What the Delta variant could mean for Covid-19 in the US - CNN

[Michael Arent]

FYI.

What the Delta variant could mean for Covid-19 in the US - CNN

https://apple.news/A_WeocgxuS8yQlgu7BJ0H7Q

PS:Potential impact re: opening the lab and the future of CCL meetups...

M i c h a e l

[Noel Carrascal]

Hey guys,

I would like to give a perspective inspired by the article shared by Michael.

I became an atheist in part because I did not trust the sermons and fears that religious leaders would give to people to control them. I was 14 when that hapened. 

In fact, that and Darwin, biographies of Einstein and Carl Sagan documentaries inspired me to become a scientist.

The parochial attitudes of people in the mountains of Colombia in my childhood are no different from what I see now in the world and even the scientific community today. Just belive what they tell you, don't question authority, no nonsense like critical thinking and fall back in line. Only that now the media and other self appointed secular  'prophets', not a church, push that on people.

We are community scientists with enough expertise to write a more informed article than CNN's. We are not institutional scientists who can be tamed, pressured or coerced by very strong institutional and political forces and fear career suicide. We are free of that, and as such we need to search the truth however COUNTER CULTURAL it is.

Science is in crisis by the publishing and grant seeking attitude of scientists driven by careerism. I was a naive and idealistic first year grad student when I got a taste of that soon after the covid epidemic of 2003/2004. I worked in computational drug design. I help my advisor on a R01 grant and he was making the same argument than the scientists and experts in the article shared by Michael. I am paraphrasing: people will die, my research is critical to help save them and there is gloom and doom ahead if no funding is given. By the time covid19 started, I was too desensitized to worry. 

I do think COVID19 is a real health issue, but it has been disproportionally over blown with other purposes. I thought community scientist could provide a cool and cautious mind during this pandemic. It seems they are going with the trends.

I do believe the mRNA vaccine is safe. I got the moderna vaccine. I am no anti vaxxer, but i am worried about the rush with which these scientifically sound vaccines are rushed for people to get when the mortality ratea are in the 10ths of 1 percent. People may already have antibodies from a Covid19 infection that was asymptomatic, and the vaccine could be unnecessary in many cases. 

I do not have enough information to tell if this vaccine can cause cytotoxic effects on people, but it should not be ruled out. In fact, we should keep an open mind on that and not rush to 'fact-check-it-wrong' acting on limited information. It may actually save lives for a small portion of people who might have severe reactions to the vaccine. Why do some people think it is the righteous thing to do to have close to 100% vaccination on the population? I believe vaccination should be voluntary and confidential.

I stopped participating in the covid19 meetings because I noticed people were just relaying information from different sources without getting into the data. 

Instead, I downloaded the sequences of about 30 covid19 spike proteins from covid viruses that include the 2003, 2004 and 2019 strains. I aligned them and I noticed 5 incertions in covid19, relative to covid 2003/04, that i did not find in sequence comparisons between other two strains that I aligned. I used software developed for protein design that I developed in grad school to align the sequence gaps to a structure of the protein and the gaps corresponded to loop regions of the spike protein. These are not secondary structure alignments, these are thertiary structure alignments in 3D and the matches had very low RMSD. Loop regions that are disordered are in the surface and for that reason they likely play roles in inmune responses and cell entry. I even built the sugars at glycosilated sites, but i stopped there.

That information was too much of a coincidence for me to rule out the virus was designed. I am not saying it is, i think it is hard to prove conclusively that it is, but then it was quickly dismissed in the covid  discussion as debunked and conspiracy theory material. No reasons given, none that would outweigh my alignment findings. 

I still can't confirm the virus is engineered. I do not guide my thinking from the puzzling term 'gain of function' of hyperpartisan politics of today that cloud our judgment. My suspicion comes from the alignments alone and i wanted to put those suspicions to the test.

I believe it is possible to estimate how likely those insertions found in alignments between spike proteins in covid19  2003/04 could happen naturally, but that is not my area of expertise.  If we could find rate of mutations of similar virus, combined that with how like those mutations happen in loop regions (as opposed to the interior of the protein), we could then have something very interesting to report whether that supports my suspicion or not. It could give an estimate of the number of year for a virus to go from 2003/04, or other found sequence, to covid2019, and the number would give us a good perspective on the 13 year gap between the outbrakes. Is there any one in this group who has done that? .

