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Beerpig's Snug No Politics Coronavirus Thread

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sg31
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Re: Beerpig's Snug No Politics Coronavirus Thread

#337679

Postby sg31 » September 2nd, 2020, 3:01 pm

I've found over the years that people believe what they want to believe and read articles/ watch programmes that support that belief. They find reason to discredit things that go against their belief. Trying to persuade them that they are wrong is impossible or at least very difficult.

I've been reading research papers since this all started, they are generally way above my competence level but I have friends in America who explain the implications of much of the information.

As Scotia has said most general newspaper reports are pretty useless, unless they are employed by one of the specialist science or medical journals they just don't understand what they are reading. If they work for one of the broadsheets they are generalists by and large, expected to cover everything thrown at them. When it gets to sharp end of medical research they don't have a prayer of understanding the complex issues . When you get to the real specialist stuff even another researcher in another medical field will struggle.

As a layman it seems to me self evident that Covid is a seriously nasty disease, it has killed tens of thousands of people around the world, even more have complications from the illness that will be with them for the rest of their lives.

Just about every Government in the world has been forced into bringing in severe restrictions and lockdowns to reduce the infection rate and manage the pressure on hospital beds. These politiciand are fallible individuals but they did have expert advice. They generally followed the science and took the recommended action. I'm prepared to assume they knew more than most of us did and give them the benefit of the doubt. They were faced with a serious threat and dealt with it. The fact that our pro business Conservative Government introduced a lockdown that damaged business interests is suggestive that they had liitle alternative

It might not be what we desire but there are flare ups around the world that need dealing with. That isn't peoples imagination it is happening.

If you don't want to believe Covid is a threat that's fine, I'm not going to try to persuade you to change your mind.

I'm lucky I live in a rural location and I'm retired, there's no need for me to interact with others unless I consider it safe. I do appreciate that others have no such luck.

johnhemming
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Re: Beerpig's Snug No Politics Coronavirus Thread

#337681

Postby johnhemming » September 2nd, 2020, 3:08 pm

sg31 wrote:I've found over the years that people believe what they want to believe and read articles/ watch programmes that support that belief. They find reason to discredit things that go against their belief. Trying to persuade them that they are wrong is impossible or at least very difficult.

I think you are right about this as a general principle. I find online debates helpful to enable me to challenge my own views and ensure that I get facts right. I also tend to read material sourced from people who I don't agree with.

The issue of confirmation bias is a key issue in investment.

However, I do have quite a bit of experience of the public sector and systems of government and am perhaps not as confident as you as to the ability of most politicians in selecting which science to follow.

scotia
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Re: Beerpig's Snug No Politics Coronavirus Thread

#337683

Postby scotia » September 2nd, 2020, 3:09 pm

JamesMuenchen wrote:He cited an experiment conducted during his time at the BMJ, in which a short paper containing eight deliberate errors was sent to 300 reviewers, as evidence of how badly the system can fail to detect errors.

“No one found more than five, the median was two, and 20 percent didn’t spot any,”

Yes - regrettably true. Going back a long time, I found that peer reviewing a paper required a lot of work - especially since I didn't have the capability of online searches. And it became increasingly obvious that others were not taking a similar amount of care.
However - on the statistics you quoted above - I reckon if I had discovered 5 errors, I wouldn't have bothered looking for more - I would simply have reported it as not worthy of publication.
But yes - I still think a flawed system of reviewing is better than none.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337710

Postby Nimrod103 » September 2nd, 2020, 5:14 pm

sg31 wrote:As Scotia has said most general newspaper reports are pretty useless,


Please, on the subject of Carl Heneghan, we are not talking about newspaper 'reports'. These are articles (the Spectator one at least) under his own name, and presumably carry his full authority and approval. If he is wrong, it is his neck on the line.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337722

Postby scotia » September 2nd, 2020, 5:46 pm

Nimrod103 wrote:
sg31 wrote:As Scotia has said most general newspaper reports are pretty useless,


Please, on the subject of Carl Heneghan, we are not talking about newspaper 'reports'. These are articles (the Spectator one at least) under his own name, and presumably carry his full authority and approval. If he is wrong, it is his neck on the line.

