TWiV 1349: Smallpox and mummies

Welcome and introductions

0:00This Week in Virology, the podcast about viruses, the kind that make you sick.

0:10From Microbe TV, this is TWIV. This Week in Virology, episode 1349, recorded on August 14th, 2026. I'm Vincent Racaniello, and you're listening to the podcast all about viruses. Joining me today from Madison, New Jersey, Brianne Barker. Hi, it's great to be here. It's a lovely summer day out there. It's 86, but it doesn't seem as humid as it has been. Pretty nice. Looking forward to a nice weekend.

0:45I think it's nice here too, but it's all dark in here. I can't tell. I think this morning when I walked in, it was nice, but that was hours ago. Also joining us from College Station, Texas, Jolene Ramsey. Hello, hello. It is nice here, I think. A nice Texas summer day of only 93 degrees Fahrenheit, 34 C. But it's a little humid. It looks like it's going to rain, but it's not. Yeah. And from Austin, Texas, Rich Condit.

1:19Hey, my weather is like Jolene's.

1:25Yeah, we've got two New Jerseyans and two Texans here today. How about that?

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Tribute to Dr. Frederick Murphy

2:37We have a bunch of news for you today. We have already talked about the passing of Fred Murphy, but now there is an article in the Journal of Virology by Michael Lairmore. Biographical feature, Dr. Frederick Murphy, a tribute to a pioneer in virology. So he... That's a really nice bio. Yes. 92. That's pretty good, Frederick. Yeah. Good on you, Fred. Yeah. Rich and I went to visit him in... I know the date because it was 2020, the beginning of the

3:14pandemic. It was February, right? Or March, something like that. Something like that. And the masks were just starting to pop up here and there. We went to his apartment and when we released the video. We released the video like six months later and people were yelling at us, why aren't you wearing masks? Well, it was way at the beginning when it wasn't yet going. Anyway, so that is TWIV 625. You know, despite the fact that we interviewed him and did his whole history and stuff there,

3:47I guess I'd kind of forgotten it because, you know, Fred to me was this guy who took the cool pictures of Ebola and wrote the cool book on the history of virology and was just a nice guy, right? But there's a whole lot more to it than that. And the bio does a really nice job in outlining it. Fred did a lot of cool stuff in a fashion that people enjoyed and respected. Good for

4:19him. And of course, his, uh, his electron, his famous EM of Ebola virus is on the wall here at the incubator. And, uh, because that's, that was the subject of the painting that's on the wall called Ebola. Uh, too bad he never got to come and see it. I told him when I bought it, you should come see it. And he said, well, maybe one of these days and that's it. Can't see it now. All right. Uh, we have

Midge-borne orthobunivirus in cattle

4:47from Alan, a new midge-born orthobunivirus making cattle sick in Western Europe. It reduces milk production and it affects ruminants. Um, so this is an article in science by Kai Cooper Schmidt. If you remember Schmallenberg virus a number of years ago, it was a new midge-born virus to, it got introduced into Europe and it, uh, I think it caused birth defects in ruminants.

5:23But now this is another one. It's a, it's a orthobunivirus. Uh, and it's very closely related to Shamonda virus, which I've never heard of, but I like the name Shamonda. It's spread by midges, isolated from cattle in Nigeria in 1965. So this is new. It seems like there are, um, an increasing number of orthobuniviruses that are transmitted obviously by different arthropods that are being detected recently. Um, perhaps, you know, with climate change or things like that,

5:58whether it's, you know, things like Jamestown Canyon and La Crosse or now, um, this midge-born virus, um, clearly a reason why we need to care a lot about what's happening with arthropods and their viruses. And, um, we should actually, you know, do something about that. Uh, in this article, they actually cite, uh, climate change and, uh, elevated temperatures for exacerbating the, uh, transmission from midges. I forget quite the mechanism. It has

6:29to do with promoting the replication in the midges or something like that. Mm-hmm. Yeah. Too many. It feels like deja vu.

6:39So Martin Beer says, the virus is racing through herds. And once you get a virus like this spreading locally, you don't get rid of it again. Martin Beer. Okay. So that's another news. And then

Executive order on childhood vaccines

6:52this, uh, week, the U S president, uh, signed an executive order, uh, really, a really ridiculous executive order, which, uh, attempts to reduce the number of vaccines that kids get. And also to split the measles, mumps, rubella vaccine. So you want to reduce the number of vaccines and then you want to split the MMR into three components. I'm sorry. This is just so dumb. And that will never happen by the way. Anyway, we have two articles that are really good. One is

7:25a New York times article, what to know about vaccines targeted by Trump's executive order. But then I like the commentary in Sidrap by Jake Scott. He's been on with a couple of times what the vaccine executive order gets wrong and what it will cost us. And this is really good. So Trump says at a press conference or the overall office, he says, he's seen proof that kids get a bottle of soda worth of vaccines poured into their body. He's seen proof of this.

7:57Of course, he doesn't, doesn't give any, any of that proof. And, and Jake goes on to say, well, you know, a vaccine is typically a half a milliliter. So you're not getting a soda bottle. He said, that's a gap of more than 200 fold between the 20 ounce bottle of soda and the, and a couple of mils of vaccine. And he says, if you go on blue sky, there are people who actually have photos of the different volumes. And the, an executive order was signed on the strength of that.

8:26So anyway, it also dose numbers. He goes through the fallacy in the dose numbers. And then there's just some crazy stuff that happened at this, uh, well, the splitting up of the MMR is ridiculous. There's no reason to do that. Well, Trump's Trump says that, uh, if you do that, the rates of autism are going to go down. And there's no evidence for that, of course, because vaccines do not cause autism. So that's crazy. There's a, there's a quote here by Strauss. Um, I saw the press conference somewhere

8:58that he had said the MMR can kill 5% of kids. He just said, yeah, that's the number I've heard. And of course there's no such number. It doesn't exist. Standing behind, beside the president, deputy chief of staff, Stephen Miller, who we dislike very much said, parents are pressured into five, six, or seven shots when their children are weeks out of the hospital. And nobody has studied it. Nobody has looked at it. Nobody has thought about it. And Scott writes, nothing could be more detached from reality. And then he goes on to talk about why, what he said is all wrong.

9:28Well, uh, uh, these guys have absolutely no respect for the truth or facts at all. It's just whatever fits their narrative. They say it shamelessly. It's just, it's disgusting. I mean, the whole point is that they're appealing to their base, right? Who are, who like this stuff. And that is not a reason to put kids health in jeopardy. Come on folks. Politics is not that yet. They're doing anyway. This is a great article by Jake Scott. I really like the American association

10:00for pediatrics has done a really good job of promoting what they think is a science and evidence based vaccine schedule. Um, and a lot of people have also been, uh, sharing that a lot more recently. So I would highly recommend if people have questions about, um, what a vaccine schedule ought to look like and what is really, um, recommended to look at the American association of pediatrics. Uh, I think a little, uh, a little more background on this might be helpful. That is that, uh, RFK

10:33took up his position and he fired the existing advisory committee on immunization practices, which over decades, uh, has, this is a body of really expert professionals, uh, have made the recommendations on which the states rely in order to, um, uh, to distribute vaccines, uh, and a vaccine schedule. Uh, and, uh, RFK fired that panel and put in place his own panel, uh, that, uh, were not experts,

11:08uh, and were, uh, ideologues, uh, following his, uh, ideology. They came up with a vaccine schedule scheme that I think is probably pretty much this one, uh, that came out with Trump's order that was challenged in the courts and the committee was, uh, declared illegal and the scheme was declared illegal. So they're back to square one on paper, at least though, it's still wrapped up in a political process. And the way I see it, this executive order is an attempt as with so many of these things,

11:42just, I'm not going to give up. I'm going to now do this challenge and do an executive order. This will be challenged as well. It won't go anywhere, but the result is chaos and confusion for the parents and not knowing what to do with their kids. And people are going to suffer from that. Yeah. I mean, many parents are going to say, Oh, a soda bottle worth of vaccines. That's not good. He's right. You know, not even thinking about it and distrust in the healthcare system, which is, uh, a tragedy. This is going to take a long time to repair, but folks just think, I mean,

12:17the people listening are low hanging fruit. Yeah. I'm not preaching to the right, but just think that you're using kids to get their political goals in. It just is horrible. Uh, well, this is interesting because we're going to talk about this a little bit later, the whole, uh, anti-vax thing, because, uh, one way to look at this, uh, is that, um, parents have a responsibility to care for their kids. If you don't feed and clothe and shelter your children, you're liable for criminal

12:49prosecution, right? Vaccinations are part of childcare. We know that they're, that they're really important. And so pushing back against, uh, well-studied and recommended vaccines is essentially child abuse. And here we have now federally mandated child abuse. Yeah. No, but nobody, but nobody gets prosecuted. I mean, look at the parents in Texas who didn't vaccinate their kids against measles and one of them died that nothing happens. Right. Um,

13:19I will also tell listeners to be on the lookout. I don't know when it's going to, uh, be posted, but, um, the, um, the episode that we did at ASV, um, I learned a lot about a complication of measles virus called SSPE. I always knew it was a terrible, uh, outcome. And now I understand that it's even more terrible than I originally thought. Um, and so, um, you know, I, I did see something with RFK,

13:50um, the other day where he was talking about how not serious measles was, um, and how you just need some chicken soup. And, um, I would recommend you either read the book booster shots that's behind Jolene right now, or, um, listen to that upcoming episode on SSPE to learn just how wrong that is. Yeah. He, he, so the article you're referring to is talking about his, uh, his talk in Pennsylvania,

14:22Lancaster PA a number of years ago, where there's a lot of measles right now. And he said it was just nothing disease and everyone applauded him for saying that. Um, the other thing that's interesting anyway, the, the last executive order on this has been stayed, as you know, Rich, that's not going anywhere. A judge said this is illegal. So we'll see what happens to this. But another interesting article in CIDRAP is about the new CDC director, Erica Schwartz, who, and the title is new CDC

14:54director faces first major tests before she even begins work. So it will be interesting to see if she, you know, supports this executive order or says it is not correct. We want to protect our children and then maybe get fired before even starting work. I don't know. That's what the article is all about. And finally, I want to mention Trudy Ray's 100th post at Virology blog.

Virology blog milestone

15:22So Trudy Ray started writing there on March, 2018 and, uh, has done a hundred posts. So I used to write, well, I started Virology blog and, uh, now other people are writing it, which is great because I don't write there anymore. Um, and Trudy does Virology. David Tuller talks about post, post-acute viral syndromes there a lot. Uh, but Trudy has written a hundred posts. And so congratulations,

15:52Trudy. Hope you keep it up to the next, uh, hundred.

