I’ve been trying to find a word for this? Structural isomorphism? Methodological similarity? I’m very open to suggestions! How about CONCEPTUALLY ANALOGOUS?
Epistemology: The theory of knowledge, especially with regard to its methods, validity, and scope. Epistemology is the investigation of what distinguishes justified belief from opinion.
“there are a lot of meta-features of different kinds of events that create conceptual tool-kits that can be brought over, even though on the surface, the event is a different category. I’ve been trying to find a word for this? Structural isomorphism? Methodological similarity? I’m very open to suggestions!”
Structural isomorphism is too restrictive. Think of oat milk. It’s not cow milk (or goat or sheep) but many people want them to behave similarly. When they don’t behave in the same way, people try to find work arounds. That makes it functional or behavioral isomorphism, if isomorphism itself is the right word.
Methodological similarity is similarly too restrictive, since this is behavior that people exhibit under everyday circumstances, not just academic research. Again, oat milk.
It’s more a form of analogy: using an example you know well as an analog for what you don’t know. It can often get you into the new example because there are similarities, or can yield incredible insights because of how the two differ,
I've been struggling with the same thing you've mentioned about classifying the domain-independent structural similarities of how we should properly handle knowledge. Informally I've been using "information kinematics" to try to capture that spirit of "the science of things hitting other things in such a way where the composition of the things is tremendously important, but you can still draw general lessons if you're careful about it." But I'm still not totally sure if it's self-explanatory enough that I can just slip it in to my writing.
Anyway, I completely agree and think this is the kind of thing we all need to be broken records about. We're so conditioned to think of rare events like lottery tickets - especially when so many modern institutions only exist because of the human affinity for gambling - but the real world has tons of control processes and unexplained correlations. So a rare event is a lot more likely to be a correspondence break from the base state of the system in a way we don't understand yet, and our base assumptions should be cryptic factors over bad luck. Honestly, I think the modern crop of self-proclaimed Bayesian's have no small hand of blame in this, since the very act of setting a prior implies that you think your *available language with regard to the system is complete*. For all of the supposed humility in laying out and updating your thoughts, I think the real world often turns on distinctions between outcomes A and A' that are similar enough that we didn't even think to define a difference between them until the impact of that difference suddenly presented itself.
How much do we understand about the factors influencing the scientists who signed the Lancet letter indicating that Covid was not lab-related? I know that Peter Daszak had some pretty serious conflicts of interest (which I believe the Lancet has now admitted). I know Zeynep indicated in several different writings that a number of the original signers have now indicated that a lab-leak is a possibility. Why did the different "experts" sign-on in the first place? This also seems an area that would benefit from some rigorous examination. That letter and the tone behind it provided more fodder for people who want to dismiss science and expertise. I wonder if there are ways scientific communication can be more transparent than it currently is (signing a conflict of interest form when submitting a grant or publication is woefully insufficient).
"Looking at the post-molecular biology era, when we were more in a position to be the cause of a pandemic, the known incidence is that two out of three pandemics were completely zoonotic: the same odds that Nate Silver had assigned to Hillary Clinton winning the presidency in 2016. It’s actually not saying that much either—again, given a rare outcome—except that ruling out pathways without evidence isn’t warranted."
I'm trying to figure out which list of events is being discussed here. I'm thinking that HIV is one of the completely zoonotic pandemics, and the 1977 flu pandemic is the one that isn't obviously zoonotic. I guess SARS, MERS, Zika, and Ebola were never pandemics, and I had to go to the Wikipedia tab on pandemics and epidemics and look at their list of global ones before I remembered that 2009 swine flu was probably the third one you were mentioning. But it does seem worthwhile to have a canonical list of the events that count as "pandemic" so that people can have more systematic discussions of them.
I’m wondering what those of us reading along at home are supposed to do with this:
> First, going forward, we should consider all possibilities as potential pathways and think about what can be done. I people don’t understand the evidentiary basis on which people are assigning precise(ish) likelihoods to the paths leading to a rare, perhaps once-in-a-century rare, event when a lot of paths have been demonstrated as viable.
