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Mina Markham's Formation, tweaked for folks who use R

Mina Markham’s Formation is awesome.

Formation is a shell script to set up a macOS laptop for design and development. It can be run multiple times on the same machine safely. It installs, upgrades, or skips packages based on what is already installed on the machine.

It’s based on other scripts with a similar idea (see thoughtbot’s laptop, for example). I tweaked it for those of my usage — R + packages, a lightweight TeX install, and the “productivity” and “creative” applications I commonly use. My variant is available here.

Emptying and Deleting Amazon S3 Glacier vaults

For a period, I used Arq Backup with Amazon S3 Glacier as archival storage for my photos. I’ve got an alternative, faster, more convenient solution now and wanted to stop paying for storage at Amazon. Turns out clearing out a Glacier vault is neither easy, fast, nor straightforward. In the end, I used Leeroy Brun’s Glacier Vault Remove. While it couldn’t delete the vault automatically, it did empty it out overnight. I logged into AWS console to delete the vault. Here as reference for me and others who may run into this problem and need a tidy solution.

Machine-learned modeling of PM2.5 exposures in rural Lao PDR

Hill LD, Pillarisetti A, Delapena S, Garland C, Pennise D, Pelletreau A, Koetting P, Motmans T, Vongnakhone K, Khammavong C, Boatman MR, Balmes K, Hubbard A, Smith Kr. 2019. Machine-learned modeling of PM2.5 exposures in rural Lao PDR. Science of The Total Environment, https://doi.org/10.1016/j.scitotenv.2019.04.258.

Helvetica Now and Public Sans

Excitement in the world of typography!

Monotype’s marketing text for Helvetica Now:

Helvetica Now is a new chapter in the story of perhaps the best-known typeface of all time. Available in three optical sizes—Micro, Text, and Display—every character in Helvetica Now has been redrawn and refit; with a variety of useful alternates added. It has everything we love about Helvetica and everything we need for typography today. This is not a revival. This is not a restoration.

From an interview with Charles Nix, type designer at Monotype:

If I had to put them in order of what we wanted to change, the first thing — from the customer’s point of view, the user’s point of view, the designer’s point of view — are those alternate characters because they’re the most visible change. The second most important thing to us and to designers is the optical sizing. It’s super important to me because it’s just, it’s one of those things when you say a new Helvetica, I mean, I would shrug. “Does there need to be a new Helvetica?” But then when you see it and you use it, because of the optical sizing, it’s like being reintroduced to an old friend. It’s amazing. I thought I knew Helvetica. I thought I didn’t need Helvetica. And then I see this Helvetica Now and I suddenly realize that’s it not what I thought it was.

Public Sans was released as part of the the US Web Design System announcement of USWDS 2.0:

USWDS 2.0 adds built-in support for custom typefaces, and sometimes you need one that’s simple, neutral, and isn’t Helvetica. Public Sans is an open source, free license typeface (SIL Open Font License 1.1) designed and maintained by USWDS, adapted from Libre Franklin. Just as with our components, we intend Public Sans to be an example of how to design an accessible open source typeface with contributions and feedback from the public — to deliver a useful, neutral, sans serif and continuously improve it.

Modeling the Impact of an Indoor Air Filter on Air Pollution Exposure Reduction and Associated Mortality in Urban Delhi Household

Liao J, Ye W, Pillarisetti A, Clasen TF. Modeling the Impact of an Indoor Air Filter on Air Pollution Exposure Reduction and Associated Mortality in Urban Delhi Household. Int. J. Environ. Res. Public Health 2019, 16(8), 1391; https://doi.org/10.3390/ijerph16081391    Supplementary Information

Indian annual ambient air quality standard is achievable by completely mitigating emissions from household sources

Chowdhury S, Dey S, Guttikunda S, Pillarisetti A, Smith KR, Di Girolamo L. Indian annual ambient air quality standard is achievable by completely mitigating emissions from household sources. Proceedings of the National Academy of Sciences Apr 2019, 201900888; DOI: 10.1073/pnas.1900888116. Supporting Information.