That's what citizen scientist should be doing, not just relaying information from compromised sources and passing it as fact and not the opinions they are.

Noel

P.S. Michael, please dont take this as a personal attack for sharing that article. My point is that the world needs citizen scientists that are free from trends and narratives and think for themselves.

P.S. asside from my spanished infused grammar, there might be typos because I wrote this on my cellphone from Iceland where people in crowded places have asked me why do I wear a mask?... that was so liberating... i could not agree more. See... 'facts' vary across borders...

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[Michael Arent]

Thank you both, Noel and Cere, for your responses to my email. 

@Noel: I did by no means take your response as a personal attack. My intention in forwarding the email to the organization was indeed to spark the kind of deeper discussion that both you and Cere have replied with. I'm neither academically nor professionally trained as a scientist and I rely on those in or connected with our organization to conduct fora and have in-depth discussions on these type of important topics that affect not only the science community but the wider populace who are impacted by these health, climate and many other scourges that plague our planet, Earth -- and which science has a key role in trying to tame.

@Cere: I wholly agree with your sentiment, "I think CCL should probably have more discussions (not less) about how it can balance openness with playing an effective role in the scientific process and scicomm." 

Hopefully, we'll receive the thoughts on this topic from others in our organization as well...

M i c h a e l

[yann lala]

Hi Noel,

I will reply to some points of your pamphlet.

 -"Science is in crisis by the publishing and grant seeking attitude of scientists driven by careerism."

This is a weird way to put it. Scientist don't have a choice in the matter, they need to publish and do grant seeking if they want to survive. For everybody who had the luck (or bad luck, depending of your point of view) to met me at CCL when I was in California, they know that in the French system researcher is a status, you are a unfirable state employee, allow to work on everything you want, and in the past, you had some money for your research without the grant bullshit. So my point is that it is possible, and it is a political choice from governements, scientists are a not responsable of that. (unless you think they should do strike and such, which the french tried of course, without success https://www.lexpress.fr/actualite/societe/loi-sur-la-recherche-pourquoi-les-chercheurs-se-mettent-en-greve-ce-jeudi_2120119.html)

-"I do think COVID19 is a real health issue, but it has been disproportionally over blown with other purposes. I thought community scientist could provide a cool and cautious mind during this pandemic. It seems they are going with the trends."
I am not sure what this is suppose to mean. Over blown with other purposes? Which purposes? I guess for the overblown part, it depends how many death are acceptable for you. Since we have as example a lot of countries which managed to suppress the virus from their territory, I do think that is reasonable to be a little bit upset at the imcompetence of governements, don't you think? Also, this a a bit of fallacy, not going with the trend is not necessary right.

-"I do believe the mRNA vaccine is safe. I got the moderna vaccine. I am no anti vaxxer, but i am worried about the rush with which these scientifically sound vaccines are rushed for people to get when the mortality ratea are in the 10ths of 1 percent."

Mortality rates is not the end all be all criteria to determine the dangerosity of a virus. You have hospitalisation rate, which can lead to a lot more death because of deprogrammation, long covid issue which will affect the quality of life of a lot of people. And also, letting the virus circulating mean that you increase the chance of mutation and the apparition of more dangerous variant. And it has been proven that vaccines decrease the viral load if you get contaminated, which will help for that.

-"I do not have enough information to tell if this vaccine can cause cytotoxic effects on people, but it should not be ruled out. In fact, we should keep an open mind on that and not rush to 'fact-check-it-wrong' acting on limited information."

We have enough statistics to rule out short term effect of the vaccines on people.

-"It may actually save lives for a small portion of people who might have severe reactions to the vaccine. Why do some people think it is the righteous thing to do to have close to 100% vaccination on the population? I believe vaccination should be voluntary and confidential."

I know it is a hard concept to grasp for north americans sometimes, but there is things which works only if everybody does it. The vaccines, since it conceptions, is not designed to be an individual protection but a collective one. You can't achieve herd immunity, which will protect people who can't get vaccinated because of immuno-deficiency, if too many people don't get vaccinated. It is always the righteous thing to have close to 100% vaccination on the population.

-"I stopped participating in the covid19 meetings because I noticed people were just relaying information from different sources without getting into the data."

I don't know the details, but maybe the goal is not necessary to do a heavy data driven meeting, no? And more a conversation?