To continue your analogy, this sounds like good advice for the investigators of a plane crash, but we aren’t plane crash investigators. We aren’t going to figure this out ourselves; we lack expertise and access to the relevant evidence. At best we can be supportive of those who are in a position to investigate and wait for future developments.
Since it seems there isn’t going to be a real investigation, I’m not sure what we can do other than shrug and move on. “Sure, it could have happened that way. So what? Flying is very safe in general, so I’m still going to buy a plane ticket.”
As the meme goes, this seems like both the simple and adept way of looking at it?
"1-More about that furin cleavage site debate (it ended up being too wonky for the article but it’s actually an interesting intersection between science, evolution and academic incentives)."
I work as copy editor for a science magazine (not a journal but a sort of trade mag for biologists). I have been closely following the lab leak debate since April 2020 and was first struck by Yuri Deigin's breakdown of the virus's genome in Medium, which first pointed to the furin cleavage site. Deigin and Segreto then wrote a paper about it, which in turn pointed to this one
"'You cannot, in a normal cell culture, maintain the furin cleavage site,”'he told me. When the COVID-19 virus is replicated in a cell culture in a lab, he said, the furin cleavage tends to delete itself. A peer-reviewed paper, published in late April in Nature, noted that habit and identified seven other papers that found a similar deletion. [LINK: https://www.nature.com/articles/s41564-021-00908-w#author-information]
"So if researchers were using traditional methods and their preferred cell lines to try to force the virus to replicate, mutate, and change, the furin cleavage site would likely disappear.
"The gain-of-function proponents say this furin site is too well adapted for humans to be an accident. But Goldstein said the opposite is true. The cleavage site is imperfect, so odd, that it could have only been a freak of nature. 'No virologist would use that cleavage site,' he said."
LONG STORY SHORT, I proposed to my science magazine employers that they host a debate between, say, Goldstein and Deigin, Segreto, or another proponent of considering a gain-of-function origin. They declined: they seem to find Deigin and Segreto a little shady (and in any event, neither is a virologist).
Maybe you could host that debate. In the absence of hard evidence, it really does come down to scientists' informed opinions on the question of how SARS-CoV-2 sprang into the world so seemingly pre-armed to cause a human pandemic.
Zeynep, this is even above and beyond your normal (casual and profound) connection: "Looking at the post-molecular biology era, when we were more in a position to be the cause of a pandemic, the known incidence is that two out of three pandemics were completely zoonotic: the same odds that Nate Silver had assigned to Hillary Clinton winning the presidency in 2016." Bam.
I see some openings for further understanding, even lacking participation by China. For example, do people eat horseshoe bats? Do they house them nearby, perhaps to control insects? If not, that eliminates whole areas of inquiry and lets us focus on others.
Regarding Biden calling on intelligence agencies to produce a report: I took this to suggest a belief that we have more information than we have surfaced in the information stream. (Because finding stuff in information streams is a big part of what intelligence agencies do. And sometimes fail to do...) Recently we have seen news reports of the content of previously overlooked messages of various sorts, and the great sleuthing that noted the deletion of the sequences from the database and the finding of a number of them once researchers knew that they existed. It became like finding the car keys, not having to hypothesize the existence of the car.
Being more of an interested spectator than a stakeholder in identify with clarity the source of this global pandemic, I will follow your endeavors. Unfortunately, China's actions seem not to want or publicly identify your goal, and the desire of the world health community to solve this mystery with sufficient data. Assuming the origin is from the wet market, and China collected all the animals at this market, it is strange that they say they destroyed these animals rather than saving them from finding the source and bringing more clarity to this vector.
My concern and memory are that with the Spanish Flue, the second year caused a more significant loss of life, maybe through a more deadly variation of the flue. However, since the world will be the incubator for Covid in the next few years, and examples like the Delta variation, what are the rare odds that a new variation dominates but does not kill or kill millions?
