COVID19 update, June 21, 2020: Current understanding of clinical features; vitamin D finally hitting the UK media

Very briefly after a long workday.

Dr. John Campbell summarizes our current understanding of clinical features:

 

 

And again Dr. John Campbell on vitamin D finally hitting the media in the UK

 

 

Finally, a brief video from the Israeli news channel (in Hebrew) about the latest COVID19 testing facility coming online, set up by the MyHeritage.com human genetics company with a Chinese partner (a spokesperson of whom speaking briefly in English). Located in the central town of Petach Tikva, it can process 10,000 samples per day in batches of 96.

ADDENDUM: seems New Zealand’s claim of having eradicated the virus (with an official count of zero active cases) was a little premature. (Via Instapundit.)

And (hat tip: Erik W.) The Gold Opinion, a blogger who is both an emergency physician and  a lawyer, on how hydroxychloroquine became a political football, not just in the political arena but (sadly) in medical journals. Read the whole thing.

COVID19 update, June 4, 2020: is the virus a picky eater; co-authors of influential Lancet hydroxychloroquine study retract paper

(1) Somebody quipped to me the other week: “the virus is a picky eater”. Now, Prof. Karl Friston of UC London, a well-known neuroscientist and computational modeler who is a member of “the independent SAGE committee” is interviewed here on UnHerd.

Now, from the unlikely source of a prominent member of the “Independent SAGE committee”, the group set up by Sir David King to challenge government scientific advice and accused by some of being populated with Left-wing activists, comes a claim that the true portion of people who are not even susceptible to Covid-19 may be as high as 80%.

 

A written essay is here. His thesis: 

Theories abound as to which factors best explain the huge disparities between countries in the portion of the population that seems resistant or immune — everything from levels of vitamin D to ethnic-genetic and social and geographical differences may come into play — but Professor Friston makes clear that it does not primarily seem to be a function of government coronavirus policy. “Solving that — understanding that source of variation in terms of this non-susceptibility — is going to be the key to understanding the enormous variation between countries,” he said.

Controversial? We link, you decide.

(2) The Washington Examiner reports that the influential The Lancet paper, which claimed hydroxychloroquine was more harmful than helpful in the treatment of COVID19 based on dodgy Surgisphere data, has now been retracted by 3 of the 4 authors (the 4th is the CEO of Surgisphere). Here is the original retraction notice:

https://www.thelancet.com/lancet/article/s0140673620313246

After publication of our Lancet Article,1 several concerns
were raised with respect to the veracity of the data
and analyses conducted by Surgisphere Corporation
and its founder and our co-author, Sapan Desai, in
our publication. We launched an independent third-
party peer review of Surgisphere with the consent of
Sapan Desai to evaluate the origination of the database
elements, to confirm the completeness of the database,
and to replicate the analyses presented in the paper.

Our independent peer reviewers informed us that
Surgisphere would not transfer the full dataset, client
contracts, and the full ISO audit report to their servers
for analysis as such transfer would violate client
agreements and confidentiality requirements. As such,
our reviewers were not able to conduct an independent
and private peer review and therefore notified us of their
withdrawal from the peer-review process.

We always aspire to perform our research in accordance
with the highest ethical and professional guidelines. We
can never forget the responsibility we have as researchers
to scrupulously ensure that we rely on data sources that
adhere to our high standards. Based on this development,
we can no longer vouch for the veracity of the primary
data sources. Due to this unfortunate development, the
authors request that the paper be retracted.

We all entered this collaboration to contribute
in good faith and at a time of great need during
the COVID-19 pandemic. We deeply apologise to
you, the editors, and the journal readership for any
embarrassment or inconvenience that this may have
caused.

The accompanying statement by the Lancet editorial board:

Statement from The Lancet
Today, three of the authors of the paper, “Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis”, have retracted their study. They were unable to complete an independent audit of the data underpinning their analysis. As a result, they have concluded that they “can no longer vouch for the veracity of the primary data sources.” The Lancet takes issues of scientific integrity extremely seriously, and there are many outstanding questions about Surgisphere and the data that were allegedly included in this study. Following guidelines from the Committee on Publication Ethics (COPE) and International Committee of Medical Journal Editors (ICMJE), institutional reviews of Surgisphere’s research collaborations are urgently needed.