John Balmes: Don't Let a Killer Pollutant Loose

Professor John Balmes, close colleague and friend, and physician member of the California Air Resources Board:

PM 2.5 kills people. There has been little dispute that microscopic particulate matter in air pollution penetrates into the deepest parts of the lungs and contributes to the early deaths each year of thousands of people in the United States with heart and lung disease.

One recent study called PM 2.5 “the largest environmental risk factor worldwide,” responsible for many more deaths than alcohol use, physical inactivity or high sodium intake.

The Environmental Protection Agency’s own website says: “Numerous scientific studies have linked particle pollution exposure to a variety of problems, including: premature death in people with heart or lung disease, nonfatal heart attacks, irregular heartbeat, aggravated asthma, decreased lung function, increased respiratory symptoms.”

Which makes it deeply troubling that the very people at the helm of the Trump administration’s E.P.A. responsible for protecting public health and the environment are now pursuing a course that would make the air we breathe even more hazardous.

Promoting LPG usage during pregnancy: A pilot study in rural Maharashtra, India

Pillarisetti A*, Ghorpade M, Madhav S, Dhongade A, Roy S, Balakrishnan K, Sankar S, Patil R, Levine DI, Juvekar S, Smith KR (2019) Promoting LPG usage during pregnancy: A pilot study in rural Maharashtra, India. Environment International 127:540-549.     Supporting Information (.docx)

Understanding Air Pollution with Art: "The Air of the Anthropocene" and "Mutual Air"

Playground, India Institute of Technology Campus, Delhi, India - PM2.5 500 - 600 µg/m3

Artist Robin Price and Professor Francis Pope use experimental photography to “see” small particles as part of their “Air of the Anthropocene” project (h/t Zoe Chafe). The photos are stunning. From a Guardian piece highlighting many of the photos:

Using a custom-built digital light painter and wearable particulate sensor, I take long exposure photographs that paint the amount of PM2.5 particles in the air as particles of light. As the light painter’s sensor detects more pollution it draws correspondingly greater numbers of light particles into the photograph. The effect is as if the microscopic pollution has been enlarged and lit up, shedding light on the invisible particles.

Meanwhile, in the Bay Area, Artist Rosten Woo uses chimes to make air pollution audible:

Mutual Air is a network of roughly thirty specially designed bells that generate a soundscape reflecting and responding to the changing composition of our local and global atmosphere. By sonifying air-quality fluctuations, Woo hopes​ to engage the public in an experiential understanding of climate science and how aspects of our atmosphere, while a shared resource, reflect socioeconomic disparities.

His work was featured on PBS News Hour:


See also Smog Meringues and British Pathe - Air Pollution

Indian Election Analysis: Election manifestos feature air plan but little action on ground

A new report titled “Political Leaders Position and Action on Air Quality in India” released by Climate Trends also highlighted that members of parliament in 14 Indian cities, among the most polluted cities globally as per the WHO 2018 urban air quality database, have done little to get their cities to comply with safe air quality standards locally.

“The manifestos of both the national parties have proven that political parties cannot ignore and neglect air pollution related health emergency any more. This rhetoric is a good sign. But the bigger question is - if this electoral promise will translate into strong enough political will to push for hard action with accountability and show results,” said Anumita Roychowdhury, executive director, Centre for Science and Environment. Delhi’s air pollution levels recorded a fall in 2018 because of multiple strategies, she added.

Energy and Health in the 2019 BJP Manifesto

The BJP’s Manifesto was released in the last few days. A little hard to hunt down, initially, though a PDF is hosted at documentcloud.

In a section that is partly a list of achievements and partly a description of next steps:

We have evolved technologically better strategies and devices to map the level of pollution in cities and rivers and have taken effective steps to reduce the level of pollution in major cities, including the national capital. We will convert the National Clean Air Plan into a Mission and we will focus on 102 most polluted cities in the country. Through concerted action, we will reduce the level of pollution in each of the mission cities by at least 35% over the next five years.

