The CHAZ & the virus & labs & bibliographies & a guy on a bike.
The CHAZ and All That Jazz
As monuments are toppling & state legislatures are agreeing to take down confederate state flags, a great mountain of indignation is pouring out of America. Even the meme “Democracy in a can” [tear gas can] was looking poignant. The lockdowns had given with one hand what corporations and bankers had for most of history taken away with the other: free time for engaging in politics as the payoff for having driven the system with crippling debt, plus lockdown during a pandemic. Mayors & governors were having to figure out which side they were going to dance for, the epidemiology probability models, or the oligarchs.
Somewhere in between was the capacity for sweeping away what wasn't working & building something much, much better. Cynicism, made out of deprivation & a lack of nutrients in the basics [food, mutual care, time, quiet, money, art, conscience, reason] force the end "For whom?"
The CHAZ appealed to that old-time anti-authoritarian impulse. For some it was May '68 all over again. In others it stimulated a need for law & order. In between there were frauds, fakes, criminals, utopians, how-tos about showering off tear gas, or avoiding kettling, & a whiff of the danger of conscience. At the center is the demand for racial equality & justice. Everyone was getting real & had something to lose. I bet Adam Curtis and Errol Morris are drinking a lot of coffee right now.
And then things got weird in the CHAZ. Street party by day, tear gas and shootings by night. But it was the bizarre reports that showed the gaps in purpose. For many reports of free stores, cooperation & communing were a few that were bizarre, medieval as if you were reading something written by Umberto Eco.
One from Columbus OH emerged on Twitter, was of the hemiplegic rolling on the ground, separated from his prosthetic legs & pants, with protesters around him summoning a medic. One account said that the cops had pushed him down, stolen his legs, & tear gassed him. Another account was that he had traumatized some cops by lying partly under their car & with the same motion making them think they had run over him, though in the videos there is no auto near him. The incident led to the bizarre defense, “The cops absolutely did not steal his legs,” and an unforgettably absurd scene.
That just about captured the weird side of the prima facie puzzle of the street actions. The sheer power of the state & deep opposition to it all on display in a blaze. It's not very often you get to see the possibilities for good & evil right next to each other, right out in the open.
One thing was certain, the authorities from all levels would eventually use whatever forces of the state to halt the unrest, in the name of law & order. That's the only place this goes, short of the internal factions collapsing the effort first. On July 1st the police raided the original Seattle CHAZ & it withered under the attack. The media may have reported it incidentally that day.
Some mayors & governors agreed to reform police practices. I read somewhere recently [forgive me, I forget where] that others probably reason that the only type of police force that can persistently oppose the protesters & maintain phalanx morale were individuals who were, or were sympathetic to, the alt-right. The materiel of militarization of law enforcement was out in the open now & not only a cliché of a statist dissent. Just wait til they remember they also have to contend with anti-authoritarians on the populist Right. Hawaiian shirts became the uniform of the Bugaloo, who are cast in the media as unified by guns without unified politics. This was not your grandmother's direct action.
Whatever force is used it will be in service to preserving the economy, capitalization. It is tricky to both want people to be able not to starve & become homeless by wanting them to be able to go back to work, and to want fundamental change in the economic system that could mitigate that tendency by stopping economic progress. Whether you are compulsively checking Lew Rockwell dot com or being constantly texted by the Bernie Sanders campaign [still], there are strange bedfellows. But don’t think about that. There isn’t time right now.
It does seem like something is going down. Good.
Sars-cov2
Pre-print servers are starting to heat up and a few biologists recognize the urgency of piecing together the history of coronavirus research before the field gets hopelessly noisy.
In principle, the science isn’t that hard to understand. In principle. Anyone who has done serious reading can get the basics.
As biologists from various sub-fields start to look at the research, and then place it in a complete lit review, they are finding weird tendencies. Some of them. I'm going to explain why some scientists think Sars-cov2 is not constructed in a lab, for example by CRISPR, but could have been lab mediated & then escaped by accident. I'm amplifying their alert. There are a lot of branches in this decision tree, but here I'm just dealing with one: could Sars-cov2 have been adulterated & not a straight zoonotic jump? Why are some credible scientists starting to say this?
In this massive task of tracking down bibliographic coherence in order to backtrack genomic coherence in the Sars-cov2 virus haplotypes, every person trained in lit review or research library skills can contribute. This is real citizen-science. Bakunin has entered the chat. The mega-media messaging can still be turned down.
It turns out now that the problems with explaining the origins of Sars-cov2 as a zoonotic jump lie in its extraordinary genomic genealogy. It is unlike any contemporary coronavirus genomes, which in fact is evolutionarily unlikely. And also, its genome is nearly completely identical [96%] to a much older bat coronavirus, which was reported as early as 2013 [old in virus-years] as being sequenced in a lab.