Phage transcriptional regulation and condensates

15:55All right. Now onto the literature. And since Jolene is here, you know that we are going to do a phage paper. If it's Tuesday, it's Belgium. If it's Jolene, it's phage. I wonder if Jolene would ever do. So there was a movie many years ago, which predates everyone but rich. It was called, if it's Tuesday, it's Belgium. It's one of those kind of tours where every, every day you would go to a different country. And if it's Tuesday, it's Belgium. But I wonder if one day Jolene will,

16:28will surprise us and not do a phage paper. Who knows? I suppose it's not like there's a process. I could pick something else. Well, you know, just keep tuning in and then you'll see what I pick next time. But this time, uh, I have selected a paper published in Nucleic Acids Research, uh, just this year. It's called Liquid-Liquid Phase Separation and a Phage-Encoded Inhibitor Cooperatively

16:59Drive Transcriptional Transcription During Phage SPO1 Infection. And, um, there are actually four co-first authors on this paper. Zong Lan, Yi Yu, Jun Yue Hu, Qian Qian Jin, Haoran Zhang, uh, are the four first, co-first authors. And then there are three senior authors, uh, which are Yen Li, Shui, uh, Shui Yuan, and Bing Liu. And this, these individuals are coming from several

17:36institutions. There are, um, six of them by how I counted. The first affiliated hospital, um, of Xi'an Jiao Tong University in China, the Wuhan Institute of Virology, Hujiang University of Science and Technology, Imperial College London, and King's College London. And- That's what, before you start- Yeah. I just want to point out that I really love that Nucleic Acids Research puts the methods right after the introduction. Yeah, that's almost-

18:06All the other journals are putting it at the end now because they don't think it's so, but I think it's really important. It could be because I was raised that way, right? All my journals had. But I also think it's important because I always want to look at the methods and you have to scroll to way at the bottom and, and some journals put them in the supplementary data as well. So thank you, Nucleic Acids Research. You got to know how to do the experiments before you read about the experiments. Yes, yes. It's key. I do want to know how it was done. Yeah. I do like Nucleic Acids Research and a lot of the, the work that is published there is

18:37great. So to the, the subject of today's paper is basically transcriptional regulation in a bacillus subtilis phage by this really cool thing that I don't know a lot about that I've heard go by different names. And here they're using liquid, liquid phase separation. And another name that I hear it go by a lot is biomolecular condensates. And so I think we have to start by talking about this because this is generally not considered when we're thinking

19:10about cells. And so there's this really cool image, you know, if you think about what you see inside of a cell in a textbook, it looks super empty, but it's not empty. It's full of molecules and those molecules are moving around all of the time and they're diffusing around inside the cell in an organized fashion, but even more organized than we think. So if you look at, at pictures that model the interior of a cell, so many things touching each other, how does anything get

19:41concentrated in the right spot to do the interactions that you, that they need to be doing? And so there's this phenomenon where some molecules will associate with each other in such a way that they are effectively membraneless organelles. So the molecules in that concentrated region are considered a condensate or a phase-separated liquid. So it's still liquid around it and inside of it, but they're not moving around as much relative to each other. And they're definitely almost still compared to

20:17everything around them. So Jolene, this figure that they have, this graphical abstract, right? Yeah, yeah. So the condensate looks like it has something around it. Is that right? I think that's an artistic choice. It's not right. Yeah. There are no, there's not like a bound, there is maybe a fluid boundary, maybe. I'm not entirely sure how to describe that part, but there's not a wall. There's not a lipid wall. There's not a protein wall. There is a transition between the speed of the molecules and how they

20:51relate to each other inside the condensate and outside the condensate. But I don't know so much about the actual boundary. Yeah. So when I, my understanding of this was very much helped by a chemist here who was sort of talking, reminding me about, you know, phase changes from solid to liquid and sort of that kind of idea. And, you know, this in some ways being a type of phase change. Sometimes I've seen it described as sort of that self-organization

21:24that you see with oil droplets and water where there's nothing keeping the oil in its separate area, but because of chemical principles, it sort of makes its own aggregated area. And so it seems as though this is really important for changing a lot of proteins, at least again, based on the things I'm familiar with in a cell, changing their localization or changing their function based on the chemical environment of that protein. And so certain proteins seem to move a lot into different aggregates that

22:00happen because of liquid, liquid phase separation. But even though one of the proteins I care very much about, it seems to be regulated by this process. I don't feel like I understand it nearly as well as I need to either. So I was super excited to see this paper. So I, just because this is very different from what I usually think about, I thought it might be helpful for other people. I put a link in the show notes to a series of videos, almost like a tutorial

22:32from Janet Iwasa's group in Utah, where they have a nice introduction to phase separation. They have short animations, videos, some narration, some reading. And there's one video in particular that has the, model of the interior of a cell and the molecules. And it kind of, it really just illustrates how you have the, the liquid, liquid phase separated section in the middle, and there are molecules there and they're wiggling around relative to each other and everything else is wiggling very fast. And that is kind of what we imagine it looks like and what it models to, to functionally do.

23:07And which kinds of proteins and what kinds of cells have these, all cells have these kinds of condensates. The eukaryotic cells and bacteria, I'm sure, RK, although I didn't read so much about that, in eukaryotic cells where it has been studied, these are particularly known to be important for the regulation of processes that involve transcription, RNA metabolism, chromatin organization, and signal transduction. So lots of these small condensates inside of the nuclei of a eukaryotic

23:43cell are going to look like spots in a, that you can label them and they look like little spots inside of the nucleus. And in bacteria, they're also known to be important for processes that involve RNA, various different processes. But today we're going to be focusing on transcription. I was so, again, I just want to thank Jolene for this paper because, again, I spend some time thinking about liquid-liquid phase separation with regard to a few specific proteins. And it had not

24:18occurred to me to think about whether it happened in prokaryotic cells until this paper. It hadn't even occurred to me to ask that question. And I was both excited to think about the question and learn the answer.

24:32I picked this paper because I learned a lot from it when I read it before. And also it has some cool phage biology. It kind of helps explain some, you know, sometimes I just think about life and I'm like, how does life even happen? How do reactions happen in the cell when they're supposed to, with who they're supposed to? And this kind of helps me understand the way that reactions can happen when and where they're supposed to. And many different ones in the same cell, but in different

25:05spots all happening. And others study these condensates in the context of the evolution of life. And that is something that maybe can be explored at a later time. But yeah, I learned a lot too. So I don't know everything about these condensates, but here they did see that it is important for transitions to different stages of transcription in the phage life cycle. So any more comments about condensates? Lots, but I'll save them.

25:37Okay. Okay. All right. So with that little bit of background about the condensates, they happen and they are known to be involved in regulation of processes that have nucleic acids and proteins involved. Here they're looking at transcription in Bacillus subtilis infection. And in bacteria, the RNA polymerase, not molecule, complex that binds to DNA is going to have multiple

26:08subunits. So there are multiple different subunits. This is kind of important for what we're thinking about here. The process is regulated. So you have this core enzyme with these five to seven subunits and there is an adapter protein. So the core enzyme is okay for doing transcription, but it's not very specific. It can kind of transcribe anywhere. But to go to the right place in the DNA where there's a gene, a specific kind of promoter, you need in bacteria something called a sigma factor. And that sigma

26:38factor, there are many of them, but there are some that are considered the housekeeping sigma factor or just the one that's on all the time. And that housekeeping sigma factor in Bacillus is called sigA or sigma factor A. This is going to be the one that's necessary to tell the core polymerase to transcribe at all of the genes that the cell uses all the time. And when something stressful happens, then the cell will turn on another sigma factor and that will direct it to the genes that are

27:10necessary to respond to a stress. Okay. And so it turns out that bacteriophages, as all viruses, they often either encode alternative sigma factors or they can direct the cell to use one sigma factor over another. And that's because that will help the polymerase be favorable towards phage promoters rather than host promoters. It's part of taking over the cell to make more phage and drive the gene expression that is necessary. Now there's another interesting layer about the way that just viruses

27:45in general regulate their gene expression. You know, if you have more than one gene, how do you turn them on in the correct order? So in phage, there's an organizational temporal strategy where we divide things by early genes, middle genes, and late genes. These are, you know, boxes that we put that help us understand how some genes are expressed first. And oftentimes the next genes are dependent on the first ones and so on and so forth. And there is some, you know, bleed over back and forth, but generally

28:17early, middle, and late transcription. And in most phage where the sigma factor is what's determining the switch between early, middle, and late, the first genes, the early genes are going to be transcribed by the host RNA polymerase using the host housekeeping sigma factor. And then they might switch to a phage encoded sigma factor and then the polymerase will transcribe those middle genes. But the question here is how does the phage direct, how does it get the RNA polymerase to the correct promoters and how does it

28:51prevent it from using the previous promoters? So that's what this paper is all about. In a particular phage called SP01. So it's not necessarily super important, but just because I am a phage person, I like to look them up, right? So this is about 140 kilobases of double-stranded DNA in the phage. It has a large head, a contractile tail, so that makes it a myovirus. And it always undergoes a virulent replication cycle. It doesn't have a temperate replication cycle. So it's going to come

29:27in, take over the cell, make phage, and get out. Okay. So now the question that they had here was about how does transcriptional regulation occur over time in the context of these liquid-liquid-phase separated areas of the cell? And I was looking this up a little bit. It doesn't seem like people have really looked in the context of phage infection. While it's known that bacteria have these condensates, how do phage take advantage of them? So they were interested in, are there phage proteins

30:01that drive condensate formation and how could that interact with the transcriptional regulation in the phage? And they did find that there are these condensates. I'm going to say condensates because it's shorter than liquid-liquid-phase separation, but they also abbreviate it as LLPS, which is confusing to me because I work on gram-negative bacteria that have LPS. So I'm going to say condensates. Sometimes people say droplets. That's an option too. I really, I really, conceptually condensates works better for me. I like that word.

