Naked Science Forum
Life Sciences => Physiology & Medicine => COVID-19 => Topic started by: L_D_G on 20/12/2020 18:34:05
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So I read about this a while ago, but am now trying to track down answers to questions I have.
The NYT has an article from 16 March titled "White House Takes New Line After Dire Report on Death Toll".
The report, which was not released in a peer-reviewed journal but was authored by 30 scientists on behalf of Imperial College’s coronavirus response team, simulated the role of public health measures aimed at reducing contact.
What is the difference between peer-reviewed and being authored by (what reads to me) as 30 peers? I'm guessing people involved in the study/the writing of it vs people completely separate from it?
Presumably, in the 20 some days between the Imperial College study being published, and Fauci/Birx meeting with Trump at the White House for the first time, one of them read the thing.
Then I come across an interesting breakdown on Columbia.edu's Statmodeling site in a post titled "So the real scandal is why did anyone ever listen to this guy" in talking about Neil Ferguson.
So I guess my question for the science community is: what would have been the thought process and reasoning-back in April-for our CDC leaders to accept the Imperial College study? And why?
I'm not trying to say any direction was right or wrong. We are where we are now. I'm just trying to understand stuff and this seemed weird. Thanks for your inputs!
As an additional question- how does everyone feel about going from "don't wear masks" to "wear a mask". I wear a mask, I'm just trying to take advantage of smart minds while I have your attention.
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So I guess my question for the science community is: what would have been the thought process and reasoning-back in April-for our CDC leaders to accept the Imperial College study? And why?
At some point, anyone who calls himself a scientist ignores what he has been told to think by a philosopher, priest or politician, and tells the truth. It's what distinguishes us from the arselicking idiots in the White House or Downing Street.
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The way I'm reading this is that a potentially questionable study (rebukes in the columbia post I referenced) was not peer reviewed, but used as the argument to usher in quarantines.
I'm not trying to question anything so much as I am trying to understand it...if that makes sense.
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Imperial College/Neil Ferguson Covid model
This is an April 2020 overview of Neil Ferguson's COVID model: https://www.nature.com/articles/d41586-020-01003-6
It is an opinion piece from a scientific journal.
What is the difference between peer-reviewed and being authored by (what reads to me) as 30 peers? I'm guessing people involved in the study/the writing of it vs people completely separate from it?
Yes, that is a reasonable summary.
A journal aims to get experts who are not connected with the original study to critique it, and feed this back to the original authors to update and resubmit the study. Sometimes this process takes several months.
Like everything with a pandemic, there isn't several spare months before it grew to a major disaster, so a lot of communication about COVID-19 has been through pre-print servers like medrxiv ("medical archive"), and via press release. These are not peer-reviewed, and should be taken with a grain of salt.
See: https://connect.medrxiv.org/relate/content/181
Nature, one of the traditional peer-reviewed publishers, set up a podcast to cover the rapidly-changing COVID-19 landscape, with professional science reporters providing an overview of these less-reliable sources.
Columbia.edu's Statmodeling site in a post titled "So the real scandal is why did anyone ever listen to this guy"
See: https://statmodeling.stat.columbia.edu/2020/05/08/so-the-real-scandal-is-why-did-anyone-ever-listen-to-this-guy/
This web page seems to be a rant, based on the following inflammatory article in the National Review:
https://www.nationalreview.com/corner/professor-lockdown-modeler-resigns-in-disgrace/
I'm not familiar with this US-oriented news organisation, but it appears to be a strongly pro-Trump site.
- If so, it was probably an opinion piece echoing Trump's priority that economics is more important than health and welfare.
As far as I can see, Neil Ferguson is still employed at Imperial College:
https://www.imperial.ac.uk/people/neil.ferguson
The person who resigned was not Neil Ferguson, but a White House COVID-19 adviser Scott Atlas (the video won't play for me).
The point of a successful epidemiologist is that they will state the uncertainties, but ensure people are aware of the potential risks.
- The uncertainties with mad cow disease were huge, and he predicted a range of fatalities from 50 - 50,000
- But if the government takes prompt action, the results will be at the lower end of the range.
Back to the Nature article: near the end, it hopefully suggests that if restrictions remain in place, the UK COVID-19 deaths could remain below 20,000 (today it is above 67,000). So he is clearly not a panic - monger.
