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Old 1st June 2021, 06:19 PM   #841
RecoveringYuppy
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Originally Posted by Myriad View Post
If the natural mechanism of protein formation can't overcome the repulsive changes, then the virus can't replicate that protein when it infects a cell. In which case it can't function as a virus.
Having tried to google this a bit I realize that it may not be a question of whether the protein formation mechanism can produce them but whether mutations would be more likely to move away from those configurations rather than toward them. But I also realize I'm unlikely to find an answer to this via google with my level of understanding.
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Old 1st June 2021, 06:21 PM   #842
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Originally Posted by RecoveringYuppy View Post
Is this verifiable? It seems like this point would be very persuasive in favor of recombination in nature so would lead to a greater consensus on this issue. I was under the impression this had been looked for and not found.
Yeah, it's verifiable. The elements are there and a lot of recombinant events take place in the bat population. Even the pangolin gene segment can be found in the horseshoe bats in Yunnan.

But the sequence all in one bat has not been found. That's my understanding of it anyway.

I'll hunt back in the thread for the citations.
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Old 1st June 2021, 06:52 PM   #843
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Try here and this paper angrysoba actually linked to: Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

It's hard to keep going back through the thread to find stuff. There were 2 lines of discussion, one about this "generalist" CoV in horseshoe bats and one that discussed finding a regular soup of coronaviruses recombining within the bat population and it included RNA from pangolin CoVs.
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Old 1st June 2021, 07:09 PM   #844
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Thanks very much. Hope you didn't do that on my account, I'm perfectly willing to traipse through the thread if I care enough.
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Old 1st June 2021, 09:31 PM   #845
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Originally Posted by Skeptic Ginger View Post
OK here it is on page 4 and there's nothing new there, neither is there some post with me siding against Dalgleish. I don't see I even replied to that particular post but I didn't look past page 5.

Here's the quote from your citation:

From your link, so claims Mr Racaniello:We know that is bull ****. It's not impossible and that particular attitude is what Dalgleish alluded to when he said no one wanted to look at the lab accident hypothesis a year ago and they dismissed the paper out of hand.

This is how that is described in the Daily Mail:

I'm not claiming this paper is going to be the definitive smoking gun. I haven't even seen it yet. But I am interested in critiques of their work.
No, I don't think you replied to it, but I only remember the claims that were made.

I assume that these counterclaims remain as well:

Quote:
"No scientist or group of scientists created this virus in a laboratory. That would require insight into [viral] pathogenesis and protein engineering that does not exist," said Robert Garry, Ph.D., virologist at Tulane University.

Garry explained that much of the genetic material of the virus that caused COVID-19 is similar to that found in viruses sampled from animals, and was unknown to science until after the pandemic, ruling out the possibility the virus was created beforehand in a lab.

The genetic material and genetic changes to the novel coronavirus are "all what you would expect from natural evolution and an animal source," said Amesh Adalja, MD, infectious disease fellow and senior scholar at Johns Hopkins Center for Health Security.

"There've been multiple rumors and conspiracy theories," he said. "And I do think you'll probably see more."
The thing is, whenever there are "made-in-a-lab" claims, you seem to think they are worth investigating. Whenever you find someone saying, "The virus wasn't made in a lab" you say, "Strawman! Nobody claims that! This is an attempt at misdirection because the claim is it escaped from a lab."

It seems to me that the virologists who dispute it are saying that a Gain of Function research cannot produce Covid-19, or at least not from known viruses such as RaTG13.

This means in order for the Gain of Function argument to work, it requires a virus we don't know about.

But then, if you claim that the virus we don't know about escaped from a lab after gain of function, then maybe we don't even need the gain of function part of the argument.

But then, gain of function isn't doing much work in the theory.... hmmm...
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Old 1st June 2021, 10:15 PM   #846
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Originally Posted by angrysoba View Post
No, I don't think you replied to it, but I only remember the claims that were made.
Then go find it. Go to the link which you already got wrong claiming names had been said when they weren't. If you think I replied please post the quote or a link to the post.