I should possibly bear part of the blame. I was referring to two newspaper references - one from the Daily Mail, the other from the Spectator. The headline in the Daily Mail would not, I hope, have been written by Carl Heneghan - so all trust in such an article evaporated very quickly. The Spectator article is considerably more scholarly - but my personal past experience of national newspapers and TV does not always support the claim that all that is reported is exactly as the author intended. So I'll stick to scientific journals - and am willing to read internal reports on authors' sites - although I hope they will subject their work to appropriate scrutiny.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337727

Postby scotia » September 2nd, 2020, 6:17 pm

Interesting newly published set of experimental results from Iceland in the New England Journal of Medicine
https://www.nejm.org/doi/full/10.1056/NEJMoa2026116?query=recirc_curatedRelated_article
and the accompanying editorial is
https://www.nejm.org/doi/full/10.1056/NEJMe2028079?query=recirc_curatedRelated_article

dealtn
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Re: Beerpig's Snug No Politics Coronavirus Thread

#337728

Postby dealtn » September 2nd, 2020, 6:18 pm

bungeejumper wrote: and accounts of trips to the supermart are laden with horror stories about non-distancing and non-masking.


I think we were brought up on different versions of horror stories!

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337736

Postby sg31 » September 2nd, 2020, 7:07 pm

This is an interesting article. It is a study of work done on a supercomputer which threw up some interesting observations.

https://elemental.medium.com/a-supercom ... cb8eba9d63

This is the paper itself. It doesn't really draw any definite conclusions but points a possible way forward and suggests existing drugs which may be worth proper studies.

https://elifesciences.org/articles/59177

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337884

Postby scotia » September 3rd, 2020, 11:24 am

scotia wrote:has anybody on this board been attempting to extract Covid-19 data from the government source using the instructions contained in an on-line manual
https://coronavirus.data.gov.uk/developers-guide.
I find this manual opaque, and its suggestion that you need to develop an api to get at the data seems crazy.
It also is subject to changes which can trash an application - but there are no change lists in the updated guide to warn a developer
However I wanted to get at the data, and I set forth to carry it out, using curl on a Windows PC.
After a bit of a struggle, I got it working, then they changed "newDeathsByPublishDate" to "newDeaths28DaysByPublishDate" - and the application crashed. So I worked out from error messages what had happened, and got it back into action.
However a few days ago it ceased working - no error messages - and it simply returned zero data.
Is anyone out there using a similar app? Have you run into similar difficulties? Do you have a soluion?
I have emailed the address on the developers guide - but have had no response.

From the lack of feedback It looks like nobody on this board has been attempting to extract Covid-19 data from the government source using an application based on their developers' guide
But just in case anyone is thinking of trying it out, I can now report that it is back working - but I have received no response on why it stopped working.
When working, its an excellent source of up-to-date Covid-19 data, with selective granularity down from country to local authority level.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#337908

Postby johnhemming » September 3rd, 2020, 12:36 pm

Here is a peer reviewed editorial in the BMJ essentially making the same point as I have made on a number of occasions.

https://www.bmj.com/content/370/bmj.m3364

Current antibody tests fail to identify people who had mild infections

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Re: Beerpig's Snug No Politics Coronavirus Thread

#338012

Postby servodude » September 4th, 2020, 5:59 am

Here's a link to a meta analysis that looks to have quite wide and deep coverage
https://onlinelibrary.wiley.com/doi/10.1002/jmv.26326

this bit from the abstract struck me as interesting:
A total of 50 155 patients from 41 studies with confirmed COVID‐19 were included.
The pooled percentage of asymptomatic infection is 15.6% (95% CI, 10.1%‐23.0%)