(3) Elsewhere in the Lancet is an article with a “meta-analysis” of other studies (in plain English: a study in which the raw data of several original lstudies are combined into a larger dataset and the statistical analysis repeated in order to achieve greater productive power than the individual studies)  on the effectiveness of distancing, face masks, and eye protection, in both  healthcare and non-healthcare (community) settings.

https://doi.org/10.1016/S0140-6736(20)31142-9

From the summary (paragraphing and emphasis mine):

Our search identified 172 observational studies across 16 countries and six continents, with no randomised controlled trials and 44 relevant comparative studies in health-care and non-health-care settings (n=25 697 patients).

Transmission of viruses was lower with physical distancing of 1 m or more, compared with a distance of less than 1 m (n=10 736, pooled adjusted odds ratio [aOR] 0·18, 95% CI 0·09 to 0·38; risk difference [RD] –10·2%, 95% CI –11·5 to –7·5; moderate certainty); protection was increased as distance was lengthened (change in relative risk [RR] 2·02 per m; p_interaction=0·041; moderate certainty).

Face mask use could result in a large reduction in risk of infection (n=2647; aOR 0·15, 95% CI 0·07 to 0·34, RD –14·3%, –15·9 to –10·7; low certainty), with stronger associations with N95 or similar respirators compared with disposable surgical masks or similar (eg, reusable 12–16-layer cotton masks; p =0·090; posterior probability >95%, low certainty).

Eye protection also was associated interaction with less infection (n=3713; aOR 0·22, 95% CI 0·12 to 0·39, RD –10·6%, 95% CI –12·5 to –7·7; low certainty).

Unadjusted studies and subgroup and sensitivity analyses showed similar findings.

 

ADDENDUM: “WHO frustrated by China’s info delays as coronavirus started to spread, report finds”. Is this damage control/reputation management on the part of the WHO, or the genuine expression of frustration by the technical levels of the organization? More about this tomorrow, G-d willing.

COVID19 update June 3, 2020: serological study in Israel; Surgisphere data scandal [UPDATED]

(1)  Israel is planning to test a sample of 70,000 people for antibodies. Earlier, preliminary result from a smallish sample of 1,709 Israelis found that 2.5±0.5% had antibodies for the virus. With official infection numbers (positive tests in RT-PCR) reaching only 0.2% of the population, this implies a Dunkelziffer  (stealth infection rate) of 10-15 times the official one — not dissimilar from what Prof. Hendrik Streeck found in Germany or the team of Ioannides, Bendavid et al. found in Santa Clara County, CA. [For non-American readers: Santa Clara County is almost synonymous with Silicon Valley.] 

With just 291 dead out of 17,377 confirmed cases — a raw case fatality rate (CFR) of 1.67%, this implies that the infection fatality rate is just 0.11–0.17%. This is considerably lower than even the drastically downward-revised CDC figures,  (IFR of about 0.26%), but Israel has a much younger population pyramid than the USA, and is sunny enough that vitamin D deficiency should not be as prevalent as in  northern US states.

Meanwhile, Israel is seeing a flare-up of cases in schools that has some people speaking of a second wave, although it might actually be more like a ripple, or a round of the dance in Tomas Pueyo’s “Hammer and Dance” strategy. Rungholt blogs in German about her experience as a kindergarten teacher in a kibbutz in the far North of the country.

(2) h/t: Cathe Smith: several papers, including the one that led to suspension of the hydroxychloroquine trials, now under a cloud owing to suspect medical database

On its face, it was a major finding: Antimalarial drugs touted by the White House as possible COVID-19 treatments looked to be not just ineffective, but downright deadly. A study published on 22 May in The Lancet used hospital records procured by a little-known data analytics company called Surgisphere to conclude that coronavirus patients taking chloroquine or hydroxychloroquine were more likely to show an irregular heart rhythm—a known side effect thought to be rare—and were more likely to die in the hospital.

Within days, some large randomized trials of the drugs—the type that might prove or disprove the retrospective study’s analysis—screeched to a halt. Solidarity, the World Health Organization’s (WHO’s) megatrial of potential COVID-19 treatments, paused recruitment into its hydroxychloroquine arm, for example. (Update: At a briefing on 3 June WHO announced it would resume that arm of the study.)

But just as quickly, the Lancet results have begun to unravel—and Surgisphere, which provided patient data for two other high-profile COVID-19 papers, has come under withering online scrutiny from researchers and amateur sleuths. They have pointed out many red flags in the Lancet paper, including the astonishing number of patients involved and details about their demographics and prescribed dosing that seem implausible. “It began to stretch and stretch and stretch credulity,” says Nicholas White, a malaria researcher at Mahidol University in Bangkok.