Originally Posted by angrysoba View Post
I assume that these counterclaims remain as well:

The thing is, whenever there are "made-in-a-lab" claims, you seem to think they are worth investigating. Whenever you find someone saying, "The virus wasn't made in a lab" you say, "Strawman! Nobody claims that! This is an attempt at misdirection because the claim is it escaped from a lab."

It seems to me that the virologists who dispute it are saying that a Gain of Function research cannot produce Covid-19, or at least not from known viruses such as RaTG13.

This means in order for the Gain of Function argument to work, it requires a virus we don't know about.

But then, if you claim that the virus we don't know about escaped from a lab after gain of function, then maybe we don't even need the gain of function part of the argument.

But then, gain of function isn't doing much work in the theory.... hmmm...
Your memory is grossly inaccurate. Please quit making assertions about me without a quote. It's annoying.

And I don't know what you are on about with the GoF statements. Your post is confusing.

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Old 1st June 2021, 10:16 PM   #847
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Originally Posted by Skeptic Ginger View Post
Then go find it. Go to the link which you already got wrong claiming names had been said when they weren't. If you think I replied please post the quote or a link to the post.

I never said you replied. In fact, I said the opposite.
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Old 1st June 2021, 10:31 PM   #848
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Originally Posted by angrysoba View Post
I never said you replied. In fact, I said the opposite.
She's talking about the posts you might find in regards to her new request to "go find it".
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Old 1st June 2021, 10:50 PM   #849
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Originally Posted by angrysoba View Post
I never said you replied. In fact, I said the opposite.
So now you are playing games? You said:
Quote:
The thing is, whenever there are "made-in-a-lab" claims, you seem to think they are worth investigating. Whenever you find someone saying, "The virus wasn't made in a lab" you say, "Strawman! Nobody claims that! This is an attempt at misdirection because the claim is it escaped from a lab."
Post a quote or stop with the false assertions, thank you.
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Old 2nd June 2021, 02:37 AM   #850
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Here is the abstract of the original paper by the Dalgliesh and Sorenson. There is also a third writer, Susrud, about their vaccine Biovacc-19.

Quote:
This study presents the background, rationale and method of action of Biovacc-19, a candidate vaccine for corona virus disease 2019 (Covid-19), now in advanced preclinical development, which has already passed the first acute toxicity testing. Unlike conventionally developed vaccines, Biovacc-19’s method of operation is upon nonhuman-like (NHL) epitopes in 21.6% of the composition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)’s spike protein, which displays distinct distributed charge including the presence of a charged furin-like cleavage site. The logic of the design of the vaccine is explained, which starts with empirical analysis of the aetiology of SARS-CoV-2. Mistaken assumptions about SARS-CoV-2’s aetiology risk creating ineffective or actively harmful vaccines, including the risk of antibody-dependent enhancement. Such problems in vaccine design are illustrated from past experience in the human immunodeficiency viruses domain. We propose that the dual effect general method of action of this chimeric virus’s spike, including receptor binding domain, includes membrane components other than the angiotensin-converting enzyme 2 receptor, which explains clinical evidence of its infectivity and pathogenicity. We show the nonreceptor dependent phagocytic general method of action to be specifically related to cumulative charge from insertions placed on the SARS-CoV-2 spike surface in positions to bind efficiently by salt bridge formations; and from blasting the spike we display the NHL epitopes from which Biovacc-19 has been down-selected.
https://www.researchgate.net/publica...or_Infectivity
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Old 2nd June 2021, 03:26 AM   #851
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Originally Posted by angrysoba View Post
Here is the abstract of the original paper by the Dalgliesh and Sorenson. There is also a third writer, Susrud, about their vaccine Biovacc-19.



https://www.researchgate.net/publica...or_Infectivity
Hmmm, I don't think that is peer-reviewed. Antibody-dependent enhancement has not been observed for COVID vaccines and is pretty much considered a non-issue.

"Gus" Dalgliesh is well known for discovering that CD4 is the receptor for HIV-1.
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Old 2nd June 2021, 06:13 AM   #852
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Originally Posted by RecoveringYuppy View Post
Here's what Tedros has to say:

https://news.un.org/en/story/2021/03/1088702
He is discussing the WHO's readiness to conduct follow-up missions. There was a follow planned for further investigating the frozen food chain as well. As I stated before, I have no particular objection to further investigation into these unlikely possibilities but the fact remains there is no supporting evidence for either hypothesis.

