
Deep learning to predict the lab-of-origin of engineered DNA - Katydid
https://www.nature.com/articles/s41467-018-05378-z
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ulam2
Can 48% accuracy or 70% top10 accuracy be used for attribution? How high the
accuracies have to be before this model is useful?

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dr_teh
Well, consider that if airplanes were 99% safe, nobody would fly. And the way
I understand it (not very well), the lab-of-origin discovery is based on
design choices rather than inherent factors. This means that it could be
copied to create false positives? Hopefully someone more educated on the
subject can elaborate.

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carbocation
Before someone unleashes their malignant creation upon the world, they'll make
sure their design choices look boringly common to this tool.

As an aside, the introductory paragraph is an extremely strong piece of
writing that gives a great intuition for their motivation.

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sampo
Are they talking about traditional transgenics, or also modern gene editing?

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gravelc
Neither - they are talking plasmids, which are a precursor to both. Plasmids
are circular DNA that are used in cloning. Cloning is the step-by-step process
by which a construct is engineered (e.g. promoter and gene sequence placed in
the correct orientation, along with a selectable maker in traditional GM).
Plasmids are amplified in bacterial systems to generate loads more, and a very
stable. Good for storing and passing around to other labs. Often the same
plasmid backbone is used in multiple constructs, hence why the approach in the
paper works. You could not use this approach to detect which lab CRISPRd an
organism (the tell-tale signs are not retained), but it would have some
effectiveness in traditional GM if the insert were sequenced, as some of the
lab-specific cloning decisions and mutations could be present.

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rgclark
Shades of “Blade Runner”.

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curiousgal
Tangent: I wish papers that get published contained a section with the
reviewers' notes.

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sampo
> I wish papers that get published contained a section with the reviewers'
> notes.

At least the journals published by the European Geosciences Union publish the
whole review process in the open. Reviewers' comments, and authors' responses
to them.

[https://www.egu.eu/publications/open-access-
journals/](https://www.egu.eu/publications/open-access-journals/)

(When you open the view to any article in any of those journals, you need to
click on the "Peer review" tab, and you get to see the original manuscript as
"Discussion paper", and all of the review process.)