Today, The Lancet issued an Expression of Concern (EOC) saying “important scientific questions have been raised about data” in the paper and noting that “an independent audit of the provenance and validity of the data has been commissioned by the authors not affiliated with Surgisphere and is ongoing, with results expected very shortly.”

Hours earlier, The New England Journal of Medicine (NEJM) issued its own EOC about a second study using Surgisphere data, published on 1 May. The paper reported that taking certain blood pressure drugs including angiotensin-converting enzyme (ACE) inhibitors didn’t appear to increase the risk of death among COVID-19 patients, as some researchers had suggested. (Several studies analyzing other groups of COVID-19 patients support the NEJM results.) “Recently, substantive concerns have been raised about the quality of the information in that database,” an NEJM statement noted. “We have asked the authors to provide evidence that the data are reliable.”

A third COVID-19 study using Surgisphere data has also drawn fire. In a preprint first posted in early April, Surgisphere founder and CEO Sapan Desai and co-authors conclude that ivermectin, an antiparasitic drug, dramatically reduced mortality in COVID-19 patients. In Latin America, where ivermectin is widely available, that study has led government officials to authorize the drug—although with precautions—creating a surge in demand in several countries.

Chicago-based Surgisphere has not publicly released the data underlying the studies, but today Desai told Science through a spokesperson that he was “arranging a nondisclosure agreement that will provide the authors of the NEJM paper with the data access requested by NEJM.”

UPDATE (h/t LIssa Hailey): much more at The Guardian (archive copy here) “Governments and WHO changed Covid-19 policy based on suspect data from tiny US company”

A search of publicly available material suggests several of Surgisphere’s employees have little or no data or scientific background. An employee listed as a science editor appears to be a science fiction author and fantasy artist. Another employee listed as a marketing executive is an adult model and events hostess.

[…] Until Monday, the “get in touch” link on Surgisphere’s homepage redirected to a WordPress template for a cryptocurrency website, raising questions about how hospitals could easily contact the company to join its database.

[…] At a press conference on Wednesday, the WHO announced it would now resume its global trial of hydroxychloroquine, after its data safety monitoring committee found there was no increased risk of death for Covid patients taking it.

The article refers to an earlier expose at MedicineUncensored.

Change: Narcissism no longer a psychiatric disorder

Via Insty , we learn news that must be a great relief to the current occupant of 1600 Penn and his dwindling band of sycophants:

CHANGE: Narcissism no longer a psychiatric disorder. Well, that’s a relief:

[More here. In fairness, the basic idea apparently is narcissism being reclassified as a symptom of a deeper personality disorder rather than a disorder in itself. The change, being pushed by researchers, is vociferously opposed by practicing clinical psychiatrists — apparently not the first example of a rift between researchers and clinicians in the community.]

C2 commenter “buzzsawmonkey” had some pithy comments in yesterday afternoon’s C2 thread:

“Any discipline in which something can be declared a “disorder” or not by vote is the province of charlatans.”

Reply to Lucius Septimius in #220:

I was working for the ACLU in the ’70s, on gay-rights issues (if you can believe it), when the American Psychiatric Association decided by vote that homosexual behavior was “no longer a disorder.”  While this was certainly useful to me in my professional capacity, even then I realized that any outfit that could decree what was or was not a “disorder” by vote of its membership was of necessity a fraud from top to bottom.”

But… “the science is settled”, dontcha know!

UCSB physicist Hal Lewis resigns from the American Physical Society with a screed against climate alarmism and its enablers

Watts Up With That reports that UCSB physicist Hal Lewis (more about him here) resigned from the American Physical Society with a blistering resignation letter in which he dares to call the organization’s position on AGW:

Hal Lewis: My Resignation From The American Physical Society - an important moment in science history I don’t believe that any real physicist, nay scientist, can read that stuff without revulsion. I would almost make that revulsion a definition of the word scientist.

In the interim the ClimateGate scandal broke into the news, and the machinations of the principal alarmists were revealed to the world. It was a fraud on a scale I have never seen, and I lack the words to describe its enormity. Effect on the APS position: none. None at all. This is not science; other forces are at work.- Hal Lewis

Read More at Watts Up With That? who call the letter the scientific equivalent of Martin Luther nailing his Ninety-Five Theses to the church gate at Wittenberg.

NAS compiles dossier on AGW “deniers”, including… NAS members

This is the sort of thing that, if this were even possible, would make me feel ashamed to call myself a scientist. Frank Tipler:

The National Academy of Sciences, in its official journal Proceedings of the National Academy of Sciences, has just published a list of scientists whom it claims should not be believed on the subject of global warming. I am number 38 on the list. The list of 496 is in descending order of scientific credentials.