Originally Posted by RecoveringYuppy View Post

You said that we have an answer. Please indicate the timestamp in your video where they tell us what that answer is.
They did discuss their access to information on the mission early on, around the 11 min mark and say that they asked for a lot of information and were generally satisfied with what they were provided.

With most conspiracy theories no investigation is ever enough for those that buy into the conspiracy, and I expect that will be the case here. If the follow up mission to the lab happens the CT'ers will still find reasons to insist the investigation was inadequate.
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Old 2nd June 2021, 06:38 AM   #853
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Originally Posted by Capsid View Post
Hmmm, I don't think that is peer-reviewed. Antibody-dependent enhancement has not been observed for COVID vaccines and is pretty much considered a non-issue.

"Gus" Dalgliesh is well known for discovering that CD4 is the receptor for HIV-1.
That is either an earlier abandoned paper or it is a pre-print.

Earlier there was a claim that they had not had their paper published because people thought the lab leak theory was a crackpot one. However, apparently they will now get something published.

I wonder how much will be the same.
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Old 2nd June 2021, 06:48 AM   #854
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Originally Posted by Skeptic Ginger View Post
Here you go, an article to be published in a couple of days has been previewed by the Daily Mail. You can get a head start dismissing their thesis. That it's in the Daily Mail with all the accompanying sensational language and that the thesis was rejected last year should give you all some ammo.

I was going to wait until the paper was published but the Daily Mail has quite a bit of it excerpted already. Scroll down to the actual paper excerpts. They are copy protected so I can't quote from the paper.

EXCLUSIVE: COVID-19 'has NO credible natural ancestor' and WAS created by Chinese scientists who then tried to cover their tracks with 'retro-engineering' to make it seem like it naturally arose from bats, explosive new study claims

I'm sure a number of people in this thread will see the bit about the claims being rejected earlier and dismiss the paper.

The 2 scientists have serious credentials and have authored or co-authored hundreds of papers published in scientific and medical journals.

PubMed: Dalgelish

Who are Angus Dalgleish and Birger Sørensen?


The lower level biosafety labs have been noted in citations in this thread.


I don't have any background in the paper's claim:
I understand the positive and negative charges, just not that amino acids have these charges. I'll look for more relevant information on that and await critique by contributors to the thread.


QRB Discovery to save people time looking for the paper when it's published.
This looks like just another rehash of speculation about the furin cleavage site. This was examined a year ago and found to be consistent a natural origin and inconsistent with a lab origin. Since then the evidence for it being natural has grown. It's discussed extensively around the 55 min mark of the TWiV podcast linked previously.

https://www.youtube.com/watch?v=IxwrDSYrhjU&t=5527s

A few of the points made:
- no one would have thought to create a furin cleavage site this way unless they had already studied Covid-19
- There is regulatory RNA for the furin cleavage site no one would have thought to use unless they had already studied Covid-19
- Since it was studied in Covid-19 similar structures of various ranges of completeness and efficiency have been found in a wide range of corona viruses, including some of Covid-19's close relatives.
- It's not a full furin cleavage site. If someone was actually designing it they would have used a full furin cleavage site because that would bind even more efficiently than the structure that exists in Covid-19
- it's an example of un-intelligent design commonplace in evolution. there are other "mistakes" in the way the furin cleavage site is constructed that no competent designer would make.
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Old 2nd June 2021, 07:08 AM   #855
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Originally Posted by Skeptic Ginger View Post
Yeah, it's verifiable. The elements are there and a lot of recombinant events take place in the bat population. Even the pangolin gene segment can be found in the horseshoe bats in Yunnan.
Evidence?

There have been similar spike features found in a number of viruses, but this doesn't mean the genetic sequences are identical. The RNA from the Pangolin Sabercorona virus spike structure is 98% - 99% identical to Covid-19 so while the closest know, it's still possible something even closer may yet be found in bats.