A clear reminder: If you want science, pay attention to a science reporter, not a political pamphlet.
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National Review isn't exactly objective, you are correct. I just sometimes find it helpful to understand an argument before fully grasping where it is wrong-kind of like a piece by piece deconstruction.
I found the Columbia post to bring up interesting points on why Ferguson was trusted. He did end up resigning, but it wasn't over the study. It was because he broke quarantine rules. I am however appreciative of you taking the time to go in and read that post from a scientific stand point and conclude it as politically motivated. Without a proper understanding of the sciences involved here, I simply was unsure where the line was in that post.
The last thing I think I'm still trying to reconcile is why Fauci and Birx used this paper if it wasn't peer reviewed. From a novice point of view, isn't that a bad thing? I get the accelerated timeline we were forced into, but I'm having trouble understanding how a scientist can justify it.
I think a lot of the political disagreement surrounding covid-at least in the US-has been around govt overreach, the effect on the economy, and going from "save masks for medical professionals" to "everyone wear a mask".
Appreciate the thoughtful and prompt response...as well as posting of the links. I tried to and this thing told me I couldn't post external links.
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The way I'm reading this is that a potentially questionable study (rebukes in the columbia post I referenced) was not peer reviewed, but used as the argument to usher in quarantines.
The argument to introduce quarantines goes back to Roman times, or even Leviticus. If you have an infectious disease for which
(a) the known vector is humans
(b) there is no known cure and
(c) the outcome is unacceptable
quarantine is the only method of minimising its impact. Fortunately the governments of Australia and New Zealand were more interested in protecting their populations than their popularity, so a shred of civilisation has been saved from economic and social disaster by the swift and complete introduction of quarantine.
why Fauci and Birx used this paper if it wasn't peer reviewed
Formal peer review takes time (which you don't have in a pandemic) and doesn't guarantee that the paper does anything more than support the prejudices of the reviewer. This has been demonstrated time and again by submitting the same paper to different groups of established reviewers but ascribed to authors with different names, institutions, or nationalities. White, British, male, Imperial College, professor, OBE, FMedSci, pretty much guarantees a favorable review, regardless of the content, so you'd just be wasting time and lives by insisting on it.
Fauci and Birx are experts in the field and as well qualified to review the paper as anyone else, given that very little was known about the transmission and progress of the disease at the time they were required to advise the Idiot in Chief about it.
In science, an expert is someone who is considered competent to express an opinion.
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So it feels like in the absence of a proper, lets say science-friendly(?) timeline, the experts went off of not only their own knowledge in the field, but the recent studies of their own colleagues-even if not officially fully vetted. Of course when you disagree and have no reasonable argument, you seek to discredit.
I get it. And I get why people might object.
I really like that infectious disease treatment you laid out. Never knew any of that.
Side question: why was personal health-in the good diet and exercise realm-not pushed more?
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The point of peer review is not to say if a paper is right.
It can't be. The people who write papers are at the forefront of their fields- that's why they are the ones writing the papers.
So the reviewers do not know as much about the subject as the authors.
But that's OK because the reviewers' job is to check that the authors have done the job properly. To ensure that they haven't missed any stages or failed to take account of other known stuff. It's the reviewers' job to check that the right process was followed and that there aren't any non sequiturs .
Obviously, they will also point out errors of fact if they spot any.
But fundamentally the only real review of science is repetition. When another scientist does the same experiment and gets the same result.
The flip side is that you can't really do all the experiments in a pandemic. You can't, for example, deliberately expose people to the two different strains of virus and see which spreads fastest.
Almost all you can do is look at epidemiology.
And that, at best, can't happen faster than cases pile up.
So the idea that the scientists are "withholding" information is just absurd.
If they were doing that you wouldn't have heard that there was a new strain of the virus, would you?
And, to a great extent the problem isn't the science.
The science is the same in New Zealand.
The politicians are different.
The outcomes were different.
What can you deduce from that?