I hope you're all keeping well (this thread seems to grow too quickly to keep up with you all)

-sd

johnhemming
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Re: Beerpig's Snug No Politics Coronavirus Thread

#338030

Postby johnhemming » September 4th, 2020, 8:40 am

servodude wrote:this bit from the abstract struck me as interesting:
A total of 50 155 patients from 41 studies with confirmed COVID‐19 were included.
The pooled percentage of asymptomatic infection is 15.6% (95% CI, 10.1%‐23.0%)



I think the difficulty is one as to how one identifies all of the people with asymptomatic infection. Hence one would expect most studies based upon confirmed infection to identify a lower bound.

I had a good discussion yesterday with an A&E consultant who has been dealing with Covid cases. He agrees with my view that in England in the urban areas we are essentially at the HIT. It will take a while for this to seep through to government and so I expect them to continue doing the rain dance for a while longer.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#338035

Postby johnhemming » September 4th, 2020, 9:03 am

Looking at the detailed chart as to asymptomatic cases the highest figure is about 89%. There are quite a few over 50%. The analysis itself is meaningless.

scotia
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Re: Beerpig's Snug No Politics Coronavirus Thread

#338077

Postby scotia » September 4th, 2020, 12:04 pm

scotia wrote:
scotia wrote:has anybody on this board been attempting to extract Covid-19 data from the government source using the instructions contained in an on-line manual
https://coronavirus.data.gov.uk/developers-guide.
I find this manual opaque, and its suggestion that you need to develop an api to get at the data seems crazy.
It also is subject to changes which can trash an application - but there are no change lists in the updated guide to warn a developer
However I wanted to get at the data, and I set forth to carry it out, using curl on a Windows PC.
After a bit of a struggle, I got it working, then they changed "newDeathsByPublishDate" to "newDeaths28DaysByPublishDate" - and the application crashed. So I worked out from error messages what had happened, and got it back into action.
However a few days ago it ceased working - no error messages - and it simply returned zero data.
Is anyone out there using a similar app? Have you run into similar difficulties? Do you have a soluion?
I have emailed the address on the developers guide - but have had no response.

From the lack of feedback It looks like nobody on this board has been attempting to extract Covid-19 data from the government source using an application based on their developers' guide
But just in case anyone is thinking of trying it out, I can now report that it is back working - but I have received no response on why it stopped working.
When working, its an excellent source of up-to-date Covid-19 data, with selective granularity down from country to local authority level.

I spoke too soon. The government site is now responding with data - for only for some of the areas. In these reporting areas the number of (Covid-19) Cases (new and cumulative) seems reasonably up to date - at least until until the end of August. But all of the (Covid-19) Deaths Data (new and cumulative) has disappeared. E.G. for London we have apparently zero (Covid-19) deaths (new and cumulative) from the end of January to the present. So we are left clueless as to what is actually happening.
And I'll modify an earlier statement from its an excellent source of up-to-date Covid-19 data to it should be an excellent source of up-to-date Covid-19 data
For those interested in what is currently shown for the number of new daily Cases in the London data - it peaked around 1000 at the beginning of April, then fell to around 30 towards the end of June, but is now back up around 130 in late August. The cumulative number of Cases in London is currently around 40,000.

Itsallaguess
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Re: Beerpig's Snug No Politics Coronavirus Thread

#338105

Postby Itsallaguess » September 4th, 2020, 2:07 pm

The numbers of people testing positive for coronavirus in England remain unchanged in the week to 25 August, according to the Office for National Statistics.

Its latest survey found there were about 2,000 new cases per day and an estimated 27,100 people in the community had the virus during that week.

This is similar to the previous week and several weeks before, which suggest that, despite outbreaks in some areas, overall cases continue to be stable and infections remained at a constant level during August.

Based on tests on people in households whether they have symptoms or not, the figures are thought to give one of the most accurate pictures of whether or not new infections are increasing.