The flip side, however is that RaTG13 is only 95% - 96% similar to Covid-19. If\when something closer is identified there is no guarantee it will be in a bat. A LOT of bat samples have been studied in comparison to other animals so the fact that the closest know relative was found in bats may just be a sampling issue.
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Old 2nd June 2021, 08:30 AM   #856
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Originally Posted by lomiller View Post
[Blather snipped]
You said we had an answer. You have not cited that answer.

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Old 2nd June 2021, 08:42 AM   #857
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Originally Posted by RecoveringYuppy View Post
You said we had an answer. You have not cited that answer.
I said the investigation team found no evidence and was satisfied with the information they provided and backed that up with comments provided by members of that investigation team.

You have had ample time to provide evidence for a lab leak and have failed to do so.

You have also had ample time to provide evidence for the conspiracy and cover-up the lab leak hypothesis is built on, and again you have failed to do so.

What it comes down to is that there IS no evidence to support either of these.
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Old 2nd June 2021, 08:50 AM   #858
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JFC you've provided evidence for the coverup. It was discussed in the video you presented.

And, pray tell, what am I supposed to be providing evidence for? And, what? Agreeing with Fauci makes me a conspiracy theorist now? Where the heck do you see anyone arguing for a conspiracy theory in this thread (I assume the off topic posts got moved to the correct thread).

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Old 2nd June 2021, 09:14 AM   #859
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You want evidence for coverup ? It happened in China. That's all you should need to know. Of course there was coverup. Even if the virus did not escape from the lab.
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Old 2nd June 2021, 09:44 AM   #860
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Originally Posted by RecoveringYuppy View Post
JFC you've provided evidence for the coverup. It was discussed in the video you presented.
In the mind of the conspiracy theorist every failure to find evidence for their pet theory is evidence someone is covering it up. This is the lifeblood of a CT.

Originally Posted by RecoveringYuppy View Post
And, pray tell, what am I supposed to be providing evidence for? And, what? Agreeing with Fauci makes me a conspiracy theorist now?
What makes you think you agree with Fauci? All he's said is that he's in favor of a follow-up investigation of the lab itself. I expect he's also in favor off a follow-up investigation into the possibility the virus emerged elsewhere and was carried to China on frozen food. Even if thinks that either of these things are extremely unlikely he's going to support follow-up to everything mentioned in the WHO report.

This is VERY different than suggesting either of these be considered legitimate possibilities at this point. Hell even I have said that I have no objection to further investigation of the lab and cold food chain, I just happen to think it's extremely unlikely any supporting evidence will ever be found.
Originally Posted by RecoveringYuppy View Post
Where the heck do you see anyone arguing for a conspiracy theory in this thread (I assume the off topic posts got moved to the correct thread).
Every version of the lab leak hypothesis requires numerous scientists to be actively participating in a cover-up. At a minimum it requires that scientists actively destroyed data and samples to hide the fact Covid-19 was in the lab. It also required scientists to be lying about illness within the lab, the work they were conducting, etc, etc, etc.

How many times have we seen Peter Daszak slandered in this very thread? The mans active field of research is the possibility of a pandemic coronavirus emerging in China. The "justification" for slandering him has been that most of the scientists working on this subject are Chinese and he's "suspect" simply because he works with these Chinese scientists.
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Old 2nd June 2021, 09:59 AM   #861
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JFC Not every conspiracy is a conspiracy theory and we do have proven activity that a database was taken offline at a suspicious time.


I give up. I have no mechanism to cauterize the hydra.
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Old 2nd June 2021, 10:37 AM   #862
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Originally Posted by RecoveringYuppy View Post
JFC Not every conspiracy is a conspiracy theory and we do have proven activity that a database was taken offline at a suspicious time.
The "database" was taken down in Sept the first real human case was likely in Oct, so the timelines don't work. There are other copies of the data around the world and they contain nothing suspicious.
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Old 2nd June 2021, 11:54 AM   #863
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Originally Posted by lomiller View Post
Evidence?...
It's in this thread. I'm done hunting **** down for people who didn't read it the first time.
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Old 2nd June 2021, 11:56 AM   #864
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Originally Posted by angrysoba View Post
Here is the abstract of the original paper by the Dalgliesh and Sorenson. There is also a third writer, Susrud, about their vaccine Biovacc-19.

https://www.researchgate.net/publica...or_Infectivity
That is not the paper. That one was published a year ago.
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Old 2nd June 2021, 12:03 PM   #865
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Originally Posted by Capsid View Post
Hmmm, I don't think that is peer-reviewed. Antibody-dependent enhancement has not been observed for COVID vaccines and is pretty much considered a non-issue.