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Neil Ferguson's model was used to by the UK government in february in deciding their approach. Mathematically I agree with what they said in Columbia. The equations are degenerate, I said so at the time. Degeneracy means that a small change in the equations brings a large change in the outcome. Anyone who has studied optimisation knows not to act on the predictions of a degenerate set of equations. Although in this case it would be pretty clear to anyone who asked 'what if they have got the doubling time wrong?' You don't base life and death decisions on set of equations which includes an exponential function unless you are sure you have that function nailed down.
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Let's say that I don't know much about optimization, I don't think, as it pertains to this. Search Engine Optimization? Yes.
Can you elaborate a little on the last three sentences?
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this thing told me I couldn't post external links.
That is a precaution against spammers posting links to their own website.
Unless the policy has changed recently, you can still paste in a link which others can see (and copy/paste to view).
- It's just not "clickable", and it's not followed by search engines
- Forum contributors earn the right to post clickable links
- Spammers get banned
The equations are degenerate, I said so at the time. Degeneracy means that a small change in the equations brings a large change in the outcome.
Degenerate in mathematics means "simpler" or "limiting case".
See: https://en.wikipedia.org/wiki/Degeneracy_(mathematics)
Perhaps you mean "Ill-conditioned"?
https://en.wikipedia.org/wiki/Condition_number
I agree that exponentials change very rapidly - those unfamiliar with exponentials (ie most politicians and most of the public) are often shocked at how fast things change, when exponentials are involved.
You don't base life and death decisions on set of equations which includes an exponential function unless you are sure you have that function nailed down.
On the contrary - in the early days of a pandemic, the growth is always exponential.
- That means epidemiologists must do something quickly, or it will turn into a major disaster before you publish anything or initiate actions to control it.
Even in March/April, Neil Ferguson had estimated the incubation period and infectious period fairly close to the accepted figure we have today.
-The R0 figure was known fairly well (I have seen suggestions that the current UK strain might have an R0 higher by about 0.4)
- The death rate for severe cases was fairly well known (assuming the hospital system was not overloaded)
- He guessed (worst-case) that the susceptible population was pretty much everyone, which was pretty much right.
You can plug those figures into an SIR model, and come up with an enormous death toll, after which you will have herd immunity.
- It took a while for the message to get through to some politicians, but the rational ones finally accepted that "enormous death toll" is not acceptable to the voters and is really bad for the economy too...
- That's where the modeling gets really complex, trying to estimate the costs and benefits of wearing masks vs closing schools vs closing pubs vs lockdown of "non-essential workers" (and figuring out who these were, and how to identify them). And the hardest part is figuring out how to stop a portion of the population from starving (and starting food riots).
See: https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology#The_SIR_model
So I think Neil Ferguson did the right thing, and despite a lot of dithering, the UK has (so far) avoided millions of deaths, and kept most of these people alive long enough to receive a vaccine sometime next year.
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You don't base life and death decisions on set of equations which includes an exponential function unless you are sure you have that function nailed down.
Then what do you base them on?
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even if not officially fully vetted.
By whom? Who better than the head of CDC and a military physician who actually served under a sane president, neither of whom has any connection with Imperial College, and who will be given the responsibility (and take the blame - politicians are above blame) for doing something about it?
The editor-in-chief of the British Medical Journal gives pretty much the same lecture at every meeting I've attended, pointing out that peer review confers consistency, not quality or originality.
Side question: why was personal health-in the good diet and exercise realm-not pushed more?
because (a) there's no evidence that the virus knows or cares what you last ate and (b) even if it did, it's a bit late to start running marathons in the hope of dying from a heart attack rather than respiratory failure. Nobody has ever dissuaded anyone from good food and exercise, nor would a sane person consider Donald Flump to be a lifestyle guru.
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You don't base life and death decisions on set of equations which includes an exponential function unless you are sure you have that function nailed down.
Nor on the best-case prediction. General principle of survival is to enact the most probable and prepare for the worst. Political response is to rubbish the worst case, do nothing, and blame the experts for their misleading pessimism.`
Worth remembering Stalin's dictum: "One death is a tragedy. A million deaths is a statistic." And then watch the TV news to see it come true.
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That is a precaution against spammers posting links to their own website.
That's what I figured...especially since this was my first post. Glad the links got posted though!
But that's OK because the reviewers' job is to check that the authors have done the job properly. To ensure that they haven't missed any stages or failed to take account of other known stuff. It's the reviewers' job to check that the right process was followed and that there aren't any non sequiturs .
