This is an awesome writeup that really helped me understand what's going on under the hood. I didn't know, for example, that for the limited number of PTMs AF3 can handle it has to treat every single atom, including those of the main and side chain, as an individual token (presumably because PTMs are very underrepresented in the PDB?)
Thank you for translating the paper into something this structural biologist can grasp.
It's true that Science is very invested in this bad (for everyone else) publishing model, and I suppose if somehow, by omission, they managed to convince the population that open access is inherently scammy, that's all the more convenient for them. I wouldn't necessarily group Derek in with that, though, and he's not wrong about this.
This topic has broken the brains of so many otherwise reasonable people. Is a lab leak possible? Of course it is. But the purported evidence for it is so weak, repeated by the same cranks who seem to have made up their minds.
Also, it's not like the authors of the Nature Medicine paper thought one thing and wrote another. Read their correspondences! Their thoughts evolved over time. It's almost as if that's how science is supposed to work.
From the original paper:
"Although the evidence shows that SARS-CoV-2 is not a purposefully manipulated virus, it is currently impossible to disprove the other theories of its origin described here."
And
"More scientific data could swing the balance of evidence to favor one hypothesis over another."
But there was no new evidence at that time. What there was though, was discussions on how a lab origin's negative impact on research and future funding! You can read more about some of their conversions before and after the paper was published here: https://public.substack.com/p/top-scientists-misled-congress...
> Wrote Andersen on February 1, 2020, “I think the main thing still in my mind is that the lab escape version of this is so friggin' likely to have happened because they were already doing this type of work and the molecular data is fully consistent with that scenario.” A few days later, he and the other authors were searching for a plausible intermediate host such as a pangolin that would allow them to refute the theory.
> That line, especially the “friggin’ likely,” has been the standout quote from the 140-page document. (Taibbi headlined his summary, “‘So Friggin' Likely’: New Covid Documents Reveal Unparalleled Media Deception.”) But there are a few things that the screenshot quote elides. One is the specific context in which was said. ... I don’t read this as a conversation between people who all know, or even suspect, that COVID didn’t come from nature. It’s a searching discussion — an argument in some ways — about the structure of the virus itself: whether it looks like it was engineered in some way or a product of natural evolution. ... The “friggin’ likely” is not a secret admission of wrongdoing. It’s a scientist talking to himself and his (skeptical) peers, saying, this is my assumption, this is what we need to test. ...
> If you keep reading though, a funny thing happens: the scientists get new data and start revising their conclusions. ... This conviction seems to have grown among the authors over the course of February. On Feb. 25, Holmes sends new data about a virus in a Yunnan bat from March 2019. Garry says: “Holy crap.” Andersen, revising his conclusion, says it “provides a template for how all of this happened in animals.” ...
You write "no new evidence" but in the link I gave, "Feb. 25, Holmes sends new data about a virus in a Yunnan bat from March 2019", and the Slack history shows it was new evidence for them.
> "Feb. 25, Holmes sends new data about a virus in a Yunnan bat from March 2019"
But the Furin cleavage site is missing from this bat virus which the authors speculated the following after Holmes shared it:
In reference to it, Holmes said, “Bob [Garry] said the insertion was the 1st thing he would add.”
“Yeah,” agreed Andersen, “the furin site would be the first thing to add for sure.”
Garry explained how easy it would be to engineer the virus. “Transmitting a bat virus like RatG13 in HeLa cells and then asking your graduate student to insert a furin site…” he wrote. “It’s not crackpot to suggest this could have happened given the GoF [gain of function] research [which increases infectiousness] we know is happening.”
So no the virus from Yunnan only fueled speculation, it did not provide evidence ruling out a lab origin.
Silver's argument wasn't that the scientists secretly knew it was the lab leak; it's that there was a lot more uncertainty than the view that they published. And that became a problem because journalists used their paper to push misleading information that the lab leak was right wing conspiracy instead of a very possible scenario.
Agreed on all counts, though it's important to note that this protein has bacterial homologs that almost definitely have the same function (5'-3' RNA ligase activity).
>Ridiculous not in a political sense (I have no strong feelings one way or another about the economic fates of career writers) but in the sense of being incoherent.
It is not incoherent if you believe art to be an expression of the human condition. You still need humans in the writer's room to know what they want the audience to get out of a show. That is not something that ChatGPT can understand.
Also, maybe people should have some feelings "about the economic fates of career writers." Who are we even building this hyper-efficient economy for?
Yeah, this. As humans and as the inventors of these technologies, we get to decide what kind of values we uphold and how our politics and policies should reflect them.
These think pieces that subscribe to an unspoken underlying technological determinism are so disgusting to me, they have a really narrow and pathetic view of what it means to be human (it mostly boils down to "economic agent") Half the time I wonder if the authors themselves even have requisite humanity, and I also wonder if the obsession around digital technology is partially driven by our having made machines of ourselves in the first place (all we care about is economy, work, etc. We've lost the old notion of the "human spirit" at great cost).
More people in power and decision making positions need to start broadening their reading lists with Goethe, William Blake, Novalis, and other awakened poets and start letting some of these imaginative ideas about humanity's potential drive their lives more than purely economically motivated crapped out thinkpieces.
Make sense. Plastics are notorious for absorbing in the UV range- for most useful spectroscopy experiments below ~400 nm we have to go straight to quartz cuvettes.
Yes. I've often wondered about how previous generations got certain things so wrong, but this is the first time I've been fully aware of a revolution taking place right under my nose and I feel mostly powerless to do anything about it.
Even if mining all of the lithium and copper weren't such a disastrously extractive and exploitative process, big personal steel boxes would still be an awful mode of transportation for most people. Our insistence on building infrastructure such that cars are the only truly viable method of getting around diminishes my enthusiasm about what is otherwise amazing technological progress.
reply