I can say that I know Aussie scientists have been asked. I didn't respond as I'd just say, we need testing. Perhaps responses will be forthcoming in the next round of media outputs?
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I've now responded to The Conversation. To me, the heatmap in Figure 3A links 2019-CoV to bats, not snakes. Who reviews this stuff?
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Als antwoord op @edwardcholmes @stgoldst en
I was wondering.. JMV, for which this stuff was never in the wheelhouse, got taken over a little while ago. Noticed some language issues too. A shame for this journal (but no APCs)
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Wiley have a lot to answer for. They publish the paper AND write an editorial on it AND put out a press release entitled “Researchers Trace Coronavirus Outbreak in China to Snakes”.
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Als antwoord op @edwardcholmes @evogytis en
Is there any doubt the analyses are flawed and the conclusions erroneous?
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Als antwoord op @EvolveDotZoo @evogytis en
None on the basis of the data provided.
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Als antwoord op @edwardcholmes @evogytis en
It begs the question of whether the reviewers of this manuscript had the relevant expertise in molecular evolutionary analysis.
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Als antwoord op @EvolveDotZoo @evogytis en
And why the journal pushed it through so quickly, wrote an editorial on it and hawked it to the world’s press.
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Als antwoord op @edwardcholmes @EvolveDotZoo en
I have done these types of analyses - looking at how well codon usages of viruses match those of (known) hosts to train a model to predict putative hosts for novel pathogens. Good idea, but it can’t be done - rarely is the top match a know host and there is no meaningful signal!
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Als antwoord op @K_G_Andersen
Out of curiosity - given that ML-based projects on this especially aren't likely to slow down in the next 10 years, what do you think good work on this would look like? (I realize this might be a conversation for over beers instead of twitter)
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Oh yes, AI to the rescue
. Issue one - small training dataset and that's hard to overcome. But otherwise, integration of other data - trees, kmer profiling, restriction sites, host gene interactions, structures, known receptors, etc.
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Als antwoord op @K_G_Andersen
I'd love to pick your brain about this sometime when there's not a coronavirus pandemic
We're wrangling a proposal around this now, and I think I see eye to eye with you on a lot of this - we've struggled to figure out how to appropriately articulate what those data look like1 antwoord 0 retweets 1 vind-ik-leuk -
Als antwoord op @wormmaps @K_G_Andersen
(Happy to email that proposal over if it's of any interest)
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