Obviously, they will also point out errors of fact if they spot any.
This was the catalyst for my own research and eventual decision to post this. The rushed timeline that the pandemic caused seems to have eschewed normal protocol of peer reviewed science.
That means epidemiologists must do something quickly, or it will turn into a major disaster before you publish anything or initiate actions to control it.
...which means in the event of going worst case, they are happy to be wrong...but then they get criticism for being wrong. The whole "you're an expert?" thing. Not unlike a weather forecast.
You can plug those figures into an SIR model, and come up with an enormous death toll, after which you will have herd immunity. It took a while for the message to get through to some politicians, but the rational ones finally accepted that "enormous death toll" is not acceptable to the voters and is really bad for the economy too...
Depends on the politicians AND their constituents.
Was there ever a number attributed to "enormous death toll"? Also, what would count towards that-test positive, but have no symptoms and get in an accident? Pneumonia caused by Covid? I have found the Covid deaths to be a slippery slope in terms of what counts, but I'm learning a lot in this thread, so maybe I can be enlighten on this aspect as well.
Quote from: L_D_G on Yesterday at 22:00:06
even if not officially fully vetted.
By whom?
What I mean here is actually being peer reviewed.
Political response is to rubbish the worst case, do nothing, and blame the experts for their misleading pessimism.`
Like when 6 inches of snow ends up only being 2?
The editor-in-chief of the British Medical Journal gives pretty much the same lecture at every meeting I've attended, pointing out that peer review confers consistency, not quality or originality.
...shouldn't it go for quality though? I mean, maybe not as the sole aspect, but at least in part?
Side question: why was personal health-in the good diet and exercise realm-not pushed more?
because (a) there's no evidence that the virus knows or cares what you last ate and (b) even if it did, it's a bit late to start running marathons in the hope of dying from a heart attack rather than respiratory failure. Nobody has ever dissuaded anyone from good food and exercise, nor would a sane person consider Donald Flump to be a lifestyle guru.
I'm of the understanding that kids and seniors were most susceptible. I infer this to mean the weakest immune systems (also why there is extra caution for immunocompromised). With proper diet and exercise, you do build up your immune system, don't you? Maybe not an exact science, but you'll be doing better than you would be as a lump. Avoidance just seemed to be the single strategy. Not saying it's not a good strategy, but why not go multipronged and encourage the strengthening of the immune system?
I think there is a difference between not dissuading and not encouraging.
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...shouldn't it go for quality though?
How?
Who knows enough to say if the new stuff is right or wrong?
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...shouldn't it go for quality though?
How?
Who knows enough to say if the new stuff is right or wrong?
The results or the work? If the equations are seen as poor, does that not invite questioning?
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I'm of the understanding that kids and seniors were most susceptible.
Oddly, not kids. Which is why the amoral morons insisted on opening the schools so kids could become asymptomatic carriers and kill their grandparents. Saves money on pensions and benefits, and lets the parents go back to work, for the greater good of The Holy Economy.
Avoidance just seemed to be the single strategy. Not saying it's not a good strategy, but why not go multipronged and encourage the strengthening of the immune system?
If you really know what you are doing, you can wrestle a bear. But the time to hit the gym is about 20 years before you meet the bear. Still best to avoid contact, even if you've trained for it.
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If the equations are seen as poor, does that not invite questioning?
The equations are good. It's the input data that's unknown (infectivity) and uncontrolled (behavior). Hence a wide range of outcome predictions, because the epidemic process is extremely sensitive to small changes in inputs. If R > 1 you will have a disaster, even if it's only a tiny bit greater than 1, if you wait long enough. If R<1 by even a tiny bit, you may have some survivors.
And you have to remember that whilst deaths make the headlines, chronic infections damage the economy and the lives of the survivors.There are at least 25 infections per death, 5 requiring long hospital stays and probably 10 resulting in 6 month disability. I haven't heard of a single case of full recovery.
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The equations are good.
I'm going off of this exchange:
Quote from: set fair
The equations are degenerate, I said so at the time. Degeneracy means that a small change in the equations brings a large change in the outcome.
Degenerate in mathematics means "simpler" or "limiting case".
