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The lab-leak hypothesis is meta-scientific. When it was first tossed around, the lab leak hypothesis generated two predictions: 1. We would find evidence that
by throwawaymaths 4y ago
The lab-leak hypothesis is meta-scientific. When it was first tossed around, the lab leak hypothesis generated two predictions:
1. We would find evidence that someone was doing experiments on furin cleavage sites in coronaviruses.
2. We would find that the furin cleavage site matched a known sequence.
We did not find 2, which should have been easy to find. Eventually, we found 1, since a rejected DARPA grant proposal affiliated with the lab in Wuhan emerged.
Then, we found 2!! with a plausible explanation of why no one had found it earlier -- you had to turn on "patented sequence search" on NCBI blast, which is turned off by default. An easy mistake to make. As a professional biochemist for a decade I had no idea that blast had a patent sequence search, much less that it was turned off by default (which, btw is a sensible setting).
The scientific method says given a model it should make independent predictions (ideally unlikely) which are later verified. The evidence for a lab leak should be considered relatively strong.
- whatshisface 4y agoSomeone should contact the patent holder and let them know they're being infringed upon. ;)
- throwawaymaths 4y agoThat would be, ironically, moderna. Will the patent court award them negative damages? On a more serious note, to stave off conspiratorial thinking, it should be "not crazy" that a moderna furin sequence appear. If I told a biochemist to go and insert a furin cleavage site into a virus, that grad student would do an NCBI blast search and get a list of all sequences. Maybe they are more knowledgeable than me and did know that patent search was enabled (or maybe they were used to ripping off parents :| -- I'm anti-patent myself so this is not an indictment of the general process). Then that library of say a few hundred sequences is applied. Then the grad student, say, drops the 96-well plate with the virus samples, and gets infected -- It should not be surprising that the moderna sequence is the winner in the competition amongst the viruses in that grad students body because moderna has engineered that site to be a very effective site, and we know that having the furin cleavage site is correlated to virulence, so "natural selection" kicks in.
- EA_itsinthegame 4y agoIs the founder of Moderna meta-scientific for claiming that COVID leaked from a laboratory? Or would that be too ironic?
- Izkata 4y ago> On a more serious note, to stave off conspiratorial thinking, it should be "not crazy" that a moderna furin sequence appear. If I told a biochemist to go and insert a furin cleavage site into a virus, that grad student would do an NCBI blast search and get a list of all sequences. The weird part is, prior to 2020, a BLAST search only results in Moderna patents. There wasn't anything there for them to copy from. https://arkmedic.substack.com/p/how-to-blast-your-way-to-the-truth https://arkmedic.substack.com/p/how-to-blast-your-way-to-the...
- throwawaymaths 4y agoI presume moderna had a small army of DNA synthesizing robots to cover and optimize the shit out of that sequence from whole cloth.
- antiverse 4y agoBack up a bit. What the fuck is "meta-scientific"?
- __alexs 4y agoIt's a polite way of saying that it was nonsense.
- rwmj 4y agoBut the comment seems to go on to say it's not nonsense.
- decebalus1 4y agoIt means pseudo-scientific bullshit
- nopenopenopeno 4y agoIt’s literally a hypothesis. It’s in the name.
- throwawaymaths 4y agoI'm using it to refer to applying the scientific method to the process of science itself.
- EA_itsinthegame 4y agoYou are intellectually and scientifically dishonest by presenting the lab leak like this. Take your own theory and argument for it. You could only stare at a honest list of for and against regarding the lab leak, and conclude that lab leak is meta-scientific. When you call for evidence, remember the information blackouts and destruction of samples ordered by the Chinese. Chinese citizens and scientists were dissapeared for following the science and doing proper journalism. To conclude their legacy as meta-scientific is ugly. That is not my science, but maybe that is your job here...
