Alina Chan Profile picture
8 Dec, 20 tweets, 6 min read
New perspectives piece in ⁦@NatureComms
Wonder what all these scientists could be talking about...
⁩“actors may be incentivized to be reckless if they believe they are unlikely to be held accountable for any accidents arising from their actions.” nature.com/articles/s4146…
"A key security challenge involves attribution: determining, in the wake of a human-caused biological event, who was responsible."

Any chance this is about COVID?

nature.com/articles/s4146…
"if an incident occurs.. near laboratories working on the causative agent, there is a greater chance of it being attributed to an accidental release."

Wonder which recent incident occurred near a lab working on the causative agent. nature.com/articles/s4146…
On "technical forensics: the properties and characteristics of the agent that caused.. outbreak may provide clues as to who made it and/or who was responsible for releasing it" - recommend reading @ScolesSarah article on the limitations of this approach. futurehuman.medium.com/how-do-we-know…
tldr technical forensics can be severely limited because scientists often do not publish their discoveries in a timely manner, which is exactly the situation we are in re: covid and the type of situation we anticipate in the future.
“Everyone who’s trying to engineer knows just as much as the people who’re trying to detect engineering,” says Plant. “So you have, functionally, an arms race. You’re never going to have completely the ability to detect something that’s engineered.”
Why would scientists, especially those engaging in covert research, start publishing all their pathogen data in a timely manner if they know that this can be used to hold them accountable for accidental leaks in the future?
It's fine to keep funding technical forensics R&D, but this seems, imo, to be a sizeable misunderstanding of why scientists can't tell even today where SARS-CoV-2 came from, nature or lab-based scenarios - if that is even what this article could possibly be alluding to.
The reasons why we cannot pinpoint whether SARS-CoV-2 came from a lab is not because our Machine Learning or other tools to detect traces of engineering are underdeveloped.
The reasons are (1) it is so damn difficult to get access to information regarding even research that was funded by the US for years. Case in point: RaTG13, collected in 2013, inaccurately reported sample history and data in Jan 2020, addendum in Nov 2020. nature.com/articles/s4158…
This is not at all a technological issue. This is a transparency issue. A human issue. No amount of machine learning is going to overcome this barrier.
(2) Politics in science, conflicts of interests, an aversion among scientists to engaging in politics.

Many scientists won't even voice the possibility of lab origins publicly. The majority of the public and scientists believe the scientific consensus is covid=natural.
How can scientists across different disciplines openly and rigorously analyze natural vs lab origins when, right from the start, one entire category of hypotheses is disparaged as harmful conspiracy theories?
usrtk.org/biohazards-blo…
Imo, ensuring an open, public platform for scientists (established and trainees) to analyze origins data/evidence is much more crucial than more technologies to detect engineering - which again is not at all the key to solving the origins of covid.
The solutions to this challenge are again not better forensic tech, but human ones. There needs to be a better way of identifying conflicts of interest other than self-declaration. There needs to be open editorial+peer review, open tracking of funding (organization, individual).
On a related note, (3) the ability to assemble and enforce, without delay, an international investigation by a team free from pre-existing relationships or interests that can compromise the credibility of the investigation.
Troubling that more than a year has passed since covid emerged and no international team of investigators has received permission to even go to ground zero or talk to doctors (reportedly silenced) or index patients. US journalists expelled from China. inews.co.uk/opinion/china-…
If another pandemic arises in the future under similar circumstances (no clear traces of engineering), my bet is that its origins are not going to be predicted by ML.

Advocate the powers that be to invest in better research tracking + accountability & investigation mechanisms.
Sometimes there's a temptation to think that if we throw enough millions of $$$ at technological solutions, we can solve the greatest challenges in the world.

But I don't think we are going to be able to machine learn, AI, or blockchain our way to the origins of covid.
Afaik internet sleuths have done more than any cutting edge technology or international investigation team to uncover key facts pertaining to the origins of Sars2. Story by @emmecola

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More from @Ayjchan

9 Dec
I was recently asked what I would like to see come out of SARS-CoV-2/covid origins investigations.

I would like to know that, the next time a pandemic like this occurs, the world is better prepared, better informed as to how to determine its origins and prevent future outbreaks.
I'm going to break down 3 key publications that I think relate to covid origins. What were the questions they asked to determine whether SARS-CoV-2 came from nature vs from a lab?

