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Not that important but that piece is from New York Magazine, not the New Yorker

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"They didn’t find any live viruses, but there were able to recover a few shreds of useful DNA."

You're wrong. Live Spanish flu was indeed revived and used to infect a bunch of monkeys (and kill them).https://www.nature.com/articles/nature05495

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> Here is a great article about a guy who digs up ancient Indian burial grounds, searching for samples of especially severe flus. If only we had some sort of cultural folk memory that warned people against doing that kind of thing!

Hah, I'm actually not sure if this is a reference to anything in particular. Is it referencing Pet Sematary or something?

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> But I haven't the proper experts address this properly

I think there's a typo in this sentence.

Also several typos in the quote from the magazine, but that might be on them, I didn't check.

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Yeah, there's cause for optimism. We're not adapted to weird ancient diseases, but they're also not adapted to us.

Some of the most fascinating scientific questions relate to aliens. (By "aliens" I mean any lifeform dropped into a totally new environment, not grays with anal probes.) You'd think the alien would die in the strange environment - often this is true! But sometimes aliens have a competitive advantage.

Rabbits in England are preyed upon by a host of animals, which holds their fitness in check. But when they were brought to Australia, a place with few or no natural predators, they took over. Their alienness gave them an advantage. The country now has a hundred and fifty million feral rabbits - about eight times more rabbits than people.

Agricultural crops often do best far away from their native land, where pests and pathogens are adapted to them. New-world maize and cocoa are among the biggest crops in Africa. Conversely, most coffee is grown in South America. Sometimes being far from home is a good thing.

The diseases spread by the Columbian expansion were famously very bad for the Native Americans, and that's definitely the alien advantage in action. So why won't permafrost viruses do the same to us?

Probably because "alien advantage" falls off quickly. You can't be too ill-suited for your environment or your fitness goes away. So there's a weird curve in play: "close" diseases (that we come into contact with regularly) normally aren't that bad: our bodies have built up defenses to them. "Far" diseases (such as the smallpox that wiped out the Taino) are worse. But VERY far diseases hit a species barrier and become harmless, unless they can cross over.

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Supposing smallpox reappeared, how long would we need to be able to restart vaccine production? I assume patents on smallpox vaccines are now expired and anyone who wants to can produce a vaccine, but I'm also sure it would take some time.

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An important point about the Spanish flu - most of the deaths caused by the 1918 Spanish flu were actually as a result of bacterial pneumonia. If it had happened just a decade later it would have been significantly less deadly, as bacterial pneumonia is immensely helped by antibiotics.

https://www.nih.gov/news-events/news-releases/bacterial-pneumonia-caused-most-deaths-1918-influenza-pandemic

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> No mystery why smallpox died out - we killed it.

Well except for some lab samples. And now it's not even relevant - smallpox is literally open source, and there's even even instructions for "compiling" it (paper from a few years ago, about doing it with horsepox).

https://www.ncbi.nlm.nih.gov/nuccore/L22579.1

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0188453&type=printable

I'm not sure if current situation qualifies to call it truly dead.

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> An envelope fell out of a book containing a note and some weird red stuff; the note said that it was smallpox scabs from a past infection, kept as souvenirs. This sounds like a scene for a horror movie aimed at epidemiologists.

The note is in English and says "scabs from vaccination of W. B. [?] Yarrington's children".

This would strongly suggest that no smallpox is present. You don't vaccinate for smallpox with smallpox.

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Not relevant to ancient plagues, just a modern one.

In a world where a ridiculous number of people refuse vaccination for Covid, perhaps Omicron is good news. That is a variant that is more infectious but less lethal than Delta to search out and variolize unvaccinated persons.

Just a thought.

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I was listening to https://twitter.com/vaccinepodcast and they described how, shortly after smallpox was wiped out, an archeological team dug up a crypt in England known or strongly suspected to contain victims of smallpox. They took precautions and I'm glad to hear that recovering live virus from these conditions is rare. But I was struck by the idea that there is no possible universe in which the benefits of a single archeological dig outweigh the risk of re-releasing smallpox, even if minuscule.