Another part of he Manifesto is framed around 75 milestones for India’s 75th anniversary, including some focusing on health, energy, air pollution, and water & sanitation.

Under Infrastructure:

Ensure a pucca house to every family. Ensure the LPG gas cylinder connection to all poor rural households. Ensure 100% electrification of all households. Ensure a toilet in every household. Ensure access to safe and potable drinking water for all households. Bharat Mission to achieve ODF+ (Open Defecation Free) and ODF++ in cities and villages. Ensure ODF status for all villages and cities.

Under good governance:

Work towards substantially reducing the current levels of air pollution. Work towards completely eliminating crop residue burning to reduce air pollution.

Energy and Health in the 2019 Indian National Congress party Manifesto

The opposition Congress party in India released their “manifesto” — a party statement across a range of issues — a few days ago. It is long and has rough (sometimes detailed, sometimes vague) policy outlines. Of particular interest are a number on energy and health.

Under infrastructure:

Congress promises to enhance availability of, and access to, electricity in rural areas by encouraging investment in off-grid renewable power generation with ownership and revenues vesting in local bodies. Every village and every home will be electrified in the true sense. In the long term, we aim to substitute LPG used in homes by electricity and solar energy.

Under environment and climate change:

Congress promises an action agenda that will place India at the forefront of the battle against global warming and for the protection of the environment. At the same time, Congress will defend and advance India’s interests in international negotiations on Climate Change and the Environment.

We will constitute, by law, an independent, empowered and transparent Environment Protection Authority (EPA) to establish, monitor and enforce environmental standards and regulations. The EPA will replace all other bodies that currently exercise jurisdiction and powers.

Congress recognises that air pollution is a national public health emergency. We will significantly strengthen the National Clean Air Programme in order to urgently tackle the problem of pollution. All major sources of emission will be targetted, mitigated and reduced to acceptable levels. Sectoral emission standards will be set.

Congress promises to provide clean cooking fuels at affordable prices to all the households of the country. We will monitor the price of LPG cylinders and mitigate through subsidies the burden of price increases on the homemaker.

Under healthcare:

We will expand the ASHA programme and appoint a second ASHA worker in all villages with a population exceeding 2500 persons. Congress will implement a programme that will enable State Governments to revamp and equip the network of primary health centres (PHCs). PHCs will provide all primary health services, including preventive measures and wellness services, and become referral centres for serious medical cases.

Under jobs:

Para-state workers such as Anganwadi workers, ASHA workers, rozgarsahayaks, preraks, and anudeshaks, form the backbone of the public service delivery system. We will increase funding for the relevant programmes and work with State Governments to ensure that all arrears are paid immediately. We will also work with State Governments and attempt to address all pending contentious issues regarding their salaries and work conditions. In addition, we will expand the ASHA programme and appoint a second ASHA worker in all villages with a population exceeding 2500 persons.

A running list of how President Trump is changing environmental policy

McClatchy reporting today:

The Trump campaign is seeking a list of “climate change victories” that can be attributed to Donald Trump’s presidency, reflecting a shift in strategy ahead of the 2020 election as polls show growing voter concern over global warming, two sources familiar with the campaign told McClatchy this week.

To hell with that. National Geographic has provided an excellent rebuttal with “A running list of how President Trump is changing environmental policy”. They peg it at a 70 minute read.