Professor Freeman Dyson of the Institute for Advanced Study, a member of the National Academy of Sciences and a fellow of the Royal Society, is number 3 on the list. Dyson is a friend of mine and is one of the creators of relativistic quantum field theory; most physicists think he should have shared the Nobel Prize in Physics with Richard Feynman. MIT professor Richard Lindzen, a meteorologist who is also a member of the National Academy, is number 4. Princeton physics professor William Happer, once again a member of the National Academy of Sciences, is number 6.

I’m in good company.

The list is actually available only online. The published article, which links to the list, argues that the skeptical scientists — the article calls us “climate deniers,” trying to equate us with Holocaust deniers — have published less in climate “science” than believers in anthropogenic global warming (AGW).

True.

But if the entire field of climate “science” is suspect, if the leaders of the field of climate “science” are suspected of faking their results and are accused of arranging for their critics’ papers to be rejected by “peer-reviewed” journals, then lack of publication in climate “science” is an argument for taking us more seriously than the leaders of the climate “science.”

Freeman Dyson, for example, was not trained as a physicist but as a mathematician. His contribution to quantum field theory was applying his mathematical skills to showing that Feynman’s work was mathematically rigorous and mathematically equivalent to another formulation due to Julian Schwinger (who shared the Nobel with Feynman). Freeman has spent the fifty years after this work switching from field to field, always making important contributions to these fields, and making them precisely because he has looked at the evidence from a different point of view.

Dick Lindzen actually is an insider in real climate science, but he is an insider who can’t be bought, an insider who follows the evidence rather than the grant money.

Will Happer is mainly an experimental atomic physicist, but a physicist who has a decades-old reputation for investigating extraordinary claims in all areas of physics.  Will was one of the experimentalists who exposed the cold fusion scam a number of years ago.

As for myself, I’m a cosmologist, with a special interest in the anthropic principle, as my National Academy of Sciences security police dossier correctly notes. Twenty odd years ago, I co-authored a book, published by Oxford University Press, on the anthropic principle. As my co-author and I pointed out, the essence of the anthropic principle is eliminating human bias from the interpretation of observations, and we focused mainly on eliminating such bias from cosmology.

“Seek the truth wherever thou mayest find it” has, sadly, become “seek grant money wherever thou mayest find it” for all too many.

For rather more refreshing reading, have a look at the website of Israeli astrophysicist Nir Shaviv, http://www.sciencebits.com,  A couple of suggestions: “Cosmic rays and climate“, and “ClimateGate and the hockey stick: not news to me“.

Cathy Young: Tea Partiers Racist? Not So Fast

In RealClearPolitics, Cathy Young of Reason Magazine [h/t: one of the fine denizens at C2] looks at surveys that ‘prove’ that the charge that Tea Partiers are raaaaacist, and basically finds: ‘no more or less than the general population’.

Ever since the “Tea Parties” gained national attention, the debate has raged on whether they are a grass-roots protest movement in the proud tradition of American dissent, or a hysterical mob driven by fear, intolerance and selfishness. Recently, two much-discussed surveys — a CBS/New York Times poll and a multi-state University of Washington poll — have been bandied about as proof that the leftist caricatures of the Tea Partiers as mean-spirited rich white bigots are accurate. Yet a look at the data suggests that this interpretation is highly skewed by political bias.

In a Salon.com article titled “The Tea Partiers’ racial paranoia,” editor Joan Walsh notes that in the University of Washington poll, only 35% of pro-Tea Party whites regarded blacks as “hard-working,” 45% as “intelligent,” and 41% as “trustworthy.” Walsh scoffs, “And Tea Party supporters don’t like it when anyone notices the racists in their midst?”

Not so fast. The respondents in the UW poll were asked to rate on a 1-7 scale how intelligent, hardworking, and trustworthy they perceived “almost all” blacks (and, in separate questions, whites, Latinos, and Asians) to be. Whether the findings expose Tea Party bigotry hinges on two things: how the “Tea Partiers'” opinions of blacks compare to their views of other groups, and how their answers compare to those of other, non-Tea-Partying Americans.

The UW researchers’ initial analysis compared only whites who were strongly pro-Tea Party and strongly anti-Tea Party, concluding that the latter held a much more positive view of blacks. These data are no longer on the UW website; instead, there are tables for other race-related questions (such as “Over the past few years blacks have gotten less than they deserve”), with separate results for whites who were either neutral toward the Tea Party movement or had never heard of it, as well as for all whites.