-"Instead, I downloaded the sequences (...)"

I don't understand what your demonstration is supposed to show. You should maybe find papers who talk about that and go into the data? Just looking at sequence is pointless, you want to do follow the evolution, which other scientist did.  I am too lazy to look too much into it, but with a quick search you have those papers: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293463/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7415347/

-"That information was too much of a coincidence for me to rule out the virus was designed. I am not saying it is, i think it is hard to prove conclusively that it is, but then it was quickly dismissed in the covid  discussion as debunked and conspiracy theory material."

Thinking the chinese governement did it on purpose and contaminated their own population to spread it to the world is conspiracy material. A lab leak is not, but very unlikely. You would have to demonstrate that they work on those specific mutation. Gain of function are really valuable tool and to my knowledge done in a lot of different lab around the world. The possibility of a lab leak already created discussion about safety process, but beyond I don't see the benefit to focus on this topic.

-"That's what citizen scientist should be doing, not just relaying information from compromised sources and passing it as fact and not the opinions they are."

Which source are compromised? What does that mean? Compromised by who or what?

To Cere

You can't critizices CCL leadership to use appeal to authority when two sentences after you do one "As one well respected cardiologist and science youtuber". Truth is, when you are a scientists (a real one, somebody who publish paper, not like me), you are selling your integrity and honesty to other researcher and the public. Because when I read a scientific paper, I need to be sure that the scientists who did the work did it with a certain standard and didn't cheat on the results. Appeal to authority is embedded in the science practice, because you need to become an authority to do sciences to be credible and taken seriously. I think it can explain why acadamic scientist sometimes have issue to understand the point of citizen scientist.

"Recently, I listened to a podcast run by two university professors/scientists interviewing a couple of (currently) well respected scientists who believe that we should be focusing more on developing vaccines which target the innate immune system and they cite the role that financial incentives play in vaccine development as one of the reasons why it is not being researched. "

This is an really interesting topic, and for sure science is influenced by economic and political consideration. And sometimes it is creating really bad situation, like when the french scientific community and the cdc claimed that mask are not effective because they didn't had enough stock of it. It destroyed the trust in those institution for a lot of people.

If we want a better incentive system, we probably should not support only private effort to produce vaccines and start pouring money into academia.

"In light of this, I think CCL should probably have more discussions (not less) about how it can balance openness with playing an effective role in the scientific process and scicomm."

In principle, I don't desagree. But in practice, there is a danger to fall into some kind of relativism where all the idea seems to have the same weight. I don't see the value to entertain ideas which are not based on any data, or giving too much weight on obviously wrong idea. (like vaccine cause autism for example) I do believe that those idea should not treated like they have any scientific basis, because they don't, and can be discarded rapidly.

I have a lot of anti vaccine and conspiracy theorist in my family, and they can speak about it for hours without stoping. Nobody have the time and energy for that. (and time and energy is a really valuable and scarce ressource at CCL)

   Best,

      Yann

On Fri, Jun 25, 2021 at 11:36 AM Cere Davis <cere...@gmail.com> wrote:

Hey Noel,

I am an old (past in some sense) member of CCL.  I have no opinions of the cytotoxicity of spike proteins as I haven't researched it.  I have however, since a long time, noticed that some of the leadership at CCL do tend to get the difference between rigorous science and appeals to authority confused.

Throughout this pandemic there has been changes in opinion and dissent even among institutional (grant funded) scientists about various aspects of how to handle this health crisis.

As one well respected cardiologist and science youtuber gives a fun rundown of all the different incidents of COVID-19 (up to August of 2020) "giving the science community a good wedgie" revealing many weaknesses in our own internal systems of scientific verification. 

https://www.youtube.com/watch?v=7leWXMr3ayk

Therein he even points out the falling of even one of his former biostatistics heros, who falls from public graces due to a sloppy publication and FOX media promotion of an erroneous idea based on many classically known forms of bias that he himself has published books on.

https://youtu.be/7leWXMr3ayk?t=457

Recently, I listened to a podcast run by two university professors/scientists interviewing a couple of (currently) well respected scientists who believe that we should be focusing more on developing vaccines which target the innate immune system and they cite the role that financial incentives play in vaccine development as one of the reasons why it is not being researched.  

https://www.bigbiology.org/season-3#episode66

I must say that this interview left me with more questions than answers, but it's yet another example of the fact that scientific opinion, even among institutional grant-funded players, is not (yet) a monolith.  So we shouldn't be too surprised when there is disagreement among citizen scientists.