In comparing airplane crashes and the efforts to identify the details around why this crash event happened. The goal being so that new actions are taken to either better train pilots, repair a broken part, create another safety break when the systemic system of safety has a rare flaw is a perfect analogy. I seem to recall a French plane crash in the South Atlantic that took years and millions of dollars to find the plane, concluding it was a pilot error. A few years ago, an Indonesian plane disappeared, and radar and satellite data showed it crashing somewhere in the Indian Ocean to the west of Australia. This plane and mystery may never be solved unless its actual location, recovery happens.
Today I read this article that points out an outsider's insider perspective on the professional standards at the viral lab and media rumors that would challenge her experiences.
Bloomberg article "The Last-And Only-Foreign Scientist in the Wuhan Lab Speaks Out."
"Virologist Danielle Anderson says half-truths have obscured an accurate accounting of Wuhan lab's functions, but she does think an investigation is needed to nail down virus's origin."
"Once a plane crash does occur, we don’t tell the investigators that planes are really really safe, so let’s not worry about it. In fact, the thoroughness of that investigation is exactly what makes planes really really safe, in the future: we figure it out and fix it."
I'm not sure the airplane safety comparison works here- airplanes are human-designed and human-built machines, under human control, and humans have the ability to fully reconstruct a failure sequence and directly address it. This is even down to the level of airliner CPUs being hardened against extremely rare but known failure modes- comic rays causing a digital bit somewhere to flip from 0 to 1.
In contrast, it can very difficult to understand and manipulate the biological world, including viruses, to the same level of precise causality. For the original SARS, the best we have found more than a decade later is a cave where bats have different viruses that contain all of the constituent parts of the virus.
Additionally, this argument almost sounds like great justification for pursuing gain-of-function research on coronaviruses after the 2003 SARS outbreak!
Rare Events Need Different Methods
I’ve been trying to find a word for this? Structural isomorphism? Methodological similarity? I’m very open to suggestions! How about CONCEPTUALLY ANALOGOUS?
Epistemology: The theory of knowledge, especially with regard to its methods, validity, and scope. Epistemology is the investigation of what distinguishes justified belief from opinion.
“there are a lot of meta-features of different kinds of events that create conceptual tool-kits that can be brought over, even though on the surface, the event is a different category. I’ve been trying to find a word for this? Structural isomorphism? Methodological similarity? I’m very open to suggestions!”
Structural isomorphism is too restrictive. Think of oat milk. It’s not cow milk (or goat or sheep) but many people want them to behave similarly. When they don’t behave in the same way, people try to find work arounds. That makes it functional or behavioral isomorphism, if isomorphism itself is the right word.
Methodological similarity is similarly too restrictive, since this is behavior that people exhibit under everyday circumstances, not just academic research. Again, oat milk.
It’s more a form of analogy: using an example you know well as an analog for what you don’t know. It can often get you into the new example because there are similarities, or can yield incredible insights because of how the two differ,
I've been struggling with the same thing you've mentioned about classifying the domain-independent structural similarities of how we should properly handle knowledge. Informally I've been using "information kinematics" to try to capture that spirit of "the science of things hitting other things in such a way where the composition of the things is tremendously important, but you can still draw general lessons if you're careful about it." But I'm still not totally sure if it's self-explanatory enough that I can just slip it in to my writing.
Anyway, I completely agree and think this is the kind of thing we all need to be broken records about. We're so conditioned to think of rare events like lottery tickets - especially when so many modern institutions only exist because of the human affinity for gambling - but the real world has tons of control processes and unexplained correlations. So a rare event is a lot more likely to be a correspondence break from the base state of the system in a way we don't understand yet, and our base assumptions should be cryptic factors over bad luck. Honestly, I think the modern crop of self-proclaimed Bayesian's have no small hand of blame in this, since the very act of setting a prior implies that you think your *available language with regard to the system is complete*. For all of the supposed humility in laying out and updating your thoughts, I think the real world often turns on distinctions between outcomes A and A' that are similar enough that we didn't even think to define a difference between them until the impact of that difference suddenly presented itself.
