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kottke.org posts about science

A Scientific Portrait of the SARS-CoV-2 Virus

posted by Jason Kottke   Oct 12, 2020

A model of the SARS-CoV-2 virus

This is a great piece from Carl Zimmer about how much scientists have learned about SARS-CoV-2 through imaging, including how the virus works and prospects for treatment and a vaccine.

Thanks to the work of scientists like Dr. Li, the new coronavirus, known as SARS-CoV-2, is no longer a cipher. They have come to know it in intimate, atomic detail. They’ve discovered how it uses some of its proteins to slip into cells and how its intimately twisted genes commandeer our biochemistry. They’ve observed how some viral proteins throw wrenches into our cellular factories, while others build nurseries for making new viruses. And some researchers are using supercomputers to create complete, virtual viruses that they hope to use to understand how the real viruses have spread with such devastating ease.

I’ve been watching the lectures for MIT’s online Covid-19 class and the thing that has struck me most is just how much scientists have learned about the SARS-CoV-2 virus in such a short amount of time. To be clear, there are many things that they still do not understand about it (and viruses in general), but scientists know this thing upside down and backwards. The depth and breadth of their knowledge is so impressive and I wish more people were aware of it.

Winter Is Coming. Is It Safe to Socialize Indoors?

posted by Jason Kottke   Oct 12, 2020

In an article that The Atlantic classifies as “politics” rather than “science” or “medicine”, Olga Khazan explores why, more than 8 months into the pandemic, Americans still have little idea about the safety of gathering with others indoors.

For months now, Americans have been told that if we want to socialize, the safest way to do it is outdoors, the better to disperse the droplets that spew from our mouths whenever we do anything but silently purchase grapefruit. But in many parts of the country, this is the last month that the weather will allow people to spend more than a few minutes outside comfortably. And next month, America will celebrate a holiday that is marked by being inside together and eating while talking loudly to old people.

In a nutshell, the lack of federal support/guidance/action is the main reason why people are still so confused about what safety measures to take to reduce their Covid risk:

Still, Ranney says, this [Covid risk] app is the kind of thing the federal government really should have developed by now. It’s odd that in a wealthy, industrialized country, a random researcher is the one designing a tool to keep citizens safe from public-health threats, using data she scraped from a newspaper.

One thing that Khazan doesn’t really get into is the whole aerosols thing, which in my mind is something that most people are still not familiar with, many local & state governments are not taking into account w/r/t recommended safety measures, and requires different risk guidance about the safety of the indoors than if we were just dealing with fomites & droplets. Again, from the excellent Time magazine piece by aerosol chemist Jose-Luis Jimenez:

When it comes to COVID-19, the evidence overwhelmingly supports aerosol transmission, and there are no strong arguments against it. For example, contact tracing has found that much COVID-19 transmission occurs in close proximity, but that many people who share the same home with an infected person do not get the disease. To understand why, it is useful to use cigarette or vaping smoke (which is also an aerosol) as an analog. Imagine sharing a home with a smoker: if you stood close to the smoker while talking, you would inhale a great deal of smoke. Replace the smoke with virus-containing aerosols, which behave very similarly, and the impact is similar: the closer you are to someone releasing virus-carrying aerosols, the more likely you are to breathe in larger amounts of virus. We know from detailed, rigorous studies that when individuals talk in close proximity, aerosols dominate transmission and droplets are nearly negligible.

If you are standing on the other side of the room, you would inhale significantly less smoke. But in a poorly ventilated room, the smoke will accumulate, and people in the room may end up inhaling a lot of smoke over time. Talking, and especially singing and shouting increase aerosol exhalation by factors of 10 and 50, respectively. Indeed, we are finding that outbreaks often occur when people gather in crowded, insufficiently ventilated indoor spaces, such as singing at karaoke parties, cheering at clubs, having conversations in bars, and exercising in gyms. Superspreading events, where one person infects many, occur almost exclusively in indoor locations and are driving the pandemic. These observations are easily explained by aerosols, and are very difficult or impossible to explain by droplets or fomites.

The science is there — it’s the lack of connection between scientists, public health experts & officials, and the government that continues to be a problem.

Dr. Fauci: Earliest We’ll Be “Back to Normal” Is the End of 2021

posted by Jason Kottke   Oct 08, 2020

A few weeks ago during the Q&A session after his lecture for MIT’s online biology class about the pandemic, Dr. Anthony Fauci shared his expert opinion on when things might return to “normal” in the US. Here was my paraphrased tweet about it:

With a very effective vaccine ready in Nov/Dec, distributed widely, and if lots of people take it (i.e. the best case scenario), the earliest we could return to “normal life” in the world is the end of 2021.

At the New Yorker Festival earlier in the week, Michael Specter asked him about a return to normalcy and Fauci elaborated a bit more on this timeline (starts ~10:22 in the video).

When are we gonna get back to something that closely resembles, or is in fact, normal as we knew it?

We’re already making doses, tens and hundreds of millions of doses to be ready, first at least, in graded numbers at the end of the year in November/December. By the time we get to April, we likely will have doses to be able to vaccinate anybody who needs to be vaccinated. But logistically by the time you get everybody vaccinated, it likely will not be until the third or even the beginning of the fourth quarter of 2021.

So let’s say we get a 70% effective vaccine, which I hope we will get, but only 60% of the people get vaccinated. There are going to be a lot of vulnerable people out there, which means that the vaccine will greatly help us to pull back a bit on the restrictions that we have now to maintain good public health, but it’s not going to eliminate things like mask wearing and avoiding crowds and things like that.

So I think we can approach normality, but I don’t think we’re going to be back to normal until the end of 2021. We may do better than that; I hope so but I don’t think so.

Leaving aside what “normal” might mean and who it actually applies to,1 there’s some good news and bad news in there. The good news is, they’re already producing doses of the vaccine to be ready if and when the phase 3 trials are successful. Ramping up production before the trials conclude isn’t usually done because it’s a waste of money if the trials fail, but these vaccines are so critical to saving lives that they’re spending that money to save time. That’s great news.