"Gus" Dalgliesh is well known for discovering that CD4 is the receptor for HIV-1.
If you scroll down 13 papers cite their work.
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Old 2nd June 2021, 01:07 PM   #866
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Originally Posted by Skeptic Ginger View Post
If you scroll down 13 papers cite their work.

Fairly certain it’s still not peer reviewed.


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Old 2nd June 2021, 01:20 PM   #867
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Here is one of the papers that cites the June 2020 paper:

An open debate on SARS-CoV-2’s proximal origin is long overdue
Quote:
There is a near consensus view that SARS-CoV-2 has a natural zoonotic origin; however, several characteristics of SARS-CoV-2 taken together are not easily explained by a natural zoonotic origin hypothesis. These include: a low rate of evolution in the early phase of transmission; the lack of evidence of recombination events; a high pre-existing binding to human ACE2; a novel furin cleavage site insert; a flat glycan binding domain of the spike protein which conflicts with host evasion survival patterns exhibited by other coronaviruses, and high human and mouse peptide mimicry. Initial assumptions against a laboratory origin, by contrast, have remained unsubstantiated. Furthermore, over a year after the initial outbreak in Wuhan, there is still no clear evidence of zoonotic transfer from a bat or intermediate species. Given the immense social and economic impact of this pandemic, identifying the true origin of SARS-CoV-2 is fundamental to preventing future outbreaks. The search for SARS-CoV-2’s origin should include an open and unbiased inquiry into a possible laboratory origin.


A reminder to those that keep repeating the Seafood Market origin:
Quote:
However, three of the four patients with the earliest recorded onset of COVID-19 symptoms, none had an association with the seafood market (Huang et al., 2020), and the ancestral T8782 and C28144 genotype was not associated with the seafood market (Chen et al., 2020). Phyloepidemiologic analysis of early cases (Yu et al., 2020) also discounted this theory.
Garry claimed in his piece that the other cases were connected to other wet markets. I have yet to find any evidence supporting his assertion. As I noted a few times, one patient's son had been to a wet market but he did not have COVID 19.

The WHO paper mentioned 2 other markets and only found evidence of COVID in one. If the other early cases had a connection to this other market one would think there would have been stronger evidence for that hypothesis.

Unless there is a source for COVID infection connected to another market, for me this discredits Garry as someone just a tad too confirmation biased.



And for those who keep repeating the pangolin as an intermediary species:
Quote:
Although two pangolin-CoV’s (Xiao et al. 2020, Liu, P. et al., 2020) exhibited strong binding to human ACE2, binding to pangolin ACE2 was approximately tenfold weaker, and binding to bat Rhinolophus ferremequinum ACE2 was very weak, which is comparable to that exhibited by SARS-CoV-2 (Wrobel et al. 2021).
And this was brought up in the thread:
Quote:
All published pangolin-CoV genome sequences with a nearly identical spike RBD to SARS-CoV-2 were sourced from a single batch of smuggled pangolins (Chan and Zhan 2020), raising the question whether pangolins may have been infected from another host species or from humans during trafficking (Choo et al. 2020; Wenzel, 2020). ...

Finally, the discovery of synthetic DNA sequences in pangolin CoV metagenomic raw sequence reads by Zhang, D., (2020) and the interpretation that the pangolin-CoV genomes were generated from a synthetic construct,...


