Justin Mason's Weblog Posts
The numbers are in, in this _Science_ paper —
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
Some context — European telcos no longer operate their equipment:
As an icebreaker, [telco operators] were asked if they thought the Chinese could eavesdrop through “backdoors” in Huawei equipment. Every single hand went up. One of the bankers then asked, for balance, if they thought the US could access communications through key Cisco equipment. “All the hands went straight back up without hesitation” [….] In a modern telecommunications service provider, new equipment is deployed, configured, maintained and often financed by the vendor. Just to let that sink in, Huawei (and their close partners) already run and directly operate the mobile telecommunication infrastructure for over 100 million European subscribers. The host service provider often has no detailed insight in what is going on, and would have a hard time figuring this out through their remaining staff. Rampant outsourcing has meant that most local expertise has also left the company, willingly or unwillingly.(via ITS slack)
“The evidence supporting airborne transmission is overwhelming, and evidence supporting large droplet transmission is almost non-existent” (Greenhalgh et al., Lancet, 2021) (via Daniel Lemire)
France’s official “Repairability Index” site
Very impressive level of detail here
This is chilling:
I love tech. But watching it intersect with a Hindu nationalist government trying to crush dissent, choke a free press, and destroy a nation’s secular ethos doesn’t feel like something I bought a ticket to. Writing about technology from India now feels like having a front-row seat to the country’s rapid slide into authoritarianism. “It’s like watching a train wreck while you’re inside the train,” I Slacked my boss in November.
This is the best news to happen in Ireland’s emissions situation for a while! The ESB plan to turn off the highly polluting coal power station at Moneypoint, switching it to be a hub for offshore wind energy, including energy storage using hydrogen. Moneypoint has massive connections to the Irish grid, and the amount of available wind power on the west coast is simply huge. Great stuff!
Using DD-WRT to turn off the internet for certain devices during night-time hours
‘[River] wanted to use a Raspberry Pi to bring the fans into his home automation system, but the Raspberry Pi doesn’t have a 304.2 MHz radio. What it does have is user-programmable GPIO and the rpitx package, which converts a GPIO pin into a basic radio transmitter. Of course, the Pi’s GPIO pin’s aren’t long enough to efficiently transmit at 304.2 MHz, so [River] added a proper antenna, as well as a low-pass filter to clean up the transmitted signal. The rpitx package supports OOK out of the box, so [River] was quickly able get the Pi controlling his fan in no time’
Zeynep Tufekci hits the nail on the head here — 3 particular factors were wilfully overlooked in Western countries’ early response to the COVID pandemic:
Put all three together: airborne transmission, clusters driving the epidemic, and presymptomatic transmission. Not only do we get a clear and consistent picture of many things that have happened since, we also get the mitigation strategy. Further, all three dimensions support each other: transmission from people not (yet) coughing or sneezing very much argues in favor of aerosol transmission, which explains how large clusters can be driving the epidemic and how transmission in a situation like that ship can occur. And the mitigation and other strategies become clear: pay attention to clusters and ventilation, universal masks, different policies for indoors and outdoors, etc.
Holy cow this could have been pretty serious:
A software mistake caused a Tui flight to take off heavier than expected as female passengers using the title “Miss” were classified as children, an investigation has found. The departure from Birmingham airport to Majorca with 187 passengers on board was described as a “serious incident” by the Air Accidents Investigation Branch (AAIB). An update to the airline’s reservation system while its planes were grounded due to the coronavirus pandemic led to 38 passengers on the flight being allocated a child’s “standard weight” of 35kg as opposed to the adult figure of 69kg. This caused the load sheet – produced for the captain to calculate what inputs are needed for take-off – to state that the Boeing 737 was more than 1,200kg lighter than it actually was.
Excellent thread on privacy and security of the proposed Digital Green Certificate for intra-EU safe travel during the COVID-19 pandemic, from Carmela Troncoso. tl;dr:
My conclusion is: this is an immature design of an extremely complex infrastructure with no guaranteed security. The proposed scheme is likely to go down the slippery slope of discrimination and surveillance. I’d like to end reminding my wild thought: Given that fraud is possible anyway, a simple paper-based solution with enough protection to deter cheating may be sufficient to get us through this summer, avoiding long-term consequences.