30:35Okay. Droplet reminds me of lipid droplets, which is different. Uh, yes. Yep. They are different. Uh, so many, it's hard, you know, there's only so many words in language. Anyway. Okay. So here, um, to give the overview of the phage itself, there are several proteins and the, the proteins themselves come with numbers. They're called GP something, something, and the GP stands for gene product. Pretty much every phage gene starts with GP, not all of them,

31:08but most of them. And then the numbers are not random. They're generally in order on the genome, but the early, middle, and late genes aren't always next to each other. So the numbers might feel kind of random. Uh, and I'll try to keep those straight as we go along. So the first thing that they did was to look at whether or not an inhibitor of condensate formation had an effect on phage infection. They just, there's this apparently well-known inhibitor of condensate formation that

31:40we're going to call hex. It's hexane diol. They added that during an infection to the cells and they saw that it reduced plaque formation. Um, it changed the dynamics of when the lysis occurred in a liquid infection, but it didn't prevent the phage from infecting. So the phage could still adsorb and get in and transcribe some of their genes, uh, but not all of their genes. So when they looked specifically at transcription of early, middle, and late genes, they saw the early genes were fine, which makes

32:14sense because SPO1 uses the RNA polymerase sigma factor A complex to drive its early gene transcription. Uh, but the middle genes were delayed and somewhat inhibited and the late genes were pretty inhibited from being transcribed. So that suggested that the inhibitor was preventing the later genes from being transcribed. I have a peripheral question, Jolene. Okay. Um, you may or may not know the answer to this and that's okay. Does SPO1 do this multi-step injection phenomenon of its genome? I wanted to know the answer to

32:52that question, but I didn't have time to look it up. So I, I think that it does. Um, what Rich is referring to is that some phage will bind and then they'll in, they'll release a little bit of the DNA and it's kind of dangling there. And then the polymerase will come and start transcribing that helps pull the rest of the DNA into the cell. Right. And the early genes are organized on that little bit that's dangling in there. Yep. And the early gene products, and as I understand it, transcription itself helps ratchet the rest of the DNA into the cell. Yes. Um, I don't know if SPO1 does it, but from some of the things I was seeing, I suspect so. There

33:25is a nice map of SPO1 and I think it has been studied. I'll look it up. Okay. Okay. So they established that these condensates seem to be important for infection. They didn't exactly know how. So they did an analysis of the proteins that are encoded in the SPO1 genome to look for which ones might be involved in this process. And they're able to do that because it's well documented that the kinds of proteins that help form these condensates have what are called intrinsically disordered regions. And this means that there are, the protein sequence itself doesn't adopt

34:03necessarily a fixed structure with what we are taught in school, you know, these alpha helices and beta sheets. Maybe they have that, but maybe in solution, they're more floppy. And these are the kinds of proteins that whose structures are hard to solve. And they might adopt a confirmation when they bind with binding partners. But before that, they have what is called an intrinsically disordered region or an IDR. And that, um, can be predicted bioinformatically. You can look at the sequence and, uh, they did that with these proteins that are encoded in SPO1 and they found a few candidates.

34:37And they're like, okay, let's see if these are the ones that are important for, uh, formation of, uh, condensates. And they did identify that two of them are important. And this was really cool to me because even though I have a colleague who studies condensates, I don't see the data very often. So they purified the proteins. One of them is called 25.1 and the other one is called 27. And then they just put it on a slide and they see nothing, which is what you would expect. And then, um, they add PEG, which is, um, which is a molecule that helps to crowd things together and helps to, um, initiate

35:15the formation of these condensates. And on the slide of just purified protein with PEG, you can start to see the condensates like by eye for light microscopy. And they also had their protein labeled GF with GFP. And so they could also see, um, spots by fluorescent microscopy. So that, that was just, it's just really cool to see. This is just a pure protein that is condensing into these bodies that you can physically see. And they were able to go ahead, Brianne. Oh, I was just going to say that I think that the

35:49intrinsically disordered protein piece of this, um, or region of this is also sort of interesting to think about because at least once upon a time, um, I feel like in structures, those regions were removed to get good crystal structures. That's right. And so I think there's a certain amount of things that are not known about, um, proteins with intrinsically disordered regions. Um, I think that this is so cool and there's, it's clear that they're obviously important and it's clear that, um, some of that

36:23work may need to be thought about a little bit more and maybe people should be thinking about some of those proteins in terms of condensates. Mm-hmm. Right. Agreed. While we're paused, SPO1 does not do the multi-step DNA. It doesn't. Okay. One fell swoop. Hmm. All inside. Okay. And all the more reason that it needs to regulate which promoters are getting transcribed in order, uh, okay. So they can see

36:54the condensates and they can inhibit their formation in vitro just with pure protein by adding the hex molecule. Um, and then they were able to get slightly larger condensates when they added purified RNA polymerase as well. And that would make sense if the, if this is actually a process that's occurring, um, in conjunction with transcription. So then they did this neat assay where they took pieces of DNA

37:24that were, uh, that contained the promoter sequences for early genes, middle genes, and late genes. And, um, initially they just put a promoter sequence that should be recognized by the polymerase and they didn't get any transcription. And then they added PEG so that the protein should form a condensate and the polymerase is in the condensate. And then they got transcription and they could inhibit that. Um, they could inhibit that by not having the correct, um, the correct proteins in the

37:58condensate. And then what they did was they said, okay, can we encourage transcription of a middle or a late gene or an early gene? If we put multiple promoters together, what's going to happen? Is there a preference one way or another? And so initially when they mixed together the, um, the GP27 that induces condensate formation with a late gene sigma factor, then they got late gene synthesis. When they mixed

38:30together the condensate forming GP27 with the sigma A factor, then they got early gene synthesis. And then if they added a phage protein that they suspected was an inhibitor that, um, would prevent early gene synthesis, they got reduction in early gene synthesis. And concomitantly, they then got increase in middle gene synthesis, which is what we would have predicted. And the way that they were telling which RNA got made in their in vitro, uh, method was they had this sequence, um, of RNA that's

39:06called mango three, which is, uh, folds into a particular structure that can bind to a reporter fluorophore. And so they could know whether it made a late gene or an early gene or a middle gene. Okay. Um, so then they, they briefly, very briefly moved into cells and they looked inside of cells and they saw that when they were expressing this GP27 protein that seemed to be forming the condensates necessary for middle gene transcription, they, they could see, um, that the GFP on the protein

39:39would become slightly more organized inside the cell. And it became much less organized inside the cell when they added hex. So they think that this is occurring in vivo. They did not actually show it in the phage infection with the labels, uh, but they went on to do a whole bunch of other assays. So they suspected that if this GP27 protein was important for recruiting the RNA polymerase to DNA,

40:10that it would interact with DNA. And they did get some DNA interaction. And then they did some things that not all of them. I'm entirely clear why, but they did some condition testing. Uh, it interesting to me though. So I'll just mention it that temperature affects the amount of condensate and the size of the condensate. So like higher temperatures had, um, more and larger condensates. And then, uh, the condensates actually don't stay in the condensate form forever. Uh, so they checked after 10 minutes

40:46of, um, adding PEG and they had condensates, but after 16 hours, the condensates had kind of fallen apart. And I'm, I'm not clear exactly why, but that was interesting. And then one other, uh, cool method that, uh, was the way I was initially introduced to condensation, which is why I explain them as like slow moving molecules relative to fast moving ones is this fluorescence recovery after photo bleaching. So here they are looking in vitro, they made the condensates and they're green, right? And

41:18then they take a laser and they, um, basically zap it to get rid of all the signal. And so there's a dark spot in the middle of the green. And then if the molecules are moving around, then they should just quickly fill in the dark spot and it will all look green again. But if the molecules are moving very slowly relative to each other, then that dark spot will persist for a longer time. And that is what they see that they can make these spots and it can take quite a while, um, before they get recovery of the regions that they have photo bleached. Okay. So then they, for the rest of the

41:53paper, they look into, um, this GP27 protein and then they look into GP33. So GP27 is the one that forms condensates at the beginning that helps transition to middle gene transcription. And then GP33 is what they are going to show us is an inhibitor of the host sigma A factor. So it inhibits host gene transcription, which means that it will also inhibit early gene transcription. So for GP27, they do, um, kind of what I would call a deep dive of the importance of the intrinsically

42:27disordered region. They look at the structure in a couple of different ways. They use, um, NMR, they use, um, size exclusion chromatography, they use molecular dynamics simulations, and they see that the intrinsically disordered region is disordered and there is a more, um, uh, what do you call it? Ordered region in one of the termini. And they also see that the, the intrinsically disordered region is important for DNA binding. And they do some modeling for where does this GP27 protein interact with

43:05RNA polymerase. And they see that, uh, one of the folded regions of GP27 interacts with one of the beta subunits of the RNA polymerase. And then they do a really cool experiment, which is a competition experiment. So they have the GP27 formed condensate with RNA polymerase, and then they add, uh, the sigma factor to get middle gene transcription. And then they also add in the host sigma factor. And when the

43:36host sigma factor is present, then they get less middle gene transcription. And this is explained as the host sigma factor just has a better affinity, um, for the complex than the phage transcription factor. So that was another thing that motivated them to look for how does the phage inhibit the host sigma factor? Since basically all of the later sigma factors that they looked at that are needed for middle and late gene transcription, they're not as good as the host sigma factor at, um, inducing transcription. So there had to be a way to inhibit transcription, um, mediated by sigma A. So then

44:13they turned their attention to this GP33 protein. Uh, what they did initially, so GP33, they, um, are pretty confident is essential. You can't delete it from the phage. So they took the opposite approach and they overexpressed it in the cell. And if GP33 was, uh, competing with sigma A, they expected to see some toxicity if they overexpressed it. And they did see a delay in host growth, uh, although eventually it was able to grow. And they also looked at, um, the, they did infect cells with SP01 that were

44:52overexpressing GP33 and they got early gene transcription, but it was, uh, not nearly as much as they would get if there was no GP33 being expressed. So it was much less, which is consistent with GP33 inhibiting sigma A mediated transcription. And then they, they, uh, were looking at how this GP33 interacts with the RNA polymerase and sigma A factor complex. And kind of the summary of those studies

45:24is that GP33 is binding next to sigma A and also is sandwiched between, um, the beta, one of the beta subunits and sigma A. And that is what they think is basically trapping the complex so that it does still form the complex, but it can't then move on with transcription. Uh, it can't be a productive, um, transcribing complex. And they do another competition experiment. And this is, uh, in vitro

45:57with mixing with DNA. And it's consistent that basically if they mix it together at the same time, then the GP33 can inhibit sigma A activity of binding DNA. But if the complex with sigma A was already formed, then GP33 is not good enough to knock it off. Um, and then the last thing I wanted to mention is actually something that they, they talk about kind of in their supplementary information. So it turns out that GP33 is not the only inhibitor of transcript of the RNA polymerase

46:35complex. Other phages make inhibitors, but they did this modeling and they showed that every inhibitor that, that is known either by structure or by modeling is binding the RNA polymerase complex in a different place. Uh, so there are many ways to inhibit transcription or to favor transcription towards a different promoter, uh, that maybe we haven't discovered because they're not all in the same place. Uh, that, and I thought that was really cool. And the other thing I wanted to bring up is