In the process of doing science, there will (likely) be places where institutes of citizen science get it right and there will be places where they get it wrong.  Depending on how that happens, it runs the risk of sullying CCL's reputation and prospect for future grants. This is the credibility risk that I think that some of the established CCL members (who have PhD level credentials) worry about. (...that and, of course, the risk to their own name by association with CCL). I don't see an easy answer to that problem, but I think closing down discussion by shaming members into submission is not a the best approach. 

In light of this, I think CCL should probably have more discussions (not less) about how it can balance openness with playing an effective role in the scientific process and scicomm. Hopefully there is a way CCL can do this without inadvertently contributing to its own demise, amidst the vagaries and volatility of our current socio-political climate.

-Cere

On Fri, Jun 25, 2021 at 4:42 AM Noel Carrascal <noelca...@gmail.com> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/CCLmembers/CAAzQ6rZ26qxXETf-61Wt3u-nwgOi6j9VjvRJsSP_JfZPzDLb2w%40mail.gmail.com.

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[yann lala]

Fair. I have not been involved in Covid meetings and discussion, or CCL meeting in general for a long time so I can't really comment on that. Finding this balance is indeed difficult, and I don't have a clear answer to how to achieve it.

  Yann

On Fri, Jun 25, 2021 at 2:58 PM Cere Davis <cere...@gmail.com> wrote:

Yann,

I think we both agree, fundamentally on various idealized points.  The devil is in the details, as you have pointed out in your own way.  I am not suggesting that CCL should "fall into some kind of relativism" but I think a better balance can be struck than I have seen in past conversations.  

-Cere

[rece...@ianmathews.com]

Noel,

Very good email, very heartfelt, and I am sure many people on this thread share your experiences and frustrations. I have lurked for a year, and your email has brought me out of hibernation.

CCL on the internet is not a good filter, we used to be able to have side conversations and bypass a top down hierarchy. Are we back open? Can we start to safely congregate and discuss these matters together to grow together?

There is a lot to unpack here, but I agree with the sentiment of your email in many ways,

1) Vaccines can cause damage, and the spike protein does travel to the ovaries in disturbing amounts, and vaccines increase variant breakthroughs if vaccines are applied after local viral landfall.

           However, there are weak people everywhere, and many see it as our civic duty to submit to a national vaccination effort to help herd immunity.

2) I see a lack of data around the viral structure, machine learning, and inter-genera or inter-species comparisons. I hope other researchers have proven without a doubt that this statistically is not a Frankenstein engineering, but I have yet to see this, and in fact a few researchers on a TV channel not to be named have said the opposite.

I have included a great paper, and I would like to see this level of analysis applied to not only whole virus analysis, but spike proteins, RdRp protein, and other regions

There may be no smoking gun, and the natural genomic plasticity of betacoronaviruses may be our biggest foe in this battle

3) Are the inserts you mention in line with the virus's "high mutation rates, reaching from 1 in 1000 to 1 in 10000 nucleotides during replication" or can we show statistically the likelihood or unlikelihood of this occurrence

I do agree that CCL meetings generally can be frustrating, and some people are professionals at wasting time and obfuscating real forward momentum.

I also really appreciate your endeavor to computationally look at COVID and I would like to join you in this effort,

We COULD start a COVID statistics meeting, let's expand upon this conversation

[Patrik D'haeseleer]

And to all of you who would love to discuss these topics more - keep in mind that CCL and BioCurious have been doing a weekly 2-hour in-depth discussion session on all the latest Covid news and research every Saturday morning for the last (...checks...) 65 weeks now!

Please do join us for Covid Chat this Saturday 10am: https://www.meetup.com/Counter-Culture-Labs/events/bjvldsyccjbjc/

https://us02web.zoom.us/j/820128495?pwd=dE1kMHcxQ2o4UlI5dWdudk9YV1Q4Zz09

Some of the topics we have lined up this week include:

• The discovery of some SARS-Cov2 sequences from the very early days of the pandemic that had apparently been deleted from the databases by Chinese researchers
• Vaccine equity in our communities
• And yes, the coming surge in Delta variant, and what it might mean for us here in the Bay Area

We typically have a good mix of covering the latest news from around the world, digging into the data, publications and preprints underlying the news, linking to analyses by the some of our favorite scientists and science communicators that have done an excellent job in the past, and keeping an eye out for the latest science misinformation and conspiracy theories doing the rounds.