The bad news is that we’re not even halfway through the pandemic in the best case scenario. We’re going to be wearing masks in public for at least another year (and probably longer than that). Large gatherings of people (especially indoors) will continue to be problematic — you know: movie theaters, concerts, clubs, bars, restaurants, schools, and churches — and folks staying within small pods of trusted folks will likely be the safest course of action.

A change in national leadership in both the executive branch and Senate could change the outlook for the better. We could get some normalcy back even without a vaccine through measures like a national mask mandate/distribution, a real national testing & tracing effort, taking aerosol transmission seriously, and easing the economic pressure to “open back up” prematurely. We’re never going to do as well as Vietnam or Taiwan, but I’d settle for Greece or Norway.

Update: In an interview posted yesterday, Johns Hopkins epidemiologist Dr. Caitlin Rivers gives her best guess at a return to normalcy:

Topol: When do you think we’ll see pre-COVID life restored?

Rivers: I wish I knew. I’m thinking toward the end of 2021. It’s really hard to say with any certainty. We should all be mentally prepared to have quite a bit ahead of us.

  1. It’s America. If we know anything by now about this country, it’s that access to healthcare and economic opportunity is going to apply unevenly to the people who live here. For instance, it’s likely that Black & brown communities, which have been disproportionately affected by the pandemic, may face difficulty in getting access to vaccines compared to wealthier, predominantly white communities.

The Science Is In: Wear. A. Mask!

posted by Jason Kottke   Oct 07, 2020

Back in June, in a post called Jesus Christ, Just Wear a Face Mask!, I presented a bunch of evidence and arguments for wearing face masks to prevent the spread of Covid-19. Even then it was pretty clear that masks were working. In piece published by Nature yesterday, Lynne Peeples summarizes what the data and science currently says about the effectiveness of wearing face masks. Here is her one-sentence summary:

To be clear, the science supports using masks, with recent studies suggesting that they could save lives in different ways: research shows that they cut down the chances of both transmitting and catching the coronavirus, and some studies hint that masks might reduce the severity of infection if people do contract the disease.

And importantly, even ardently pro-mask scientists agree that masks should be worn in conjunction with taking other precautions: limiting large gatherings, maintaining distance, limiting the time you spend indoors with others, etc.

David Attenborough: A Life on Our Planet

posted by Jason Kottke   Oct 06, 2020

Now streaming on Netflix, David Attenborough: A Life on Our Planet, a documentary about the 94-year-old broadcaster, naturalist, and international treasure.

In this unique feature documentary, titled David Attenborough: A Life On Our Planet, the celebrated naturalist reflects upon both the defining moments of his lifetime and the devastating changes he has seen. Coming to Netflix October 4 2020, the film addresses some of the biggest challenges facing life on our planet, providing a snapshot of global nature loss in a single lifetime. With it comes a powerful message of hope for future generations as Attenborough reveals the solutions to help save our planet from disaster.

In the trailer (embedded above), Attenborough says “I had the most extraordinary life. It’s only now that I appreciate how extraordinary.” In saying that, he’s speaking not only as a living legend whose long career in television and science has brought him nearly universal acclaim, but also as someone who can look back and see how recognizably and thoroughly the Earth has changed during his lifetime. The depletion of animal populations, the changing climate, the shifting habitats — he’s witnessed firsthand how much humans have fucked up the planet. We should listen to his testimony and suggestions for fixing what he calls “our greatest mistake”. I hope it’s not too late.

Like Humans, Crows Can “Ponder the Content of Their Own Minds”

posted by Jason Kottke   Oct 05, 2020

A recent study that looked at the brain patterns of crows when performing tasks found evidence that they “know what they know and can ponder the content of their own minds”, an attribute that was previously thought to exist only in humans and some monkeys.

The birds were aware of what they subjectively perceived, flash or no flash, correctly reporting what their sensory neurons recorded, Nieder told STAT. “I think it demonstrates convincingly that crows and probably other advanced birds have sensory awareness, in the sense that they have specific subjective experiences that they can communicate,” he said. “Besides crows, this kind of neurobiological evidence for sensory consciousness only exists in humans and macaque monkeys.”

(via kottke ride home)

Totally Under Control

posted by Jason Kottke   Oct 02, 2020

In secrecy over the past several months, filmmaker Alex Gibney has been making a documentary film about the US government’s response to the Covid-19 pandemic called Totally Under Control. He and co-directors Ophelia Harutyunyan and Suzanne Hillinger interviewed “countless scientists, medical professionals, and government officials on the inside” to produce the film.

Academy Award-winning filmmaker Alex Gibney, directing with Ophelia Harutyunyan and Suzanne Hillinger, interrogates this question and its devastating implications in Totally Under Control. With damning testimony from public health officials and hard investigative reporting, Gibney exposes a system-wide collapse caused by a profound dereliction of Presidential leadership.

Gibney previously directed Enron: The Smartest Guys in the Room, Going Clear, and Zero Days (all excellent documentaries). The film comes out in theaters on October 13 and on Hulu on October 20.

How to Protect Yourself from the Aerosol Spread of Covid-19

posted by Jason Kottke   Oct 02, 2020

A group of scientists who believe that WHO and the CDC are being too slow in acknowledging the role of aerosol transmission in spreading Covid-19 have written up a Google Doc of advice for the public: FAQs on Protecting Yourself from COVID-19 Aerosol Transmission.

The goal of these FAQs is to provide information to the general public in an efficient manner about how to prevent aerosol transmission of COVID-19, with the hope that this will allow more informed decision making by individuals or organizations. All of this information has been posted in Twitter and other forums, but can be difficult to find. Having multiple experts working together, and having the ability to update this information also improves its quality. These FAQs represent our best understanding at this time, and should always be similar or more stringent than information provided by CDC, WHO, and most regional & local health authorities. If your authority has a more stringent guideline than discussed here, follow that more stringent guideline.