Some highlights:

TRUMP SIGNS ORDER GREENLIGHTING KEYSTONE XL PIPELINE

EXECUTIVE ORDER CALLS FOR SHARP LOGGING INCREASE ON PUBLIC LANDS

EPA CRIMINAL ENFORCEMENTS HIT 30-YEAR LOW

TRUMP ADMINISTRATION ROLLS BACK OBAMA-ERA COAL RULES

FIRST OFFSHORE OIL WELLS APPROVED FOR THE ARCTIC

Washington Post: If I were still working at the EPA, I would resign

Bernard D. Goldstein, former chairman of the Clean Air Scientific Advisory Committee and EPA assistant administrator for R&D under Reagan:

I had hoped that Wheeler would reverse Pruitt’s initial policies. Instead, he has taken them well beyond the point that, were I a member of CASAC, I would have resigned. Neither my conscience, nor my concern for the respect of my peers, would have allowed me to provide advice on a complex health-related subject when I cannot interact in a scientific consensus advisory process with those who have the necessary expert credentials.

I cannot ask President Trump’s EPA assistant administrator for research and development to resign. That position remains unfilled. Nor is it likely that any credible scientist would accept such a nomination. But I urge the current members of CASAC to step down rather than seemingly acquiesce to this charade. The EPA’s leadership is destroying the scientific foundation of environmental regulations, to the detriment of the health of the American people and our environment.

Read the whole thing.

New Yorker: The Hidden Air Pollution in Our Homes

Nice piece by Nicola Twilley, co-host of Gastropod:

“So there is a big question here,” Marina Vance pointed out. “If all these studies have found an association between outdoor air pollution and a decrease in life quality and life expectancy, but we’re not outside, how does that relationship still hold?”

One possibility is that the brief moments we spend outdoors have an outsized impact on our health. Another consideration is that outdoor pollutants can and do come inside. But one homechem researcher, Allen Goldstein, recently co-authored a paper that suggests a fascinating inversion. The dominant source of VOCs in Los Angeles is now emissions from consumer products, including toiletries and cleaning fluids. In other words, vehicle emissions have been controlled to such an extent that, even in the most car-clogged city in America, indoor air that has leaked outdoors may create more smog than transportation does.

It’s true — some surveys done in the last couple of decades show that people in North America spend, on average, 90% of their time indoors. It’s unlikely that our air pollution exposures — measured as ambient concentrations at central sites, far from where we live and spend time — capture what’s really going on.

One point of contention with this article — despite some nice historical thinking on the relationships between indoor and outdoor air, there was no mention of the very large exposures that continue in the developing world, where solid fuels like wood, grass, dung, and coal are used indoors. A substantial oversight.

Update: Nicola Twilley wrote on twitter that mention of the developing world didn’t make the final version.

Four Gallup polls related to energy and climate

Gallup conducted its annual Environment poll between March 1-10. They have released four snippets of fascinating data related to global warming, reliance on fossil fuels, and nuclear energy.

A/ More people are attributing warmer and colder weather to climate change than previously

Seventy percent of the subset of U.S. adults experiencing warmer temperatures this winter, and 44% of those experiencing colder than normal temperatures, attribute their atypical weather to human activity.

In 2012, when temperatures nationwide were 3.69 degrees higher on average than normal, 38% of those experiencing warmer than usual weather blamed it on human activity. The percentage blaming warmer weather on human activity rose into the 50s from 2013 to 2017 before rising to 70% this year.

The sample sizes of those experiencing colder than normal weather in 2012 and 2013 were too small to allow reporting of these respondents’ views on the cause. However, in 2014, when the sample size was sufficient, just 29% thought colder-than-normal weather was due to human activity. That rose to 37% in 2015, to 40% in 2016, and has since been above 40%.

B/ The data on climate change indicate greater concern overall among the populace, but dramatic differences across party and ideological lines.

… the public’s concern about global warming and belief that humans are responsible are holding steady at or near the trend high points. While Americans as a whole are concerned about global warming, the partisan differences between Democrats and Republicans are stark. Most Democrats take the issue seriously and are troubled by it. Republicans remain skeptical and largely unconcerned.

First, some graphs on the overall concern.

