Wuhan, Wuhan-U, and Woohoo!

OK, this came from a threaded discussion I'm having off line. It sent me down a rabbit hole. The initial question is whether or not Anthony Fauci lied to Congress about gain of function research being done at the Wuhan Institute of Virology. I wanted to make use of the formatting here because there are a lot of quotes.

My reply: 

OK, I can see how you get to where you are.

Obama paused certain types of gain of function research for the right reasons. It was for an ethical review and risk-benefit evaluation that led to enhanced safety procedures for gain for function research into transmissibility. Then, with those protections in place, it was back to the science; the pause of gain of function research was lifted given special protections. In the case of the research we're gonna be looking at, it was done in a biosafety level 3 lab. 

Research on coronavirus was done in Wuhan by EcoHealth, who was studying coronavirus in bats, to see if: "spike proteins from naturally occurring bat coronaviruses circulating in China were capable of binding to the human ACE2 receptor in a mouse model." This sounds to me that researchers know 1) where there is a risk of emergence and 2) likely routes of infection--because both were true in the case of SARS-CoV-2. SCIENCE! But it also establishes the fact that there is a very good reason for the outbreak to start where the lab was, not because of an escape but because prior probability suggested that Wuhan was a likely point of origin for the next coronavirus spillover. So, there's a real relationship, but it's not a causal one, but a correlational one.   

So, EcoHealth's funding was provided by the NIH, and EcoHealth picked its own collaborators including WIV. Gain of function research was not covered by the grant (although I'll point out that the strains of mice with human ACE2 receptors are the product of gain of function research, which isn't always "let's make diseases worse," as so many people seem to think). It looks like when some of the mice were infected with naturally occurring virus (the subject of the study), and there was a control that was infected with a modified virus that... I think it was the control--it was a comparable, very similar non-infectious agent. The modified virus was the same virus with a spike that had never infected people (or, more specifically, bound to the human ACE2 receptor before). It was, then, apparently not something designed to make it more virulent, which people seem to assume. Surprisingly, the mice who got the altered virus got sicker than the ones exposed to the wild virus. EcoHealth did not report this to the NIH, though they were required to by the terms of the grant, as pointed out by a director in a letter he sent to Congress, referenced here in the only link I will ever have to the NY Post.

This points, to my mind, to the possibility Fauci and others at NIH were not fully informed at the time about this unexpected result. 

This is the study in question, done by UNC and Wuhan: https://pmc.ncbi.nlm.nih.gov/articles/PMC4797993/  

From the abstract, which clarifies (ha!) how the viruses were used in the research, actually one of the papers that came out of this larger research project:

Therefore, to examine the emergence potential (that is, the potential to infect humans) of circulating bat CoVs, we built a chimeric virus encoding a novel, zoonotic CoV spike protein—from the RsSHC014-CoV sequence that was isolated from Chinese horseshoe bats1—in the context of the SARS-CoV mouse-adapted backbone. The hybrid virus allowed us to evaluate the ability of the novel spike protein to cause disease independently of other necessary adaptive mutations in its natural backbone. Using this approach, we characterized CoV infection mediated by the SHC014 spike protein in primary human airway cells and in vivo, and tested the efficacy of available immune therapeutics against SHC014-CoV. Together, the strategy translates metagenomics data to help predict and prepare for future emergent viruses.

I also looked for the original grant proposal, to see what was proposed.

DESCRIPTION (provided by applicant): This project will examine the risk of future coronavirus (CoV) emergence from wildlife using in-depth field investigations across the human-wildlife interface in China, molecular characterization of novel CoVs and host receptor binding domain genes, mathematical models of transmission and evolution, and in vitro and in vivo laboratory studies of host range. Zoonotic CoVs are a significant threat to global health, as demonstrated with the emergence of pandemic severe acute respiratory syndrome coronavirus (SARS-CoV) in China in 2002, and the recent and ongoing emergence of Middle East Respiratory Syndrome (MERS-CoV). Bats appear to be the natural reservoir of these viruses, and hundreds of novel bat-CoVs have been discovered in the last two decades. Bats, and other wildlife species, are hunted, traded, butchered and consumed across Asia, creating a large scale human-wildlife interface, and high risk of future emergence of novel CoVs. This project aims to understand what factors increase the risk of the next CoV emerging in people by studying CoV diversity in a critical zoonotic reservoir (bats), at sites of high risk for emergence (wildlife markets) in an emerging disease hotspot (China). The three specific aims of this project are to: 1. Assess CoV spillover potential at high risk human-wildlife interfaces in China. This will include quantifying the nature and frequency of contact people have with bats and other wildlife; serological and molecular screening of people working in wet markets and highly exposed to wildlife; screening wild-caught and market sampled bats from 30+ species for CoVs using molecular assays; and genomic characterization and isolation of novel CoVs. 2. Develop predictive models of bat CoV emergence risk and host range. A combined modeling approach will include phylogenetic analyses of host receptors and novel CoV genes (including functional receptor binding domains); a fused ecological and evolutionary model to predict host-range and viral sharing; and mathematical matrix models to examine evolutionary and transmission dynamics. 3. Test predictions of CoV inter-species transmission. Predictive models of host range (i.e. emergence potential) will be tested experimentally using reverse genetics, pseudovirus and receptor binding assays, and virus infection experiments across a range of cell cultures from different species and humanized mice.