47:08when I was thinking about how, if you are inhibiting, basically the important thing is if you have this RNA polymerase complex and the sigma A factor in the condensate with the inhibitor, it can't do transcription. So how does the phage do transcription if all the complexes are kind of bound up? So they, they, um, tell us that only between two and 50% of the RNA polymerase in the cell is actively associated with sigma A at any given time. So that's like, you know, up to half of the polymerase

47:42complexes would still be available to use for transcription. So that was a helpful thing to mention, I thought. Yeah. I thought that the, that was one thing that sort of clicked for me as I was like, oh, uh, I guess I was, I was imagining, you know, the RNA polymerase goes and does transcription and I wasn't imagining how many excess complexes there were that were doing nothing. Um, because it, um, in the, um, GP33 experiments, I was realizing, I was like, this, the only way this works is if that complex is in extreme excess, um, so that some of it can be inhibited and you can still

48:18do transcription. And so I was really glad that they addressed that. Um, and that was the same kind of thing that I started thinking a whole bunch about here. Yeah. Yeah. Yeah. Okay. So to summarize, when the phage infects, it uses the host RNA polymerase and its sigma factor to make early genes, but then it needs to transition. So one of the early genes is this GP27 protein that induces a condensate formation. In that condensate, there's RNA polymerase from the host with its sigma

48:50factor trapped. And then the phage inhibitory factor binds that and keeps it trapped. So then no more early genes are getting made and now middle genes are getting made and then eventually late genes can be made and that will complete the phage life cycle. Uh, so they're showing that these liquid, liquid phase separated condensates are important for the regulation of transcription and possibly other things. And I, I hear Brianne say this all the time. This made me kind of want to go like

49:21study this in my life. I was like, so how many IDR containing proteins are there in the phages that I study? And how does that work for my transcription? Yeah. Yeah. I was interested in understanding how hex works. Yeah. I didn't have a chance to look. I don't know. I was like, okay. So I'll tell you. Oh, okay. Great. I looked it up. So it's hexane diol, right? And it basically disrupts hydrophobic and aliphatic interactions between the proteins and the RNA. It's, it's pretty straightforward.

49:54I guess. Okay. So, uh, kind of something I glossed over is at the beginning, they had to do a concentration check. Like how much do we need to add to inhibit without like inhibiting the cells too much? And so I guess that would make sense that if you add too much, then it will disrupt all of these kinds of generic interactions, but just a little bit will specifically affect that. And also will, yeah. So it will, at a high concentration, it will disrupt, uh, other proteins independently of phase, uh, these, these droplets. So, um, so as I read this paper,

50:26um, my reaction was, man, this is really familiar in particular when they started talking about a structured region and an intrinsically disordered region. And it's because we spent years working on a vaccinia protein called H5, uh, that was a real mystery that did all kinds of stuff. And, um, uh, it turns out it was discovered, uh, what, um, must be now 10 years after I retired

50:58that H5 is one of these proteins that, uh, promotes condensates. And it's the same thing. It's got a, it's, uh, same, same, only different. It's got an intrinsically disordered region. We figured that out. Uh, in this case, it binds DNA and we didn't, uh, determine this, but that's gotta be a function of the ordered region. And, uh, mutants in this protein, uh, basically crashed the whole infection. Uh, and we could see other sort of specific effects. We originally got interested in it because it,

51:32uh, seemed to be, um, associated with, uh, uh, a particular kind of RNA processing that, uh, goes on in the cell. We also, you know, it had a native molecular weight of, uh, 35 kilodaltons, but if you put it on a size exclusion column, it was like 300 KD. Okay. It was always in the excluded. Well, it wasn't quite in the excluded volume. So it was, uh, essentially aggregating or something like that. Now it turns out that vaccinia makes these

52:04viral factories that you are very distinct in the cells. Matter of fact, they show up as, uh, intracellular inclusions, uh, in microscopy, this diagnostic of a hox virus infection. It's where DNA replication, a lot of other stuff happens. Um, and, uh, in this paper that came out afterwards, they demonstrate that H5, uh, basically is critical for formation of those factories, you know, and there's an, so for me, uh, there's a, uh, there's a cool thing

52:38that happens after you retire and you figure nobody's going to care about anything you did anymore. And then 10 years later, somebody publishes a paper on something that you didn't understand at all. That brings a clearer under all the stuff that you wondered about kind of falls into place. And then I looked because in the, later in my, in the closing stages of my career, I personally got into, uh, fluorescence confocal microscopy. We had a wonderful collection of

53:10antibodies that we could use to, uh, look at specific viral proteins and how they localized intracellularly under various conditions of infection and with various mutants. And I just spent hours in the dark looking at these things because they were fascinating, uh, with all these proteins and all these mutants. And I must have dozens and dozens of experiments looking at H5 under different conditions, none of which are published, all of which are stored on a server at the university that

53:41somebody decided, uh, was no longer, uh, in use. So all that stuff is gone, but I would have loved to look at some of those pictures and, uh, and make sense of them. But so it turns out, I think that in terms of vaccinia factories, H5 is not just in the factories, it is the factories. It makes them happen. Okay. Or at least that's one approach. Yeah. I, I don't know why I didn't think of any of this before this conversation. Um, again, because I've been thinking so much about liquid, liquid phase

54:18separation and immune responses and interactions with immune proteins. But as we've been discussing it, um, the thought occurred to me, I was like, wow, I bet that this process could be really useful in terms of viral assembly. I wonder how many viruses might you have a protein that induces some kind of phase separation to help with assembly. Um, and I did a very, very quick search, um, after I spelled things correctly and it looks like the answer is yes, this, this, there seems to be,

54:51I'm getting a lot of hits. I haven't, you know, gone through and read them all. Um, but as I think about it, I'm sort of like, why, why would I have not thought of that before? It makes perfect sense that this would be a great way to help viral assembly happen, uh, to make a particle. Um, I think Rich has mentioned of the, the factories in pox virus triggered it. Um, but yeah, so I bet that there's a lot more of this in virology than perhaps we, it's a, it's a way of making a compartment, you know, there are a lot of these, uh, Vincent, I forget whether polio does this or not,

55:26but there's a lot of these viruses that have membrane bound complexes of one sort or another that are little factories. And I'll bet you there's some of this stuff going on. It's a way of compartmentalizing stuff. Uh, we decided, we called the H5 a hub protein. Okay. Cause our model was that, uh, the ordered region maybe binds DNA and the disordered region could flop around and do an induced fit to grab on to different other enzymes to help them do stuff.

56:01But I think it's the reverse is true. It seems to me like the disordered region is helping, uh, make a condensate that includes this ordered region that can bind DNA that probably nucleates this whole factory thing and says, okay, DNA is going to be here and all the ancillary processes surrounding DNA replication and transcription are going to happen in this compartment and assembly as well. Very cool. Yeah. It, it just makes, uh, I don't know if the term would be like biophysical

56:35sense that reactions happen more efficiently if things are next to each other. Yep. So it makes sense to condense them together. That's the effect of PEG, right? Is to, is to concentrate things. Yeah. Yeah. Yeah. That was the original reason the RNA viruses were thought to make these membrane complexes, put everything you need there instead of having to diffuse around the cell, which takes forever, right? Diffusion doesn't happen really quickly at all. So thank you, Jolene. This was a

57:09wonderful adventure for me. I really appreciate it. Well, I'm, I'm grateful to the authors and that I found the paper because it's not something I usually read about. All right, let's, let's move

Ancient smallpox genomes in South America

57:21to eukaryotes now and we will do a paper, um, in science. This is, uh, called the Genomic Identity of Early Smallpox in South America. The authors are Bruno Romero Gonzalez, Margarita Reyes Madrid, Bernardo Ariaza, Lara Cassidy, Mauricio Moraga, Constanza de la Fuente Castro, and Shigeki Nakagome from Trinity College in Ireland, the Universidad de Chile, Universidad de Tarapaca, and Kanazawa

58:00University. And the, the summary here, the brief summary is, um, smallpox was introduced into the Americas by the European colonizers. It caused complete population collapse in the Americas, but we don't have any actual proof of, we don't have a virus, right, or a sequence. So these are the first ancient smallpox genomes from the Americas. They date to about 1492 to 1631 CE, the common era.

58:35Uh, they were recovered from two Inca colonial individuals in Northern Chile. And, um, they form a lineage that clearly arose from, uh, the medieval lineage that had been previously identified in Europe. So clearly this is, and you'll see the phylogenetics shows that this is derived from them. And so the first evidence for smallpox introduction through European colonization. Uh, so, uh, uh, Rich, you want to give us the smallpox summary, the, the virus and all that?

59:08Uh, sure. Okay. So, uh, smallpox, uh, the virus, uh, the family is called poxviruses. These viruses, there are poxviruses of, uh, all sorts of organisms, both vertebrates, uh, and invertebrates. A, what used to be a very large double-stranded DNA virus until we discovered that there are double-stranded DNA viruses out there that are much larger. Okay. Has a very unusual, uh, structure that's, uh, generally called complex, doesn't fit any of the normal paradigms.

59:45Uh, replicates entirely in the cytoplasm. So you infect the cells and the DNA stays in the cytoplasm rather than go to the nucleus, which means that it has to encode all of its own transcription and DNA, uh, replication apparatus, which is why, uh, it's so complicated. Uh, one of the reasons it's so big. And it's also known for, uh, its, uh, facility with, uh, immune evasion. Uh, there's a good, this is about 200 kilobases, so that's about 200 genes.

1:00:15And there must be, uh, up to half of the genes, uh, that are involved in tinkering with the intracellular environment or even extracellular, uh, environment in terms of, uh, immune evasion at all levels of the immune response. And it's been actually very useful in, uh, probing the immune response in that respect. Uh, of the pox viruses, the most notorious is smallpox, uh, which, uh, in Europe, uh, uh, it's been with humans for, uh, as long as humans have been around as far as we know.

1:00:49Uh, though there's some debate about, uh, its early evolution. Um, but in, um, Europe in, uh, you know, uh, 15, 16, uh, 17 centuries, if you lived in a populated area like London or Paris, you would get smallpox. That was a certainty. And the mortality rate was about 30%. And the disease is absolutely terrifying.

1:01:22You catch it as a respiratory disease. It spends about two weeks cooking through your system and, uh, making you feel miserable. And then in the late stages erupts in this all over your body, blistering skin lesions that are painful and itch, uh, and, uh, then you die. Or if you serve, or if you survive, uh, you're scarred for life. Other sequelae like, uh, uh, bone deformities and blindness and et cetera.