Allow Minecraft Bedrock Edition clients on mobile devices, Switch, PS4 and XBox to connect to your Java edition Minecraft server. Works particularly nicely as a plugin in a PaperMC server — will definitely give this a go and see how the kids get on….
Official guidance from the CDC is toning down the “bleach everything!” messaging:
People can be infected with SARS-CoV-2 through contact with surfaces. However, based on available epidemiological data and studies of environmental transmission factors, surface transmission is not the main route by which SARS-CoV-2 spreads, and the risk is considered to be low. The principal mode by which people are infected with SARS-CoV-2 is through exposure to respiratory droplets carrying infectious virus. In most situations, cleaning surfaces using soap or detergent, and not disinfecting, is enough to reduce risk. Disinfection is recommended in indoor community settings where there has been a suspected or confirmed case of COVID-19 within the last 24 hours. The risk of fomite transmission can be reduced by wearing masks consistently and correctly, practicing hand hygiene, cleaning, and taking other measures to maintain healthy facilities.Can we tone down the cleanliness theatre now?
The short version is this: we think about 1% of applications and traffic “out there” are still using TLS1.0/TLS1.1. Given where browsers are at, I think this percentage is an under-estimate of the usage on Java applications – I suspect it’s even higher there. When we dig in with customers “Why are you still using TLS1.0 or TLS1.1” the most common reasons are legacy appliances and applications. Think of hardware load balancers that were never updated, or can’t be, to support TLS1.2 or better. Compliance mandated traffic inspection devices that force TLS1.0 in certain industries are another reason. For these applications, the change will break them, and they’ll get a low-level exception. The users can re-enable TLS1.0 and TLS1.1, but they may suffer an outage because they likely weren’t expecting a breaking change low in the networking stack.
oh god this brings back painful memories —
On a particularly large deployment, I eventually had to layer in a second pgbouncer tier. One tier ran on the application servers and another tier on the database servers. Altogether it aggregated connections for around 1 million client processes. Tuning it was 40% dark art, 40% brute force, and 10% pure luck.Amazing to see that these issues are still something that Postgres users have to worry about :)
Good article on the topic of COVID-19 airborne transmission, with some decent graphics and charts
This is going to be one of the big scandals of COVID-19, when we get around to looking back from a position of safety in the future:
On 28 March 2020, two months after the WHO had declared COVID-19 a global health emergency, the agency broadcast a public-health message on Twitter and Facebook. “FACT: #COVID19 is NOT airborne,” it said, labelling claims to the contrary as misinformation. But evidence quickly established that the virus is transmitted by air, and researchers roundly criticized the agency. The WHO updated its advice on SARS-CoV-2 transmission three months later, acknowledging the possibility that airborne transmission might occur in some community settings. Airborne transmission in “crowded and inadequately ventilated spaces over a prolonged period of time with infected persons cannot be ruled out”, the updated advice says. Yuguo Li, a building environment engineer at the University of Hong Kong, says that he is disappointed it took the WHO and other health authorities so long. “We would have saved a lot of people” if airborne transmission was recognized earlier, he says.