- kolanos 4y agoFrom June 9: > Over two years after the coronavirus was first detected in China, and after at least 6.3 million deaths have been counted worldwide from the pandemic, the World Health Organization is recommending in its strongest terms yet that a deeper probe is required into whether a lab accident may be to blame. > That stance marks a sharp reversal of the U.N. health agency’s initial assessment of the pandemic’s origins, and comes after many critics accused WHO of being too quick to dismiss or underplay a lab-leak theory that put Chinese officials on the defensive. [0]: https://www.wivb.com/news/world/who-covid-origins-unclear-but-lab-leak-theory-needs-study/ https://www.wivb.com/news/world/who-covid-origins-unclear-bu...
- nopenopenopeno 4y ago
- edvards 4y agoCan you tell more about 1 and 2, maybe with some sources added? this is pretty big
- Izkata 4y ago2: https://arkmedic.substack.com/p/how-to-blast-your-way-to-the-truth https://arkmedic.substack.com/p/how-to-blast-your-way-to-the... Search for "moderna" then scroll up a bit.
- dekhn 4y ago"Using BLAST is easy". Yes, it's very easy to use BLAST to convince yourself of something that is not correct. It's a power tool being used by idiots most of the time, no wonder fingers get cut off.
- throwawaymaths 4y agoBefore implying it's not correct, do the math yourself. Calculate the relative drift among natural sequences and see if the moderna sequence is an outlier. How many single point mutations would it take to get from a known sequence to the moderna one.
- dekhn 4y agoDo what math now? I spent 10 years as an academic doing bioinformatics, with deep expertise in BLAST (I helped demonstrate that BLAST E-values accurately represent homology). If you look, he shows some pages with resuults where the E-value is 282. Normally, an evalue should be 1e-2 or better (ideally 1e-6) before you start making ANY claims. I've seen hundreds of examples where a person did the math, convinced everybody they were right, and either subtle errors or mistaken assumptions meant the work was useless. These days, if somebody starts with "Here, I'll show you how to use blast to demonstrate that the lab leak hypothesis is true", my priors say "most likely just garbage".
- 4y ago
- NationalPark 4y agoCan you link some sources here? Call me skeptical, but if the evidence is as convincing as you make it sound, then it implies a pretty widespread conspiracy among experts (of many countries and affiliations) who would understand the implications yet are deliberately mis-communicating via their podcasts, news appearances, papers in famous journals, etc. Are there any papers published on this or is it just in the book that the authors of this article are selling? I'm not sure if I'm confusing this author with a Matt Ridley who seems to be an eccentric but minor British noble who writes about fringe climate change ideas? Edit: Ok I figured out the source of the claims, it's the Alina Chen (I didn't realize she was co author) stuff. And it is indeed the Viscount Matt Ridley himself!
- throwawaymaths 4y agoYou can find the primary source for the DARPA leak on hn; if you care to verify that the sequence comes from a patent yourself directly from primary sources, you can find instructions on how to do that on hn too. I've done the search myself, it's real. I can't provide direct sources for the fact that these predictions preceded the discoveries, but I can tell you they ran through my head, and others I talked to, and the lack of a sequence match bothered me. If you want to get meta-meta-scientific I would not be surprised if there was at least a blog post by someone out there saying "if it was a lab leak, where's the sequence match?" Out there that preceded the sleuth who found it hidden in plain site (behind an NCBI search option) Edit: I have not read the ridley/chen book, I know most of the stuff from when they were emergent reports by reading this site and applying my intuition as a former biochemist (and some of my actively working biochemist friends) ti judge relative merits of hypotheses.
- etcet 4y agoIf you've done it could you link to or provide instructions on how we may reproduce your findings rather than just saying "the truth is out there"?
- throwawaymaths 4y agoYeah, sorry, here it is: https://arkmedic.substack.com/p/how-to-blast-your-way-to-the-truth https://arkmedic.substack.com/p/how-to-blast-your-way-to-the...
- fabian2k 4y agoI don't find any arguments around the furin cleavage site convincing. This kind of cleavage site is pretty small and the number of variations that have good efficiency is limited. The presence of a specific furin cleavage site is not clear evidence of genetic manipulation.
