N95, KN95 masks provide best protection against covid, CDC study shows Washington Post (furzy). Will the CDC next study whether water is wet? And why report this now and not in 2020?
China’s Challenges Project Syndicate (David L)
US temporizing trade terms with China Asia Times (Kevin W)
‘Go down in history as one of the all time worst led political parties….’ Slugger O’Toole (PlutoniumKun)
New Cold War
Look at the map! Where are the Ukrainian military forces concentrated and where are they absent? Gilbert Doctorow. Another recent vid I found randomly that looks germane too: https://www.youtube.com/watch?v=w-rbYFMFjrw.
A war with Russia would be unlike anything the US and NATO have ever experienced Scott Ritter, RT (guurst)
The Year of the Tiger Starts with a Sino-Russian Bang Pepe Escobar, The Saker (Chuck L)
The Reason Putin Would Risk War Anne Applebaum, Atlantic (Kevin C). The projection, it burns, since at least the time the US (wellie along with the UK) arranged for the installation of the dictator the Shah of Iran. More recently, it was the US that sponsored the successful coup against Yanukovich….a mere six weeks before elections where his poll numbers were so low that he was assured to be defeated and there was no indication he intended to scupper the election. And before you object to the word “coup” the incoming bunch tore up the current Constitution and implemented a different one…with no democratic process.
ADL changes definition of racism RT (Kevin W)
The death of an inconvenient Palestinian Al Jazeera (resilc)
‘We’re Outraged’: Liberal U.S. Jews Feel Betrayed by New Israeli Government Haaretz. This story comes from the early 2000s, so things can only have gotten worse since then. A friend is Reform and very pro-Israel. Has >30 cousins in Israel and visits pretty regularly, like at least every other year. She and her Jewish husband adopt a boy from Thailand (and yes, bring him up in the faith; I went to his bar mitzvah). On his first trip to Israel, when they are leaving Tel Aviv (you have to go through elaborate security checks), the guard starts raking them over the coals about their then six year old, who has a perfectly proper US passport. It is immediately evident that this interrogation has nothing to do with security but with the guard’s disapproval of the adoption.
The mother explodes (she’s a negotiator and has control over her register, so she intended to make the point to everyone there, not just the dickhead). She tells him she has cousins in the Knesset (true) and if he does not stop this immediately she will get him fired. Husband is embarrassed but they are resentfully waved through.
Israel, Bahrain sign security cooperation agreement in Manama Al Jazeera Resilc: “Sad day.”
How the Establishment Functions Craig Murray (guurst)
Imperial Collapse Watch
Defiant Pentagon hides poor testing results behind phony firewall Responsible Statecraft (resilc)
Richelieu’s ghost almost solves America’s problems Asia Times (resilc). Ouch:
“Why do you think the Germans have all but dismantled their military?” continued Richelieu. “Because you Americans turned NATO into a bloated, indefensible swamp. You are as stupid as the Austrian Hapsburgs, who acquired Spain, Flanders, Naples and Sicily with clever dynastic marriages. They had twice the population of France during the Thirty Years War, and all the silver of the Indies, but France bled them dry and erased Spain for all time from the list of great powers.”
Lack of Coast Guard Icebreakers Disrupts Shipping on Great Lakes, Says Task Force qCaptain (guurst). Hhhm. When I was a kid, icebreakers didn’t get to Escanaba (the biggest iron ore shipping port on Lake Michigan) till March.
Biden Withdrawing Student Debt Appeal After Outcry Daily Poster. Sirota can take credit for this!
Democrats en déshabillé
GOP Clown Car
Forget reading Thomas Piketty. Try a bit of Terry Pratchett Financial Times
Federal Job Fakery Hits Peak Balderdash The Great Recession Blog. You need to read past some hyperventiliating to get to the data and the abnormally large adjustments.
Google wants schools to teach Chromebook repair classes ars technica (resilc). Ahem, how about making less breakable Chromebooks?
Gigantic Semi-Submersible Ship Transformed into Superyacht Core77 (resilc)
Amazon workers in Alabama say they’re torn over historic union vote Washington Post. Um, the Bezos fish-wrapper, so discount. But the vote did fail before by a hefty margin and that alone creates an aura of defeat.
Kevin W adds: “Related article: Starbucks Is Desperately Trying To Slow A Union Campaign That’s Caught Fire HuffPost
I confess to not having read yet. But headline suggests this is a borderline or actual hit piece on Adolph Reed, for starters by conflating liberals with “the left”. The Marxist Who Antagonizes Liberals and the Left New Yorker (furzy)
National Treasure Harpers (Anthony L). On Nicholas Cage. Have to say, he’s not a favorite of mine.
Antidote du jour. Tracie H:
Gold Koi: “She’s staring at us, do you think she’s going to feed us?”
White, Poorly-Applied-Lipsticked Koi: “No, I saw her look at the don’t-feed-‘em sign, we should move on to that little kid.”
White spotted Koi: “You go ahead, I’m sneaking up on something here.”
Gold Koi: “That’s a LEAF Spotty. Come on, let’s go.”
And a second bonus. I’ve seen several versions of this account but this one seems more comprehensive than the others…and in a very compact presentation.
See yesterday’s Links and Antidote du Jour here.