Simulating an Epidemic: Using Data to Show How Diseases Like COVID-19 Spread

Disease modeling as a science has come into its own lately, for heartbreakingly obvious reasons. What may not be so obvious to those of us who aren't scientists is just how critical data can be in changing the course of events in an outbreak. Virus outbreaks may be “acts of God” or acts of unregulated black markets and agribusinesses, but in either case, statistical models can show, concretely, how collective human activity can save lives—and show what happens when people don’t act together.

For example, epidemiologists and biostatisticians have shown in detail how social distancing led to a “decline in the proportion of influenza deaths,” one study concludes, during the 1918 flu pandemic. The same researchers also saw evidence in their models that showed “public risk perception could be lowered” when these practices worked effectively, leading people think they could resume business as usual. But “less social distancing could eventually induce another epidemic wave.”

To say that it’s a challenge to stay inside and wait out COVID-19 indefinitely may be a gross understatement, but hunkering down may save our lives. No one can say what will happen, but as for how and why it happens, well, “that is math, not prophecy,” writes Harry Stevens at The Washington Post. “The virus can be slowed,” if people continue “avoiding public spaces and generally limiting their movement.” Let’s take a look at how with the model above. We must note that these are not models of COVID-19 specifically, but a detailed look at how a hypothetical epidemic spreads.

Created by YouTuber 3Blue1Brown, the modeling in the video draws from a variety of sources, including Stevens’ excellent interactive models of a hypothetical disease he calls “simulitis.” Another simulator whose work contributed to the video, Kevin Simler, has also explained the spread of disease with interactive models that enable us to visualize difficult-to-grasp epidemiological concepts, since "exponential growth is really, really hard for our human brains to understand” in the abstract, says YouTube physics explainer Minute Physics in the short, animated video above.

Deaths multiply faster than the media can report, and whatever totals we come across are hopelessly outdated by the time we read them, an emotional and intellectual barrage. So how can we know if we’re “winning or losing” (to use the not-particularly-helpful war metaphor) the COVID-19 fight? Here too, the current data on its previous progress in other countries can help plot the course of the disease in the U.S. and elsewhere, and allow scientists and policy-makers to make reasonable inferences about how to stop exponential growth.

But none of these models show the kind of granularity that doctors, nurses, and public health professionals must deal with in a real pandemic. “Simulitis is not covid-19, and these simulations vastly oversimplify the complexity of real life,” Stevens admits. Super-complicating risk factors like age, race, disability, and access to insurance and resources aren’t represented here. And there may be no way to model whatever the government is doing.

But the data models show us what has worked and what hasn't, both in the past and in the recent present, and they have become very accessible thanks to the internet (and open source journals on platforms like PLOS). For a longer, in-depth explanation of the current pandemic's exponential spread, see the lecture by epidemiologist Nicholas Jewell above from the Mathematical Sciences Research Institute (MSRI).

It may not sway people who actively ignore math, but disease modeling can guide the merely uninformed to a much better understanding of what’s happening, and better decisions about how to respond under the circumstances.

Related Content:  

Spring Break vs. COVID-19: Mapping the Real Impact of Ignoring Social Distancing

Watch “Coronavirus Outbreak: What You Need to Know,” and the 24-Lecture Course “An Introduction to Infectious Diseases,” Both Free from The Great Courses

The History of the Plague: Every Major Epidemic in an Animated Map

Josh Jones is a writer and musician based in Durham, NC. Follow him at @jdmagness

The “Feynman Technique” for Studying Effectively: An Animated Primer

After winning the Nobel Prize, physicist Max Planck "went around Germany giving the same standard lecture on the new quantum mechanics. Over time, his chauffeur memorized the lecture and said, 'Would you mind, Professor Planck, because it’s so boring to stay in our routine, if I gave the lecture in Munich and you just sat in front wearing my chauffeur’s hat?' Planck said, 'Why not?' And the chauffeur got up and gave this long lecture on quantum mechanics. After which a physics professor stood up and asked a perfectly ghastly question. The speaker said, 'Well, I’m surprised that in an advanced city like Munich I get such an elementary question. I’m going to ask my chauffeur to reply.'"

That this intellectual switcheroo never actually happened didn't stop Charlie Munger from using it as an opener for a commencement speech to USC's Law School. But when a successful billionaire investor finds value even in an admittedly "apocryphal story," most of us will find value in it as well. It illustrates, according to the Freedom in Thought video above, the difference between "two kinds of knowledge: the deep knowledge that Max had, and the shallow knowledge that the chauffeur had." Both forms of knowledge have their advantages, especially since none of us have lifetime enough to understand everything deeply. But we get in trouble when we can't tell them apart: "We risk fooling ourselves into thinking we actually understand or know something when we don't. Even worse, we risk taking action on misinformation or misunderstanding."