1:01:54It was absolutely horrifying. Just, I can't imagine living with this. So if you had kids in one of these cities when you were growing up, you knew that they were going to get this disease and there was a 30% chance that they were going to die of it. So people were absolutely terrified of this. Go ahead. Oh, I was just going to say, I, it didn't, it occurred to me at one point when I was learning more about virology, um, at some point when I had been reading, you know, novels set in,

1:02:25uh, those sorts of time periods, um, some person would be referenced as pockmarked. Um, and I think I always read that, um, before thinking about viruses as just like a synonym for ugly. Um, but in fact, no, they were pockmarked because of those scars from smallpox. And I realized how frequently that was in fact discussed when discussing people of that era was their, their pockmarks. So there's a long, there's a history of trying to, uh, immunize people against this.

1:03:00There was a, an early practice that originated, uh, in Africa and the Middle East, uh, called that was ultimately called variolation, where you would actually take a little bit of material from one of these blistering lesions and carefully, um, seed it into a scratch in the skin. Uh, and I think because it was an, uh, an alternate route of infection rather than a, uh, uh, a respiratory infection, the chances that the, uh, infection seeded in that fashion would go systemic were lower,

1:03:36but it gave a, just a, a horrible reaction and made you feel terrible and had about a 1% mortality rate, but that's 30% better than getting the disease. And then ultimately, as we'll discuss a little bit later, Edward Jenner, uh, in the late 1700s figured out that you could use a related pox virus that he initially called cowpox, but we now, uh, pretty well understand it was probably horsepox, uh, to artificially inoculate people

1:04:09in a fashion using the same methods as, uh, uh, inoculation with smallpox. Uh, but it would give a single mild lesion, uh, very transient, uh, discomfort and confer. It was basically serologically cross-reactive with smallpox and confer immunity to smallpox. That became, that was the first vaccination. Vaca is the Latin for cow, right? Yes. Imagine if you knew it was horsepox and then we would all talk about equination. Yeah.

1:04:40Actually, equination is a word that was used because people deliberately used horsepox, uh, in, in some circumstances. And that practice spread worse worldwide and ultimately, uh, uh, resulted in the eradication of the disease. And you can be really thankful for that because this would be awful to live with. Oh, the things humanity was subject to before the onset of public health, right? And now we don't have to deal with it except in, in a certain country where certain leaders

1:05:11want to inflict it back upon us. Slight exaggeration, but yeah. Some people, well, except this virus. Well, this virus won't come back, but, um, measles was gone from the U.S. and now it is back and, uh, others will follow. So, um, I think exaggeration is important to, to impact the seriousness of this on people sometimes because measles is not a delicate disease, folks. Anyway, back to smallpox.

1:05:43So the official name for this virus is now orthopoxvirus variola or variola. I don't know how that you're supposed to say, but I've heard people say it's both. I think people mostly say variola. That's what I say. Yeah. I remember, uh, McFadden always said variola. Um, so we'll call it variola introduced to the Americas by the European colonizers after 1492, right? As soon as Columbus got here, more people came and they brought smallpox and it spread through three routes through the Caribbean, through the Southern routes and the Northern routes.

1:06:14And the first outbreak. So these are historically documented outbreaks. The first one in the Americas, 1518 during the Spanish conquest of the Caribbean. And then the virus spreads across Central and South America. It reaches Mexico in 1520, goes through the isthmus of Panama, and then into the northern frontiers of the Inca empire by 1525. It gets to Chile in the mid 16th century. Now these epidemics are reported.

1:06:46You can find them in the literature, 1554, 1556 in Chile, particularly. But, uh, we, we don't know if it was smallpox. Uh, for example, an outbreak in 1561 is, is thought to be the first, uh, confirmed introduction of the disease into the region. It occurred in waves. You know, we have an estimate of three to four million deaths, but probably more. There would be a wave and then there'd be a little bit of recovery and then another wave and it would just wipe out subsequent generations.

1:07:18And that's how it had this incredible effect because there was no immunity. There was poor, some poor living conditions. There was the oppression of the, uh, the colonists and so forth. And that all added up to wiping out many peoples. Now, the problem is the historical record isn't great because this, these are mostly by the colonizers, right? Who, and, and they don't know anything about the transmission among the indigenous populations because they're not there most of the time. And so, uh, that's all we've had until now.

1:07:50And now we're going to see in this study where you're going to use ancient DNA to document the first introduction. Well, you could also imagine, you know, most of these reports that we have are based on symptoms or are based on, um, looking at remains and sort of what types of pathological changes are made. And you could imagine one could debate, are you sure it was smallpox that they're talking about in this literature or could it have been some other type of, of, uh, infectious disease?

1:08:23Uh, and so I think it's also really key here that this sort of makes it more clear that in fact, smallpox, um, was a causative agent here, not, uh, some of the other hypothesized or, uh, agents. Actually, uh, speaking of wondering what disease it is, the reason it's called smallpox is to differentiate it from bigpox, which is secondary syphilis. And by the way, there was a fair, there was a fair trade here because we gave the Western

1:08:55world smallpox and they gave us syphilis in exchange. Okay. Now we've, we've known a bit about the, uh, uh, varilla genomes across Europe. We've actually done some of these studies on TWIV before. So there've been genomes recovered from early medieval individuals across Northern Europe. That would be 600 to 1050 CE. That includes the Viking age. And these are basal to 20th century smallpox viruses, right?

1:09:26Just before, uh, eradication. There's also a strain from a 17th century Lithuanian child mummy. Uh, that one had an ancestor about 1700 years ago. Uh, and then it is an 18th century English varilla that forms a sister clade to these modern strains. And what's interesting, that 18th century guy comes from the Huntington museum in London, which I really need to visit because this guy Huntington was a surgeon, but also a collector

1:09:57of all kinds of stuff. And when he died, he left his collections behind. And, and that sample came from some sort of human sample in his collection. In the museum. Yeah. That's cool. So I wanted to clarify here. I was confused when I read this and I want to make sure I understand. So modern strains means things from like within the most recent century, because there are no varilla strains except the ones that are possibly in tubes somewhere, but they mean this century. Up until eradication.

1:10:29Yeah. Okay. 20th century. Yeah. They, uh, on this, well, on this, uh, map on figure two. Yeah. Yeah. You can see the modern. You can see the modern strains and they actually talk about some of the modern strains. Well, I, it's a little confusing to me because they've got things labeled M varilla virus that go way back, but most of it I think is, uh, I would say 18th century onward.

1:11:01Something like that.

1:11:05Yeah. We had a letter last week. Um, I think it was read on Twiv. Uh, a guy went to see some park in London and he was disappointed and then he saw the statue of Jenner and he said that made it worthwhile. Was that last week? It was last week. It was pretty cool. So actually, actually, if you look at that, uh, figure two thing, what you see is in terms of samples that are available, uh, very few, uh, that have dates before about, uh, 1900 and

1:11:37then a whole slug because people started keeping samples, uh, in the, in the modern age that we can go back and get sequenced. Yes. Although if you look at the, the axis here, it has 2000s as the most recent year. And I, I was sort of confused in the same way that Jolene was until I really, wait a second. Yeah. Until I, until I looked carefully and realized that each tick mark was 50 years. So the tick mark before 2000 was 1950 and most of these are sort of closer to that 1950 or just after.

1:12:07And I was like, oh, that makes sense. That's not, you know, 1990 right before 2000. Yeah. Smallpox eradication wasn't declared until 1978, 1980. The 79. I get confused about 79. So I, uh, smallpox vaccination, uh, was compulsory, uh, for me when I was a kid, I had to be vaccinated against smallpox to go to kindergarten.

1:12:38Yeah, me too. Yep. I still got my scar. Yep. All right. Um, no, what's interesting. It's going to come up later now is during this period, we're talking about, you know, the ancient to the modern, there is reduce, a reduction of gene content or gene inactivation. And this is thought to reflect the specialization or the adaptation of the virus to humans. Right. All right. So the current study, they have, they looked at 13 bone samples from the Camarones 9 site.

1:13:14So these samples are going to be called Cam 9 in Northern Chile. They've identified two cases of smallpox infection, a female, uh, 20 to 35 years and an adult male, 18 to 20 years old, adult female and adult male. And this was first determined through bone assessments. Okay. Um, they were able to tell changes in the bones that are consistent, osteological manifestations of smallpox, um, which are pretty rare, but they found them here.

1:13:45And then they recovered the genome from these bones. And these two genomes, Cam 9 and Cam 9, Cam 9, 208 and Cam 9, 205 have 99.912% sequence identity, which says that probably from the same, uh, outbreak. Now, these individuals were naturally mummified and buried together. They were, I'm sorry, not together. They were bundled up like mummies, right? Oh, that's what that meant.

1:14:17Okay. Yes. Bundled. Yeah. Not together. I love the, in the methods, the description of the archeological sites. And I just love this stuff. So this site is associated with the late period, which would be 1400 to 1536. It's culturally affiliated with the Inca and, uh, there is some European influence from the archeological evidence. The, the radiocarbon dates of, of faunal and botanical remains puts it between 1320 and 1680 CE.

1:14:47And they had hair from one of the two, Cam 9, 208, which they could radiocarbon date. And it would, it agreed with that. It gave a range of 1398 to 1700, which either proceeds or broadly coincides with the early phase of, uh, Spanish colonial reorganization. And, um, they found, they, they, they saw skin lesions, uh, um, at Cam 9, of which were one to five millimeters in diameter concentrated on the trunk.

1:15:20They were previously thought to be caused by arsenic exposure because the tissues of this individual had elevated arsenic, but they thought that it would, uh, be smallpox. And of course, they, the DNA shows that, that it was. And this DNA is ancient DNA. So you have to make sure it's really ancient and not a contaminant. And there are different things that you can do like deamination patterns of the DNA and short fragment lengths, of course, and that sort of thing.

1:15:51Um, so then they compare these sequences to the, they have a panel of many different, uh, 728 present day individuals, present day meaning before 1979, right? Um, so these DNAs, these DNAs cluster with present day indigenous populations in the Americas, no detectable European ancestry. Sorry, this is, this is the DNA from the humans I'm talking about now.

1:16:21Uh, these cluster with present day indigenous populations in the America, no detectable European ancestry. Uh, the mitochondrial DNA, uh, haplogroups are consistent with that. And these are observed in, in populations through the Americas just to show that these are actually people from that region and not Europeans that happened to die and were, were buried. So basically the evidence suggests local varioly transmission among these, they call them unadmixed. They hadn't bred with any Europeans, uh, from the Inca sphere.

1:16:56Okay. So what do these genomes tell us? They compare these genomes to a large data set of both ancient and modern varioly, varioly genomes. They do phylogenetic analysis of various sorts, but the result of all this is that both of the CAM samples are in a lineage between two major clades. One, the early medieval European strains, these are called ancient varioly, ancient varves, and the modern strains, which include the 17th century genome.