Also, the most recent episode of rationally speaking (http://rationallyspeakingpodcast.org/261-dangerous-biological-research-is-it-worth-it-kevin-esvelt/) seems to conclude similarly to what you conclude here: Scientists looking for risks may cause the very problems they are trying to prevent.

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And then there's the David Drake thing where you go back in time and bring modern bird flu to the dinosaurs 65 million years ago.

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Something I've never understood about smallpox: why were native Americans and Australians affected so badly by it, when it was a relatively minor problem in Europe?

Is it that smallpox had already swept through Europe centuries ago, before recorded history, and wiped out the ~90% of people who weren't especially resistant to it? Or is it something more complicated?

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Not really about ancient plagues, but we already have engineered plagues and Australian rabbits in this thread so what the hell, I'll just continue.

So, there's been a considerable amount of effort going into eradicating those rabbits through biological warfare, and without real success. If actual scientists with government funding and a 100 years of effort failed to wipe out a species from a single continent, isn't it a strong evidence against bioweapons being an X-risk, at least in the near future? One big difference I see is that rabbits breed much faster than humans and so maybe they can outbreed a disease, but I feel like it should be more than offset by hygiene, quarantine and medicine.

To be clear, I'm asking specifically about the risk of wiping out the entire species or at least the civilization, death rates in 10-50% still look possible and of course that'd till be horrible.

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> And doctors whose knowledge of medicine doesn't begin and end with "look like a creepy bird"

I love that picked a picture that is titled "the doctor's beak of Rome[?]". But to be fair, as the text at the bottom points out ("clothes against the death in Rome"), they also wore protective clothing. Maybe COVID wouldn't have been as bad if a lot of people had chosen to dress like this when going outside.

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Maybe this is because my primary language isn't English and it's mapping funny to English in this occasion, but when I read a virus is worse, my brain first thinks it's stronger because a stronger virus would be a worse thing. I have to stop and think for an instant to realize it's a worse virus (and that's a better thing).

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I'm less sure about how worrying or not worrying this might be. A good reference is pre-Columbian America: since there were no close human relatives in the American continent for millions of years, all the pathogens there were poorly adapted, and selection on human immune genes was relaxed, they didn't seem to have much issue, until Eurasian diseases got to them ultra hard (so a disconnect or just some dozens of thousands of years of evolutionary time)

FWIW (this doesn't speak to virulence in particular) using reconstructions of ancient adenoviruses is deemed a promising approach to get gene theraphy that isn't rejected by the immune system, as in https://www.sciencedirect.com/science/article/pii/S2211124715007597?via%3Dihub

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"millions of years"

Can DNA really survive this long?

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The whole premise is ignorant anyway, resting as it does on the delusion that we are (or could be) seriously different, down at the molecular level where infective invasion and defense happen, from our ancestors 50,000, let alone 5,000 years, ago. We're not. If all you had access to was information on the 50 micron length scale and below, you'd be extremely hard pressed to tell the difference between a sophisticated 21st century journalist tapping out doom pr0n clickbait and a Cro-Magnon grunting[1] tales of boogey-men in the wild woods to his hairy naked children squatting around a fire in a cave.

Viruses and eukaryotes have been slugging it out for 600 million years, and not a lot has changed at the level where the battle is fought since an uneasy truce was called some 7-digit number of years ago (at least). The idea that viruses preserved from 1 million BC are potentially dangerous in a way a brand-spanking-new virus cannot be is goofy. The molecular weapons and defenses are unchanged, over that time span, and so are the potential chinks in the armor, zero-day exploits, et cetera. There's no reason a virus frozen in Antarctica ice for 10,000 years would be any more, or any less, dangerous then one created by an unfortunate mutation 10 minutes ago, and you'd think HIV and SARS-CoV-1 (and -2 to some extent, and for that matter the 1918 flu, the Black Death, practically the entire history of pandemic disease, really) would be pretty obvious illustrations of that fact.

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Just a note about smallpox - the US maintains a supply of vaccine sufficient for every American.

https://www.cdc.gov/smallpox/bioterrorism-response-planning/public-health/vaccination-strategies.html

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I embarrassed myself in a movie theater by saying something out loud (much shorted than your essay) about it when an an ancient virus was supposed to be especially scary. I think it was the X files movie.