Even if you put little stock into a made-up anecdote about one Nobel-winning physicist, surely you'll believe the documented words of another. Richard Feynman once articulated a first principle of knowing as follows: "You must not fool yourself, and you are the easiest person to fool." This principle underlies a practical process of learning that consists of four steps. First, "explain the topic out loud to a peer who is unfamiliar with the topic. Meet them at their level of understanding and use the simplest language you can." Second, "identify any gaps in your own understanding, or points where you feel that you can't explain an idea simply." Third, "go back to the source material and study up on your weak points until you can use simple language to explain it." Finally, "repeat the three steps above until you've mastered the topic."

We've featured the so-called "Feynman technique" once or twice before here on Open Culture, but its emphasis on simplicity and concision always bears repeating — in, of course, as simple and concise a manner as possible each time. Its origins lie in not just Fenyman's first principle of knowledge but his intellectual habits. This video's narrator cites James Gleick's biography Genius, which tells of how "Richard would create a journal for the things he did not know. His discipline in challenging his own understanding made him a genius and a brilliant scientist." Like all of us, Feynman was ignorant all his life of vastly more subjects than he had mastered. But unlike many of us, his desire to know burned so furiously that it propelled him into perpetual confrontation with his own ignorance. We can't learn what we want to know, after all, unless we acknowledge how much we don't know.

Related Content:

Richard Feynman’s “Notebook Technique” Will Help You Learn Any Subject–at School, at Work, or in Life

Richard Feynman’s Technique for Learning Something New: An Animated Introduction

The Feynman Lectures on Physics, The Most Popular Physics Book Ever Written, Is Now Completely Online

The Cornell Note-Taking System: Learn the Method Students Have Used to Enhance Their Learning Since the 1940s

Based in Seoul, Colin Marshall writes and broadcasts on cities, language, and culture. His projects include the book The Stateless City: a Walk through 21st-Century Los Angeles and the video series The City in Cinema. Follow him on Twitter at @colinmarshall or on Facebook.

Watch “Coronavirus Outbreak: What You Need to Know,” and the 24-Lecture Course “An Introduction to Infectious Diseases,” Both Free from The Great Courses

COVID-19 is a serious, highly communicable disease. It is not a hoax, and it will continue to spread until it is contained with widespread testing and a vaccine. At present, scientists seem to know little about all the forms of transmission or the possibility of reinfection. Older people and the immunocompromised are certainly more at risk than others, but the virus can kill the healthy and the sick. It doesn’t care where it starts or ends. It doesn’t care if someone is a U.S. Senator or someone a senator deems disposable. These plain facts should put us all on notice, but the response has not only been slow but nearly nonexistent in countries where leaders are daily making the situation worse.

In the U.S., hospitals and city and state governments cannot expect the kind of response from the federal government needed to meet the threat. We must all educate ourselves and do our part, both for ourselves and our neighbors—which seems, after all, to amount to the same thing.

To that end, we can thank The Great Courses company for offering their entire online lecture series, An Introduction to Infectious Diseases, for free, as well as the short video at the top from Dr. Roy Benaroch, who debunks rumors and explains the history and inevitability of COVID-19. “It’s no longer a question of if this virus is going to strike your community, but when.”

While most cases are mild, this should not lure us into a false sense of security. Infected people who appear healthy and present no symptoms are responsible for the spread of the disease, and if they continue to move around and infect others, the chances of it striking us or those we love increase exponentially. This is why social distancing is so important. “We’re past the time when containment can separate us from them, the contagious people from the rest of us.” Every time we go out, we risk exposing others or ourselves.

“Of course, you should seek medical attention if you experience shortness of breath or more severe symptoms,” but people with milder symptoms should stay away from doctors and hospitals. Dr. Benaroch gives us several other preventative measures we can employ to slow the spread and “flatten the curve.” COVID-19 is a viral infection, and as such, it makes sense for us to brush up on our virology via the third lecture in the Infectious Diseases course, above, “Viruses: Hijackers of Your Body’s Cells.” Catch the full 24-video course from Dr. Barry Fox here, and watch lecture six, “Six Decades of Infectious Disease Challenges,” below. Great Courses promises more “relevant content to help inform, enlighten, and understand the world around us and to counter mistruths and rumors.” We'll keep you posted.