It does not cover people in hospital or care homes.


https://www.bbc.co.uk/news/health-54025713

Cheers,

Itsallaguess

scotia
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Re: Beerpig's Snug No Politics Coronavirus Thread

#338117

Postby scotia » September 4th, 2020, 3:11 pm

London in August - extracted from the (partially working) government Covid-19 data site.
date name cases
31/08/2020 London {'daily': 135, 'cumulative': 39893}
30/08/2020 London {'daily': 128, 'cumulative': 39758}
29/08/2020 London {'daily': 126, 'cumulative': 39630}
28/08/2020 London {'daily': 214, 'cumulative': 39504}
27/08/2020 London {'daily': 226, 'cumulative': 39290}
26/08/2020 London {'daily': 165, 'cumulative': 39064}
25/08/2020 London {'daily': 168, 'cumulative': 38899}
24/08/2020 London {'daily': 195, 'cumulative': 38731}
23/08/2020 London {'daily': 143, 'cumulative': 38536}
22/08/2020 London {'daily': 117, 'cumulative': 38393}
21/08/2020 London {'daily': 166, 'cumulative': 38276}
20/08/2020 London {'daily': 203, 'cumulative': 38110}
19/08/2020 London {'daily': 152, 'cumulative': 37907}
18/08/2020 London {'daily': 181, 'cumulative': 37755}
17/08/2020 London {'daily': 190, 'cumulative': 37574}
16/08/2020 London {'daily': 87, 'cumulative': 37384}
15/08/2020 London {'daily': 105, 'cumulative': 37297}
14/08/2020 London {'daily': 127, 'cumulative': 37192}
13/08/2020 London {'daily': 124, 'cumulative': 37065}
12/08/2020 London {'daily': 150, 'cumulative': 36941}
11/08/2020 London {'daily': 149, 'cumulative': 36791}
10/08/2020 London {'daily': 142, 'cumulative': 36642}
09/08/2020 London {'daily': 67, 'cumulative': 36500}
08/08/2020 London {'daily': 55, 'cumulative': 36433}
07/08/2020 London {'daily': 119, 'cumulative': 36378}
06/08/2020 London {'daily': 105, 'cumulative': 36259}
05/08/2020 London {'daily': 115, 'cumulative': 36154}
04/08/2020 London {'daily': 103, 'cumulative': 36039}
03/08/2020 London {'daily': 87, 'cumulative': 35936}
02/08/2020 London {'daily': 72, 'cumulative': 35849}
01/08/2020 London {'daily': 58, 'cumulative': 35777}

sg31
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Re: Beerpig's Snug No Politics Coronavirus Thread

#338503

Postby sg31 » September 6th, 2020, 11:04 am

https://phys.org/news/2020-09-nanobody- ... ction.html

"We hope our findings can contribute to the amelioration of the COVID-19 pandemic by encouraging further examination of this nanobody as a therapeutic candidate against this viral infection," says Gerald McInerney, corresponding author and associate professor of virology at the Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet.

"Using cryo-electron microscopy, we were able to see how the nanobody binds to the viral spike at an epitope which overlaps with the cellular receptor ACE2-binding site, providing a structural understanding for the potent neutralization activity," says Leo Hanke, postdoc in the McInerney group and first author of the study.

Nanobodies offer several advantages over conventional antibodies as candidates for specific therapies. They span less than one-tenth the size of conventional antibodies and are typically easier to produce cost-effectively at scale. Critically, they can be adapted for humans with current protocols and have a proven record of inhibiting viral respiratory infections.

"Our results show that Ty1 can bind potently to the SARS-CoV-2 spike protein and neutralize the virus, with no detectable off-target activity," says Ben Murrell, assistant professor in the Department of Microbiology, Tumor and Cell Biology and co-senior author of the publication. "We are now embarking on preclinical animal studies to investigate the neutralizing activity and therapeutic potential of Ty1 in vivo."