Keith Dawson has written up a great summary of a paper by Dr. Zoë Hyde:
The general perception and belief for the last year has been that children are less likely than adults to be infected with SARS-CoV-2. A new paper in the journal Clinical Infectious Diseases casts serious doubt on this assumption. The author of that paper, Zoë Hyde of the University of Western Australia, argues that there are two principal reasons why the myth of a lower attack rate in children developed: we don’t test kids much, and they may only be infectious for a very short window of time. The CDC’s stance on kids and Covid seems to be overly sanguine. The metric used in their paper is hospitalization rate. It is true that hospitalization rates for teenagers and younger people are extremely low, but that may not be strongly indicative of infection rate. Kids’ infections are more likely to result in a mild or even asymptomatic case of Covid-19 — about twice as likely as for adults, according to Hyde. Combine this fact with the US bias towards testing only once symptoms appear, and you can see how this could contribute to an undercount of childhood cases. Compounding the dearth of testing is the (fairly robust) finding that, when infected, children may be shedding virus for a shorter time than adults: only two days on average, compared to five days for adults. So kids are more than twice as likely to show up PCR-negative even in the rare instances in which they are tested. Looking at seroprevalence surveys, Hyde cites studies from Italy and Brazil pointing to similar levels of children and adults who have antibodies indicating they have recovered from the disease. (In the Italian study from last year, children’s seroprevalence was even higher than that of the oldest adults, the result of what Hyde calls “survivorship bias” — i.e., the older people who got Covid-19 mostly died.) The hosts on This Week in Virology went over Hyde’s paper in last week’s podcast, TWiV #731. If you can spare the time, listen to 11 minutes’ worth of their discussion beginning at 23:33. One compelling point the TWiV team brought out: children are not immune from long Covid. A UK study found that 12.9% of kids had symptoms weeks after clearing the disease, compared with 22% of adults. The belief that children don’t get infected much should no longer be used as an argument for why schools ought to be reopened.
Turns out they accidentally released some charts back in Feb, modelling vaccination/reopening scenarios — these were probably used in private briefings to the cabinet, and not intended for public consumption (via Andrew Flood)
Well done, Slovakia — massive decrease in prevalence after 2 rounds of mass testing.
Slovakia conducted multiple rounds of population-wide rapid antigen testing for SARS-CoV-2 in late 2020, combined with a period of additional contact restrictions. Observed prevalence decreased by 58% (95% CI: 57-58%) within one week in the 45 counties that were subject to two rounds of mass testing, an estimate that remained robust when adjusting for multiple potential confounders. Adjusting for epidemic growth of 4.4% (1.1-6.9%) per day preceding the mass testing campaign, the estimated decrease in prevalence compared to a scenario of unmitigated growth was 70% (67-73%). Modelling indicated that this decrease could not be explained solely by infection control measures, but required the additional impact of isolation and quarantine of household members of those testing positive.
Testcontainers is a Java library that supports JUnit tests, providing lightweight, throwaway instances of common databases, Selenium web browsers, or anything else that can run in a Docker container.
Lovely little service to draw a map with ridgelines, Joy Division “Unknown Pleasures” style (via Nelson)
‘tl;dr: The time when Microsoft banned my entire country for cheating at Club Bing.’ This is a great story — though it must have been driving the MS Asirra anti-abuse team up the wall. Quite interesting to hear about low-cost/grassroots ways to accomplish some of the tech tasks, e.g. instead of firing up a farm of EC2 instances to crack a Captcha, he farmed out that work using thumbdrives, manually distributed to his friends.
‘The club’s name is synonymous with idiocy in Africa’s most populous nation. How on earth did this happen?’ — what a great story! (via Ben)
Interesting blog post from Nelson about Speedify, a proprietary multipath VPN service to bond two internet links to improve reliability
Amazing well-preserved human footprints from between 4200 and 4600 years ago:
The Centro Nacional de Investigación sobre la Evolución Humana (CENIEH) has participated in chapter 17, which covers the prints of bare feet preserved in the soft floor sediment of Palomera Cave in the Ojo Guareña Karst Complex (Merindad de Sotoscueva, Burgos, Spain). These footprints, ascribed to traces left by about ten individuals who explored the caves between 4200 and 4600 years ago, were discovered in 1969 by Grupo Espeleológico Edelweiss (GEE) at the Sala y Galerías de las Huellas site, some 1200 m from the entrance to Palomera Cave. The fragility of the footprints and their environment meant it was not possible to study them, and doing so has had to await the development of the new non-invasive teledetection techniques.
Great essay on the shitfest that is NFTs and cryptoart:
During unprecedented temperature increases, sea level rise, the total loss of permanent sea ice, widespread species extinction, countless severe weather events, and all the other hallmarks of total climate collapse, this kind of gleeful wastefulness is, and I am not being hyperbolic, a crime against humanity.