- throwawaymaths 4y agoEvidence comes with context. We're asserting that something like this would be found. Then we found it! After not finding it initially, even. The inability to find it initially should tell you something about the general evolutionary drift around these sites to begin with.
- bandyaboot 4y agoI haven’t been fixated on this by any means but I remember reading an article months back that looked at the timeline and locations of the early cases and compared them against the locations of the market and the research facility. I came away thinking that the animal market hypothesis seemed much more likely than the lab leak.
- mikeyouse 4y agoYep - there are a ton of such points of evidence. The strict "lab leak" proponents have essentially made an unfalsifiable hypothesis akin to the intelligent design people's "God of the Gaps" where each time there's new research that disproves a core assumption, that just means the conspiracy goes deeper. I linked it above, but aside from the fact that every other pandemic we've seen came about the same way, there's a ton of specific evidence from this pandemic: https://protagonistfuture.substack.com/p/natures-neglected-gof-laboratory?s=w https://protagonistfuture.substack.com/p/natures-neglected-g... Including the timeline/locations of the earliest cases: https://zenodo.org/record/6299600#.YjSWqDUxmUk https://zenodo.org/record/6299600#.YjSWqDUxmUk One thing the lab leak crew haven't been able to answer is how there could possibly be two different lineages at the market -- which you'd 100% expect from multiple spillover but is essentially impossible if your working theory is that an infected lab worker brought it to the market.
- secondcoming 4y agoBrought what to the market? Themselves or animals from a lab?
- mikeyouse 4y ago> Infected worker To be honest, I hadn't even encountered the idea that lab employees were what, selling infected animals at the market? Is this a real thing people are arguing? Who even comes up with this stuff.
- coupdejarnac 4y ago
- deleted 4y ago[deleted]
- ttpphd 4y agoSorry but the post above is unscientific sophistry. Science is about weighing competing theories by examining the relative strength of evidence. The evidence is strongly in favor of zoonotic origin. What's posted here is an exercise in confirmation bias, not rigorous scientific thinking.
- throwawaymaths 4y agoGiven that I used to believe the zoonotic hypothesis the assertion of confirmation bias is a bit surprising to me.
- ttpphd 4y agoThe comment this is a reply to is what's known as rhetoric. The goal of rhetoric is to persuade the audience in the absence of logic or evidence. The comment is offering "testimony of conversion" which is not scientific.
- kaitaincps 4y agoNot really. The poster is saying they used to believe X but was persuaded subsequently that ~X was more likely. This seems to indicate at least a recent pattern of avoiding confirmation bias.
- ttpphd 4y agoIf you find "I changed my mind" to be the message, then you agree with me that it is rhetoric. It is testimony of conversion.
- secondcoming 4y agoAren’t you assuming that you’re being shown all the evidence?
- ttpphd 4y agoI'm very clearly and obviously doing the exact opposite
- gmiller123456 4y agoRather than just saying "we found..." and expecting people to take it at that, provide sources. If I went and looked up everything anyone claimed, that's all I'd ever do.
- flobosg 4y agoYou can BLAST that furin cleavage sequence and find matches in other non-patented sequences, though. Here’s one from 2011 (bases 286 to 304, reverse complement): https://www.ncbi.nlm.nih.gov/nucleotide/DN616748.1 https://www.ncbi.nlm.nih.gov/nucleotide/DN616748.1
- TameAntelope 4y agoWe did not "find" 1 from any rejected DARPA grant proposal, that's nonsense and completely unsupported by the actual grant proposal. You cannot presume one leads to the other, that'd be like trying to cite a patent on a perpetual motion machine as conclusive proof perpetual motion machines exist. I would argue that continuing to state what you have here qualifies as disinformation, and think HN should remove it immediately, lest HN become yet another breeding ground of this kind of anti-intellectual memetic drivel.
- YeGoblynQueenne 4y ago>> The lab-leak hypothesis is meta-scientific. When it was first tossed around, the lab leak hypothesis generated two predictions: When and where were those two predictions published? Can you give a link?