1:17:30So that's included in the modern strain, the 18th century English genome, and all the 20th century strains. So that's why the, the M rich go back a bit. Right. So this is intermediate between the ancient, uh, and the European varioly strains. Um, and, uh, so that's, we don't have all that many strains, old world strains, right? European strains. So that's the best you can do. They say that the CAM nine strains cluster within the ancient European diversity, but we really can't tell where it came from because we don't have any data from anywhere else.

1:18:04It could be closer to something from another region, but we don't have any sequences from there. But it definitely is time-wise, um, sort of makes sense in terms of where it's clustering. Well, it, it came from, it, from all the samples we have, it's clearly related. It's a descendant of the European strains, but it could also, some others could be closer and it would be descended from them, right? But right now it looks like it came from the European strains. Um, these, so these individuals, they estimate, died between 1492 and 1631 and, uh, basically

1:18:41suggests colonial transmission of these, uh, lineages. And these, by the way, these CAM lineages are no longer seen, right? All the modern genomes are not the CAM. So they went extinct. Likewise, the ancient ones no longer. The ancient ones too, yeah. So there's a real evolution going on here. Mm-hmm. Yeah.

1:19:06All right. So then they wanted to look at, uh, the gene inactivation in the genome, right? Because this is a unique set of samples. And so can we use this? And, and they are intermediate between the ancient and the modern. So could we use these to understand this gene inactivation, uh, process? Uh, and so they have really high coverage of this gene, of one of these genomes, 208. So they use this. They could annotate 205 open reading frames, uh, from 214 genes.

1:19:38And they use that to infer gene inactivation status. And so basically you look at the protein sequences and you can tell when the protein has been inactivated, um, truncated or fragmented and so forth. And they find in total 49 genes in the CAM208 genome are absent or inactive. And 37 of those are also inactive in all the other ancient and modern genomes.

1:20:11Okay. So this, this CAM has inactive genes that are also seen in the ancient and the modern genomes. Uh, two, though, are unique to the CAM9 lineage, two inactivated genes, which I don't see, uh, anywhere else. And so basically these 37 genes that are inactive are already dispensable. We're already dispensable before the emergence of this, um, CAM lineage. Uh, then they have 10 genes that are inactive in both CAM208 and the modern, uh, variala, uh,

1:20:45half of these, and they, they go through some of these, uh, genes and half of them are associated with host range function. Um, and so they see variation in the, in the status of these genes, which they suggest means that some of these 10 genes were already under inactivation of them or was already underway by the early medieval period. And then they accumulated prior to the emergence of the ancestor of these CAM and modern lineages.

1:21:16So, uh, you, uh, obviously dug in this, uh, more deeply than I did. Did I hear you say that, uh, some of the CAM genes that were inactivated are not inactivated in either the ancient or the modern lineages? No, so we have 37 genes that are inactivated in the CAM, uh, the strength, the 208 that they're looking at, right? Let me see. I lost my place. Yeah. 37 genes were inactivated.

1:21:48Sorry, 49 genes are absent or inactive in CAM208, of which 37 are also inactive in ancient and modern genomes. So 37. Okay. And so there's, there's a 10 left over. Yeah. That gives you 10. And of those 10, they are inactive in both CAM9 and modern and their status varies among the medieval genomes. Okay. So all supporting the notion that this is an ongoing, inactivation is an ongoing process.

1:22:18Okay. It's on between the, between the ancient and the CAM, there's, there's evolution going on. Right. Right. And we, and we interrupted it. Okay. So let me, this may be an appropriate point to try something out on you because I've had a bit of a difficult time wrapping my head around this. Um, the implication all through this, I mean, we, we only have samples going back. Um, uh, what is it?

1:22:49Is that 1500 years? I think it was 17. Back to about 500 CE, something like that. That's not all that long. No. Um, and, uh, humans have been around for millions of years. It's not clear where the human, this is a highly specific. Uh, one of the reasons we were able to eradicate it is this virus, smallpox doesn't replicate in anything other than humans. So it's very specifically adapted to humans. And I think it's a wide open question of where humans picked it up originally.

1:23:22Okay. But they may have picked it up from somewhere else. Uh, and I'm imagining, this is where I'm going to space out here a little bit. I'm not supposed to say I made it up, right? This is a hypothesis. No, you shouldn't. I still have a note here. Tell me not to say you need to do that.

1:23:38That somewhere way back, remember I said these things are loaded with immunomodulatory genes. So somewhere way back in time, this virus, uh, came into the human population loaded for bear with immunomodulatory stuff, which over time, because of the, over time, because it's replicating in humans, it figures, oh, well, wait a minute. I don't need this guy. Okay. Because the humans don't do something that I need to inactivate with that. And they let go of that gene, let go of another.

1:24:09So over time, this inactivation happens as the virus becomes more and more specialized for humans. Does that make sense? Yeah. So it's sort of like the virus came in full of inhibitors, um, adapted well to whatever other species it was in. Or maybe multiple species. Or maybe multiple species. And, um, the ones that were not relevant or useful in humans were sort of lost over time. Or the ones that killed the host and didn't allow for spread.

1:24:41That too. Also lifted against. Yes. And that process was still happening in 500, um, and in 1250 and in, in all of the years we're seeing here. Yes, exactly right. And I would, I would take it even a step further and say that the way we make attenuated viral vaccines is to passage them in either cell culture or eggs or something like that, where there is no immune system. And one of the classics in the case of vaccinia is a thing called MVA, which is a vaccinia that's been pastured in, uh, chicken eggs 500 times, where it doesn't have to deal with immunity at all.

1:25:20Uh, and that has huge deletions in it of, uh, mostly immunomodulatory genes of one sort or another. So, if you don't need it, you get rid of it. That was interesting to me that they estimated a rate of one to two gene inactivation events per century. Yeah. So, I guess when we're, when we are passaging, we drastically speed that up. Oh, yeah. Yeah. Oh, yeah. So, I mean, this probably went into people thousands or tens of thousands, not hundreds of thousands of years ago, okay?

1:25:53So, I mean, the estimate is three, four, or 5,000 years ago. So, sometimes, it started to lose genes, and we're catching it right in the middle here, right? Because of the ancient genomes, we already see evidence for gene loss. Then we interrupted it completely because we squashed it. And the reason, the reason we can say that the CAMs are, are, are telling us this evolutionary position is that, you know, two genes are unique to the CAM lineage, and then 10 are common to both CAM and, and, and, and, uh, modern, but variable among the ancient genomes, right?

1:26:26So, that tells you that this evolution is still going on. So, then they, they further look at, look at this by looking at the ratio of synonymous to non-synonymous mutations, because they want to get a little more information on, on what, what's going on here, right? So, they, for genes that are inactive across all the samples, the, the ratio is comparable, because there's no point in doing any purification, because the genes are already inactive.

1:27:03So, it doesn't matter what kind of mutations happen in them, right? But then, so, a non-synonymous gene messes up the, a non-synonymous mutation messes up the protein. A synonymous mutation does not change the protein. So, the ratio does not vary in these already broken genes. If a gene is already broken, you don't care about what happens to it. But then the intact genes have differences. They see a disproportionate drop in synonymous substitutions. These are usually neutral, right?

1:27:35So, seeing them constrained more than non-synonymous changes, which is usually the case that you get non-synonymous constraint, that's unexpected. And so, they say something's going on beyond ordinary purifying selection. And they call this a period of evolutionary stasis, right? That there's some kind of broad constraint on the genome, but not on just the individual protein sequences. And they say, okay, now the virus has reached some kind of adaptive peak in its relationship with the human hosts.

1:28:11But then, after this constrained period, they see substitution rates return to normal. And the authors suggest in the discussion that maybe this shift happened because of vaccination, right? And that shifts the immunological landscape. That shifts the selective environment. And now you're seeing a change in this synonymous substitution rate once again. We don't know if that's true. I mean, the caveat in this whole study, right, is this is a long period of time where they're looking at this.

1:28:45And the molecular clock is quite uncertain. We don't have a lot of genomes. And so, the pattern looks really good. But you have to realize that this is some signal which is coming from a pretty sparse data set with a model that's not great. So, it's not definitive. And I don't know how it will get more definitive because, you know, we don't generate these isolates by the ton, right? So, this is what we're stuck with now. Anyway, the first molecular evidence for the introduction of smallpox into the Americas, I think that's the real big story here and why it got a lot of press.

1:29:24Very cool. I like that. It's a very cool story. It's difficult to do. I mean, when they're talking about the depth of coverage of one of their CAM samples, it's 3x, which is very low. So, the way they were able to assemble it to check on G9 activation required some tricks to be able to get it all there to have enough to do the analysis. So, it's difficult to get the ancient DNA.

1:29:54For the lay people out there, this coverage refers to the number of times that you have been able to sequence a certain region of DNA, actually a certain nucleotide. So, the more times that you get sequence information out of a certain region, the more certain you are that what you've got is correct. So, 3x is, man, when we were first doing this, the goal was to get both strands.

1:30:25That was your, just once, that was your conformation, okay? But now, 3x is, eh. But this other sample is 84x. That's kind of a record for ancient box samples. That's pretty good. Yeah, I did, sorry. I did polio at 2x coverage. I did both strands. There you go. It's just, like, for kind of, I guess, modern DNA reference, I had a 100x genome that I deposited recently.

1:30:55And a reviewer told me, you know, that's kind of really low. Are you sure about that? And I'm like, come on.

1:31:03That's pretty good. We regularly get, like, 600x. It's pretty incredible that they can, I mean, this is technologically not simple. No. Getting these ancient samples. And that you can actually get a contiguous genome of 200 kilobases out of a sample that's 500 years old or so. It's just incredible. Well, it wasn't simple in the old days either. You know, they were different. So, the way I sequenced the genome of polioids, I made a DNA copy. And then I cut it with restriction enzymes into manageable pieces.

1:31:37And I would phosphorylate the ends. And then you'd take that fragment and cut it again to separate the two ends on the gel. And then you could sequence it. Because you could only have label at one end. You had to sequence across every cut site, though. Okay? Because if you cut with an enzyme, then you had to have another one that would overlap the cut site. Because you could be fooled. And I got fooled. I sequenced across every cut site except one. It was a BAM H1 site, which is a pretty rare enzyme.

1:32:09I was done with the sequence. I said, hell with this.