The group was organized by chemist Jose-Luis Jimenez, who has been studying aerosols for 20 years. You may remember Jimenez from his excellent piece in Time magazine, where he used the analogy of smoke to explain aerosol transmission. Here’s a snippet from the FAQ, highlighting something I’ve been concerned about lately: people wearing face shields instead of masks and employees in stores not wearing masks behind plexiglass shields:

7.13. Are face shields and masks interchangeable?
No, face shields do not offer much protection against aerosols (also see this video), while masks do. Face shields are good for blocking ballistic droplets released by the wearer or that might fly into the wearer’s face when close to others. Face shields are considered a supplement to masks for partial eye protection (but less useful than closed glasses, as discussed above), but not a substitute for them.

7.14. Are plexiglass barriers helpful?
Plexiglass barriers are generally useful to avoid direct droplet infection and direct aerosol transmission whenever people are in close proximity and distance cannot be kept. Therefore, it is recommended to use them as a direct transmission suppression tool at such places, such as a supermarket checkout.

However, as aerosols follow the air movements indoors, the protective effects of the plexiglas barriers against aerosols will be limited. Plexiglas barriers alone are not a sufficient approach to protect against aerosol transmission. Their installation alone cannot protect against indoor aerosol transmission and should not be regarded as safe and sufficient protection.

MIT Technology Review’s Charlotte Jee interviewed Jimenez about the FAQ document.

We update the document all the time. We’re effectively having to be a little WHO or CDC. We’re saying the things that they should be saying. This is frustrating, but it’s the situation we find ourselves in. These organizations have been flat-out refusing to consider if aerosol transmission is important, which leaves people unprotected. So we feel it’s our duty to communicate directly with the public.

Right now, in my opinion as someone who has done a ton of reading about Covid-19, the most best accessible information on how individuals and societies can protect themselves and others during the pandemic (and why) is available in Jimenez’s Time article, Aaron Carroll’s NY Times piece about how to think about risk management, Zeynep Tufekci’s piece in the Atlantic about dispersion and superspreading, and now this Google Doc by Jimenez et al.

“This Overlooked Variable Is the Key to the Pandemic”

posted by Jason Kottke   Oct 02, 2020

Zeynep Tufekci says that we are paying too much attention to the R value of SARS-CoV-2 (basically the measure of its contagiousness) and not nearly enough attention to the k value (“whether a virus spreads in a steady manner or in big bursts, whereby one person infects many, all at once”).

There are COVID-19 incidents in which a single person likely infected 80 percent or more of the people in the room in just a few hours. But, at other times, COVID-19 can be surprisingly much less contagious. Overdispersion and super-spreading of this virus is found in research across the globe. A growing number of studies estimate that a majority of infected people may not infect a single other person. A recent paper found that in Hong Kong, which had extensive testing and contact tracing, about 19 percent of cases were responsible for 80 percent of transmission, while 69 percent of cases did not infect another person. This finding is not rare: Multiple studies from the beginning have suggested that as few as 10 to 20 percent of infected people may be responsible for as much as 80 to 90 percent of transmission, and that many people barely transmit it.

We’ve known, or at least suspected, this about SARS-CoV-2 for awhile now — I linked to two articles about superspreading back in May and June — but Tufekci says we have not adjusted our thinking about what that means for prevention. We should be avoiding superspreading environments/events (“Avoid Crowding, Indoors, low Ventilation, Close proximity, long Duration, Unmasked, Talking/singing/Yelling”), doing backwards contact tracing, and rapid testing.

In an overdispersed regime, identifying transmission events (someone infected someone else) is more important than identifying infected individuals. Consider an infected person and their 20 forward contacts-people they met since they got infected. Let’s say we test 10 of them with a cheap, rapid test and get our results back in an hour or two. This isn’t a great way to determine exactly who is sick out of that 10, because our test will miss some positives, but that’s fine for our purposes. If everyone is negative, we can act as if nobody is infected, because the test is pretty good at finding negatives. However, the moment we find a few transmissions, we know we may have a super-spreader event, and we can tell all 20 people to assume they are positive and to self-isolate-if there is one or two transmissions, it’s likely there’s more exactly because of the clustering behavior. Depending on age and other factors, we can test those people individually using PCR tests, which can pinpoint who is infected, or ask them all to wait it out.

Part of the problem is that dispersion and its effects aren’t all that intuitive.

Overdispersion makes it harder for us to absorb lessons from the world because it interferes with how we ordinarily think about cause and effect. For example, it means that events that result in spreading and non-spreading of the virus are asymmetric in their ability to inform us. Take the highly publicized case in Springfield, Missouri, in which two infected hairstylists, both of whom wore masks, continued to work with clients while symptomatic. It turns out that no apparent infections were found among the 139 exposed clients (67 were directly tested; the rest did not report getting sick). While there is a lot of evidence that masks are crucial in dampening transmission, that event alone wouldn’t tell us if masks work. In contrast, studying transmission, the rarer event, can be quite informative. Had those two hairstylists transmitted the virus to large numbers of people despite everyone wearing masks, it would be important evidence that, perhaps, masks aren’t useful in preventing super-spreading.

The piece is an important read and interesting throughout: just read the whole thing.

Is It Too Late To Stop Climate Change?

posted by Jason Kottke   Sep 29, 2020

For Kurzgesagt’s latest video, they explore the challenges the world faces in attempting to get the rate of climate change under control before it’s too late and how to get there.

Climate change is just too much. There is never any good news. Only graphs that get more and more red and angry. Almost every year breaks some horrible record, from the harshest heat waves to the most rapid glacier melt. It’s endless and relentless.

We have known for decades that rapid climate change is being caused by the release of greenhouse gases. But instead of reducing them, in 2019 the world was emitting 50% more CO2 than in the year 2000. And emissions are still rising. Why is that? Why is it so hard to just stop emitting these gases?

According to the video, global population growth and economic growth will be working against us over the next few decades and that increasing our energy efficiency and lowering emissions from energy sources are the main ways in which we will be able to slow things down. It’s worth noting that on the wizard vs. prophet continuum, this video is firmly in the wizard camp. That’s not wrong or bad; it’s just that other people have different ideas about how to combat climate change.