Prof. Akiko Iwasaki on Twitter: “This video shows that vaccines have helped some people with #longCOVID with their symptoms. While the numbers are still small in some groups, there are encouraging signs (also via @DanielGriffinMD). I present my hypothesis on how vaccines might improve #LongCovid (1/)”
Reverse-engineered by an external user, it seems: ‘This information below is gathered from sporadic developer posts and videos, salted with my own experience and experiments, various forum threads, and watching streams. Note that since Blizzard does not give exact algorithms, I do have to fill in some gaps, or leave some items unknown.’ The matchmaking systems are very complex and a key component of what makes games like Overwatch playable, so this is interesting stuff. (via Shevaun)
This is great. An amulet is ‘a kind of poem that depends on language, code, and luck. To qualify, a poem must satisfy these criteria: Its complete Unicode text is 64 bytes or less; and the hexadecimal SHA-256 hash of the text includes four or more 8s in a row.’
The hash is a cold hexadecimal spew – 9a120001cc88888363fc67c45f2c52447ae64808d497ec9d699dba0d74d72aab – and, like a fingerprint, it doesn’t tell you anything about the entity it identifies. That’s by design, but even so, it feels strange for a value so pivotal to be totally disconnected from the underlying content, especially when it is this value that’s being collected and traded in cryptographic marketplaces. Ostensibly, the hash provides an immutable link between unique cryptographic object and free-floating digital media. The amulet asks: what if we took that link seriously? In a sense, the definition of the SHA-256 hash function created, at a stroke, all amulets of all rarities. Common to mythic, trashy to lovely, they have been hiding in the manifold combinations of language; we just didn’t know we ought to be looking for them. Until now!
This is comedy gold. Turns out some digital phrenology software used for AI-aided interviewing will produce higher results for candidates who simply have a bookshelf as a background. As Daniel Bilar puts it: it’s the “Clever Hans” phenomenon, […] ‘spurious correlations, can occur when there is a feature in the data that is highly correlated with the correct outcome, but is not the cause for the answer being correct.’
Via Colman Reilly — this really sounds like outright fraudulent behaviour by FB:
The filing also reveals that a Facebook product manager for the “potential reach” tool warned the company was making revenue it “should never have” off of “wrong data”. The unsealed documents pertain to a U.S. class action lawsuit, filed in 2018, which alleges that Facebook deceived advertisers by knowingly including fake and duplicate accounts in a “potential reach” metric. Facebook denies the claim but has acknowledged accuracy issues with the “potential reach” metric as far back as 2016 — and also changed how it worked in 2019. […] Redacted documents from the lawsuit, reported by the WSJ last year, included the awkward detail that a Facebook employee had asked “how long can we get away with the reach overestimation?”
This is pretty solid real-world data, IMO — even if they’re not testing correctly to find it, it’s there in the ONS data
Testing people with any of the three ‘classic’ symptoms would have spotted 69% of symptomatic cases, with 46 people testing negative for every person testing positive. However, testing people with any of seven key symptoms – cough, fever, anosmia, fatigue, headache, sore throat and diarrhoea – in the first three days of illness would have detected 96% of symptomatic cases. In this case, for every person with the disease identified, 95 would test negative. Researchers also found users of the Symptom Study App were more likely to select headache and diarrhoea within the first three days of symptoms, and fever during the first seven days, which reflects different timings of symptoms in the disease course. Data from the ZOE app shows that 31% of people who are ill with COVID-19 don’t have any of the triad of symptoms in the early stages of the disease when most infectious.
working on the maths on outage probabilities.
via Paddy Mallon on twitter: ‘results (pre-print) of an analysis examining SARS-CoV-2 variants in Ireland from hospital cases during 2020. This is the largest analysis of its kind to date in Ireland and provides some important insights into #COVID19Ireland.”
