Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966 • Hacker News Board

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#221

Post by DiogenesKynikos » Sun, May 31, 2020, 8:04 PM UTC

yters wrote: post #220

DiogenesKynikos wrote: post #219

Earlier quoted context omitted.

> So, there is some sort of non accidental relationship between sars and sars2. Yeah, they're both betacoronaviruses. You've just discovered something called "common descent." Charles Darwin published about it in 1859. I'm sorry, but this is getting comical. You really have to step back and learn some basics about biology before you go on this dive into conspiracy theories.

Hmm, still not following. Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I blasted sars2 against sars and against ratg13. 88% coverage for the first and 99% for the second, so ratg13 seems to be a much more recent ancestor. - sars2 v. sars: https://blast.ncbi.nlm.nih…

> Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13?

I'm saying that it's complete nonsense to say that there's a (1/20)^7 chance of 7 amino acids matching. We're talking about viruses that are descended from a common ancestor, not random, independently distributed coin flips.

> ratg13 seems to be a much more recent ancestor.

RaTG13 is not an ancestor of SARS-CoV-2. The two viruses share a common ancestor.

> Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13?

ACE2 is a human protein. Neither SARS-CoV-2 nor SARS-CoV have ACE2. If you're talking about the RBD of the S protein, then note that the RBDs of SARS-CoV-2 and SARS-CoV are only 73% homologous, which is a pretty massive difference.

Stepping back for a second, you're diving down the conspiracy-theory rabbit hole with very little prior knowledge of the subject. That's just going to make you easy prey to a lot of nonsense. Really, instead of reading blogs that claim to have found the secret truth about SARS-CoV-2, listen to what respected virologists have to say about it. Do some basic background reading on virology and coronaviruses. Read some review articles from scientific journals.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#222

Post by yters » Sun, May 31, 2020, 9:06 PM UTC

DiogenesKynikos wrote: post #221

yters wrote: post #220

Earlier quoted context omitted.

Hmm, still not following. Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I blasted sars2 against sars and against ratg13. 88% coverage for the first and 99% for the second, so ratg13 seems to be a much more recent ancestor. - sars2 v. sars: https://blast.ncbi.nlm.nih…

> Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I'm saying that it's complete nonsense to say that there's a (1/20)^7 chance of 7 amino acids matching. We're talking about viruses that are descended from a common ancestor, not random, independently distributed coin…

I've done a bit of reading from the experts. I read the main debunking article about this lab theory, and personally did not really understand why the authors were so confident their evidence eliminated the lab theory.

- https://www.nature.com/articles/s41591-020-0820-9

Their two claims are:

1) ace2 binding is much better than humans can engineer with computer simulations

2) virus does not come from any known backbones

Regarding #1, I've found another article where the author was able to induce zoonosis from a feline coronavirus to a mouse by exposing the virus to mouse genetic material. So, the fact humans cannot directly engineer zoonosis very well does not preclude lab induced zoonosis.

- https://www.nature.com/articles/news030331-4

In fact, this is a theory posited at the end of another debunking article, which doesn't actually debunk that particular theory.

- https://www.livescience.com/coronavirus-wuhan-lab-complicate...

Regarding #2, as I mentioned before, it seems this line of reasoning is a non sequitur. A virus backbone used to create a bioweapon is exactly the sort of sequence you are not going to upload to NCBI.

The fact the reasoning does not seem very solid in what is considered the official and definitive debunking of the conspiracy theory is itself odd.

So, it is my reading of some respected virologists that in part motivates me down this rabbit hole.

Anyways, I greatly appreciate your feedback. I'll keep learning more about virology, and hopefully get some clarity on the whole matter.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#223

Post by DiogenesKynikos » Sun, May 31, 2020, 10:08 PM UTC

yters wrote: post #222

DiogenesKynikos wrote: post #221

Earlier quoted context omitted.

> Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13? I'm saying that it's complete nonsense to say that there's a (1/20)^7 chance of 7 amino acids matching. We're talking about viruses that are descended from a common ancestor, not random, independently distributed coin…

I've done a bit of reading from the experts. I read the main debunking article about this lab theory, and personally did not really understand why the authors were so confident their evidence eliminated the lab theory. - https://www.nature.com/articles/s41591-020-0820-9 Their two claims are: 1) ace2 binding is much better than humans can engineer with computer simulations 2) virus does not come from any known backbon…

The WIV is not a bioweapons laboratory. It's an academic research institution. Any gain-of-function experiments they would do would be aimed at understanding viruses, not creating weapons. They would use known backbones, not a virus nobody has ever heard of, that they've never even uploaded to a database.

I'm going to suggest to you that the reason you don't find the reasoning in the debunking to be solid is that you don't understand the field very well. I don't know what your specialty is, but imagine someone who has no experience in it. They might have a lot of weird conceptions about your specialty, they might have no idea how things work in your field, they might find a lot of things surprising. Things that you find obvious might seem dubious to a novice. The arguments made in the debunking are considered very strong by experts in the field. That's what matters.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#224

Post by yters » Sun, May 31, 2020, 11:56 PM UTC

DiogenesKynikos wrote: post #223

yters wrote: post #222

Earlier quoted context omitted.

I've done a bit of reading from the experts. I read the main debunking article about this lab theory, and personally did not really understand why the authors were so confident their evidence eliminated the lab theory. - https://www.nature.com/articles/s41591-020-0820-9 Their two claims are: 1) ace2 binding is much better than humans can engineer with computer simulations 2) virus does not come from any known backbon…

The WIV is not a bioweapons laboratory. It's an academic research institution. Any gain-of-function experiments they would do would be aimed at understanding viruses, not creating weapons. They would use known backbones, not a virus nobody has ever heard of, that they've never even uploaded to a database. I'm going to suggest to you that the reason you don't find the reasoning in the debunking to be solid is that you…

Yes, that is a fair point. I just wish the experts were better communicators to us lay people.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#225

Post by foldr » Mon, Jun 01, 2020, 11:05 AM UTC

wsgeorge wrote: post #198

foldr wrote: post #124

Earlier quoted context omitted.

And in Africa most transmissions are between heterosexuals. But you never hear the same rhetoric about irresponsible promiscuous heteros.

>But you never hear the same rhetoric about irresponsible promiscuous heteros. We did. Sort of. Heterosexuals weren't singled out for caution about promiscuous sex, because most of the public messaging assumed heterosexual relations anyway. But the emphasis was always on promiscuity.

No, you did not see rhetoric accusing heterosexuals as a class of being prone to promiscuous behavior. Unfortunately, even in 2020, it seems to be necessary to spend paragraphs and paragraphs explaining what homophobia is until people get it. Here is an article from 1987 that does some of the work:

https://www.latimes.com/archives/la-xpm-1987-07-20-me-2954-s...

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#226

Post by ekianjo » Tue, Jun 02, 2020, 3:36 PM UTC

koheripbal wrote: post #171

ekianjo wrote: post #84

Earlier quoted context omitted.

High risk but most infected have close to no symptoms which is nothing like AIDS which used to be a death sentence.

That's not accurate. "mild cases" is not the same as "no symptoms".

Read again: "close to no symptoms"

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#227

Post by TamaraBoyle » Wed, Jun 03, 2020, 10:11 PM UTC

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