The Delightful New “Universe in a Nutshell” App

posted by Jason Kottke   Sep 22, 2020

The breadth of scale of measurable objects in the universe — our distance from the most distant objects we can observe (billions of light years away) to particles measured in something called a yoctometer (1×10-24 meters) — is staggering to think about. That’s where the Universe in a Nutshell app comes in. Developed by Kurzgesagt & Wait But Why (both kottke.org favorites), you can use the app to quickly and easily zoom in and out through objects at all the scales of the universe, like quarks, DNA, cells, earthworms, Europe, Jupiter, the black hole at the center of our galaxy, the Crab Nebula, galaxies, and galaxy superclusters.

Universe In A Nutshell

Universe In A Nutshell

You can tap on any object you encounter to learn more about it, like an interactive Powers of Ten. I spent 20 minutes just now playing around and it’s really fun. You can download the app for $2.99 from the App Store or on Google Play.

To mark the release, Kurzgesagt made a video comparing the sizes of stars:

And Wait But Why’s Tim Urban wrote a post about the scales of objects: The Big and the Small.

In Search of a Flat Earth

posted by Jason Kottke   Sep 16, 2020

In Search of a Flat Earth is a documentary essay by Folding Ideas’ Dan Olson that starts out talking about people who believe the Earth is flat (and why it’s so difficult to convince them otherwise) but then takes a sharp turn toward a more recent and much more worrying conspiracy theory, QAnon. Lots of interesting information and observations throughout.

See also QAnon, Conspiracy Theories, and the Rise of Magical Thinking.

Scientists Detect Signs of Possible Life on Venus

posted by Jason Kottke   Sep 14, 2020

The planet Venus

A group of astronomers have announced that they’ve discovered evidence that there may be life in the atmosphere of Venus.

The astronomers, who reported the finding on Monday in a pair of papers, have not collected specimens of Venusian microbes, nor have they snapped any pictures of them. But with powerful telescopes, they have detected a chemical — phosphine — in the thick Venus atmosphere. After much analysis, the scientists assert that something now alive is the only explanation for the chemical’s source.

Some researchers question this hypothesis, and they suggest instead that the gas could result from unexplained atmospheric or geologic processes on a planet that remains mysterious. But the finding will also encourage some planetary scientists to ask whether humanity has overlooked a planet that may have once been more Earthlike than any other world in our solar system.

“This is an astonishing and ‘out of the blue’ finding,” said Sara Seager, a planetary scientist at the Massachusetts Institute of Technology and an author of the papers (one published in Nature Astronomy and another submitted to the journal Astrobiology). “It will definitely fuel more research into the possibilities for life in Venus’s atmosphere.”

Ultra Slow-Motion Video of Insects Taking Flight

posted by Jason Kottke   Sep 09, 2020

Research biologist Adrian Smith, who specializes in insects, recently filmed a number of different types of flying insects taking off and flying away at 3200 frames/sec. Before watching, I figured I’d find this interesting — flying and slow motion together? sign me up! — but this video was straight-up mesmerizing with just the right amount of informative narration from Smith. There’s such an amazing diversity in wing shape and flight styles among even this small group of insects; I had to keep rewinding it to watch for details that I’d missed. Also, don’t miss the fishfly breaking the fourth wall by looking right at the camera while taking off at 6:07. I see you, my dude.

Smith has previously captured flying ants in slow motion and this globular springtail bug that spins through the air at more than 22,000 rpm. (via moss & fog)

Radioactive Diamond Batteries That Last for Thousands of Years

posted by Jason Kottke   Sep 01, 2020

A pair of researchers from the University of Bristol have formed a company called Arkenlight to try to make diamond batteries out of nuclear waste that can potentially power devices for thousands of years. The betavoltaic batteries work by releasing beta radiation, which excites semiconductor material to produce electricity. These types of batteries don’t put out much power — they can’t replace your iPhone battery for example — but they do their thing for a loooong time.

Arkenlight is focused on creating batteries that have a diamond-like structure out of irradiated graphite, which is quite common.

But that’s where a radioactive isotope called carbon-14 may be able to help. Best known for its role in radiocarbon dating, which allows archaeologists to estimate the age of ancient artifacts, it can provide a boost to nuclear batteries because it can function both as a radioactive source and a semiconductor. It also has a half-life of 5,700 years, which means a carbon-14 nuclear battery could, in principle, power an electronic device for longer than humans have had written language.

I mean, it’s little more than a theory at this point so maybe it won’t be feasible after all, but what a brilliant idea: combining the radioactive source and the semiconductor (thereby upping the efficiency) and using nuclear waste to build the whole thing. Science at its most poetically useful. (via geoff manaugh)

Ammonite

posted by Jason Kottke   Aug 27, 2020

Ammonite is an upcoming romantic drama from director Francis Lee. It takes place in the 1840s and stars Kate Winslet as a palaeontologist & Saoirse Ronan as her assistant; the pair clash then fall in love. The story is based on the life of Mary Anning, who made several important contributions to paleontology.

Paleontology wouldn’t be the same without Mary Anning. She scoured the dreary coast of southern England for secrets not seen since the Jurassic, fueling the nascent 19th-century field of fossil studies with evidence of strange sea dragons, flying reptiles and other fascinating fragments of life long past. And now, over 170 years after her death, she’s got her own movie.

However, there’s no evidence that Anning and her friend, Charlotte Murchison, ever had a romantic relationship.

I have to wonder what Anning would say to this. As she wrote in a letter, “The world has used me so unkindly, I fear it has made me suspicious of everyone.” In the sexist, male-dominated world of 19th-century science, Anning’s finds were celebrated while she herself was barred from joining academic societies or even finding a path to gain equal footing with the likes of William Buckland, Gideon Mantell and other traditional heroes of paleontology who parasitized her labor. Now, in having her life’s story made a fiction, is the world using Anning again?