How much do we understand about the factors influencing the scientists who signed the Lancet letter indicating that Covid was not lab-related? I know that Peter Daszak had some pretty serious conflicts of interest (which I believe the Lancet has now admitted). I know Zeynep indicated in several different writings that a number of the original signers have now indicated that a lab-leak is a possibility. Why did the different "experts" sign-on in the first place? This also seems an area that would benefit from some rigorous examination. That letter and the tone behind it provided more fodder for people who want to dismiss science and expertise. I wonder if there are ways scientific communication can be more transparent than it currently is (signing a conflict of interest form when submitting a grant or publication is woefully insufficient).
"Looking at the post-molecular biology era, when we were more in a position to be the cause of a pandemic, the known incidence is that two out of three pandemics were completely zoonotic: the same odds that Nate Silver had assigned to Hillary Clinton winning the presidency in 2016. It’s actually not saying that much either—again, given a rare outcome—except that ruling out pathways without evidence isn’t warranted."
I'm trying to figure out which list of events is being discussed here. I'm thinking that HIV is one of the completely zoonotic pandemics, and the 1977 flu pandemic is the one that isn't obviously zoonotic. I guess SARS, MERS, Zika, and Ebola were never pandemics, and I had to go to the Wikipedia tab on pandemics and epidemics and look at their list of global ones before I remembered that 2009 swine flu was probably the third one you were mentioning. But it does seem worthwhile to have a canonical list of the events that count as "pandemic" so that people can have more systematic discussions of them.
I’m wondering what those of us reading along at home are supposed to do with this:
> First, going forward, we should consider all possibilities as potential pathways and think about what can be done. I people don’t understand the evidentiary basis on which people are assigning precise(ish) likelihoods to the paths leading to a rare, perhaps once-in-a-century rare, event when a lot of paths have been demonstrated as viable.
To continue your analogy, this sounds like good advice for the investigators of a plane crash, but we aren’t plane crash investigators. We aren’t going to figure this out ourselves; we lack expertise and access to the relevant evidence. At best we can be supportive of those who are in a position to investigate and wait for future developments.
Since it seems there isn’t going to be a real investigation, I’m not sure what we can do other than shrug and move on. “Sure, it could have happened that way. So what? Flying is very safe in general, so I’m still going to buy a plane ticket.”
As the meme goes, this seems like both the simple and adept way of looking at it?
THIS question. A suggestion follows.
"1-More about that furin cleavage site debate (it ended up being too wonky for the article but it’s actually an interesting intersection between science, evolution and academic incentives)."
I work as copy editor for a science magazine (not a journal but a sort of trade mag for biologists). I have been closely following the lab leak debate since April 2020 and was first struck by Yuri Deigin's breakdown of the virus's genome in Medium, which first pointed to the furin cleavage site. Deigin and Segreto then wrote a paper about it, which in turn pointed to this one
This article in Foreign Policy magazine
https://foreignpolicy.com/2021/06/15/lab-leak-theory-doesnt-hold-up-covid-china/?fbclid=IwAR0xkHA4DbSgZtGH9VrunZlrwFAYwuP9lsl1eSAGIQChGGm1LH6-E3GHELk
is mostly geopolitical pooh-poohing, but at the end cites some scientists and papers arguing that the furin cleavage site is more likely natural, acquired by recombination. Stephen Goldstein of the University of Utah, a human geneticist, is one, https://cellvolution.org/stephen-goldstein.htmlhttps://cellvolution.org/stephen-goldstein.html
"'You cannot, in a normal cell culture, maintain the furin cleavage site,”'he told me. When the COVID-19 virus is replicated in a cell culture in a lab, he said, the furin cleavage tends to delete itself. A peer-reviewed paper, published in late April in Nature, noted that habit and identified seven other papers that found a similar deletion. [LINK: https://www.nature.com/articles/s41564-021-00908-w#author-information]
"So if researchers were using traditional methods and their preferred cell lines to try to force the virus to replicate, mutate, and change, the furin cleavage site would likely disappear.
"The gain-of-function proponents say this furin site is too well adapted for humans to be an accident. But Goldstein said the opposite is true. The cleavage site is imperfect, so odd, that it could have only been a freak of nature. 'No virologist would use that cleavage site,' he said."