But what about the racial stereotyping items? The lead investigator, political science professor Christopher Parker, graciously provided me with the fuller data — which strongly contradict the notion of the Tea Parties as a unique hotbed of racism.

Thus, while only 35% of strong Tea Party supporters rated blacks as hardworking, only 49% described whites as such. While the gap is evident, these responses are close to those for all whites (blacks are rated as “hardworking” by 40%, whites by 52%). While whites who are strongly anti-Tea Party seem free of bias on this item — blacks and whites are rated as “hardworking” by 55% and 56%, respectively – this is not true for intelligence and trustworthiness. Whites in every group are less likely to rate blacks than whites as “intelligent” by similar margins: 14 points for Tea Party supporters (45% vs. 59%), 13 points for all whites (49% vs. 62%), 10 points for Tea Party opponents (59% vs. 69%). On “trustworthy,” the gap is smaller in the pro-Tea Party group (41% vs. 49%) than in the anti-Tea Party group (57% vs. 72%). One could write headlines about the “racial paranoia” of white liberals who consider blacks less trustworthy than whites!

The endurance of racial stereotypes in this day and age is disturbing; but Tea Party supporters differ little in this regard from mainstream Americans.  (It is also worth noting that, as in many other surveys, Asian-Americans in the UW poll are rated much more positively than whites.)

Compared to middle-of-the-road whites, Tea Party supporters show far more agreement with the statement that blacks should work their way up “without special favors” the way other minorities such as Italians and Jews did, or that blacks would be as well off as whites if they worked harder. The standard left-of-center view, shared by the UW researchers, is that such attitudes represent a subtler form of racism, or “racial resentment.” In some cases, that is surely true. Yet these sentiments may also reflect a genuinely race-neutral belief in self-reliance and self-help — or the view, shared by many black commentators, that the black community’s problems are partly rooted in damaging behavioral and cultural patterns.

John McWhorter, a noted black scholar and author whose works include the 2000 book, Losing the Race: Self-Sabotage in Black America, says that “the idea that ‘racism’ is behind the Tea Partiers is based on a lazy and vain extension of the term ‘racism’ to meaning ‘that which many black people would not approve of.'” According to McWhorter, “The position that the government does too much to help black people is not necessarily one based in inherent bias against people with black skin — it can be argued as a reasonable proposition based on the spotty record of social programs since the 1960s.”

The other charge against Tea Partiers is that they are not “the people” but the privileged defending their privilege. Walsh gleefully points out that in the Times/CBS poll, 12% of Tea Party sympathizers had an annual income over $250,000 — forgetting to mention that so did 11% of all Americans. Washington Post columnist E.J. Dionne asserts that “Tea Party enthusiasts … side with the better-off against the poor”: 73% of them, versus 38% of all Americans, say that “providing government benefits to poor people encourages them to remain poor.” (Of course, they couldn’t possibly be sincere in the belief that poor people are often harmed more than helped by government programs.)

What, then, do the new polls tell us about the Tea Partiers — or, at least, Tea Party sympathizers? (In the Times/CBS poll, only one in five self-identified Tea Party supporters reported actual involvement in Tea Party activities.) They are mostly white and more likely to be male (59%); three-quarters are 45 and older, compared to half of all Americans. They are more religious than average, though not dramatically so: 39% are evangelical Christians and 38% attend church every week, while the figures for all Americans are 28% and 27%.

Not surprisingly, the Tea Partiers are disproportionately Republican and right-wing: 39% consider themselves “very conservative” and 34% “somewhat conservative” (compared to 12% and 24%, respectively, of the general population).[…] In other words, the Tea Party movement is mainly conservative — which is hardly the stuff of headlines. That does not make it a haven for racists.

Read the rest.

ClimateGate: there’s no business like snow business

Watts Up With That: “There’s no business like snow business” starts out with Moscow (Russia, not Idaho) having the thickest snow cover since 1966. It goes on to repeat the claims of the AGW crowd that ‘snowfall will become a rare event’, and contrasting them with claims today that global warming will cause increased snowfall (no kidding). “The great thing about global warming is that you can blame anything on it, and then deny it later.” If so, statements aren’t falsifiable, and the only thing that’s “settled” about the science is that it isn’t science.

Meanwhile, Sen. James Inhofe is calling for an investigation of Johannes Tetzel Al Gore, soon to be an indulgences “carbon credits” billionaire.