A lot of horror is about fear of the past.

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There was a TV series “Fortitude” ( 2015-2018 ) that had as one of it’s major subplots a thawing mammoth carcass that introduces a bizarre disease into a small isolated Arctic village.

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Talking of archaeologists digging bodies up, a relevant clip from the 2001/02 season of Time Team, where they find a possible lead coffin burial and discuss the precautions needed - 26.26 on the Youtube video:

https://www.youtube.com/watch?v=QC76jhsoB58&list=PLWy0vReBtl9OFJpPftCA9wYzxIXk7j_IU&index=14

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Out of curiosity, is there a way to estimate how deadly smallpox would be if it were around today? Presumably modern treatments (separate from vaccination) would reduce fatality, even if only a little.

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"the 3.5 million-year-old one that a Russian scientist self-injected just out of curiosity"

At least he has a good origin story once he develops villainous superpowers.

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"...why would a flu evolve into an inferior flu? Sure, it might evolve into a less deadly flu because it's perfectly happy being more infectious but less deadly."

One thought that just struck me: maybe it makes it easier for the virus to "hide" in the general population, so to speak? IE, a really infectious flu triggers major public health responses from humans to fight it--ya know....like we did back in 1919--but if transmission from person to person seems a little more random, those precautions aren't taken and the virus' odds of hanging around over time (albeit in smaller numbers) actually go up?

I have no training or knowledge in this area at all, and this is probably 100% wrong.

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Has there ever been an interview with the kinds of people who inject ancient bacteria? Why are they doing that?

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Gretas scare the shits out of me (or they would, if I were . So the author writes: "many, many more people are not scared enough than are already “too scared.” In fact, I don’t even understand what “too scared” would mean."

You don't understand!?! Let me explain: 1 .The panic about DDT in pinguins let to a ban of DDT. Let to millions of extra-malaria deads, cuz other stuff was less efficient, not safer, more expensive. 2. The panic of the population bomb let to China's enforced one-child-terror. With women forced to abortion even weeks before birth. But, yeah, it is only about fetus (and their parents), and millions are statistics only (French diplomat, not Stalin). 3. Panic about CO2 let to "BIO-ethanol" - food converted to fuel, thus less food to eat, higher prices, hungry kids. 4. Panic about nuclear-power lead to premature closure of Germany's plants, more use of coal, esp. dirty brown-coal. By worsening air quality coal-stations kill millions (Fukushima: 2) - but QALY is again just "statistics". 5. Panic about GM-food keeps the world mal- and undernourished for much longer than needed (and forces me to buy the worse conventional stuff, not even a choice!). 6. Panic about warming forces ever stricter building codes, that make it ever harder to afford a home, even a rented one. 7. Panic about Thalidomide (at least sth. to be scared about!) lets the FDA stick to to its restrictive course - how many lifes and QALY lost, Scott and "It's a war"-Zvi may count. - Even if there really is sth. to be scared about: IT IS OFTEN FATAL TO SCARE TOO MUCH. And intentionally working up a panic, can EASILY lead to extremely wrong and harmful decisions. - Maybe it is all for the good if the NYT goes over-the top. May make more people feel suspicious about Gretas and NYT. But then: I find that stuff in school books ("Warmer climate - spread of Anopheles to the north - more Malaria in Europe"). And kids in UK cry after "lectures" by Extinction-rebellion. Hey, I believed in Armageddon (before Gorbachev) and then in DOOM, Club-of-Rome style. As a teen.

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That picture is very great.

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Here's a friendly heads up from a medievalist that a whole lot of historians of medicine no longer think the Black Death was bubonic plague. They think it was almost certainly a human-to-human airborne disease of an unknown type. It spread lightning-fast (much more like covid than plague), turned up in places where there weren't rats (like Iceland and remote mountain villages), and killed very fast (1-2 days versus bubonic plague's 7-10 days). So -- basically imagine Covid, only with pustules and bloody vomit rather than coughing, and with a 30-50% death rate. Since we don't know what the disease was, it's unknown whether good sanitation would have made a difference.

