Comment by yellowcake0 | Hacker News Reader

Comment by yellowcake0 | Hacker News Reader

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> It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome.

You could never convince me that these restriction enzymes were picked blindly, no bioinformatician I have ever met does science this way. There is a preliminary period of exploratory data analysis which is done before any hypothesis is put forward, and data dredging and leakage are rampant in the literature.

That's not to say that the spacing of BsaI/BsmBI restriction sites isn't noteworthy, just something to keep in mind.

To your point however, could someone comment on the suitability of BsaI/BsmBI for the in vitro assembly of synthetic coronaviruses? Is it all just about finding sites in the genome at the right locations which can be turned into restriction sites without disrupting any existing functional genetic elements? or is there more to it than that. If a research team were to come along and decide they wanted to engineer their own coronavirus, how likely would it be that they would choose these restriction enzymes?

> To your point however, could someone comment on the suitability of BsaI/BsmBI for the in vitro assembly of synthetic coronaviruses?

These are very commmon enzymes. Perhaps the most common today.

The GP comment is sort of misleading...you wouldn't just pick enzymes at random to do this analysis. You'd pick the enzymes in common use. These count.

> Is it all just about finding sites in the genome at the right locations which can be turned into restriction sites without disrupting any existing functional genetic elements? or is there more to it than that.

You can add or remove sites using different techniques, such as PCR mutagenesis.

> If a research team were to come along and decide they wanted to engineer their own coronavirus, how likely would it be that they would choose these restriction enzymes?

Highly likely.

> The GP comment is sort of misleading...you wouldn't just pick enzymes at random to do this analysis.

I said pick blind, not at random. I recommend reading https://info.umkc.edu/drbanderson/p-hacking-and-the-problem-...

I know what p-hacking is. There's no reason to believe that they've done that here. The choice of enzymes was motivated by the logic they outlined in the paper, the enzymes chosen are some of the most popular today, and the authors are completely forthright that the choice might affect the outcome.

To fairly make a critique like that, you need to have at least some evidence that a selection bias was applied for no other reason than to affect the p-value. Otherwise, literally every study can be accused of "p-hacking". Here, there's a very good, obvious explanation for the choice that they made, and therefore all you can really say is that the results might be different if you looked at a different set of enzymes.

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