Stay home, share the video at the top with your skeptical friends and family, and urge them to stay home too.

“An Introduction to Infectious Diseases” will be added to our list, 1,500 Free Online Courses from Top Universities.

Note: You can sign up for a free trial of Great Courses Plus and watch lectures for countless courses over the next 30 days.

Related Content:

Free Courses on the Coronavirus: What You Need to Know About the Emerging Pandemic

Interactive Web Site Tracks the Global Spread of the Coronavirus: Created and Supported by Johns Hopkins

Why Fighting the Coronavirus Depends on You

Josh Jones is a writer and musician based in Durham, NC. Follow him at @jdmagness

A Short, Animated Film Shows How a Scientific Article Gets Published: “Excitement, Baby Steps and Reams of Rejections”

When people say things like “the science is settled” or “the science has changed,” researchers tend to grind their teeth. Science can come to a broad consensus, as in the case of the coronavirus or climate change, but it isn’t ever perfectly settled as a bloc on any question. We proceed in scientific knowledge not by attaining perfect knowledge but, as Isaac Asimov once wrote, by being less wrong than those who came before.

And scientists advance in scientific publishing, as Aeon writes, not with certainty, but with “excitement, baby steps and reams of rejections.” As we see in the short film above, The Researcher’s Article, by French filmmaker Charlotte Arene, getting one’s research published can be “a patience-testing exercise in rejection, rewriting and waiting,” demonstrated here by the travails of physicists Frédéric Restagno and Julien Bobroff of the University of Paris-Saclay.

Even before submitting their findings, the scientists must carefully fit their work into the traditional form known as the “letter,” a document of four pages or fewer that condenses years of research into strictly succinct paragraphs, graphs, and references. The “letter” is “one of the most popular formats of articles in physics,” say the physicists, noting the major Nobel prize-winning discoveries to appear as letters in recent years, including the Higgs’ Boson publication that won in 2013, coming in at only two pages long.

Summing up “a massive amount of data,” short scientific articles then go on to prove themselves to their respective fields through a refereeing process in which three anonymous scientists read the work and recommend publication, revision, or rejection. This process can go several rounds and take several months. One must be persistent: Restagno and Bobroff were rejected from several journals before finally getting an acceptance.

After this significant investment of time and effort, the authors may have a readership of maybe twenty people. But crowd size is not the point, they say, “because research is made up of all these small discoveries,” contributing to a larger picture, informing and correcting each other, and going about the humble, painstaking business of trying to be less wrong than their predecessors, while still building on the best insights of hundreds of years of scientific publishing.

via Aeon

Related Content:

Read the Shortest Academic Article Ever Written: “The Unsuccessful Self-Treatment of a Case of ‘Writer’s Block'”

The Shortest-Known Paper Published in a Serious Math Journal: Two Succinct Sentences

The Emperor of Japan, Akihito, Is Still Publishing Scientific Papers in His 80s

Josh Jones is a writer and musician based in Durham, NC. Follow him at @jdmagness

The Earth Archive Will 3D-Scan the Entire World & Create an “Open-Source” Record of Our Planet

If you keep up with climate change news, you see a lot of predictions of what the world will look like twenty years from now, fifty years from now, a century from now. Some of these projections of the state of the land, the shape of continents, and the levels of the sea are more dramatic than others, and in any case they vary so much that one never knows which ones to credit. But of equal importance to foreseeing what Earth will look like in the future is not forgetting what it looks like now — or so holds the premise of the Earth Archive, a scientific effort to "scan the entire surface of the Earth before it’s too late."

This ambitious project has three goals: to "create a baseline record of the earth as it is today to more effectively mitigate the climate crisis," to "build a virtual, open-source planet accessible to all scientists so we can better understand our world," and to "preserve a record of the Earth for our grandchildren’s grandchildren so they can study & recreate our lost heritage."

All three depend on the creation of a detailed 3D model of the globe — but "globe" is the wrong word, bringing to mind as it does a sphere covered with flat images of land and sea.

Using lidar (short for Light Detection & Ranging), a technology that "involves shooting a dense grid of infrared beams from an airplane towards the ground," the Earth Archive aims to create not an image but "a dense three-dimensional cloud of points" capturing the whole planet. At the top of the post, you can see a TED Talk on the Earth Archive's origin, purpose, and potential by archaeologist and anthropology professor Chris Fisher, the project's founder and director. "Fisher had used lidar to survey the ancient Purépecha settlement of Angamuco, in Mexico’s Michoacán state," writes Atlas Obscura's Isaac Schultz. "In the course of that work, he saw human-caused changes to the landscape, and decided to broaden his scope."