Very important: I don't see gain-of-function mentioned in this proposal. I have learned that these R01 research grants can lead to follow up studies and can be renewed and ammended. Eventually it may have mentioned GoF (it looks like the last version of the updated proposal has something that sounds like it). But what's really important is that the Internet Archive captured this version of the page on April 16, 2020, two and a half months after an early email discussion (Feb 1) between Fauci and and Francis Collins and other important muckety mucks, where he relayed a conversation about a rumor floated by an Indian team that the virus was manufactured, and he said: "The suspicion was heightened by the fact that scientists in Wuhan University are known to have been working on gain-of-function experiments to determine the molecular mechanisms associated with bat viruses adapting to human infecton, and the outbreak originated in Wuhan."

OK, a few things, 1) the Wuhan Institute of Virology does not appear to be a subdivision of Wuhan University, but an independent entity. 2) The research looks very similar to what's going on in the research above, so perhaps he misspeaks here, but that suggests, 3) he's not familiar enough with the research institution to speak about it or what goes on there authoritatively. This is important if you are seeking to establish whether or not he lied to Congress--what he knows and intends are abolutely relevant, if not determinative. He can be legitimately wrong and think he is right. That's not perjury, that's sloppy. But I suspect, maybe, because his initial contact with the idea came from people who were positing a rather out-there theory that his experts generally dismissed, he dismissed the idea that that research was being done there in the first place. Possibly. That's speculation. However, it's consistent with the idea, a guiding principle I apply to accusations of malevolence, that you should usually suspect run of the mill error ahead of malevolence. I suspect that most people who have spent their professional lives testifying in front of Congress, like Fauci, don't go into those meetings intending to perjure themselves to such a hostile audience on something that is so checkable. He can be wrong.  

So, what's the takeaway, since I need to go to bed? 1) It's complicated. 2) Most of this does not speak to what Fauci knew or didn't know and therefore shouldn't be used as primary evidence of his knowingly perjuring himself to Congress. I strongly suspect that Fauci was too high up on the totem pole to be signing off on piddling research grants worth mere hundreds of thousands of dollars, and that he is at best tangentially related to this research. 3) The research seems legit and interesting and done with appropriate safety procedures, but that of course doesn't push the pudding pop one way or the other, to coin a new phrase. 4) It's not enough to establish guilt by noting that he benefitted from the outcomes of his actions; and in this case, I'm not entirely sure that he did benefit from his misstatement, since his statement has provided endless confirmation for the eager to believe that he did do something sinister. 

That's what I have for now, gents. I'm pooped. 

Vidja of a birb

 

Save Chronicling America

Via Ryan Cordell over at Bluesky comes information that Chronicling America is at risk. I use it constantly in my classes. Here is the letter I wrote to my representatives (Jeff van Drew of NJ's 2nd district, Andy Kim and Corey Booker). 

It has come to my attention that the National Digital Newspaper Program (NDNP), a partnership between the NEH and the Library of Congress, has been shut down. The NDNP is responsible for digitizing newspapers for Chronicling America, a public newspaper database used by citizens and scholars for genealogy and research purposes that is the envy of the world. This newspaper database has been a key part of my courses, up until and including this past semester, where I had college students explore the database and report on how Americans experienced major milestones in WWII, when the outcome of the war was not clear. For instance, one student reported that after Pearl Harbor (but before Germany declared war), citizens in Virginia started building bomb shelters in their yards (you know, just in case)! Chronicling America gives my students a sense of what living through history was like, and I use it in almost all of my classes. I encourage you to preserve this vital resource and to restore funding for the NDNP.

