Greg Tucker-Kellogg@gtuckerkelloggDad scientist. Biology prof in Singapore post biotech industry career. Musician on the side. Occasional tweets in Chinese. (he/him) 1.2970723339079715, 103.765121 Joined February 2008
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That's true even though rRNA depletion uses sequence hybridisation in the process. The applications with a market tend not to need species-specificity beyond the level of kingdoms, and near universal rRNA primers have been used for over 40 years. 12/
Genomic DNA depletion kits for these kinds of applications are based on broadly shared properties of eukaryotic DNA. rRNA depletion kits are based on broadly shared characteristics of rRNA. Generally speaking, these aren't species-specific 11/
which brings us back to @BiophysicsFL's question. What makes me so sure? I'm about 99% sure such kits didn't exist, about 99.9% sure Gao et al didn't use them if they did exist, and 100% sure the critique is entirely motivated reasoning 10/ en.wikipedia.org/wiki/Motivated…
I ignored it for a while, but people kept doubling down, so I wrote a thread about why it was almost surely a completely misguided critique. The kits needed to make the critique sensible weren't used (and didn't exist). 9/ twitter.com/gtuckerkellogg…
The critics (including prominent LLH advocates like Justin Kinney, Alina Chan, Alex Washburne, and Richard Ebright) argued that the report's observations of high animal/low human DNA were irrelevant because *human DNA was removed*, as Gao said right in the preprint 8/
Alex, @flodebarre, and their colleagues had identified some samples with very high amounts of wildlife trade nucleic acid and extremely low or non-detected levels of human nucleic acid. How should that be interpreted? 7/
None of that is surprising. What was surprising (to me) was how people who favoured a Lab Leak Hypothesis (LLH) focused on a particular passage from Gao et al to criticise the @acritschristoph et al analysis 6/
This ran directly against the Chinese government's claims that there was no wildlife trading at HSM, and against Gao's minimising of animal representation in the 2022 preprint. This is a contentious area, so people went right to the mattresses. 5/
While the data is three years old and the preprint over one, the data had never been available. The limited analysis that the report authors were able to do in a short time with what data they had pointed to a lot of DNA from illegal wildlife trade at the market. 4/
Background: Last week, in a widely-covered report, @acritschristoph, @flodebarre, and others described their analysis of sequencing data from SARS-CoV-2-positive environmental samples collected in early 2020, and discussed in a February 2022 preprint by Gao et al. 3/
The broad context is Covid origins, and the specific context is environmental sampling data taken at the Huanan Seafood Market (HSM) in Wuhan China, in early 2020. But you don't have to care about that: the real topic is motivated reasoning and how it takes hold 2/
Have you ever thought about how "motivated reasoning" appears, and how it poisons rational discourse? I've got a doozy of an example in a very niche thread where I also address @BiophysicsFL's question about my putative overconfidence. 🧵1/ twitter.com/BiophysicsFL/s…
An important, detailed, and even-handed thread. twitter.com/MichaelWorobey…
@MJnanostretch @BiophysicsFL @ydeigin It didn't exist, MJ. Here endeth the lesson
Weizmann Institute @WeizmannScience6 hours ago
We, at the Weizmann Institute of Science, are ashamed of, and dismayed by the Israeli government, who is threatening to crush all the conditions for the existence of a healthy civil society, and to act contrary to the law and the court’s order. (1/6)
@BiophysicsFL @ydeigin What concerns me is the gullibility of scientific readers who read those words and thought Gao was using some sort of human DNA eraser. twitter.com/gtuckerkellogg…
@BiophysicsFL @ydeigin In other words, those clinical microbiome human DNA-removal kits in 2020 were making more of a marketing claim (can remove human DNA) than a scientific one (specific to human DNA, and not other animals)
@BiophysicsFL @ydeigin EVEN IN THAT KIT, they claim to remove human DNA because it's meant to be used on human microbiome samples. The kits available at the time were not species-specific. Some of them also marketed as human DNA removal were intended for clinical use.
@BiophysicsFL @ydeigin They didn't selectively remove human DNA because, as Bauer correctly observes, it wasn't possible. It may be becoming possible, but I doubt even the makers of that brand new kit have done the comparative genomics to make that claim
@coreyum @MJnanostretch @stuartjdneil Not sure that "basic logic" hold up if they left out the samples with the animal DNA.
@MJnanostretch @stuartjdneil You answered the question better earlier. With "DNA proof of many species at SW corner of market" with "obvious relevance to origin", why were *those* samples selectively left out of the origins analysis in Gao et al?
@coreyum @MJnanostretch @stuartjdneil What positive evidence of human shedding is there? I don't there's any question humans at the market were infected, but I don't recall that discussion in the paper.
@coreyum @MJnanostretch @stuartjdneil They should have collected samples more quickly, but that's another matter.
@coreyum @MJnanostretch @stuartjdneil No, not if the place was closed and they collected samples from more relevant locations later (as they did)
@MJnanostretch @stuartjdneil So why did Gao et al not include any samples after 1 January? They don't offer a reason, yet they draw Figure 4 based on just those samples.
@DavidBahry @jeremyvancleve @EckerleIsabella Farrar and Daszak (and the-scientist.com) were referring to studies that provided data to support the estimate.
@coreyum @MJnanostretch @TheEthanIverson @stgoldst Notice they also switched primers after 12 January. So it may be that they were having a problem with their primers.
@coreyum @MJnanostretch @TheEthanIverson @stgoldst No, the NGS+ is meaningful. No reason to throw them out.
@coreyum @MJnanostretch @TheEthanIverson @stgoldst All the PCR-/NGS+ samples were collected the same day. It seems most likely to me this was degradation *during* sample collection and handling on that day.
@scotub @MJnanostretch @stuartjdneil If they don't release the data and don't include all the relevant data in their analysis, why even accept their conclusions?