1. Effective lockdown leading to low transmission rates can essentially eliminate common #SARS_CoV_2 variants contributing to disease ..BUT.. 2. ..new variants can be introduced (likely [via] travel) that seed new waves of #COVID19. As daily infections fall, hopefully correct implementation of new travel restrictions can help stop future W4 of #COVID19Ireland. We also hope that this data helps people understand how travel contributes to new #COVID19 infections (and new variants) coming into the country.
via John McClean: Imperial College COVID-19 Response Team report on premature reopening under different vaccination strategies in the UK. They find significant risk of a large 3rd wave of infections: ‘For all gradual easing of NPI scenarios explored, unless vaccination is rapidly ramped up to 3 million doses a week, gradual lifting of NPIs from 1st March to 1st July will lead to a third wave of hospitalisations which will exceed our indicative threshold of 25,000 beds national hospital capacity.’
Excellent article from Tomas Pueyo on the new COVID-19 variants:
In the race between the variants and the vaccines, the variants are the hare and the vaccines are the tortoise. We all know that, in the end, the vaccines will win. Like the tortoise. By this summer, in developed countries, vaccination rates will likely range between 50% and 80%. Since there will also be some herd immunity, and summer means outdoors in the Northern hemisphere, it’s likely that the pandemic will die down some time during the summer. The question is: Will they also be rolled out in time to prevent the new variants from taking over? Now we have our answer: Unfortunately, no.TBH, though, I am not so sanguine about the results for the Northern hemisphere. With open borders, no mandatory quarantine, and the rest of the world suffering without sufficient access to vaccines, new variants will keep passaging and keep emerging, risking putting our vaccine progress back to square one. (via Cormac)
Adam Kucharski on Twitter: “I’ve noticed people sometimes use ‘herd immunity’ to mean ‘pathogen fades to zero and stays there’ rather than the technical definition (i.e. R drops below 1 because of accumulated immunity, without NPIs). Why is the distinction important? ….”
I can confirm, zstd is awesome — must use xxHash more, too.
Newer Tar 1.32+ and Rsync 3.2.3 versions have added Facebook’s zstd compression algorithm and Rsync has added lz4 and xxHash checksum algorithms which give Tar and Rsync a tremendous boost in transfer speed.
significantly faster than Murmur3 and City32; SSE code is even faster than sequential RAM reads :)
Kai Kupferschmidt on Twitter: “Natural immunity: This was maybe the worst bit of news buried here. In the placebo group there were previously infected people and people that had not been infected. In the trial both groups ended up getting #covid19 with the same likelihood: 2%.”
Jaysus, this is terrifying.
Galvão, the lead physician in the coronavirus ward at a public hospital in the Brazilian city of Manaus, had been haunted by the wave that crashed last spring. In less than 10 days, it ruptured the city’s bewildered medical system. Sick patients were turned away. The dead were piled into mass graves. So Galvão’s hospital organized contingency plans. Additional beds were reserved, and a detailed schedule for opening them was created. But the new surge, when it came, was different. The virus had mutated, with a suite of alterations that probably made it more transmissible — and perhaps more lethal. Manaus was hit by what scientists call the P.1 variant. This time, it didn’t take 10 days to overwhelm Galvão’s hospital. It took 24 hours.
oh my, I didn’t realise you could jailbreak a Kindle and do this! Simple dashboard that HTTP fetches a rendered PNG periodically and refreshes the Kindle screen with it
“Toxic Positivity” Is Doing More Harm Than Good:
Call it FONO, or fear of a negative outlook. Also known as “dismissive positivity,” it’s expressed as an overbearing cheerfulness no matter how bad things are, a pep that denies emotional oxygen to anything but a rictus grin.(via JK)
DIY mask braces, and a shop selling premade ones, from a former Apple designer
What is a mask fitter? A soft, flexible and adjustable “frame” that significantly improves the outer seal of a mask. Why use it? Adding the Badger Seal to a 3-ply disposable mask reduces the effective particle penetration by typically 15x (see the Performance section below). What makes the Badger Seal unique? It’s cheap (< $1 in materials), easy to assemble, made from readily available materials and tools, comfortable, quickly customizable and open source. There are other fitters out there, though none seem to excel in all of these areas.