Now, Fisher and Earth Archive co-director Steve Leisz want to create "a comprehensive archive of lidar scans" to "fuel an immense dataset of the Earth’s surface, in three dimensions." This comes with certain obstacles, not the least the price tag: a scan of the Amazon rainforest would take six years and cost $15 million. "The next step," writes Schultz, "could be to use some future technology that puts lidar in orbit and makes covering large areas easier." Disinclined to wait around for the development of such a technology while forests burn and coastlines erode, Fisher and Leisz are taking their first steps — and taking donations — right now. On the off chance that humans of centuries ahead develop the ability to recreate the planet as we know it today, it's the Earth Archive's data they'll rely on to do it.

via Atlas Obscura

Related Content:

A Century of Global Warming Visualized in a 35 Second Video

Explore Meticulous 3D Models of Endangered Historical Sites in Google’s “Open Heritage” Project

Earthrise, Apollo 8’s Photo of Earth from Space, Turns 50: Download the Iconic Photograph from NASA

Download 67,000 Historic Maps (in High Resolution) from the Wonderful David Rumsey Map Collection

3D Scans of 7,500 Famous Sculptures, Statues & Artworks: Download & 3D Print Rodin’s Thinker, Michelangelo’s David & More

Based in Seoul, Colin Marshall writes and broadcasts on cities, language, and culture. His projects include the book The Stateless City: a Walk through 21st-Century Los Angeles and the video series The City in Cinema. Follow him on Twitter at @colinmarshall or on Facebook.

Meet ‘The Afronauts’: An Introduction to Zambia’s Forgotten 1960s Space Program

Broadly speaking, the "Space Race" of the 1950s and 60s involved two major players, the United States and the Soviet Union. But there were also minor players: take, for instance, the Zambian Space Program, founded and administered by just one man. A Time magazine article published in November 1964 — when the Republic of Zambia was one week old — described Edward Mukuka Nkoloso as a "grade-school science teacher and the director of Zambia’s National Academy of Science, Space Research and Philosophy." Nkoloso had a plan "to beat the U.S. and the Soviet Union to the moon. Already Nkoloso is training twelve Zambian astronauts, including a curvaceous 16-year-old girl, by spinning them around a tree in an oil drum and teaching them to walk on their hands, 'the only way humans can walk on the moon.'"

Nkoloso and his Quixotic space program seem to have drawn as much attention as the subject of the article, Zambia's first president Kenneth David Kaunda. Namwali Serpell tells Nkoloso's story in a piece for The New Yorker: not just the conception and failure of his entry into the Space Race ("the program suffered from a lack of funds," Serpell writes, "for which Nkoloso blamed 'those imperialist neocolonialists' who were, he insisted, 'scared of Zambia’s space knowledge'"), but also his background as "a freedom fighter in Kaunda’s United National Independence Party."

Born in 1919 in then-Northern Rhodesia, Nkoloso received a missionary education, got drafted into World War II by the British, took an interest in science during his service, and came home to illegally found his own school. There followed periods as a salesman, a "political agitator," and a messianic liberator figure, ending with his capture and imprisonment by colonial authorities.

How on Earth could this all have convinced Nkoloso to aim for Mars? Some assume he experienced a psychological break due to torture endured at the hands of Northern Rhodesian police. Some see his ostensible interplanetary ambitions as a cover for the training he was giving his "Afronauts" for guerrilla-style direct political action. Some describe him as a kind of national court jester: Serpell quotes from the memoir of San Francisco Chronicle columnist Arthur Hoppe, author of a series of contemporary pieces on the Zambian Space Program, who "believed it was the Africans who were satirizing our multi-billion-dollar space race against the Russians." As Serpell points out, "Zambian irony is very subtle," and as a satirist Nkoloso had "the ironic dédoublement — the ability to split oneself — that Charles Baudelaire saw in the man who trips in the street and is already laughing at himself as he falls."

Whatever Nkoloso's purposes, the Zambian Space Program has attracted new attention in the years since documentary footage of its facilities and training procedures found its way to Youtube. This fascinatingly eccentric chapter in the history of man's heavenward aspirations has become the subject of short documentaries like the one from SideNote at the top of the post, as well as the subject of artworks like the short film Afronauts above. Nkoloso died more than 30 years ago, but he now lives on as an icon of Afrofuturism, a movement (previously featured here on Open Culture) at what Serpell calls "the nexus of black art and technoculture." No figure embodies Afrofuturism quite so thoroughly as Sun Ra, who transformed himself from the Alabama-born Herman Poole Blount into a peace-preaching alien from Saturn. Though Nkoloso never seems to have met his American contemporary, such an encounter would surely, as a subject for Afrofuturistic art, be truly out of this world.