The re-evaluation of the Black Death has been going on for about 20 years; one of the earlier papers making the case against bubonic plague is here: https://www.sciencedaily.com/releases/2002/04/020415073417.htm.

In short: we better hope the lab in Wuhan stays away from this one!

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Am I the only one that incorrectly thought Anthrax was a fungus all this time? I blame the ‘spore’ terminology.

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👻👻👻👻Oooooooh👻👻👻 I am the Spooky ghost of Arthur Jensen doomed to haunted the lead contaminated streets of Baltimore for all time. I bring the curse of multiple sclerosis to all those who misrepresent heritability or believe Linda Gottfriedson’s genocidal horseshit.

Racists, worshippers of psychometric g, repent! It's just myelin and glial cells. White people are just sort of mediocre dickheads who poisoned themselves. 👻👻👻Ooooooooh👻👻👻

Scott, email me.

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I’m the archivist for a hospital, so that envelope full of scabs gives me the willies on a rather personal level.

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Wait, blog.jaibot is back up? wasnt this an old blog of yours that SSC linked to occasionaly but all the links were dead? Or am I just confusing it with your livejournal :)

(Which I know can still be dug up through wayback machine, but it’s a bit of a hassle)

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Something something The Talos Princple game something.

Good work as always!

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Another reason bubonic plague is much less deadly than it used to be might be that all the people who were particularly succeptible to it died.

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I also raised an eyebrow at this point in The Uninhabitable Earth. It is absolutely possible for ancient organisms to survive freezing, but the risk from that seems quite small relative to the apparent and pretty quantifiable risk of continual habitat destruction causing previously wilderness-only diseases to run around in human-occupied areas.

Add to that increased mosquito habitat and you have plenty to worry about from warming areas.

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Speaking of "Arctic ice" one of the most profound movies about the struggle for survival is "March of the Penguins" (2005), a documentary about the annual 70-mile walk Emperor penguins take in order to find a mate and raise a baby chick in the harsh climate of Antarctica.

The Life Lesson from this movie, which applies to all of us and all of this DOOMism, is:

"Life is a beautiful struggle—splendor and sadness co-exist for us all."

From: Movie Wisdom On Parenting Children

https://moviewise.substack.com/p/movies-on-parenting-children

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>Animal diseases can't trivially become contagious among humans. Sometimes an animal disease jumps from beast to man, like COVID or HIV, but these are rare and epochal events. Usually they happen when the disease is very common in some population of animals that lives very close to humans for a long time. It’s not “one guy digs up a reindeer and then boom”.

Or uh, you know when Ecohealth and Daszek have been doing some fishy shit along with the Chinese military.

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I think part of the answer to the flu thing is the “novelty is severity” argument that Zeynep has been highlighting. A lot of why diseases become less severe over time is not that they evolve that way, but instead that we get exposed to more and more similar diseases and our immune systems get trained. So the 1918 flu was a completely novel disease jumping from animals into people, but since then we have been exposed to lots of similar flu viruses with similar structures and therefore have some level of defence against them.

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Dec 20, 2021·edited Dec 20, 2021

"why would a flu evolve into an inferior flu"

Define "inferior"

Evolution rests on current conditions. One way diseases evolve is within individuals. It's great for a disease to spread fast, but then you also get evolution among the populations of virus in a single human.

So you may start off with a flu strain optimised to spread... but then it survives in some immune compromised or weakened individuals for months or perhaps even years and the strain that it becomes while doing so is highly adapted for evading a (weakened) human immune system over long time periods.

because viruses don't have a single environment to adapt to, it's not a matter of a single search space, rather they have different parts of their lifecycle and adapting really well to one part may make them worse in another.

Then throw in some recombination .

Viral recombination occurs when viruses of two different parent strains coinfect the same host cell and interact during replication to generate virus progeny that have some genes from both parents.

Something like 10% of people have an active influenza infection at any given time, it's just that mostly they sit quietly in your nasal cavity avoiding the interest of the immune system. Sometimes these stealthy versions swap genes with nastier versions of influenza to produce interesting combinations.

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