If you have a story or paper you'd like to add to the list, feel free to add it to this week's set of links here:

CCL-BioC COVID Zoom - Google Docs

Hope to see some of you tomorrow morning!

Patrik

[yann lala]

This video is meant to contextualize how the COVID pandemic has revealed many systemic weaknesses in "science" as it is embedded in a larger socio-cultural soup of corrupting incentives. 

I don't disagree with that. It is a crucial topic.

Obviously, it's true that science and "authority" are intermeshed in complicated ways. Which is all the more reason why it's important to examine and acknowledge the ways that authority-based incentive structures often influence science for the worse.  I mean that's supposed to be part of the point of having a "counter culture" lab.  Right?

Yes, definitively. I agree that pointing the credential is not the same as just using somebody's as an argument. I apologized, I misused appeal to authority in that case. What I tried to say is credentials are always part of the conversation to know where people talk from, and sometimes rejection of authority becomes a rejection of expertise and can be used to muddy the water and pretend all argument have the same scientific value. Some people I know are going as far as rejecting scientific paper because they don't like the conclusion of it, so they assume that there is big pharma conspiracy somewhere.

I am not saying it is what's happening at CCL, but I reacted that way because I find Noel's critics a bit light since he didn't really provided any evidence, and it seems to me that he complained that people didn't gave credit to his hypothesis even though they are not substantiated. In this specific case, Noel has a scientific training, he is higly qualified with a PhD. He should know better how to look for those kind of information and not do the "I am just asking question' thingy. There is multiple papers which looks at the evolution of the genome of the virus, and a lot of communication which talks about the lab leak hypothesis.

One published this month on Nature : https://www.nature.com/articles/d41586-021-01529-3

Or this one: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095063/

I do believe that if you have a scientific training and you have an expertise which give you some kind of authority, you do have a responsability to back up your claim, especially if it is a complicated topic. You can talk about the lab leak hypothesis, but not by just comparing few sequence and saying "that must be it".

And it is nothing personal against Noel, but disinformation against vaccines and their uses have a real impact on society. When you said previously that some members more tied to academia have to be careful of their images, it is true. For my side, if CCL become a place where anti-vaccine rethoric are nurtured, I probably will not want to be associated with it because I don't want to be associated to project which bring more harm to this planet. I don't know the balance, I don't know if the best to fight this is "in the marketplace of idea", but honestly from my experience, I am not too convinced by this strategy.

On Fri, Jun 25, 2021 at 3:56 PM Cere Davis <cere...@gmail.com> wrote:

You can't critizices CCL leadership to use appeal to authority when two sentences after you do one "As one well respected cardiologist and science youtuber". 

Would you prefer I wait to insert this youtube comment three sentences later rather than two...?  

"Appeal to authority" vs. this Youtube video seems like an incommensurate comparison in many ways.  I am not just pointing to credentials or an entire research domain and then saying "science says", I am giving you direct content from a person who happens to have some credentials in scicomm. Also, this doctor is giving a historical rundown not really a scientific one.  This video is meant to contextualize how the COVID pandemic has revealed many systemic weaknesses in "science" as it is embedded in a larger socio-cultural soup of corrupting incentives.  

I have found that acknowledgement of that simple fact has too often been downplayed in conversations with some people at CCL.  I probably should have said exactly that from the beginning.  Obviously, it's true that science and "authority" are intermeshed in complicated ways. Which is all the more reason why it's important to examine and acknowledge the ways that authority-based incentive structures often influence science for the worse.  I mean that's supposed to be part of the point of having a "counter culture" lab.  Right?

[Noel Carrascal]

Yann,

I think you missed the forrest for the trees. Take my perspective, i repeat my perspective, as a whole and do not decontextualize it argument by argument.

There is a problem with those enthroned scientists who gain tenure or the right to not get fired. That priviledge should be kept only for a very few remarkable scientists in my opinion. It blocks innovation. Oh, and scientist do have a choice.

I am not north american.

Watch out with comments like mortality is not a good measure of 'dangerosity'. It could come back and bite you. If not dead people, what is? People in history who have made that kind of calculations are not remembered as being good. One death by the virus is one too many.