Ammonite opens in US theaters in November? (I mean, they reopened schools in Florida against all expert advice and common sense, so why not theaters?) Anyway, looking forward to the third movie in the Portrait of a Lady on Fire trilogy next year.

Smoke on the Wind: the Aerosol Spread of Covid-19

posted by Jason Kottke   Aug 26, 2020

Chemist Jose-Luis Jimenez writing for Time magazine: COVID-19 Is Transmitted Through Aerosols. We Have Enough Evidence, Now It Is Time to Act. In it, he argues that while much of the early attention has been on fomites (surface contamination) and droplets as pathways for spreading Covid-19, tranmission by aerosols may be more significant. His analogy of smoke makes it quite easy to understand:

When it comes to COVID-19, the evidence overwhelmingly supports aerosol transmission, and there are no strong arguments against it. For example, contact tracing has found that much COVID-19 transmission occurs in close proximity, but that many people who share the same home with an infected person do not get the disease. To understand why, it is useful to use cigarette or vaping smoke (which is also an aerosol) as an analog. Imagine sharing a home with a smoker: if you stood close to the smoker while talking, you would inhale a great deal of smoke. Replace the smoke with virus-containing aerosols, which behave very similarly, and the impact is similar: the closer you are to someone releasing virus-carrying aerosols, the more likely you are to breathe in larger amounts of virus. We know from detailed, rigorous studies that when individuals talk in close proximity, aerosols dominate transmission and droplets are nearly negligible.

Thinking of smoke can help guide our actions:

The visual analogy of smoke can help guide our risk assessment and risk reduction strategies. One just has to imagine that others they encounter are all smoking, and the goal is to breathe as little smoke as possible. But COVID-19 is not very contagious under most situations, unlike, for example, measles: the CDC says that 15 minutes of close proximity to a COVID-19 infected person often leads to contagion, which provides an estimate of how much “exhaled smoke” one may need to inhale for infection. Inhaling a little whiff of “smoke” here and there is OK, but a lot of “smoke” for a sustained period of time and without a mask is risky. (To be clear, actual smoke does not increase the probability of infection.)

In thinking about aerosolized Covid, Jimenez recommends avoiding crowds & indoor spaces and cutting down on proximity & duration, among other things.

We should continue doing what has already been recommended: wash hands, keep six feet apart, and so on. But that is not enough. A new, consistent and logical set of recommendations must emerge to reduce aerosol transmission. I propose the following: Avoid Crowding, Indoors, low Ventilation, Close proximity, long Duration, Unmasked, Talking/singing/Yelling (“A CIViC DUTY”). These are the important factors in mathematical models of aerosol transmission, and can also be simply understood as factors that impact how much “smoke” we would inhale.

But what about masks? N95s can block most aerosols but cloth masks have “huge” holes in them relative to aerosol particles, right? They still work in lowering risk (but not eliminating it!) because your “smoke” doesn’t travel as far when you’re wearing a mask and it filters incoming smoke (if your mask fits correctly and you’re keeping your distance).

Second, masks are essential, even when we are able to maintain social distance. We should also pay attention to fitting masks snugly, as they are not just a parapet against ballistic droplets, but also a means to prevent “smoke” from leaking in through gaps. We should not remove masks to talk, nor allow someone who is not wearing a mask to talk to us, because we exhale aerosols 10 times as much when talking compared to breathing. Everyone should be careful to not stand behind someone with a poorly fitting mask, as the curvature of an ill-fitting mask can cause aerosols to travel behind the person wearing it.

Great article, full of common sense advice backed up by science.

Lovely Interactive Display of Early 19th-Century Hand-Drawn Illustrations of Minerals

posted by Jason Kottke   Aug 12, 2020

Mineralogy Zoom

Mineralogy Zoom

I love this zoomable interactive display of British & Exotic Mineralogy. To create it, Nicholas Rougeux collected 718 hand-drawn mineral illustrations by James Sowerby sourced from a pair of multi-volume books called British Mineralogy and Exotic Mineralogy, published between 1802 and 1817. Then he arranged them according to hue and brightness in a collage worthy of Knoll.

British Mineralogy and Exotic Mineralogy comprise 718 illustrations by James Sowerby in an effort to illustrate the topographical mineralogy of Great Britain and minerals not then known to it. Sowerby’s plates are some of the finest examples of hand-drawn mineral illustrations ever created. The detail and care with which these illustrations were created is incredible and worthy of close examination. See the samples below.

And, oh boy, he’s selling posters of it too.

Study Suggests That Some Masks Are Much Better than Others

posted by Jason Kottke   Aug 12, 2020

Masks comparison chart

A new study on masks that measures the number of droplets emerging from the mouth during speech shows that properly fitted N95, surgical, and polypropylene masks are best, layered cotton masks are good, bandanas are not great, and neck gaiters may be worse than wearing no mask. Here’s a Washington Post article about the study.

I have some issues with this study — most masks were tested by only one speaker and mask materials were not identified precisely1 — but when combined with other studies about masks, it is clear that surgical masks or masks that are made with similar materials (polypropylene non-woven fabric) are what you want to shoot for, you want multiple layers for more protection (no single-layer microfiber gaiters), homemade cotton masks are pretty good (but would be better with a layer of polypropylene non-woven fabric), proper fit matters, and for god’s sake, stop wearing a bandana as a mask. Yes, bandanas are convenient, but you’re probably trading safety for that convenience, especially if you factor in the amount of time you’ll be wearing a mask over the next several months. A proper mask is going to protect you and your neighbors much more over the long haul — it’s just common sense at this point.

Re: the tested neck gaiter being worse than wearing no mask: the hypothesis is that the gaiter’s material splits large droplets into smaller ones, hence the higher count.

We noticed that speaking through some masks (particularly the neck fleece) seemed to disperse the largest droplets into a multitude of smaller droplets (see Supplementary Fig. S5), which explains the apparent increase in droplet count relative to no mask in that case. Considering that smaller particles are airborne longer than large droplets (larger droplets sink faster), the use of such a mask might be counterproductive.