1:32:16It turned out there were two BAM sites within 30 bases. Wow. And so, I missed 30 bases. And they were in frame on top of it. Right? If they had been out of frame, I would have picked it up. But it was in frame. The protein kept going. And it's only until someone else saw our sequence. Said, oh, you have a different strain. It's got a 30 base deletion. I said, what? And I went back. And I sequenced across the BAM site. And lo and behold. And this was all Maximin Gilbert, right?

1:32:46Yeah. That's the problem. Maximin Gilbert has got this funny business where you have to label the ends of restriction fragments. And I'll bet you that as you talk about that, you can visualize yourself in the laboratory doing these experiments, right? I can visualize. And I can visualize when David handed me this note from Mark Girard. And he says, you've got a different strain. I said, oh, no. That's the one site I did not sequence across. Boy, did I learn a lesson from that. Pretty good. Shortcuts lead to long cuts. That's the lesson. Long cuts. That's a good one.

1:33:17Oh, God. It's going to haunt me to my grave, folks. I mean, I haven't forgot it, obviously, right? You're clearly seared deep in the memory. Seared. Seared like a steak.

COVID origins and lab leak discussion

1:33:28Okay. We have one email. Let's do it. Who would like to take the one email? It's about lab leak. Brianne, do you want to take it? Sure.

1:33:38Torsten writes, Hi, Vincent and co-virology elucidators. In case it hasn't already popped up on your radar, I expect it has. Another valuable public service from Decoding the Gurus. And he gives a link to a podcast called Lab Leak Groundhog Day, COVID Origins in 2026 with Roby Anderson and Holmes. Interesting that SARS-1 was from North Yunnan, while they now think that SARS-2 comes more from the south of Yunnan towards Laos, Vietnam and Myanmar. I remember your fascinating episode with Lori Garrett, where she talked about the Belt

1:34:13and Road Initiative driving motorway south through tropical forest so China could access ports in those neighboring countries and shortened sailing routes, and how workers would trek off to the side of the route to see what wildlife they could catch and sell in the wet markets, and how since the national swine call a few years previous to COVID caused a resurgence in wildlife selling because of the lack of pork, and how a blind eye was turned to it, even though it was supposed to be illegal. I think it was TWIV 773, worth reminding listeners, perhaps.

1:34:46I still have friends who believe in the lab leak theory, believing the misplaced certain people who are not domain experts makes my blood boil. I think the lab leak theory has been the seed of all of the damage that has been done to science and collaboration. By the way, if you are listening to the Guru's episode on iPhone, look at the way the chapters work. Very cool. Cheers and bests, Torsten. This looks like a great podcast. It's got all the superstars on it. Yep, that's good. I don't listen to that.

1:35:17I both want to listen to this podcast and revisit the TWIV podcast that he mentions here. Hey, Laurie Garrett. Yeah, I forgot about this that she was talking about here. I agree. I think the lab leak has been the seed of all this gain-of-function crap. I mean, it really started with the H5N1 experiments back in 2015, right? That set the seed. But then it exploded with the lab leak theory. And now all this attack of Tony Fauci and all of this stuff is from that. I had an interaction the other day.

1:35:47We were actually doing a singing gig at an ice cream social, after which I sat down with a couple. The woman was about my age. Her husband, actually, was a fighter pilot in Vietnam. And they discovered that I was a virologist. And she asked me, okay, so where did COVID come from? And I said, not from a lab. And she kind of gave me the side eye.

1:36:17She didn't say anything. But I got the impression that maybe she saw me as a leftist terrorist or something like that. But you're the virologist. You're the virologist. I know. But what do virologists? No, they're all ideologues. One sort or another, you know?

1:36:33I mean, she asked you because you're an expert. And then she gives you the stink eye. Well, I mean, I was reading a lot into her reaction. Okay. So it's maybe not fair. But you didn't pursue it beyond that? You didn't give her the evidence? Oh, yeah, sure. I went on a rant. Okay.

1:36:50Okay.

Picks of the week

1:36:51All right. Let's do some pics of the week. Brianne, what do you have for us? I have the astronomy picture of the day from August 7th, so basically a week ago. And I really enjoyed this one because it has to do with a telescope that I think is really cool called the Rubin Telescope. That is in Chile. And that is taking some really great images of the sky that we haven't had before.

1:37:24And so this astronomy picture of the day shows an image in the middle, which is sort of a pre-Rubin image. So that is basically actually an image that was taken by Hubble, which we all know of as, you know, this amazing telescope. And then there are little boxes throughout the image, each of which are places where Rubin has been able to take another image in much more detail.

1:37:54And so then around the outside of this image, you can see the Rubin image of that tiny piece from Hubble. And you can see how much more resolution, how many more stars we're able to see now with the Rubin telescope. I've seen estimates and now I don't remember them, so I'm not going to come up with a crazy number. But the number of additional stars that have suddenly become visible because of Rubin is pretty dramatic.

1:38:28And so I really enjoyed this. I'd seen some other types of evidence showing how great Rubin's images were. But I really liked this particular astronomy picture of the day that made it so clear how much more evidence there is that we're getting from this. And this is one of the things that I'm so fascinated about with astronomy is sort of realizing how much more there is to learn all the time. That, you know, we can look at the night sky and think there's so much out there and then so quickly can learn how much additional stuff there is as we're improving our techniques.

1:39:11And, you know, can wonder how much more is there that, you know, some future generation telescope will even be able to find on top of this. I thought you couldn't beat the Hubble out in space, right? Yeah. Especially with an Earth-bound telescope, right? Yeah. Yeah. No, you beat it a lot. It's amazing. And this is in Chile on top of it. So it connects to our paper.

1:39:33Some of the shapes of these are incredible. I didn't realize they came in galaxies, came in these shapes. Yeah. They're like, they're a bunch of different galaxy shapes. And the, so if, if you go to the, do you use some of the open sky software or go to the American Museum of Natural History Planetarium? I've seen images where they show basically the night sky pre-Rubin and post-Rubin, a model. And it's, it's amazing how much more Rubin has added. It's funny you say that, Jolene, because some people say, oh, I didn't know viruses came in so many shapes.

1:40:08So I'm just revealing my lack of astronomy exposure. Well, you stick to close to Earth. That's okay. Rich, what do you have for us? Okay. I got a bit of a rabbit hole here. I, in summary, I got two links. One's called Jenner's Inquiry Original, annotated, and the other is a link to an article called Smallpox Vaccination in Opposition by Anti-Vaccination Societies in 19th Century Britain. And this was, this was an evolution in TwivPix for me.

1:40:40First of all, I have to say that I was like stuck for a TwivPix. Like I didn't know what to do and I thought, yeah, there must be some old science thing that I've read that I can use a book or something. And I thought, how about, I think we've done it before, but how about Jenner's Inquiry? Without even thinking that it was relevant to what we were talking about. So then I said to myself, I wonder if I can find an online link to Jenner's Original Inquiry. And by the way, Jenner, the guy who pioneered, he wasn't the first to have the idea.

1:41:17He was the first to publish a rigorous set of experiments, okay? And he published them himself, right? Because that's one of the things you did that day in a document called An Inquiry into, I forget what the whole title is, but it's vaccination, okay? It wasn't called vaccination at the time, but use of cowpox to immunize against smallpox. At any rate, so I wondered if I could find a copy of the original. In fact, I don't even know whether what I'm linking here is actually an original or if it is a reproduction of the original for reasons that I will tell you.

1:41:57But I kind of assumed it was original. And I said, okay, this is okay. And it commented that it was annotated in some fashion. I thought, well, okay, I can tolerate that. And then I looked closer. And on page 15 of the PDF, which is actually page one after a bunch of preface in the book, on the top, it says, this book is property of the Southampton Anti-Vaccination League.

1:42:27And I said, okay, so let's look at the annotation. And I'll just give you, there's a lot of underlining and stuff. But just to give examples of the actual writing, marginal writing that I can identify on page 20 of the PDF, Jenner says, what renders cowpox virus so extremely singular is that the person who has been thus affected

1:42:57is forever secure from infection of the smallpox. And the marginal note says, what humbug. The next is on page 42 of the PDF, where he has a footnote, where he notes that, because remember I said that, in fact, Jenner thought, and it took us a long time to come around to this, that in fact the immunogen was probably come from horses, from a disease called grease,

1:43:28which was a blistering disease around their hooves. And farriers, guys who shooed horses, Jenner observed, or at least it had been observed, were quite often resistant to the technique that I told you about before, where they used smallpox, called variolation. And he has a footnote here. It is a remarkable fact, and well known to many, that we are frequently foiled in our endeavors to communicate the smallpox by inoculation to blacksmiths, who in the country are farriers.

1:44:03They often, as in the above instance, either resist contagion entirely or have the disease anomalously. Shall we now be able to account for this on a rational principle, implying, yeah, that they'd been infected with this. The footnote says, If true, cannot it be accounted for from the fact that their bodies, the blacksmith's bodies, are in a good state of health from constant exercise?

1:44:33All of these comments remind me of the sort of modern anti-vax clap crap that you get. Page 69. Jenner says, So he is frustrated.

1:45:13In isolating cowpox because the horses weren't getting sick because it was so dry. They usually got it when it was wet. The marginal note says, This proves conclusively that sanitary arrangements are the best means to prevent horses from having diseased heels. And then does it not follow that cleanliness is more likely to prevent smallpox than introducing that filthy matter into the human body? Page 88.

1:45:44Jenner laments the side effects of inoculation that he's now been able to get around with the cowpox. where he says notwithstanding the happy effects of inoculation with all the improvements which her practice has received since its first introduction in the country, it not very unfrequently produces deformity of the skin

1:46:15and sometimes under the best of management proves fatal. The footnote is now in light of modern science, properly made a criminal offense. Inoculation ought to be a criminal offense. So I got deep into this and I wondered about the Southampton Anti-Vaccination League. So I wrote to the Welcome Collection where this is housed and I asked for more information on this

1:46:48and they sent me back the article that I link in the second one where it turns out that somebody else went through exactly the same exercise that I've just taken you through and gone through all of these annotations. And it has some comments about these anti-vaccination leagues and they turn out Southampton Anti-Vaccination League is sort of a subdomain or spinoff from the National Anti-Vaccination League in Britain

1:47:20that was a late 18th century thing. So that's as much as 75 or 100 years after Jenner's actual thing. And this article talks about vaccination and the anti-vax movement. So my bottom line is, as we've said before, anti-vax is as old as vax. It comes from the very beginning. People resisting this and largely, to a very large extent, because they didn't want compulsory vaccination.

1:47:51In Britain, eventually it died out because people got used to compulsory vaccination. But I want to point out that this vaccine eradicated a horrific disease. There's absolutely no question about it. This is one of the most important medical advances ever. And the anti-vax stuff is nonsense.