This is like heirloom tomatoes: they are varieties that have no direct contemporary genetic sibling, but they are nearly identical to old hybrids, hence "heirloom." Sure, given enough time random choice says that a monkey will type classics. But we take that as more of a framing of the limits of probability than a possibility. And viruses aren't tomatoes b/c hybrid tomatoes are cultured, but still. It means that the heirloom seeds were revived by intervention. If you were a tomato farmer you could call Sars-cov2 an heirloom virus. Except for one thing.
It has a furin spike protein that is unusual in that it makes Sars-cov2 highly infectious to humans. A furin spike is the reaching-out molecules of the virus that is attracted to the host cells. Which is strange b/c zoonotic jumps are, by definition, not highly infectious b/c the viral fit to the new host [humans in a zoonotic jump] is barely enough to accomplish the jump. In Sars-cov2 this is a very specific alteration. It would be like cultivating heirloom tomatoes to grow in a specific type of soil they don't usually grow in. It would take some tinkering to get it to work.*[see edit note]
If the genomic sequencing puzzle isn’t enough to cause some serious questioning, then maybe the way the bibliographies of the research papers advancing the zoonotic jump of a pandemic-capacity coronavirus might: get this, a retired school teacher in NZ has located discrepancies in the updated online version of a bibliography of an archived version of a coronavirus research paper from 2015 reporting that a zoonotic jump of a coronavirus could be a serious threat.
She found 6 papers missing in the bibliography of the online version of the 2015 Nature Medicine paper that appeared in the archived version. This woman reads. It wouldn’t be a big deal to simply clean up a bibliography for a final version of a research paper. That’s done regularly.
But what is in those 6 missing papers is super-interesting: they are about using lab techniques to make coronaviruses easier to study and the genomic sequencing of the old 2012-13 bat Sars. So far, so good. It turns out that the old Sars coronavirus was hard to culture in vitro, which hampers a cheap way of creating enough of it to study. But there is another way to produce study-able quantities of virus.
If you infect an animal host with coronavirus and let the virus naturally multiply in the animal’s blood, then you can extract samples for isolation right before the animal dies of the disease. If you infect other animals with that source of the virus, you continue to reproduce viral material for study. As the virus reproduces it also becomes more fit for living in that species; the fitness is accomplished through mutation. So, while you are reproducing a greater amount of the virus, you are also accelerating its fitness to infect a new species. Which also means that at first the virus isn’t perfectly fit to infect that species.
If you were to use the acceleration process of repeated animal infection and then step-wise introduce the virus into new species having more similar receptor models to humans you would be accelerating in a lab the evolutionary capacity of a virus to infect humans, whether you injected it into a human or not. [Tsk. That would be unethical.]
That process is called gain-of-function virological research. Gain-of-function [GOF] research is ethically sensitive exactly b/c it is one way to accelerate the fitness of a virus for human-infective capacity. For this reason the NIH suspended funding for it between 2014 - 2017.
But some of the missing papers using GOF appear within this pause-on-funding period. Did that happen through a waiver by the NIH? No one seems certain.
Here are the papers:
Archived paper 2015
Current version Nature Medicine article
Archived bat paper
Airway culture paper
Look, I’m not the person who put this lit review together. I happened to run into Harvard2theBigHouse blog sometime in early March while looking at coronavirus links before I ran into the J.C. On a Bike channel, but it's going to the same place.
I am putting it in my own words so that I can figure it out. I’m just a lecturer who reads a lot & has a blog & it happens I also hike in the woods. I’m pointing to other people. One of the people doing the heavy lifting is this guy, Jonathan Couey, PhD, neurobiology. Besides some virology you'll get a tour of north Pittsburgh.
J.C. On a Bike: “Like & Subscribe” Also, Alina Chan
The rest of the paper links are in his notes on his yoo-toob channel. He does a fun job of teaching from the seat of his bike. You're never sure what's going to happen first, you learn some biology or you learn what it looks like to roll on the hood of car doing a Pittsburgh-left.
His channel is just one way into overhearing the conversation. He’s part of a bigger circle. One of the leading voices he's pointing to is Alina Chan with the Broad Institute lab at MIT and Harvard. @Ayjchan on Twitter. Here is Alina Chan, PhD's view in a pre-print:
Sars-cov2 is Well Adapted for Humans
There are a growing number of laymen & journalists publishing on the web doing exactly what I’m doing here, with more or less technical expertise.