Here’s what I’m taking away from this and other mask studies: wear the highest quality mask you can locate (multi-layered, incorporating surgical mask materials) that fits properly and, secondarily, is comfortable & convenient. For me, that’s a two-layer cotton mask (like these Vida masks) with an inserted layer of polypropylene non-woven fabric. An N95 would be much better in terms of efficacy, but it’s overkill in most situations (particularly here in VT, where rates continue to be low) and is difficult to fit properly and quickly. (via @EricTopol)

Update: Slate’s Susan Matthews goes into more detail about the problems with this study and the conclusions that others are drawing from it.

The purpose of the research was to establish that the testing method worked in principle-not to come up with meaningful or accurate verdicts about particular masks.

But she also concludes (correctly, in my mind):

Should you think twice about wearing just a gaiter inside, in close proximity to other people? Yeah, a fitted mask is probably better. But you didn’t need this study to tell you that.

(via @BrianDau)

Update: But interesting to note that in this test, scarves, bandanas, and microfiber neck gaiters came in last.

  1. What is a “gaiter type neck fleece” made out of exactly? If you look at the photo, it doesn’t look like fleece so much as microfiber polyester, which is what my kids wear for skiing. This article says the neck gaiter was “made of polyester mixed with a little spandex”, which is definitely not fleece. My guess is they tested a one-layer microfiber gaiter and that higher quality gaiters would perform better (but still not as well as a surgical mask).

QAnon, Conspiracy Theories, and the Rise of Magical Thinking

posted by Jason Kottke   Aug 11, 2020

Kirby Ferguson, creator of the Everything Is a Remix and This Is Not a Conspiracy Theory video series, has a new video out that attempts to explain the rise of QAnon, conspiracy theories, and magical thinking in America.

Ferguson zeros in on the divide between two different ways people make sense of a complex, chaotic, and uncertain world: evidence seeking and magical thinking. All of us employ both of these techniques to help ease our anxiety about the world, but those who tend towards magical thinking arrive at explanations that are based primarily on instinct, emotion, feelings, and gut reaction while evidence seekers mostly rely on scientific and empirical reasoning.

He also identifies six main aspects of magical thinking:

1. Obsession with symbols and codes (e.g. pizza as a “deep state” code for child trafficking)
2. Dot connecting (e.g. linking 5G with Covid-19)
3. Behind every event is a plan concocted by a person (e.g. Soros and the “deep state” conspiracy)
4. Purity (e.g. the Satanic panic and heavy metal music)
5. Apocalypse is nigh (e.g. the “deep state” again)
6. Preoccupation with good and evil (e.g. liberals are not only wrong but evil)

For me, the key quote about magical thinking is this one for late in the video: “These are not systems of knowledge, and they cannot build solutions. They can only criticize and second-guess.”

This Is What a Scientist Looks Like

posted by Jason Kottke   Jul 28, 2020

I Am a Scientist is an effort to introduce children to scientists outside of the narrow stereotypes that our culture typically offers (old, male, white, nerdy). They’re doing this through “scientist-of-the-month toolkits” that tell stories about contemporary working scientists who embody an “incredible range of personalities, interests, backgrounds, and pursuits”. From a blog post about the program:

Science has been the driving force in the modernization of the world as we know it, yet science as an industry has failed to adequately diversify with the times. While the new digital age offers opportunities to expand interest in and appeal of STEM careers, many barriers still hinder equitable access for all students. Conversations of famous scientists often draw answers such as “Albert Einstein” and “Bill Nye the Science Guy”. While accurate references of scientific leaders, the lack of diversity in the public image of scientists can contribute to the lack of diversity in STEM fields.

Introducing the “I Am A Scientist” initiative, which provides opportunities for students, specifically those in Junior High School and High School, to interact with the science and stories of today’s scientists-breaking down barriers like race, gender, and personal interests.

The program’s collection of classroom toolkits provide real-life stories of modern scientists, classroom resources, posters, career resources, and more. The initiative aims to help students engage with scientists that may look, act, or think like them, and are making great strides in remarkable fields that are often left out of career planning discussions. With featured scientists that range from multidimensional graduate students to globally recognized innovators at the top of their field, “I Am A Scientist” tunes into the power that comes from discovering a wide range of role models.

Only Six Weeks to Eliminate Coronavirus in the US? Sure.

posted by Jason Kottke   Jul 27, 2020

From We Can Eliminate Covid-19 if We Want To by Andy Slavitt:

We can virtually eliminate the virus any time we decide to. We can be back to a reasonably normal existence: schools, travel, job growth, safer nursing homes and other settings. And we could do it in a matter of weeks. If we want to.

Take New Zealand. With its fancy curve and life back to normal. Why can’t we? Not fair, you say. It’s an island nation. Okay. What about Germany? Not an island nation, large, growing diversity. Don’t like that comparison? What about countries that have been in big trouble? There’s Italy, France, and Spain. Those countries had it reasonably bad the same time we did. In fact, pick virtually any country you want.

But don’t tell me the United States can’t take action if we want to. And we can’t face the families of 150,000 people who didn’t have to die and tell them this had to happen. And I think it’s why our national political leaders won’t go near these families and the grieving process.

The good news — and it is good news — is we are always four to six weeks from being able to do what countries around the world have done.

I know this article is supposed to be hopeful and optimistic, but people have known what to do about Covid-19 since at least March. Instead the United States has not done it and indeed has done mostly the opposite. The “we” that are supposed to decide to lead this effort won’t because they don’t want to put in the work (it’s easier to blame the virus, Democrats, and China), they don’t want to just give money to people to stay home (a huge no-no for Republicans), and they don’t care that much about who is dying (urbanites, low-income, the elderly, Black & brown people).

