Comment by timr | Hacker News Reader

Comment by timr | Hacker News Reader

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> First and foremost the central claim is that 5 potential restriction binding sites versus 2 means that SARS-CoV2 is non natural. That does not necessarily follow. Just as SARS-CoV2 is unusually infectious and damaging to humans it could just happen to have an additional 3 restriction binding sites. So there is nothing inconsistent with natural selection of viral characteristics, only a comparison between wild and lab viruses.

No, you've completely misunderstood the analysis. The number of restriction sites is not what is important. It's the location of the sites, and the spacing between them. This is suspicious, and has a high degree of variability, as is shown in Figure 3c. They also generated 100,000 random mutations to RaTG13 and BANAL52, and found that only ~1.2% and 0.1% of these, respectively, had restriction maps as deviant as the one found in SARS CoV2 (Figure 4).

The spacing here alone is suspicious, but couple with the number of synonymous (silent) mutations, and you're looking at an outcome extremely unlikely to be found in nature.

https://www.biorxiv.org/content/10.1101/2022.10.18.512756v1....

> They also generated 100,000 random mutations to RaTG13 and BANAL52, and found that only ~1.2% and 0.1% of these

This could also be selection pressure - right? Ie imagine 99,000 yield viruses that are non viable… you’d see the same behavior of rare traits being common.

It was an in silico experiment.

But regarding your broader question: there's no reason to believe that thesse viruses experience any selective pressure for the number or location of cutting sites of the particular enzymes being investigated here. They're bacterial enzymes, entirely unrelated to coronaviruses.

We've seen horizontal gene transfer in fish, was it aliens or natural selection?

Extremely unlikely events happen when an extreme amount of attempts are made, and natural selection amplifies them if they increase fitness

Your reply after reading the explanation is like you seeing a farm of branded cows and wondering if it was due to extreme natural selection that caused that.

From the layperson article:

> In wild viruses, these cutting/pasting sites are randomly distributed because there's no evolutionary pressure for the virus to be thusly cut and pasted in nature. In infectious clones, however, the humans behind the screen tend to modify restriction sites in a regular way. For any given restriction enzyme or set of enzymes, the set of all cutting sites is called the “restriction map”, and looking at these restriction maps helps us see the fingerprint of infectious clones.

> It turns out, the sticky ends produced by BsaI/BsmBI digestion of SARS-CoV-2 are all unique, non-palindromic, and all contain at least one A or T - all criteria either required or recommended for in vitro genome assembly.

Cows don't randomly develop brands on the order of 0.1% to 1% probability. There isn't a great analogy for this and your example, as well as the hyena one in another comment, are way overstating the case.

The explanation given is based on some premises that I'm not qualified to assess, and others I am.

One of these premises is that their work properly models reality, there seems to be a lot of well informed doubt by subject-matter experts.

Another is that an event with a probability of 0.1-1% is exceptionally rare, its occurrence thus being most likely artificial, and with that I disagree, by looking at endless counter-examples nature provides.

Is the fact that humans found some optimization a proof that any occurrence of it is man-made? I believe most people would say it isn't.

> One of these premises is that their work properly models reality, there seems to be a lot of well informed doubt by subject-matter experts.

The model is fine. There's no more "well informed doubt" than for any other paper. You can certainly debate the details of what they did, but none of this debate is substantial enough to invalidate the work.

What you're seeing is a group of people who have largely pre-judged the outcome, inventing reasons to reject an experiment that disagrees with their prior conclusions. This always happens, in any scientific domain. Nonetheless, there are also a large number of well-informed people who see this as an interesting result. If you don't listen to both groups, you will be misled.

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