I still have faith in preprint servers though. Or self-publishing in the scientific writing form, instead of unorganized blog rant.
I'm not sure I buy the lab leak theory -- and certainly not solely on the basis of the information presented in this article alone -- but I do believe it's worth further investigation.
And we know lab leaks do happen; safety processes in even highly-regulated labs seem to be severely lacking. Calling attention to that, as well as the dangers of gain-of-function research (especially when considered in context of poor safety processes) is IMO critical.
At least this person has a reasoning and stands behind it, that's heads and shoulders above the tactics of those who want to bury this.
The author argued in section "weirdness 1" that the phylogentic tree implies the omicron strain is directly related to an ancestor genome from Spring 2020. I have the following concerns:
the tree is based on https://nextstrain.org/ , a database initially introduced in 2018 [1]. This is a great data source. However, for COVID, nextstrain naturally bias towards the more viable biosamples. In other words, COVID strains in wild animals such are going to be underrepresented, if represented at all. And if so, the large sequence divergence is surprising but not a direct indication of lab leak. The author can supply with a rough overview of sequencing sources of nextstrain to counter this. Or better, it would be good if the author can compare with, or cite existing literatures, phylogenetic trees of other epidemics and demonstrate that the sequence divergence is much larger than what we would expect from wild animal reservoir.
"weirdness 2" has a stand, but it should be accompanied by silent/functional mutation ratios in other COVID strains since synonomous mutation could be not entirely silent if translation efficiency is affected (correct me if I'm wrong).
Briefly on one other point, "weirdly it's exactly mice, not other animals": we use mice as lab animals for a reason. They are somewhat similar to human in terms of physiology. Therefore we can expect that they could be more prone to COVID infection, aren't we?
editted to add one more sentence: from a peer review aspect, this blog is beyond terrible and I'd probably have 10 major conerns listed if it comes in as a PR.
[1] https://academic.oup.com/bioinformatics/article/34/23/4121/5...
The "requests" I made was rather harsh, e.g. it might be impossible to check nextstrains's sequencing sources, if this is a real manuscript revision. I honestly probably won't question as harsh if it's a writting for a different topic.
However, given that the author is trying to illustrate a not-very-likely scenario, which being, not only that there's a major lab leak, but also someone has engineered a not yet fully understood non-trivial virus genome to alter its function as desired (note that COVID doesn't have a well established animal model. It would be hard to test a engineered virus even if it exists. In this case, would you assume that it's continuous lab "leak" and only the omicron strain was a success? And if yes, how could all other strains went undetected at all in the past 2 years?), I think scrutiny is justified and should be expected. It is against several odds and you really need some strong evidences to rule out other possibilities.
I don't even remotely have the expertise for that, if applicable others would have to do that. But thanks a lot for elaborating!
That original argument is interesting and is a surprising obervation to me, and I would love to read a well-written piece on that. Just keep in mind that "statistically unlikely" doesn't immediately mean "it's unlikely", you might have used the wrong presumption (in this case, silent mutation being not really silent).
In my opinion, the immediate flagging is a symptom of the hostility of even discussing the origins, lab leak or not.
I wanted to see how the post evolved as I read the article and looked into each linked source's motivations, so I made a note of the points (14 after 10 minutes) specifically because I felt there would be a lot of biased discussion.
The instant popularity of the post could have three factors: multiple votes from one source, individuals already well-versed in disease propagation and clandestine government action who support more visibility in the post, and people who believe the post could have merit without actually putting a great deal of their own research into the sources.
I'm in the fourth camp: agnostics. That's why I haven't contributed to the popularity of the post. However, two years of hearing about this disease does a lot to build resent for armchair epidemiologists.
In this case I took my time fully reading it before posting it, but not being a biotech person I posted this here also because I was interested in criticism of flaws I would have no chance of not overlooking. But just flagging it isn't that. It doesn't tell me this article is bad, it tells me too many people aren't acting in good faith, so that raises the question why that is.
Trying to turn it around on others by speculating on what they might have done (i.e. why they upvoted it, if they read it), doesn't change what was definitely done (i.e. flagging it without any substantial criticism).
(For the record, I still do believe the various lab-leak theories have legs, and should be discussed and investigated, even if this particular article ends up being unconvincing.)
And I wasn't surprised.
That's a wild state of affairs.
.. And it looks like I wasn't the only one.