As long as Republicans control the Senate and White House, the current scattershot approach of each state/county/city/person deciding what is best (or most in their self-interest) is what we’re stuck with. Treatments will improve, vaccines will be developed, many people will do the right thing and mostly stay home for many more months (sacrificing their mental health to do so), and Covid-19 will eventually come under control, but hundreds of thousands more people will die, many more will recover but carry chronic illnesses for years, vital years of the survivors’ lives will have been lost, and we will collectively grieve these losses for generations.

New Solar Telescope Finds “Campfires” on the Sun

posted by Jason Kottke   Jul 24, 2020

Sun Campfires

The European Space Agency’s Solar Orbiter is not even at its closest distance to the Sun and its telescope has already captured some images that reveal new information about our star, including features called “campfires” that are too small to have been captured by previous instruments. From the description of the video embedded above:

This animation shows a series of close-up views captured by the Extreme Ultraviolet Imager (EUI) at wavelengths of 17 nanometers, showing the upper atmosphere of the Sun, or corona, with a temperature of around 1 million degrees.

These images reveal a multitude of small flaring loops, erupting bright spots and dark, moving fibrils. A ubiquitous feature of the solar surface, uncovered for the first time by these images, have been called ‘campfires’. They are omnipresent miniature eruptions that could be contributing to the high temperatures of the solar corona and the origin of the solar wind.

The Solar Orbiter can also peek around the back side of the Sun for the first time:

“Right now, we are in the part of the 11-year solar cycle when the Sun is very quiet,” says Sami Solanki, the director of the Max Planck Institute for Solar System Research in Gottingen, Germany, and PHI Principal Investigator. “But because Solar Orbiter is at a different angle to the Sun than Earth, we could actually see one active region that wasn’t observable from Earth. That is a first. We have never been able to measure the magnetic field at the back of the Sun.”

As revealing as these first images are, at its closest approach later in the mission the Solar Orbiter’s resolving power will roughly double. Can’t wait to see what else it turns up.

A Covid-19 Vaccine Is “Only the Beginning of the End”

posted by Jason Kottke   Jul 24, 2020

The Atlantic’s Sarah Zhang has A Vaccine Reality Check for us.

Biologically, a vaccine against the COVID-19 virus is unlikely to offer complete protection. Logistically, manufacturers will have to make hundreds of millions of doses while relying, perhaps, on technology never before used in vaccines and competing for basic supplies such as glass vials. Then the federal government will have to allocate doses, perhaps through a patchwork of state and local health departments with no existing infrastructure for vaccinating adults at scale. The Centers for Disease Control and Prevention, which has led vaccine distribution efforts in the past, has been strikingly absent in discussions so far — a worrying sign that the leadership failures that have characterized the American pandemic could also hamper this process. To complicate it all, 20 percent of Americans already say they will refuse to get a COVID-19 vaccine, and with another 31 percent unsure, reaching herd immunity could be that much more difficult.

I am the least anti-vaxxer person in the world, but I have to say that getting a vaccine for Covid-19 that was rushed through trials in time for the election (October surprise!) and signed off by a Trump administration that has completely politicized science does not sound like something I want to go near. Which, for me personally, is a really really depressing thing to even think.

Update: I got a lot of flack for suggesting that I’d be skeptical of a Trump-approved vaccine rushed to market in time for the election (a very specific set of circumstances). But his buddy Putin is attempting something similar in Russia (skipping phase 3 trials), so if you don’t think Trump can try to bully the FDA and CDC into signing off on a vaccine that hasn’t been fully tested — perhaps made by a company whose CEO has donated millions to a Trump SuperPAC? — in order to salvage his reelection chances, I suggest that you haven’t paying proper attention over the past 4 years.

Update: A poll suggests that many Americans across the political spectrum are worried about a politicized FDA being forced to approve a Covid-19 vaccine before it’s adequately tested.

Seventy-eight percent of Americans worry the Covid-19 vaccine approval process is being driven more by politics than science, according to a new survey from STAT and the Harris Poll, a reflection of concern that the Trump administration may give the green light to a vaccine prematurely.

The response was largely bipartisan, with 72% of Republicans and 82% of Democrats expressing such worries, according to the poll, which was conducted last week and surveyed 2,067 American adults.

The sentiment underscores rising speculation that President Trump may pressure the Food and Drug Administration to approve or authorize emergency use of at least one Covid-19 vaccine prior to the Nov. 3 election, but before testing has been fully completed.

Viruses Explained

posted by Jason Kottke   Jul 21, 2020

Viruses Explained

In this video and accompanying infographic, scientist Dominic Walliman of Domain of Science explains what viruses are, how they infect cells, how they replicate, and what can be done to mitigate their effects on the human body.

At the beginning of this pandemic like everyone I was hearing lots about viruses, but realised I didn’t know that much about what they are. So I did a load of research and have summarised what I learned in these nine images. This video explains the key aspects of viruses: how big they are, how they infect and enter and exit cells, how viruses are classified, how they replicate, and subjects involving viral infections like how they spread from person to person, how our immune system detects and destroys them and how vaccines and anti-viral drugs work.

After watching, it’s worth checking out Walliman’s sources in the video description for a deeper dive into viruses. (via open culture)

Three Climate Change Pioneers

posted by Jason Kottke   Jul 15, 2020

From BBC Ideas, the story of three people who pioneered the science of climate change — Eunice Foote, Guy Stewart Callendar, and Charles Keeling — each of whom was under-recognized for their achievements at the time.

In particular, Eunice Foote demonstrated the greenhouse effect all the way back in 1856, but her contribution was lost to time and science until very recently.

Looking back on Earth’s history, Foote explains that “an atmosphere of that gas would give to our earth a high temperature … at one period of its history the air had mixed with it a larger proportion than at present, an increased temperature from its own action as well as from increased weight must have necessarily resulted.” Of the gases tested, she concluded that carbonic acid trapped the most heat, having a final temperature of 125 °F. Foote was years ahead of her time. What she described and theorized was the gradual warming of the Earth’s atmosphere — what today we call the greenhouse effect.

(via the morning news)

What Is Intelligence?

posted by Jason Kottke   Jul 14, 2020

How is it that I am sitting here writing this right now and you are sitting there reading this at some later point which seems like now to you? These behaviors are the result of a series of interconnected processes that have evolved over billions of years that we collective call “intelligence”.