"We have enough statistics..." really? This whole pandemic and the vaccination are still unfolding... how can you say that?

When i say i suspect the virus is designed, I admit I suspect It was created on purpose. Scientists have created polio viruses sintetically so it is not a crazy idea. That is not the same as to say they 'contaminated their own people to spread it throughout the world'. That is a different and more delicate story that i do not believe even from a goverment with a long history of human right violations, ethnic cleansing and oppressing their own people. Please don't accuse me of saying stuff i didn't say.. that is irresponsible. Measure your comments. 

I leave it here. I just felt like you misfired a lot. I just wanted to respond to a few pearls of wisdom.... not. I don't want to go on endless arguments. I would love to hear your own perspectives other than just being disagreeable. 

Noel

[Patrik D'haeseleer]

PS: almost missed a paper that just got published (thanks, This Week in Virology!) that includes four novel SARS-CoV-2-related bat viruses.
The new RpYN06 is the now closest relative of SARS-CoV-2 in most of the virus genome, although it has some deletions in Spike.

Patrik

On Fri, Jun 25, 2021 at 5:46 PM Patrik D'haeseleer <pat...@gmail.com> wrote:

On Fri, Jun 25, 2021 at 4:42 AM Noel Carrascal <noelca...@gmail.com> wrote:

> I stopped participating in the covid19 meetings because I noticed people were just relaying information from different sources without getting into the data.
>

> Instead, I downloaded the sequences of about 30 covid19 spike proteins from covid viruses that include the 2003, 2004 and 2019 strains. I aligned them and I noticed 5 incertions in covid19, relative to covid 2003/04, that i did not find in sequence comparisons between other two strains that I aligned. I used software developed for protein design that I developed in grad school to align the sequence gaps to a structure of the protein and the gaps corresponded to loop regions of the spike protein. These are not secondary structure alignments, these are thertiary structure alignments in 3D and the matches had very low RMSD. Loop regions that are disordered are in the surface and for that reason they likely play roles in inmune responses and cell entry. q_LFEQ%40mail.gmail.com.

Since Noel mentioned insertions in the Spike protein, I figured I'd put my money where my mouth is, and dig into some of the raw data. Yann already mentioned this excellent Nature paper that includes an alignment of SARS-Cov2 Spike with SARS1 and some of the closest related bat and pangolin coronaviruses. Their Figure 1 shows part of the alignment, and has accession numbers for the sequences they used. I didn't bother to assemble the pangolin viral metagenome myself, but found a pangolin coronavirus spike protein already in genbank.

A quick alignment using MUSCLE shows the following (leaving off the bottom half, where all six sequences are almost identical):

You can see that the Pangolin sequence and the closest bat sequence RaTG13 are substantially closer to SARS-CoV2 (here listed as Wuhan-Hu-1) than the original SARS-CoV and some of the other bat viruses. Yes, there are a couple of inserts, including a 7 amino acid one on the first line that is shared with RaTG13 and partially with Pangolin. And there are a few 4aa inserts and shorter, including the one creating the notorious furin-like cleavage site on the bottom line.

None of these are out of the ordinary for what I would expect from a protein alignment for viral genomes that are as far apart as these are, and almost all are shared with the closest rat and pangolin sequences we have. And if these inserts are in exposed loops of the protein that are exposed to the immune system, then that is *exactly* where the virus experiences the most evolutionary pressure, and where you would expect changes to occur. 

The furin-like cleavage site is an interesting case, because so many conspiracy theories focus on it. Note that furin cleaves canonically at RRR or RKR - the RRAR sequence found here is actually a pretty crappy cleavage site for furin, and not how anyone would engineer it! Also, similar furin cleavage sites are found all across the coronavirus phylogenetic tree and are apparently easily lost and gained during evolution. Here's an excellent paper on furin cleavage sites in coronaviruses - I think their graphical abstract really says it all:

Patrik

[Patrik D'haeseleer]

Oops - here's the paper:

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

https://www.sciencedirect.com/science/article/pii/S0092867421007091

[Noel Carrascal]

Cere, 

Thank you for your perspective. It does enrich the discussion. Your points have broaden my horizons. I do not agree 100% of some of the perspectives in the links, but it is good to know and keep in mind.