Historical newspaer databases are one of my few joys in life. Do me a solid and drop your reps a note. 

A Dispatch from Salem

 Greetings from Spring Break! 

I imagine that right now, y’all are lounging on a beach somewhere working on your tans, drinking age-appropriate beverages with little umbrellas through bendy straws, and generally being paragons of Puritan restraint and decorum.

I, however, am in Salem, MA. 

Morning, my family and I were in Plymouth, famous landing place of the Pilgrims, who had been kicked out of two countries for being too religious (and it took a LOT to get kicked out of Holland in the 1620s, let me tell you). They landed at Plymouth Rock. According to one very very very old guy. Decades after the fact. Who heard it from another guy who was supposed to have been there. The earliest mention of the rock in the historical record was as a big stone marking a boundary. But whatever, it’s a good story. Nobody warned us that the weather in Plymouth was going to be a recreation of the Pilgrims’ first winter, because it was h*cking freezing down by the water. Here is the rock:

It was fantastically good luck that the rock was stamped with the year when they got here, as calendars had not yet been invented. 

So, after we looked at the rock, I looked up the hill above the harbor and saw this brass statue of one of the indigenous people gazing out over the place where the Pilgrims landed:

I did not go up the hill to check, but I’m pretty sure the statue is titled “Oh, Shit.”

After Plymouth, we drove to Salem, about and hour and a half north. This is where the Pilgrims’ dream of killing a lot of innocent members of their own community finally came true.

Salem is goth Disneyland. 

We had an hour or so to kill before we were scheduled to meet friends of my parents for lunch, so we went to the final resting place of many of the instigators and (presumably) the victims of the famous witch hunts. The supposed witches were taken down after they were executed and put in shallow graves, but they were removed by family members presumably to this cemetery. 

The cemetery has a lot of New England charm, and you get a hint of it when you see the oldest cemeteries in Pennsylvania. The headstones are thin and very weathered so that the fronts look almost exactly like the backs. The cemetery was gated and locked (presumably because the markers there look so fragile), but you peer in over a low wall. Built into this wall are stone seats, each bearing the name and execution date of one of the accused witches. Some of them, like Bridget Bishop’s memorial, had lillies placed on them. 

For a town notorious for falsely convicting citizens for being witches, Salem sure does attract a lot of people who profess to be witches. The graveyard is bounded one side by a restaurant called “Casa Tequila” (I hear the Alamo is across from a Walgreens) and by a row of shops and mini museums on the other, all of them, I think, witch themed. I had to go in the one called Pentagram. Had to.

Had to. 

It was a fairly small shop with a large collection of gems and stones on the first floor (way more than anyone asked for on that later), books on the second floor, magic tchotchkes and divination tools throughout, and three booths with curtains drawn across them where psychics were giving readings. We arrived as one of the psychics was showing up for his shift, setting out his crystals on the little table. I really wanted to get a reading, but my family was waiting in the car and I had to be relatively quick. If I do get one, I’ll ask to film it. I did see one woman sign up for a walk-in reading.

The store sells all things “magick,” which is magic but is spelled with a “k.” 

This is a screencap of my phone. There is no movie.

There is a huge wall of herbs behind the register, I presume for spells and the types of preparations in these books:

 

I guess today is the day I learned about “plant magic.”

There also seems to be some cross pollination between Wiccan practices and other beliefs, including Jewish Kabbalah and the Golden Dawn (I am presuming that this is a reference to the offshoot of Freemasonry and the not the Greek fascist party):

They had a display with divining instruments of the type that my students might recognize:

The things that look like cookies are pendulums for divination, a type of dowsing.

And they had another thing. Among the gems and crystals. Which you would not have heard of in my class, at least not before I learned that it was a thing: a lot of amazing jewelry! 

I mean, why would you mix pewter jewelry in with the uncut gemstones and gigantic quartz peni….the hell?!! 

Like, you know me, I’ll ask anyone about anything, but not even I could screw up the courage to ask the woman behind the counter what these gigantic gizmos were in aid of. Luckily, they have a website which details everything that they sell in the shop, including the rose quartz phalluses. The text for the 8.5-incher explains: “The Phallus is a symbol of the divine masculine and fertility. Place on your Altar to bring abundance, growth and prosperity.” I kind of want to know if the 5.75-inch phallus has less potent magick. 

The website really does give you a sense of the subculture. They also sell experiences, including one that I absolutely would love to go see, a seance!