This is a scary bit:
Quote:
A very recent emergence of SARS-CoV-2 into the human population has been proposed based on the sampling of eight nearly identical complete genomes in December 2019 (Lu et al., 2020). From earliest strains in Wuhan in 2019, SARS-CoV-2 resembled SARS-CoV in the late phase of its 2003 epidemic after SARS-CoV had developed several advantageous adaptations for human transmission (Zhan et al., 2020).
I thought there was a paper before the 2019 pandemic that noted researchers were using the SARS backbone in their research. I have those details wrong but I am sure they were using the SARS virus in the WIV lab. This paper addresses that and I've quoted that part below.***



This is the first I've seen mentioned that a direct jump from bats to humans has a problem:
Quote:
However bat species are poorly infected by SARS-CoV-2 and they are therefore unlikely to be the direct source for human infection. SARS-CoV-2 does not replicate in R. sinicus kidney or lung cells (Chu et al., 2020), binds poorly to R. sinicus ACE2 (Tang, Y. et al., 2020; Li, Y. et al., 2020; Piplani et al., 2020) and exhibits no binding to R. ferrumequinum ACE2 (Tang, Y. et al., 2020). ...

... these results are perplexing as it indicates a significant and unexplained evolutionary distance between SARS-CoV-2 and bats....


Then there is this problem:
Quote:
Interestingly, there is no evidence of recombination events in studies of SARS-CoV-2 by Richard et al. (2020) (6,546 genome sequences as of September 2020) or Bobay et al. (2020) (218 sequences as of August 2020). This is in contrast with MERS-CoV, where despite a much smaller sample size, recombination events were detected.


*** Re the backbone and SARS virus used in the lab:
Quote:
The observation that SARS-CoV-2 was not derived from a previously used virus backbone was used as an argument by Andersen et al. and Liu et al. 2020 as evidence against a laboratory origin hypothesis. The Betacoronavirus RaTG13 was fully sequenced in 2018 (Zhou P. et al., 2020b) but only published after the beginning of the pandemic (Zhou P. et al., 2020a). [/More unpublished sequences existed in a WIV database that was deleted after the beginning of the pandemic (Segreto & Deigin, 2020). SARS-CoV-2 could have been engineered using one of the over 1,500 strains openly collected by institutions associated with the WIV (Sirotkin & Sirotkin, 2020), a completely undocumented backbone, or one of several fairly well correlated bat-CoV’s could have been used in combination with directed evolution, a widely used technique for introducing mutations and selection to achieve proteins with desired properties (Badran and Liu, 2015; Standage-Beier and Wang 2006; Simon et al., 2019). Specifically, this technique has been used for engineering novel virus variants (Excoffon et al., 2009; Lin et al., 2012; Meister et al., 2019). Furthermore, novel yet undocumented reverse-genetic systems could also have potentially been used. Indeed, multiple groups have developed SARS-CoV-2 reverse genetics systems for SARS-CoV-2 research in short periods of time (Hou et al., 2020; Torii et al., 2020; Thi Nhu Thao et al. 2020). Additionally, seamless “No See’em” technology pioneered nearly 20 years ago, allows reverse engineering to be used without leaving any traces (Yount et al., 2002).


The idea one cannot get COVID 19 with lab experiments to me is absurd on its face. But it has been proposed by at least one researcher along with the rationale. Here that hypothesis is disagreed with and it is addressed just how that could be done:
Quote:
Culturing and adapting CoVs and influenza A virus to different cell lines, including human airway epithelial cells, has been conducted in various laboratories (Tse et al., 2014; Menachery et al., 2015; Zeng et al., 2016; Jiang et al., 2020); furthermore, experimental creation of chimeric viruses by directed engineering as discussed above does not require prior modelling.


No conflict of interest is cited. But because DRASTIC has been naively dismissed here I add this from the paper:
Quote:
Acknowledgment
We are grateful to the D.R.A.S.T.I.C. (Decentralised Radical Autonomous Search Team Investigating COVID‐19) Twitter group for their investigative work in uncovering a significant number of previously unpublished facts about SARS‐CoV‐2 and its relative strains.

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Old 2nd June 2021, 01:22 PM   #868
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Originally Posted by Capsid View Post
Fairly certain it’s still not peer reviewed.
I think the fact they have not yet been able to produce a vaccine while other methods have been successful, discredits some of that paper. But not necessarily everything in it.
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Old 2nd June 2021, 01:47 PM   #869
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Originally Posted by lomiller View Post
The "database" was taken down in Sept the first real human case was likely in Oct, so the timelines don't work. There are other copies of the data around the world and they contain nothing suspicious.
The timelines do work. It's been explained how/why that is in the thread. You are asserting something without addressing the rebuttal posted upthread.