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Re: Beerpig's Snug No Politics Coronavirus Thread

#338504

Postby Itsallaguess » September 6th, 2020, 11:10 am

sg31 wrote:
Nanobodies offer several advantages over conventional antibodies as candidates for specific therapies. They span less than one-tenth the size of conventional antibodies and are typically easier to produce cost-effectively at scale. Critically, they can be adapted for humans with current protocols and have a proven record of inhibiting viral respiratory infections.

"Our results show that Ty1 can bind potently to the SARS-CoV-2 spike protein and neutralize the virus, with no detectable off-target activity," says Ben Murrell, assistant professor in the Department of Microbiology, Tumor and Cell Biology and co-senior author of the publication. "We are now embarking on preclinical animal studies to investigate the neutralizing activity and therapeutic potential of Ty1 in vivo."


Given the monumental human focus on these types of ultra-modern scientific advances in relation to the COVID studies, it makes me wonder when we read articles telling us that 'We may always have to live with COVID', whether they might have the completely wrong end of the stick here, and I sometimes wonder if not only may we one day be in a position to neutralise this particular strain of SARS, but perhaps even many of the other types of similar ailments that we really have had to live with for some time now...

Cheers,

Itsallaguess

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Re: Beerpig's Snug No Politics Coronavirus Thread

#338512

Postby sg31 » September 6th, 2020, 11:33 am

Itsallaguess wrote:Given the monumental human focus on these types of ultra-modern scientific advances in relation to the COVID studies, it makes me wonder when we read articles telling us that 'We may always have to live with COVID', whether they might have the completely wrong end of the stick here, and I sometimes wonder if not only may we one day be in a position to neutralise this particular strain of SARS, but perhaps even many of the other types of similar ailments that we really have had to live with for some time now...

Cheers,

Itsallaguess


I'm no expert but as I delve deeper into this and talk to friends involved in research for cancer treatments it is ovious that fantastic progress is being made. 20 years ago, maybe even 10 years ago I don't think we could have envisaged some of the things that are now being developed.

Given enough money I feel sure many current medical problems will be easily controlled but nature does seem to have a way of finding new challenges to throw at the human race. I don't think the battle will ever be won by humans. If nature comes up with the right virulent and deadly virus it could wipe out the vast majority of human life before we could find a cure.

We are our own worst enemy in many ways, we seem to organise society in away that encourages the worldwide spread of viruses as rapidly as possible and it seems a large percentage of the western population isn't prepared to take even modest precautions to avoid infection. One day, hopefully far into the future, a challenge will arise and we won't do what is required to survive until medical researchers can find the answer.

I doubt I will be around to see it happen.

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Re: Beerpig's Snug No Politics Coronavirus Thread

#338518

Postby Mike4 » September 6th, 2020, 11:50 am

sg31 wrote:I'm no expert but as I delve deeper into this and talk to friends involved in research for cancer treatments it is ovious that fantastic progress is being made. 20 years ago, maybe even 10 years ago I don't think we could have envisaged some of the things that are now being developed.

Given enough money I feel sure many current medical problems will be easily controlled but nature does seem to have a way of finding new challenges to throw at the human race. I don't think the battle will ever be won by humans. If nature comes up with the right virulent and deadly virus it could wipe out the vast majority of human life before we could find a cure.

We are our own worst enemy in many ways, we seem to organise society in away that encourages the worldwide spread of viruses as rapidly as possible and it seems a large percentage of the western population isn't prepared to take even modest precautions to avoid infection. One day, hopefully far into the future, a challenge will arise and we won't do what is required to survive until medical researchers can find the answer.

I doubt I will be around to see it happen.


I think the virulent and deadly virus you describe is more likely to originate in a laboratory than come from nature.

And as Dr Chris Martenson intriguingly points out in response to those who say there is no evidence to say SARS-CoV-2 escaped from a lab, there is no evidence it originated in nature either.


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