Are these approaches sufficient to prepare us for the next mysterious pandemic?
The 1st is the widely-read Proximal Origins article - a correspondence published in @NatureMedicine on March 17, 2020. How did the authors determine that "SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus"?
nature.com/articles/s4159…
Read 23 tweets
8 Dec
Estimated 76% Manaus and 29% São Paulo population infected by covid by October.

"These results confirm that, when poorly controlled, COVID-19 can infect a high fraction of the population causing high mortality."

science.sciencemag.org/content/early/…
In Manaus, the >70% attack rate is "above the theoretical herd immunity threshold.. Monitoring.. new cases and.. ratio of local versus imported cases.. vital to understand (how) population immunity might prevent future transmission and the potential need for booster vaccinations"
US has 15M confirmed cases, "probably, at best, diagnosing 1 in 5 cases" - former FDA commissioner Scott Gottlieb, Nov '20.

Rough calculation ~23% US population infected with covid by now + doubling time ~50 days according to @OurWorldInData + Xmas/NYE..

cnbc.com/2020/11/06/dr-…
Read 5 tweets
8 Dec
Different CDC, different covid test kit blunders. Except China already had the SARS-CoV-2 on Jan 3, 2020. apnews.com/article/china-…
*SARS-CoV-2 genome
Also, this was ~2 weeks before China told the WHO that the virus could transmit between humans, but they were already handing out contracts to buddies for test kit development & sinopharm started developing a covid vaccine once they got the SARS-CoV-2 genome.
From the AP article: “We did a brilliant job, we worked so hard,” said Gao Fu, the head of China CDC, in a videoconference in July. “Unluckily, unfortunately, this virus we are facing, it’s so special.”
Read 4 tweets
6 Dec
On the pangolin story that is still drawing breath, "(Shi Zhengli, WIV) said that if the intermediate host was the pangolin.. it’s possible the virus jumped from bats to pangolins outside China.. smuggled in from other Asian nations, including India."
theguardian.com/world/2020/dec…
Thankfully, before scientists go on a wild goose chase to sample pangolins in India, David Robertson (U of Glasgow), who was also interviewed, said, “We’re fairly confident the pangolins have picked up their virus, presumably from horseshoe bats, after being imported into China.”
If any pangolins need to be investigated, I recommend starting with the Guangdong pangolins confiscated in March, 2019. This is the only batch of pangolins with a CoV that has a SARS2-like Spike RBD. Many questions remain re: the sample histories and data. biorxiv.org/content/10.110…
Read 17 tweets
5 Dec
I'm hoping that one effect of the pandemic is that journals will start publishing peer reviews so that readers can quickly grasp the strengths and weaknesses of each paper.

Without published peer reviews, we need to rely on experts critiquing papers on twitter every weekend.
Peer reviews are performed by other experts in the same or similar fields, who spend hours to days reading and critiquing a paper.

This is real work. By highly skilled experts. That is also unpaid, no tangible incentives. Yet, not published unless a journal has open peer review.
It costs next to nothing to publish peer reviews online or as a supplementary file. But the value! Even people outside the field can see what questions the experts asked, were these addressed in the revisions? Were reviews fair, totally overboard, or negligent (just publish it)?
Read 5 tweets
4 Dec
"You may disagree with their unconventional approach, but the truth is that these people behave, to all intents and purposes, like a small scientific community: they search and analyze data, they share and discuss their findings and, more importantly, they make discoveries."
Timely piece by @emmecola on how a coalition of twitter users, several anonymous, have been at the front of investigating the origins and sample history of RaTG13 + connection to SARS-like cases among miners from a Yunnan mine full of bats in 2012. mygenomix.medium.com/the-origin-of-…
Their work and fringe (I say this positively) influence on scientists & journalists has led to measurable outcomes. Namely, this @Nature addendum, confirming that RaTG13=4991; was seq'ed in 2018, not post-covid; linked to severe respiratory cases in 2012.
nature.com/articles/s4158…
Read 9 tweets

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