If you want to debate how the timeline doesn't work, then address the reasons it does:
Incubation period before the first cases were found.

Milder cases before the serious ones came to the attention of the medical community.

The fact there were two lineages suggests there is missing time/cases, the virus might have been circulating in Wuhan for at least enough time the Sept action by the Chinese government fits the timeline.

We don't have all the genomes of those initial cases given the 3 researchers who were ill in Nov are not in the data released by China. Either the State Dept is wrong (quite possible) or the cases have been hidden by China (also possible).
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Old 2nd June 2021, 01:48 PM   #870
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Originally Posted by RecoveringYuppy View Post
I give up. I have no mechanism to cauterize the hydra.
Pace yourself. Pick and choose which posts to reply to.
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Old 2nd June 2021, 02:25 PM   #871
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Originally Posted by Skeptic Ginger View Post
I think the fact they have not yet been able to produce a vaccine while other methods have been successful, discredits some of that paper. But not necessarily everything in it.

Some of the statements are very speculative and would not have got through peer review and as a result would not be citable. It’s a bit sneaky in my opinion.


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Old 2nd June 2021, 05:14 PM   #872
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Vincent and Amy have just discussed the "it breaks the laws of physics" claim in Dalgliesh's paper (or the Daily Fail gloss on that) - and where have we heard that claim before?

Vincent and Amy say it is nonsense.

But here is a question - if it is "against the laws of physics" surely that would be true whether it is in nature or whether it is artificial, would it not?

How is "breaking the laws of physics" an indication of being man-made? It sounds like it would be evidence of being created by a supernatural being.
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Old 2nd June 2021, 05:35 PM   #873
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Apparently on Sunday, on TWiV, they will be looking at a paper that shows how the virus is natural and doesn't require any Gain of Function explanation.

(or at least that is how I understand what they said they will be looking at).
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Old 2nd June 2021, 05:50 PM   #874
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Amy and Vincent were asked what is the best evidence against a lab-leak (or presumably in favour of zoonotic spillover).

Amy cites this article as an example of an ongoing problem that has likely led to an increase in zoonotic spillover...

Quote:
The extent to which humans facilitate zoonotic transmission of infectious diseases is unclear. Human encroachment into wildlife habitats as a consequence of expanding urbanization, cropland area and intensive animal farming is hypothesized to favour the emergence of zoonotic diseases. Here we analyse comprehensive, high-resolution datasets on forest cover, cropland distribution, livestock density, human population, human settlements, bat species’ distribution and land-use changes in regions populated by Asian horseshoe bats (>28.5 million km2)—the species that most commonly carry severe acute respiratory syndrome (SARS)-related coronaviruses. We identify areas at risk of SARS-related coronavirus outbreaks, showing that areas in China populated by horseshoe bats exhibit higher forest fragmentation and concentrations of livestock and humans than other countries. Our findings indicate that human–livestock–wildlife interactions in China may form hotspots with the potential to increase SARS-related coronavirus transmission from animals to humans.
https://www.nature.com/articles/s43016-021-00285-x

The land-use in various parts of the world, and speficially in China has led to more and more of these serious viruses having contact with humans.
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Old 2nd June 2021, 06:04 PM   #875
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Originally Posted by angrysoba View Post
Vincent and Amy have just discussed the "it breaks the laws of physics" claim in Dalgliesh's paper (or the Daily Fail gloss on that) - and where have we heard that claim before?

Vincent and Amy say it is nonsense.

But here is a question - if it is "against the laws of physics" surely that would be true whether it is in nature or whether it is artificial, would it not?

How is "breaking the laws of physics" an indication of being man-made? It sounds like it would be evidence of being created by a supernatural being.
Vincent and Amy? First-name basis now?

No one here cites the Daily Mail as a source of scientific material. I cited them because they had some direct previews of the paper.