Recent preprint paper from the UK —
Adjusting for patient-level factors, mortality was higher for admissions during periods of high occupancy (>85% occupancy versus the baseline of 45 to 85%) [OR 1.19 (95% posterior credible interval (PCI): 1.00 to 1.44)]. In contrast, mortality was decreased for admissions during periods of low occupancy (<45% relative to the baseline) [OR 0.75 (95% PCI: 0.62 to 0.89)]. [...] The results of this study suggest that survival rates for patients with COVID-19 in intensive care settings appears to deteriorate as the occupancy of (surge capacity) beds compatible with mechanical ventilation (a proxy for operational pressure), increases. Moreover, this risk doesn’t occur above a specific threshold, but rather appears linear; whereby going from 0% occupancy to 100% occupancy increases risk of mortality by 92% [...]As Andrew Kunzmann noted – “To aid interpretation, the difference in risk for a 70-year-old man with no comorbidities being admitted during a period of high versus low occupancy is equivalent to the risk if they were approximately a decade older”.
A recent preprint from China — lots of “long COVID” impact, still:
Fatigue or muscle weakness (63%, 1038 of 1655) and sleep difficulties (26%, 437 of 1655) were the most common symptoms. Anxiety or depression was reported among 23% (367 of 1617) of patients. The proportions of median 6-min walking distance less than the lower limit of the normal range were 24% for those at severity scale 3, 22% for severity scale 4, and 29% for severity scale 5–6.
Andrew is keeping the receipts on restaurants and pubs reopening being a major driver for Ireland’s third wave of COVID-19: Andrew Flood on Twitter: “#Covid19Ireland cases by epi date are pretty suggestive with the sudden 50% jump Dec 14th as if something must have changed radically 10 days earlier on the 4th creating a big additional opportunity for the virus. https://t.co/aos9qb7M6T” “A Christmas season like no other”, indeed.
I never knew this existed! Code golf galore.
I had forgotten about this, but it’s a good example: Maros Bonsai on Twitter: ‘March – April 2020 in Slovakia. Border controls, mandatory quarantines for travellers from abroad in designated facilities with testing on arrival and before departure from facility. Cases brought to zero. Then abandoned suddenly. Now we have third highest fatality rate globally.’ Given that Slovakia has a capital city close to the border with another country, it’s an interesting example.
tl;dr: temperature, humidity, vitamin D are all important:
The seasonal cycle of respiratory viral diseases has been widely recognized for thousands of years, as annual epidemics of the common cold and influenza disease hit the human population like clockwork in the winter season in temperate regions. Moreover, epidemics caused by viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and the newly emerging SARS-CoV-2 occur during the winter months. The mechanisms underlying the seasonal nature of respiratory viral infections have been examined and debated for many years. The two major contributing factors are the changes in environmental parameters and human behavior. Studies have revealed the effect of temperature and humidity on respiratory virus stability and transmission rates. More recent research highlights the importance of the environmental factors, especially temperature and humidity, in modulating host intrinsic, innate, and adaptive immune responses to viral infections in the respiratory tract. Here we review evidence of how outdoor and indoor climates are linked to the seasonality of viral respiratory infections. We further discuss determinants of host response in the seasonality of respiratory viruses by highlighting recent studies in the field.
This article in _Nature Reviews Immunology_ suggests that “SARS-CoV-2 is likely to become the fifth endemic common cold virus, causing largely asymptomatic infections.”
Endemic SARS-CoV-2 will ensure maintenance of seroprevalence and mucosal immunity in the population, which will increase over time in new generations. As such, most infected individuals will ultimately endure a largely asymptomatic or mild course of disease, although similarly to the other common cold HCoVs, SARS-CoV-2 may cause fatalities in extremely vulnerable elderly or immunocompromised individuals. SARS-CoV-2 mutants will arise as already reported, but new variants will unlikely differ sufficiently to escape established immunity. Cross-reactive immunity, critically boosted by natural reinfections, should conserve good levels of population protection also against new variants, thereby preventing the occurrence of severe disease, including in the vulnerable. Therefore, we predict that the need for large-scale vaccination programmes will be transient until an endemic state for SARS-CoV-2 is reached.