J.C. is explaining the indicators in the research itself & how the research is done on Sars-cov2. He thinks that it is more likely than not that Sars-cov2 could have been enhanced in fitness in a bio-lab without having been built from molecular scratch. He’s just a neurobiologist riding his bike through Pittsburgh thinking about coronavirus research. He’s generous with his doubts as well as his thinking.
Look, I doubt that that guy & I have the same ultimate political vision. But so far as I can tell, he's a trained neurobiologist who is questioning, but mostly restrained. It's worth something to agree with what you agree with & be okay with parting ways with what you don't.
Do I think this is true? Answer: It may not matter b/c that's not my main point. My point is to demonstrate that when an expert interviewed by the media says Sars-cov2 absolutely could not have been made in a lab, you'd really have to know what made in a lab means to understand what the expert is saying. The language, the charts, the graphs, even the electron microscope pics used to educate the public on health, and other matters, are not the same as the distinctions in the reality. They are models of reality. And there's the rub.
Synthetic biology is possible. It is possible to build a virus molecularly from scratch. Though there are people who doubt even the existence of viruses, they aren’t the ones working in virology labs. There are electron microscope pics of Sars-cov2 spikes. It isn’t wrong to say that Sars-cov2 wasn’t built in a lab from scratch. It didn’t have to be. And therein is the real story.
Also, this idea doesn't extend to whether or not Sars-cov2 became feral b/c of an accidental lab breach or something else. The US government reports that there are 1, 356 Biosecurity Labs Level 3 in the US and 15 BSL-4 labs in the US in '07. There is thought to be about 55 BSL-4 labs worldwide. That's a lot of potential for an accident or lost material. Coincidentally, Fort Detrick was briefly shut down in summer '19 for inadvertent security breaches. That's just an example. Seymour Hersh wrote a book about bio-research in America in 1968 that launched his career. He also recently claimed in an interview with Errol Morris that he knows what happened to Frank Olson. But who knows, since he's not saying any more than that. But that's a digression.
The policy implication, again J.C. brought this up and I'm amplifying him today, if the mask mandates are justified then Sars-cov2 is a dangerous pathogen, suggesting that it couldn’t have been the result of a zoonotic jump b/c a virus that does that wouldn’t be fit enough to be highly virulent or deadly. If Sars-cov2 is the result of a zoonotic jump, then it isn’t that virulent or deadly in itself, but b/c of the health of people, and the mask mandates & social distancing are opportunistic for other reasons.
Either way the politics and science are tightly wound. That's my main point.
Also, BTW, Barcelona just found Sars-cov2 in a water treatment fecal sample from March 13th 2019. So, the picture is continually needing a refocus.
Sars-cov2 & HIV
Does having Sars-cov2 antibodies confer immunity? The real answer isn't known yet. But facing the possible answers presents a latent political problem.
While I was writing this post a paper on the similarity of Sars-cov2 and HIV both inactivating T-cells was both published & withdrawn. It was thought that they both inactivate T-cell recognition of the virus, impairing immunity to it. I’m not connecting to the original Chinese pre-print server b/c I’m working from home.
I'm bringing this up b/c hiding in this similarity between Sars-cov2 & HIV is a latent political issue.
Yesterday I saw a human interest story on coronavirus in which a doctor was grateful for having been treated with convalescent plasma, which he credited with saving his life. The message in this is that Sars-cov2 antibodies give at least treatment effects. The general understanding of antibodies is that they confer immunity. This is also the general justification for vaccination: if immunity is short, then vaccines can irritate the body to produce them.
In the popular press public health officials have been expressing reservations about the possibility of Sars-cov2 antibodies conferring immunity, and that the time it does that could be quite short. I haven't seen anyone saying they know what is happening with Sars-cov2 immunity yet. The HIV lit shows that HIV antibodies don't produce immunity b/c because of the number of spike proteins.
Let me just summarize with this: if Sars-cov2 were behaving like HIV and its antibodies do not confer immunity for some similar reason, then we are in for a rough ride with Sars-cov2. If a Sars-cov2 vaccine becomes available, then herd immunity could be reached fairly quickly and vaccination might be annual.
But someone who understands HIV and Sars-cov2 will need then to explain why an HIV vaccine, based on a similarity to Sars-cov2, has been elusive or couldn't be developed on the basis of that similarity. That's qualified and it's surely complicated. This report from March explains that very progress on an HIV vaccine & interestingly also broaches the issue of the capacity of some vaccine designs to risk autoimmunity.
The Uncanny Similarities paper linked above had gone further to speculate that Sars-cov2 could gain function by generating gene fragments from HIV. And that is significantly different from just noticing similarities.