And this is likely a distortion of what the paper actually says: "breaking the laws of physics".
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Old 2nd June 2021, 06:22 PM   #876
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General thoughts on amino acids

I looked up the sequences of some DNA binding proteins that fall into the class of leucine zippers. Because DNA carries a negative charge, one expects the protein to have some positively charged amino acid side chains. A portion of the sequence for Jun reads RRMR. That is three positive charges out of four amino acid residues (M is uncharged). A few residues away is a second sequence KCRKRK. That is four positive charges in a row, and 5 out of 6 (C is uncharged). Some of the residues of Fos are in a special kind of alpha-helix called a coiled-coil. In the one-letter code, K is lysine, and R is arginine.

I would point out that being close in sequence is not quite the same thing as being close in three dimensions. A typical alpha-helix makes one full revolution every 3.6 amino acids. One can consult a diagram of a helical wheel to see how the side-chains are dispersed in the standard alpha helix (although a coiled coil is slightly different). In a beta-sheet, each side chain points in an approximately opposite direction to the last one. I am not saying that the claim that 4 positive charges in a row is rare is incorrect, but I am saying that I am not convinced.
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Old 2nd June 2021, 07:36 PM   #877
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Originally Posted by Skeptic Ginger View Post
Vincent and Amy? First-name basis now?

No one here cites the Daily Mail as a source of scientific material. I cited them because they had some direct previews of the paper.

And this is likely a distortion of what the paper actually says: "breaking the laws of physics".
Heh heh! I watch them a lot and feel like they are practically family now

Yeah, I’m hedging on whether or not this is what the scientists themselves are saying or whether it is either an excitable press release or just the Daily Fail getting carried away.

I wouldn’t be surprised if we have a case of…dare I say it…. Chinese whispers*.


* I think that is the UK version of what Americans call Broken Telephone. Chinese whispers might not be considered a PC term these days.
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Old 2nd June 2021, 07:42 PM   #878
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Originally Posted by angrysoba View Post
Heh heh! I watch them a lot and feel like they are practically family now

Yeah, I’m hedging on whether or not this is what the scientists themselves are saying or whether it is either an excitable press release or just the Daily Fail getting carried away.

I wouldn’t be surprised if we have a case of…dare I say it…. Chinese whispers*.


* I think that is the UK version of what Americans call Broken Telephone. Chinese whispers might not be considered a PC term these days.
Those darn Chinese, inflicting their viruses and whisperings upon us!
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Old 2nd June 2021, 08:24 PM   #879
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Originally Posted by Chris_Halkides View Post
I looked up the sequences of some DNA binding proteins that fall into the class of leucine zippers. Because DNA carries a negative charge, one expects the protein to have some positively charged amino acid side chains. A portion of the sequence for Jun reads RRMR. That is three positive charges out of four amino acid residues (M is uncharged). A few residues away is a second sequence KCRKRK. That is four positive charges in a row, and 5 out of 6 (C is uncharged). Some of the residues of Fos are in a special kind of alpha-helix called a coiled-coil. In the one-letter code, K is lysine, and R is arginine.

I would point out that being close in sequence is not quite the same thing as being close in three dimensions. A typical alpha-helix makes one full revolution every 3.6 amino acids. One can consult a diagram of a helical wheel to see how the side-chains are dispersed in the standard alpha helix (although a coiled coil is slightly different). In a beta-sheet, each side chain points in an approximately opposite direction to the last one. I am not saying that the claim that 4 positive charges in a row is rare is incorrect, but I am saying that I am not convinced.
I appreciate your insight here. Once the paper is out I'll come back to this with some questions.
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Old 2nd June 2021, 09:01 PM   #880
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Originally Posted by angrysoba
Yeah, I’m hedging on whether or not this is what the scientists themselves are saying or whether it is either an excitable press release or just the Daily Fail getting carried away.

Are you referring to the "laws of physics" quote? Look back one page in this thread, that was a quote the Daily Mail said came from an exclusive interview.



Originally Posted by Daily Mail
The laws of physics mean that you cannot have four positively charged amino acids in a row. The only way you can get this is if you artificially manufacture it,' Dalgleish told DailyMail.com.
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