The description is: 

In a time honored tradition we will be celebrating the loved ones who have passed before us. In this small group setting we will be supporting one another as messages of love and healing are brought through. Come with an open.heart and leave with a sense of hope, love, and inspiration.

Not to be that guy, but how do they know what the departed are going to say ahead of time? Anyway, it would be interesting to see a modern take on the seance. Sadly, it’s in April. 

I saw half a dozen shops just like this in Salem, and we are going to hit some of them tomorrow. Also, I was not expecting this, but there seems to be a pirate theme running through the town as well. It’s like all of my grade school Halloween costumes come to life! 

 

Next Year is Going to Be Hard

I am checking in at the end of the year to just be on the record.

Though we have not seen the GOP do well in a single election after Trump became president, the press seems to have decided, via polls, that he is a contender for next year's GOP nomination. He may well be, pending convictions notwithstanding. With that in mind, it's going to be a bad year whether he wins or loses. Though I truly think he is unelectable, I'll never consider it unthinkable like I did in 2016. The lead-up to his loss will be brutal. The response to his loss will be also brutal.

That's as optimistic as I get this year. 2024 is going to be hard, but I strongly believe that women and others who will be victimized by a GOP win will step up. 

I am genuinely disappointed in my generation to have allowed us to reach this point. Hell, someone I went to high school with is literally Trump's lawyer. It's disheartening to have the optimism of my young adult life about the future of the country turn out to be so staggeringly wrong in just about every conceivable way. If it weren't for the compassion and empathy of the kids who I've taught (the oldest of them are in their 40s now, sweet Jesus), I'd think that there would be no hope. But the youngest, most empathetic and potentially progressive of the youth have never seen a fuctional political system in their lifetimes like we oldsters have. I get their cynicism. I think that one of my goals will be to convince those who want to hear it that I have seen better and help them see what I saw.

So, knuckle down. Keep living. Keep worried. Keep active. Keep going.

RJB

A Little Bit of Everyday Skepticism

Yesterday a student sent me an example of a weird claim to see if I could explain it. Someone on tiktok had claimed that they had seen a giant on the top of a mountain in Canada. Not long after, they died. The person claimed that they had been followed and might disappear. The tiketytokers were all aflutter over this disappearance. I did what I said I'd do, look into the report and see if there was another explanation.

Here's my report back to the student:

Alright. I'm looking into this. The mountain in Canada where this was spotted is named "Canoe Mountain." I went to Wikipedia, and it's super pretty. But look up at the peak.... Zoom in. You can see that there is something at the top of the mountain. This is looking like a candidate to me. 

Now here's a frame of the video:

The rocky ridge up front sure looks like the same as the one beneath the photo of the whole mountain, so I'm pretty confident that these are the same mountain. I don't know if the words "its a giant" appear in the original video, but if they do, well what we are seeing is ambiguous...it's certainly not obvious what it is just by glancing at it. When we are presented with something ambiguous like this (think "ghost voices" in the static between radio stations or images in random clouds) if we are given a prompt, we see what we are told to see. But anyway, look at this blurry picture of my acoustic guitar leaning up near the wall. You can see the curve of the body, you can see where the neck/fretboard meets the body, and where the sound hole is. But you can see the form of the guitar still. But the only reason you can see the guitar is because I prompted you to see it. Right? 

Actually, this is the giant from the video magnified and flipped upside down. If you saw the guitar it was because I described as a guitar and there is truly not really recognizable form to the object. I often do this when people tell me they have seen ghost faces in photos of mirrors or reflections. If you flip the image, the resemblance to a face disappears, though when you flip a photo of a person, you can still tell it's a person.

So, I think that we have established that 1) there is something there and 2) we don't know what it is. 3) Yet. 

What's at the top of Canoe Mountain, then? 

This communications tower on the peak of the mountain is almost certainly what the tiktoker saw. 

But what about his death? He does appear to have died. He died young (weird). He did not seem to have any physical ailment. But he did express that he was being followed and may have had a paranoid delusion. He hinted that he might no longer be posting. Could he have killed himself? His cause of death is not mentioned, but it's a possibility. It's not the type of thing that families are eager to publicize sometimes. I looked up the most common causes of death for young men 30- 44: accidents, heart disease, and suicide are the top three. 

My conclusion: A misidentification of a communications tower as a human form, and the sighting, absent any convincing independent evidence of him being targeted, is unrelated to his death. (Remember: the post hoc fallacy!)

B 

I love when students send me this stuff. I always take it seriously and give the claim a fair shake. I show them the research and the reasoning that leads me to a conclusion. 

Gotta do a thing...