If a relevant similarity between the 2 were to have been found, then the politics would have followed. But, again, the paper on similarity was withdrawn.
Here are a couple of sources to read about the politics of pre-prints, likening Sars-cov2 to HIV, & zoonotic jump theory:
Quick Retraction of a Faulty Coronavirus Paper Was a Good Moment for Science
HIV Did Not Contribute to the 2019 nCov Genome
Or, you could just read the titles to know their purpose.
Testing for Infection
Just a word about testing for infection.
Kary Mullis, the inventor of the PCR test said that PCR should never be used to extrapolate viral load, but should only be used to determine the qualitative existence of virus-indicating proteins in plasma. Most of the routine Sars-cov2 tests are PCR tests where there has been a technical decision about how many iterations of PCR amplification will represent a positive result. That's why false positives are the problem, not false negatives.
Kari Mullis’s view is characterized in a 2014 paper that was retracted in, let me see, October 2019.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172096/
Sars-cov2 and ventilators
Clinically, there were nurses & doctors raising the alarm about the use of ventilation on coronavirus patients in March. The questioners there started to say that the ARDS of Sars-cov2 patients looked a lot like high altitude pulmonary edema [HAPE] & the chronic fibrosis, hypoxia, & tissue damage accompanying it. Mountaineers use an old drug that forces the body to retain CO2 to shorten their respiratory adaptation to high altitude: acetazolamide. Whenever the body is blowing off too much CO2, when a person talks for a long time for example, acetazolamide can oxygenate the tissues. [See Haldane-Bohr Effect.] I’ll be looking into this more later. For now I have to call some boundaries. I mean, maybe acetazolamide was Fidel Castro's secret to talking for 20 hours.
Conclusion
These 2 posts, Parts 3 & 4, are just about what it means to think about what we are perceiving in the pandemic environment. In one of J.C.’s brain research talks he is clearly trying to cut through Rationalism in neurobiology research when he criticizes work that tries to use observed brain function to elevate the neurobiological models as more real than the phenomena they purport to indicate. Imagine what that kind of thinking does in public policy.
Rationalism is the taking of models to be more real than the empirical facts they are modeling. That leads to eliding the facts to fit the models instead of the reverse. Rationalism is insidious, especially in highly specialized abstract work.
NB: Jonathan Couey and Alina Chan don’t know me. J.C. hasn’t authorized my summary here of his presentations. So, any inaccuracies in my characterizations of his work are my own.
My purpose here is to translate the technical work into concepts understandable to generally educated people. I want to show where the culture is still vulnerable to questioning.
The scientists are working as fast as they can. But so are the political operatives. So, time is short.
To think about the meaning of empirical reality you’d want to look at what history tells us people and governments are capable of, what relationships exist, what people say about what they are doing, where the money is flowing from & to, and what is possible & likely technologically. Contextualizing also involves a little educated guessing. Like the final puzzle piece, the rest of the coherent picture can tell you pretty clearly what part of the story is absent. There is always new info to incorporate.
The masking & social distancing issues don’t mention that these policies are more effective than bands of roving thugs preventing people from associating in order to talk about what they might have in common without surveillance. OTOH, they are also saving someone's life.
The economic issues I have raised don’t approach the numbers of people who will be traumatized or die as a result of destitution, homelessness, or despair, especially if the economic system doesn’t change at all and our economy becomes even more massively corporatized through further personal debt. Massive wealth transfers in a kind of gain-of-function economic acceleration at work. But slowing the infection rate will protect the health workers & save someone's life.
Meanwhile, other critical issues are invisible. Satellite images are showing troop movements along the border of China & India, and a mild but distinctive radiation cloud has traveled over Europe, but there is disagreement about whether it came from the east [Russia] or the west [UK].
The US has launched the first new nuclear weapon since the Cold War. Like teenagers having a party betting pool over who at the party will win a cash prize for contracting coronavirus first, the world is lowering the bar for resistance to nuclear war.
We seem mostly stuck on other issues in the popular press. Contextualizing reality is a life’s work.
©Celise Schneider2020
*Edit: Since posting this explanation of GOF I since read an important distinction between gain-of-function and passaging. I learned from this article by Jonathan Latham, PhD Virology and Allison Wilson, PhD Molecular Biology & Genetics, that accelerating viral mutagenics through animals is called passaging and the insertion of genetic material specifically to enhance viral function in target species is referred to as gain-of-function. GOF can be done either with genetic material, or through keyboard insertion. Keyboard insertion is explained here. I found the nerdhaspower post & first learned of keyboard insertion from J.C. On a Bike. I found the Latham & Wilson article separately.
.