In this video, Kurzgesagt takes a crack at explaining the simple view of intelligence as “a mechanism to solve problems” that involves several aspects: information, memory, learning, knowledge, creativity, the use of physical tools, the ability to plan for the future, and culture. As usual, their extensive list of sources provides more details and opportunities for further exploration.

The New Normal

posted by Jason Kottke   Jul 09, 2020

This Is Fine

For Vox, David Roberts writes about how “shifting baselines” affect our thinking and how easily overwhelmingly large issues like climate change or a pandemic can become normalized.

Maybe climate chaos, a rising chorus of alarm signals from around the world, will simply become our new normal. Hell, maybe income inequality, political dysfunction, and successive waves of a deadly virus will become our new normal. Maybe we’ll just get used to [waves hands] all this.

Humans often don’t remember what we’ve lost or demand that it be restored. Rather, we adjust to what we’ve got.

The concept of shifting baselines was introduced in a 1995 paper by Daniel Pauly. Roberts explains:

So what are shifting baselines? Consider a species of fish that is fished to extinction in a region over, say, 100 years. A given generation of fishers becomes conscious of the fish at a particular level of abundance. When those fishers retire, the level is lower. To the generation that enters after them, that diminished level is the new normal, the new baseline. They rarely know the baseline used by the previous generation; it holds little emotional salience relative to their personal experience.

And so it goes, each new generation shifting the baseline downward. By the end, the fishers are operating in a radically degraded ecosystem, but it does not seem that way to them, because their baselines were set at an already low level.

Over time, the fish goes extinct — an enormous, tragic loss — but no fisher experiences the full transition from abundance to desolation. No generation experiences the totality of the loss. It is doled out in portions, over time, no portion quite large enough to spur preventative action. By the time the fish go extinct, the fishers barely notice, because they no longer valued the fish anyway.

And it’s not just groups of people that do this over generations:

It turns out that, over the course of their lives, individuals do just what generations do — periodically reset and readjust to new baselines.

“There is a tremendous amount of research showing that we tend to adapt to circumstances if they are constant over time, even if they are gradually worsening,” says George Loewenstein, a professor of economics and psychology at Carnegie Mellon. He cites the London Blitz (during World War II, when bombs were falling on London for months on end) and the intifada (the Palestinian terror campaign in Israel), during which people slowly adjusted to unthinkable circumstances.

“Fear tends to diminish over time when a risk remains constant,” he says, “You can only respond for so long. After a while, it recedes to the background, seemingly no matter how bad it is.”

Ok, I’ll let you just read the rest of it, but it’s not difficult to see how shifting baselines apply to all sorts of challenges facing the world today. I mean the lines “You can only respond for so long. After a while, it recedes to the background, seemingly no matter how bad it is.” seem like they were written specifically about the pandemic.

Anthony Fauci: USA on Track for 100,000 Covid-19 Cases Per Day

posted by Jason Kottke   Jun 30, 2020

US Covid Stupid Graph

The director of the National Institute of Allergy and Infectious Diseases, Anthony Fauci, told a Senate committee today that the US could be heading towards 100,000 new reported cases of Covid-19 per day. 100,000 cases per day. Yesterday the US recorded about 40,000 new cases.

“It is going to be very disturbing, I will guarantee you that,” he said.

“What was thought to be unimaginable turns out to be the reality we’re facing right now,” Fauci said, adding that “outbreaks happen, and you have to deal with them in a very aggressive, proactive way.”

Fewer than 20 countries have recorded more than 100,000 cases in total. Canada, for instance, has confirmed about 106,000 Covid-19 cases since the outbreak began.

Public health and infectious diseases experts, who have been gravely concerned about the way the U.S. response has unfolded, concurred with Fauci’s assessment.

Bars and restaurants are reopening around the country without any serious effort to test/trace/isolate/support. In the absence of strident guidance from the federal government, people are worrying less about social distancing and wearing masks to protect others. As this guy says, it’s just a matter of math:

“It’s unfortunately just a simple consequence of math plus a lack of action,” said Marm Kilpatrick, an infectious diseases dynamics researcher at the University of California, Santa Cruz. “On the one hand it comes across as ‘Oh my God, 100,000 cases per day!’ But then if you actually look at the current case counts and trends, how would you not get that?”

Absolutely nothing has changed about the virus, so its spread is determined by pretty simple exponential growth.

Limiting person-to-person exposure and decreasing the probability of exposures becoming infections can have a huge effect on the total number of people infected because the growth is exponential. If large numbers of people start doing things like limiting travel, cancelling large gatherings, social distancing, and washing their hands frequently, the total number of infections could fall by several orders of magnitude, making the exponential work for us, not against us. Small efforts have huge results.

We’ve known for months (and epidemiologists and infectious disease experts have known for their entire careers) what works and yet the federal government and many state governments have not listened and, in some cases, have actively suppressed use of such measures. So the pandemic will continue to escalate in the United States until proper measures are put in place by governments and people follow them. The virus will not change, the mathematics will not change, so we must.

Graph at the top of the post via Rishi Desai.

Covid-19 Superspreading Events and “Speech Superemitters”

posted by Jason Kottke   Jun 25, 2020

From Christie Aschwanden’s Scientific American article about How ‘Superspreading’ Events Drive Most COVID-19 Spread comes this speculation by a group of scientists that the way in which some people talk or breathe might spread many more potential coronavirus-carrying droplets than other people.

The scientists also have found intriguing evidence that a small subset of people may behave as “speech superemitters” — individuals who consistently broadcast an order of magnitude more respiratory particles than their peers. “It is very difficult to identify who is going to be a superemitter ahead of time,” he says. “One of the superemitters was a very petite young woman. And I was a bigger, bulkier guy and was not a superemitter.”

I don’t know why I find this so interesting, but I do. Add “speech superemitter” to the list of new Covid-19 vocabulary.