LONG STORY SHORT, I proposed to my science magazine employers that they host a debate between, say, Goldstein and Deigin, Segreto, or another proponent of considering a gain-of-function origin. They declined: they seem to find Deigin and Segreto a little shady (and in any event, neither is a virologist).
Maybe you could host that debate. In the absence of hard evidence, it really does come down to scientists' informed opinions on the question of how SARS-CoV-2 sprang into the world so seemingly pre-armed to cause a human pandemic.
Zeynep, this is even above and beyond your normal (casual and profound) connection: "Looking at the post-molecular biology era, when we were more in a position to be the cause of a pandemic, the known incidence is that two out of three pandemics were completely zoonotic: the same odds that Nate Silver had assigned to Hillary Clinton winning the presidency in 2016." Bam.
More thoughts on this piece: "Virologists still largely lean toward the theory that infected animals — perhaps a bat, or another animal raised for food — spread the virus to humans outside of a lab." (https://www.nytimes.com/2021/05/27/health/wuhan-coronavirus-lab-leak.html)
I see some openings for further understanding, even lacking participation by China. For example, do people eat horseshoe bats? Do they house them nearby, perhaps to control insects? If not, that eliminates whole areas of inquiry and lets us focus on others.
Regarding Biden calling on intelligence agencies to produce a report: I took this to suggest a belief that we have more information than we have surfaced in the information stream. (Because finding stuff in information streams is a big part of what intelligence agencies do. And sometimes fail to do...) Recently we have seen news reports of the content of previously overlooked messages of various sorts, and the great sleuthing that noted the deletion of the sequences from the database and the finding of a number of them once researchers knew that they existed. It became like finding the car keys, not having to hypothesize the existence of the car.
Forensic homology?
Being more of an interested spectator than a stakeholder in identify with clarity the source of this global pandemic, I will follow your endeavors. Unfortunately, China's actions seem not to want or publicly identify your goal, and the desire of the world health community to solve this mystery with sufficient data. Assuming the origin is from the wet market, and China collected all the animals at this market, it is strange that they say they destroyed these animals rather than saving them from finding the source and bringing more clarity to this vector.
My concern and memory are that with the Spanish Flue, the second year caused a more significant loss of life, maybe through a more deadly variation of the flue. However, since the world will be the incubator for Covid in the next few years, and examples like the Delta variation, what are the rare odds that a new variation dominates but does not kill or kill millions?
In comparing airplane crashes and the efforts to identify the details around why this crash event happened. The goal being so that new actions are taken to either better train pilots, repair a broken part, create another safety break when the systemic system of safety has a rare flaw is a perfect analogy. I seem to recall a French plane crash in the South Atlantic that took years and millions of dollars to find the plane, concluding it was a pilot error. A few years ago, an Indonesian plane disappeared, and radar and satellite data showed it crashing somewhere in the Indian Ocean to the west of Australia. This plane and mystery may never be solved unless its actual location, recovery happens.
Today I read this article that points out an outsider's insider perspective on the professional standards at the viral lab and media rumors that would challenge her experiences.
Bloomberg article "The Last-And Only-Foreign Scientist in the Wuhan Lab Speaks Out."
"Virologist Danielle Anderson says half-truths have obscured an accurate accounting of Wuhan lab's functions, but she does think an investigation is needed to nail down virus's origin."
"Once a plane crash does occur, we don’t tell the investigators that planes are really really safe, so let’s not worry about it. In fact, the thoroughness of that investigation is exactly what makes planes really really safe, in the future: we figure it out and fix it."
I'm not sure the airplane safety comparison works here- airplanes are human-designed and human-built machines, under human control, and humans have the ability to fully reconstruct a failure sequence and directly address it. This is even down to the level of airliner CPUs being hardened against extremely rare but known failure modes- comic rays causing a digital bit somewhere to flip from 0 to 1.
In contrast, it can very difficult to understand and manipulate the biological world, including viruses, to the same level of precise causality. For the original SARS, the best we have found more than a decade later is a cave where bats have different viruses that contain all of the constituent parts of the virus.
Additionally, this argument almost sounds like great justification for pursuing gain-of-function research on coronaviruses after the 2003 SARS outbreak!