See: https://en.wikipedia.org/wiki/Degeneracy_(mathematics)
Perhaps you mean "Ill-conditioned"?
https://en.wikipedia.org/wiki/Condition_number
Entirely possible that I read something wrong. Equations good, but results degenerate? I don't know...trying to understand.
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Degenerate is the wrong word. It turns up correctly in examples like the relativistic factor √(1 - v2/c2) which is close to 1 if you are travelling a speed v much less than the speed of light c , so the physics "degenerates" to the classical newtonian equations. That's not what this is about.
Exponential functions, which model growth rates of infection, are very sensitive to the behavior of the vector which, being human, is unpredictable and not very controllable.
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Exponential functions, which model growth rates of infection, are very sensitive to the behavior of the vector which, being human, is unpredictable and not very controllable.
This makes sense! So the decision was made to implement restrictions, but you can only do so much.
Either at the time or now, was there a feasible alternative to the restrictions (which were a way to attempt to control the unpredictability of humans) at least in terms of being social and wearing masks?
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You might provide everyone with a personal respirator and thus take all the glamor out of hard-hat diving, lunar exploration and nuclear war, but strict quarantine applied early by a competent and trustworthy administration has done the trick in Australia and New Zealand. There never was an alternative until vaccines became available. Masks and social distancing are attempts to compromise with a threat that doesn't understand the concept of negotiation.
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Masks and social distancing are attempts to compromise with a threat that doesn't understand the concept of negotiation.
More an attempt to compromise with constituents and an economy.
When the US attempted a serious lockdown closer to Spring...all of this "doing our part to flatten the curve"...what went wrong? To clarify: asking a lot of these to get science minded answers. Waters get murky when politics get involved. My guess for this is that when people heard things were getting better, they decided quarantine was over.
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but then (epidemiologists) get criticism for being wrong
Epidemiologists will quote a range of possible outcomes, given the uncertainty of the inputs.
- Typically this takes the form of a "95% confidence interval", ie we can be 95% sure that, if nothing is done, it will be worse than X, and 95% sure it won't be worse than Y.
- That's a bit hard for the news to present to the public, so they often just present the "most likely" result.
- However, I have seen it done successfully - a line graph shown on TV was overlaid on a much wider band which represented the range of uncertainty. The news just talked about the central line, but you could see that the results were a bit uncertain.
Imperial College Neil Ferguson Covid model
I heard a critique of the UK modeling, on the basis that it focused on detection of cases through hospital admissions.
- The person making these comments had worked on containing Ebola in rural Africa (where the hospital system is pretty much non-existent).
- Her comment was that the most effective way to contain an outbreak is to get out in the community, and have community members help identify cases and identify contacts both forward in time (who did this patient give it to?), and backward in time (who did this patient catch it from?).
- This is especially important for COVID, where a large number of infections do not require hospitalization (and may be asymptomatic).
Apparently, modeling played a large part in the Australian response, with the Australian government being presented with computer models as early as February 2020.
- Shutting down international travel was shown to be a major factor in Australia getting it under control.
- This is easier done for islands like Australia, New Zealand (and potentially, the UK)
When there is no cure for a new disease, the only way to get it under control is public health measures, which requires support from politicians and the community.
- The technology/pharmaceutical solutions may come later, but you can't wait that long
Anyway, an interesting panel of experts with experience in different countries, including USA (38 minutes):
https://www.abc.net.au/radionational/programs/healthreport/coronavirus-our-pandemic-year-in-review/12998796
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- This is easier done for islands like Australia, New Zealand (and potentially, the UK)
"Potentially"??? AFAIK the British Isles have been surrounded by water since the Ice Age! The big bit where most of us live has been successfully defended against the Armada, Napoleon, the Kaiser and the Luftwaffe, by swift and decisive action.
Seriously, one of our Dishonorable Members rubbished the projections by waving the whole graph around in Parliament and claiming that the worst case curve was a communist/Guardian/BBC/academic conspiracy to undermine public confidence in the Prime Idiot. So the PI "Saved Christmas", probably made a killing on the Stock Exchange, and certainly killed another 20,000 people (to date). A general would be courtmartialled for wanton endangerment of a hundred, but politicians get away with mass murder every day to line their pockets.
Pay peanuts, get monkeys. Elect monkeys, get shat on.