Related Content:

Watch a 5-Part Animated Primer on Afrofuturism, the Black Sci-Fi Phenomenon Inspired by Sun Ra

Sun Ra’s Full Lecture & Reading List From His 1971 UC Berkeley Course, “The Black Man in the Cosmos”

Sun Ra Applies to NASA’s Art Program: When the Inventor of Space Jazz Applied to Make Space Art

Wonderfully Kitschy Propaganda Posters Champion the Chinese Space Program (1962-2003)

Soviet Artists Envision a Communist Utopia in Outer Space

Based in Seoul, Colin Marshall writes and broadcasts on cities, language, and culture. His projects include the book The Stateless City: a Walk through 21st-Century Los Angeles and the video series The City in Cinema. Follow him on Twitter at @colinmarshall or on Facebook.

A Tribute to NASA’s Katherine Johnson (RIP): Learn About the Extraordinary Mathematician Who Broke Through America’s Race & Gender Barriers

We don't call it a tragedy when a renowned person dies after the century mark, especially if that person is brilliant NASA mathematician Katherine Johnson, who passed away yesterday at the venerable age of 101. Her death is a great historical loss, but by almost any measure we would consider reaching such a finish line a triumphant end to an already heroic life.

A prodigy and pioneer, Johnson joined the all-black “human computing” section at NASA’s predecessor, the National Advisory Committee for Aeronautics, in 1953. She would go on to calculate the launch windows and return trajectories for Alan Shepard’s first spaceflight, John Glenn’s first trip into orbit, and the Apollo Lunar Module’s first return from the Moon.

All this without the benefit of any machine computing power to speak of and—as Hidden Figures dramatizes through the powerful performance of Taraji P. Henson as Johnson—while facing the dual barriers of racism and sexism her white male bosses and co-workers blithely ignored or deliberately upheld.

Johnson and her fellow “computers,” without whom none of these major milestones would have been possible, had to fight not only for recognition and a seat at the table, but for the basic accommodations we take for granted in every workplace.

Her contributions didn’t end when the space race was over—her work was critical to the Space Shuttle program and she even worked on a mission to Mars. But Johnson herself kept things in perspective, telling People magazine in the interview above from 2016, “I’m 98. My greatest accomplishment is staying alive.” Still, she lived to see herself turned into the hero of that year’s critically lauded film based on the bestselling book of the same name by Margot Lee Shetterly—decades after she completed her most groundbreaking work.

Shetterly’s book, writes historian of technology Marie Hicks, casts Johnson and her fellow black women mathematicians “as protagonists in the grand drama of American technological history rather than mere details.” By its very nature, a Hollywood film adaptation will leave out important details and take liberties with the facts for dramatic effect and mass appeal. The feature treatment moves audiences, but it also soothes them with feel-good moments that “keep racism at arm’s length from a narrative that, without it, would never have existed.”

The point is not that Johnson and her colleagues decided to make racism and sexism central to their stories; they simply wanted to be recognized for their contributions and be given the same access and opportunities as their white male colleagues. But to succeed, they had to work together instead of competing with each other. Despite its simplifications and glosses over Cold War history and the depth of prejudice in American society, Hidden Figures does something very different from most biopics, as Atlantic editor Lenika Cruz writes, telling "a story of brilliance, but not of ego. It’s a story of struggle and willpower, but not of individual glory… it looks closely at the remarkable person in the context of a community.”

Katherine Johnson lived her life as a tremendous example for young women of color who excel at math and science but feel excluded from the establishment. On her 98th birthday, she “wanted to share a message to the young women of the world,” says the narrator of the 20th Century Studios video above: “Now it’s your turn.” And, she might have added, “you don’t have to do it alone.” Hear Hidden Figures author Shetterly discuss the critical contributions of Katherine and her extraordinary “human computer” colleagues in the interview below, and learn more about Johnson's life and legacy in the featurette at the top and at her NASA biography here.

Related Content:   

Women Scientists Launch a Database Featuring the Work of 9,000 Women Working in the Sciences

“The Matilda Effect”: How Pioneering Women Scientists Have Been Denied Recognition and Written Out of Science History

Women’s Hidden Contributions to Modern Genetics Get Revealed by New Study: No Longer Will They Be Buried in the Footnotes

Josh Jones is a writer and musician based in Durham, NC. Follow him at @jdmagness

More in this category... »