Noel

On Fri, Jun 25, 2021, 3:36 PM Cere Davis <cere...@gmail.com> wrote:

Hey Noel,

I am an old (past in some sense) member of CCL.  I have no opinions of the cytotoxicity of spike proteins as I haven't researched it.  I have however, since a long time, noticed that some of the leadership at CCL do tend to get the difference between rigorous science and appeals to authority confused.

Throughout this pandemic there has been changes in opinion and dissent even among institutional (grant funded) scientists about various aspects of how to handle this health crisis.

As one well respected cardiologist and science youtuber gives a fun rundown of all the different incidents of COVID-19 (up to August of 2020) "giving the science community a good wedgie" revealing many weaknesses in our own internal systems of scientific verification. 

https://www.youtube.com/watch?v=7leWXMr3ayk

Therein he even points out the falling of even one of his former biostatistics heros, who falls from public graces due to a sloppy publication and FOX media promotion of an erroneous idea based on many classically known forms of bias that he himself has published books on.

https://youtu.be/7leWXMr3ayk?t=457

Recently, I listened to a podcast run by two university professors/scientists interviewing a couple of (currently) well respected scientists who believe that we should be focusing more on developing vaccines which target the innate immune system and they cite the role that financial incentives play in vaccine development as one of the reasons why it is not being researched.  

https://www.bigbiology.org/season-3#episode66

I must say that this interview left me with more questions than answers, but it's yet another example of the fact that scientific opinion, even among institutional grant-funded players, is not (yet) a monolith.  So we shouldn't be too surprised when there is disagreement among citizen scientists.

In the process of doing science, there will (likely) be places where institutes of citizen science get it right and there will be places where they get it wrong.  Depending on how that happens, it runs the risk of sullying CCL's reputation and prospect for future grants. This is the credibility risk that I think that some of the established CCL members (who have PhD level credentials) worry about. (...that and, of course, the risk to their own name by association with CCL). I don't see an easy answer to that problem, but I think closing down discussion by shaming members into submission is not a the best approach. 

In light of this, I think CCL should probably have more discussions (not less) about how it can balance openness with playing an effective role in the scientific process and scicomm. Hopefully there is a way CCL can do this without inadvertently contributing to its own demise, amidst the vagaries and volatility of our current socio-political climate.

-Cere

On Fri, Jun 25, 2021 at 4:42 AM Noel Carrascal <noelca...@gmail.com> wrote:

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[Noel Carrascal]

Patrik,

Thanks for putting the data out. I will look at it carfully. I am overseas and away from my personal computer where i have my data somewhere. I think this exchange is healthy and i believe it is impossible to prove or disprove either side. Yet, it is always good to just lay down and consider both sides of the arguments.

A word on conspiracy theories. Dismissing them quicly is doing what a conspiracy theory intends only in reverse. 

Noel

On Sat, Jun 26, 2021, 12:46 AM Patrik D'haeseleer <pat...@gmail.com> wrote:

On Fri, Jun 25, 2021 at 4:42 AM Noel Carrascal <noelca...@gmail.com> wrote:

> I stopped participating in the covid19 meetings because I noticed people were just relaying information from different sources without getting into the data.
>

[Patrik D'haeseleer]

On Fri, Jun 25, 2021 at 5:45 PM Cere Davis <cere...@gmail.com> wrote:

One thing that you could add to the pile of questions is this BigBiology podcast link I sent.  I mean if they are claiming that the innate immune system is what we should be paying more attention to then I'm like:  Didn't we just spend months hearing about the terribleness of "cytokine storms" and how the innate immune systems is baaaad, m'kay, and must be "kept under control"?  I just didn't know how to weigh any of this against a lot of stuff I have "learned" about the innate immune system.  I was sort of annoyed that the interviewers didn't even ask about that.  To be fair, I was doing a lot of other things while this podcast was playing, so I might have missed it if they covered it. 