1:48:14Yep. By the way, I have a paper copy of the Jenner book. Oh, wow. It's an autofocus. Yeah, there you go. There you go. And the inside. Pretty cool. Yeah. That's it. Find one of the illustrations. Oh, yeah. The illustrations are very cool. This one is great. Yeah.

1:48:37He's got a picture of Sarah Nelms' hand with a lesion on it. Yeah, let's find that. I think it's before that one. That's actually a... It's... Hey, here we go. Yeah. Oh, she's got a bunch. Yeah.

1:48:53Yeah. So that was the milkmaid, Sarah Nelms, from which he isolated cowpox and stuck it into the arm of a 12-year-old kid named James Phipps. And he got the reaction you saw in the first thing, which was hardly anything. And then, because inoculation was a thing, okay, you could inoculate people with smallpox. He effectively, six weeks later, challenged the kid with smallpox by trying to inoculate him. And it didn't work.

1:49:24So that's the experiment. He weighed it enough. It's good. Yeah.

1:49:30Thanks, Rich. Sure. Jolene, what do you have for us? Uh, so I frequently am, mostly for myself, trying to find Twiv episodes or other podcast episodes and, uh, Googling. And Googling doesn't always work and it brings up a lot of the same thing, usually the recent ones. So I picked this tool made by a listener named Scott Seligman. And, uh, it's a GitHub site where you can search transcripts of Twiv for any keywords and

1:50:01you can sort by date and, uh, it's really handy. I may or may not have helped someone find a podcast recently by using this. Um, they have yet to confirm, but I was like, ah, I wish I had known about this. It's probably been brought up before on Twiv. Uh, but if not, and for those of you who are out there looking for episodes, then you can go to this site. And if you go to his GitHub site, he has many other, um, pod, similar setups, web search tools for different podcasts where you can put in the keywords that you want and the

1:50:34date range or not a date range, because it turns out our memories aren't that great for when we listen to stuff and find podcasts. And then he even has it for some comics, uh, including Calvin and Hobbes, which I thought was great because I love Calvin and Hobbes. Um, so yeah, there's just a listener who is, um, in very well versed in coding and computer science. And, uh, thank you, Scott. And I hope that this is useful for other people. Wow. This looks super useful. This is great. I'm going to link to this on the, uh, page because the, yeah, you're right.

1:51:08I have a Google search built in, but it doesn't work. That's terrible. Sometimes it gives no results for something that is obviously should be there. And you, it's not because you don't have keywords because they're there. It's just, they don't come up. I don't know. Yeah. I put keywords in every episode and people have told me, oh, you don't need keywords anymore. Google can find everything, but I still put keywords in, but this is great. I searched for Sabin and it starts with episode two. Colio is not dead. And then it goes through every line of the, how did he do this?

1:51:39Are they based on transcripts? Yeah. Transcripts. It's described. And when I, I'm not sure, I'm not sure. Maybe Scott can tell us, uh, Scott, if you're listening. So, um, it had, it was quite recent when I looked, it found something that was like within two weeks before I looked, maybe not the exact week. Cause I was looking on like, you know, Sunday, but it's real up to date. Cool. Thank you. That's great. I have an article for you in the Atlanta, in the Atlantic magazine.

1:52:12I have a gift link because I subscribed to it. So you can read this article. It's called the end of reading is here by Rose Horowitz.

1:52:22Optimists once believed that universal literacy was inevitable. Now it seems that the age of reading might be a short anomaly in human history. This is a great and scary article about the decline of reading. Um, people are reading a lot less and, uh, I can give you, let me give you a number here. Um, this is full of good stuff. Uh, they read more words because they're watching videos and stuff and they're reading texts on

1:52:57computers, but they do not read books. Where's the thing I'm looking for? Fewer than half of all adults reported having read a book of any kind in 2022. Fewer than half. Yeah. Oh my gosh. So in 1958, the top selling book in the U S was Dr. Zhivago with long sentences, long, complicated sentences. Last year's top selling novel was sunrise on the reaping. The latest in the hunger games, young adult series.

1:53:30I like young adult books. I can't blame them for that.

1:53:34Yes. But reading, you know, is really, anyway, the, the article talks about why reading is great from your brain. You know, humans are, were not originally equipped to read. They took parts of their brain that are used for other things and adapted it for reading. And you really stimulate your brain in many ways that are described in this article by, by reading. And one of the problems is that high school students are reading less and less. And by the time they get to college, they don't know a lot of things.

1:54:06And the professors have to re-educate them as Brianne well knows. Uh-huh.

1:54:14Yeah. They, they, they don't always, um, their response to being assigned reading is, um, not the same response that I had as a student. So here's the passage. Reading has never been natural. Humans have no innate cognitive machinery designed to string letters into words and connect them to their real world analogs. To read, people had to repurpose regions of their brain used for speech and object recognition, which first emerged 6,000 years ago in Mesopotamia.

1:54:46Interesting. More than any other invention, writing has transformed human consciousness, right? I mean, this is, and it talks about writing too, because that's, that's part of it, obviously. And then there's this other thing. There's a whole part of this article that talks about how first television and now the internet has consumed reading time, right? Television, you know, in, in, uh, in 1985, Americans watched more than seven hours of TV

1:55:18a day. And that number rose to nine hours a day by 2010. And TV crowded out the time needed for reading. And then the internet made it impossible. It said that basically there's, there's limitless in entertainment. It used to be a TV. You watched a program at a certain time, right on a certain channel. Now it's available all the time. Anyway, this is a really good article and, um, it's kind of scary. Too bad to get the benefit of it. You have to read it. Actually, what do you tell your students to read a book, right?

1:55:52I do. That's, that's my new advice. Whenever someone asks me who's coming to college, what they should do to, um, get ready for college is read books. You could, you could think about it. You know, you. One book. One book. I mean, you read some better than no book. You have to decode it basically, right? First you have to focus on it and you have to figure out what the words mean. And then you have multiple concepts. You have to put them all. It's really amazing exercise, right? And so I love to read and I know it's hard because sometimes I'm reading papers and they

1:56:29don't make sense. You have to read it over and over again. Now, the last thing I want to talk about is AI. That's a whole part of this article on artificial intelligence. AI produces crisp professional prose presented with human and AI produced text side by side. Even MFA candidates have been shown to prefer the work of the machines. If AI writing is pleasing and convincing, however, it is also unoriginal, often inaccurate or both. People will therefore need the powers of discernment and comprehension more than ever.

1:57:02They will need to know what they think and how to make their own judgments. And these are the exact skills that the use of AI threatens to erode. I think that was just perfect. Anyway, go read it. I don't know. A lot of people won't read it, I guess. But the link is free there and you can check that out.

Listener emails and comments

1:57:22We have two listener picks. As Tony writes, I thought you'd like, oh, I'd like to watch this cool interview with Johns Hopkins immunologist G.G. Groneval discusses a variety of topics, the demonization of gain-of-function research, the GBD. Great Barrington Declaration. Thank you. An explanation of Rand Paul's agenda. A new book she is working on regarding the history of RFK Jr.'s grievances towards Tony Fauci. Why investigating the possibility of lab leaks is still always going to be needed whenever something unusual with a virus happens.

1:57:57But also, how come there's even more confidence than ever before that COVID pandemic was zoonotic origin?

1:58:04Wow. That's a lot of stuff. Gigi's been on TWIV before. And then Charles writes, this may be getting old, but here's another Derek Lowe in the pipeline pick. There is a line about vocabulary that I thought was fantastic writing.

1:58:23Let me search for vocabulary. I think this is the same link that was in the news section. This is from 11th of August. Oh. Oh, the proposed changes in childhood vaccination. I guess not. This is the executive order, a strongly felt opinion. And so the thing, yes, here's a quote from his announcement. I have seen proof of where they have a vaccination thing that looks like the size of a bottle of soda and pour it into the little child's body. That's a quote from the president.

1:58:54And then Derek says, this is deranged nonsense expressed in the words of someone whose cerebral cortex is shedding vocabulary by the day. Vaccination thing, really? A brief reminder, this man not only imagines he is making medical policy, but he also has the nuclear launch codes. And that part is unfortunately no delusion. No delusion. Unless there's a request, I'm going to let the music of our generation arc fade away.

1:59:28No, no. I got to. I can tell you. I'll tell you, Charles, here's an album for you to go listen to. The first album, Blood, Sweat and Tears, released in 1969 without. What's his name? Without Cooper, not with the guy who just died.

1:59:47BST singer. Who died. That was David Clayton Thomas. So he was on all the subsequent albums. He had the big baritone. But Al Cooper, the first album. It is fantastic. Okay. So you can resume your arc. P.S. Thank you, Alan Dove, for the nice comment about my SIG line, which is freedom from responsibility is not liberty. It is childhood. Thank you, Charles.

Show wrap-up and credits

2:00:11All right. That's TWIV 1349. You can find the show notes at microbe.tv slash TWIV. You like our program? If you like our program, we'd love your support. Microbe.tv slash contribute. And you can send questions and comments, emails, picks of the week. TWIV at microbe.tv. Jolene Ramsey is at Texas A&M University, ramseylab.versell.app. Thank you, Jolene. Nice to see you.

2:00:42Yeah. I enjoyed that discussion today. Thank you. Brianne Barker is at Drew University Bioprof Barker on Blue Sky. Thank you, Brianne. Thanks. I learned a lot. Rich Condit is an emeritus professor, University of Florida, Gainesville. He is currently in Austin, Texas. Thank you, Rich. Sure enough. Always a good time. I'm Vincent Racaniello. You can find me at microbe.tv. Yesterday, we had visitors here, including the youngest visitor ever to visit the incubator.

2:01:18She came with her mom. Lucinda is 12 years old. And she stayed for two and a half hours because she loved it. I kept showing her virus. I gave her buckyballs, and I showed her the video, and she started building viruses. And if things work out right, the outro is going to be Lucinda today on this episode because I had her sit down here and record it. Excellent.

2:01:48That's awesome. That was just amazing. She was so curious and so smart. I was just amazed. And that's why I spent two and a half hours with her and her mom. I think her mom was really enthralled by the whole thing, too. She's a big listener. They're both from Canada, by the way. Anyway, so I said, oh, yes, I said who I am. I'd like to thank the American Society for Virology and the American Society for Microbiology for

2:02:18their support of TWIV. Ronald Jenkins for the music and Jolene Ramsey for the timestamps. You have been listening to This Week in Virology. Thanks for joining us. We'll be back next week. Another TWIV is viral.

This Week in Virology and Jolene Ramsey for the most part of this episode is a production of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Virology and Jolene Ramsey for the most part of this episode of This Week in Viro