Yes, this was actually in the news back in October. Some vaccines - especially the old fashioned ones which use killed or live attenuated whole pathogens - are so efficient at stimulating the innate immune system that they also wind up providing some protection against entirely unrelated infections. Here's an NPR story on this (from our copious Covid Chat meeting notes):

https://www.npr.org/sections/health-shots/2020/10/08/917831035/could-the-live-flu-vaccine-help-you-fight-off-covid-19

Here's some positive results from a Phase II clinical trial with the BCG vaccine for TB:

https://www.medrxiv.org/content/10.1101/2020.10.28.20221630v1

If you're interested in cytokine storms, you may enjoy last week's This Week in Virology episode, where they talked with David Fajgenbaum, who suffered from a rare and typically fatal cytokine storm disease while in med school, decided to research his own disease, and set up the Center for Cytokine Storm Treatment & Laboratory. He has since also created the CORONA project to identify and track all treatments reported for COVID-19 in an open-source data repository (which is where I found the BCG trial results!):

https://www.microbe.tv/twiv/twiv-766/

https://cdcn.org/corona-data-viewer/

Patrik

 

-Cere

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[yann lala]

Watch out with comments like mortality is not a good measure of 'dangerosity'. It could come back and bite you. If not dead people, what is? People in history who have made that kind of calculations are not remembered as being good. One death by the virus is one too many.First of all, let me say "respect" to anyone and everyone who has been holding court for this event over the period of the pandemic...

For sure.

There is a problem with those enthroned scientists who gain tenure or the right to not get fired. That priviledge should be kept only for a very few remarkable scientists in my opinion. It blocks innovation. Oh, and scientist do have a choice.

I understand this perspective. And I disagree. To all of it. Innovation is not blocked by tenure track scientists, but mostly by the patent system. Even the World Economic Forum recognized it  to some extent. (https://www.weforum.org/agenda/2013/05/do-patents-help-or-hinder-innovation/). The mechanism proposed to why patent inhibit innovation is quite clear. What would be the mechanism for tenure scientific to block innovation? They stop doing research?  They refuse to work on innovative project? Do we have any evidence of that?

No, scientists don't have a choice. If they want to do science in academia, they have to write grant and publish paper. If they don't publish paper, they will not have grants, if they don't have grant, they can't finance their science. So I don't know where the choice is here. (If we remove leaving from the equation, but if they do, they are not really academic scientist anymore)

I am not north american.

My bad, sorry about that.

Watch out with comments like mortality is not a good measure of 'dangerosity'. It could come back and bite you. If not dead people, what is? People in history who have made that kind of calculations are not remembered as being good. One death by the virus is one too many.

I am not saying that mortality is not important, I am saying it is not enough. Like I said, there is the issue of hospital being too crowded, and there is the issue of long covid. And the issue of mutations of the virus. Also, if one death by the virus is one too many, and I agree with that, than the covid response was definitively not over-blown, don't you think?

"We have enough statistics..." really? This whole pandemic and the vaccination are still unfolding... how can you say that?

I specified short term, and we have more than 6 month of history,  and there is 2.75 dose that had been admninistered. So yeah, I think scientists have enough data to say it is safe for the short term period.

I just felt like you misfired a lot.

When i say i suspect the virus is designed, I admit I suspect It was created on purpose. 

You just proved that I didn't misfired. Even if you do a huge analysis of the sequence (thanks Patrick by the way), there is no way that you can prove or disprove the validity of the lab leaks scenario, since those mutation can happen naturally. Which every paper talking about this hypothesis mention. I really don't see the value to agitate for the sake of it. Hypothetically, let's say you prove a lab leak. So what? Lab leaks happen every where, even in high security lab. Scientists are human and they do mistake. Nobody managed to create a user proof system that prevent all mistakes. Of course scientists need to improve their process, and they already are trying. To my point of view, the lab leak scenario is a meaningless excercise, unless you are interested in lab safety.

I admit I suspect It was created on purpose. That is not the same as to say they 'contaminated their own people to spread it throughout the world'. That is a different and more delicate story that i do not believe even from a goverment with a long history of human right violations, ethnic cleansing and oppressing their own people.

I never said you said that. I said ; "Thinking the chinese governement did it on purpose and contaminated their own population to spread it to the world is conspiracy material. A lab leak is not, but very unlikely."

I was making the distinction between two lab leak scenario, one accidental, and one done on purpose. The former is not conspiracy material, the latter is. Let's put this one on my bad english writing skills.

I would love to hear your own perspectives other than just being disagreeable.

I laid out all my argument. Dismissing them like that is bit disingenuous. I note that you didn't respond to my arguments about the vaccine and how it works.

As for me disagreeable, I am perfectly fine with it. I think your email needed a vigourous rebuttal, especially the vaccine part. If it makes me the villain of the story, it's ok, we French are used to that in movies. Please picture me as Vincent Cassel or Lambert Wilson.

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