The numbers from 2019 that I find most striking revolve around a question asking whether or not “global warming will pose a serious threat to your or your way of life in your lifetime.” In 2019, 45% said yes and 55% said no. If you split that up by ideology, the difference is stark: 67% of liberals, 47% of moderates, and 27% of conservatives said yes.

C/ The next two items released by Gallup deal with future energy options. The first set of questions focused on decreasing use of fossil fuels in the next 10 or 20 years. 60% of respondents thought it was likely or very likely that the US could dramatically decrease dependance on fossil fuels, with the vast majority wanting to see increased emphasis on wind and solar power.

D/ Gallup also released asked questions on the use of nuclear power. The data show an almost even split:

Americans are evenly split on the use of nuclear power as a U.S. energy source. Forty-nine percent of U.S. adults either strongly favor (17%) or somewhat favor (32%) the use of nuclear energy to generate electricity, while 49% either strongly oppose (21%) or somewhat oppose (28%) its use.

Roughly equal percentages of Americans say nuclear power plants are safe (47%) as say they are not safe (49%). This is the first time in Gallup’s 10-year trend on this question that a plurality of Americans have considered nuclear power unsafe. Even in the 2011 poll, conducted two weeks after the high-profile Fukushima Daiichi nuclear accident in Japan, a majority said they viewed nuclear power plants as safe.

More information on the sampling methodology and survey methods can be found at the bottom of each page linked above. Visualizations on this page made by downloading PDFs of data from Gallup, extracting tables, and generating plots using some R packages: readxl, ggplot2, and data.table.

And then Steve Bannon showed up: Carl Zimmer on Biosphere 2

Credit: Jessica Lehrman for The New York Times

I remember being entranced and inspired by Biosphere as a kid. Zimmer’s piece is an interesting, entertaining, and thoughtful look at the promise and perils of the project.

Many scientists looked back at the original Biosphere 2 as a colossal failure. “In short, the Biosphere 2 experiment failed to generate sufficient breathable air, drinkable water and adequate food for just eight humans, despite an expenditure of $200 million,” the ecologist Rebecca Stewart and her colleagues declared.

The scientists Joel Cohen and David Tilman wrote, “No one yet knows how to engineer systems that provide humans with the life-supporting services that natural ecosystems produce for free.”

But it would be a mistake to dismiss Biosphere 2 out of hand. For two years, eight people grew papayas, beets, bananas, rice and a host of other crops in there. Except for a sliced finger, their health remained good. The water they drank didn’t poison them. Some species went extinct, but the ecosystems endured. Biosphere 2 did not turn to slime.

Science vs Fringe Thinking: EPA Science Panel Considering Guidelines That Upend Basic Air Pollution Science

NPR, reporting on a recent EPA Meeting:

At a public meeting Thursday that ran nearly two hours long, multiple members of that committee, including Chair Tony Cox and Steven Packham of the Utah Division of Air Quality, said they do not agree that breathing air polluted with soot can lead to an early death.

“[Committee] members have varying opinions on the adequacy of the evidence supporting the EPA’s conclusion that there is a causal relationship between [particulate matter] exposure and mortality,” said Cox, reading from the committee’s draft recommendations before explaining that he is “actually appalled” at the lack of scientific evidence connecting particulate pollution to premature death.

From Nature:

A quarter of a century of research has shown that breathing in fine airborne particles emitted by cars, power plants and other sources shortens people’s lifespans. But that scientific consensus is now under attack from a top advisor to the US Environmental Protection Agency (EPA), just as the agency is rushing to revise the national air-quality standard for such pollution before the end of President Donald Trump’s first term. Scientists fear that the result could be weaker rules on air pollution that are bad for public health — and based on politics, not science.

The case has been made — repeatedly — that the health and economic benefits of the Clean Air Act and subsequent regulatory processes are clear. This is summarized succinctly in the figure below, which shows energy consumption, vehicle miles traveled, GDP, and total emissions of EPA criteria pollutants.

Figure from The Lancet Commission on Pollution and Health

Let’s put aside the economic argument and focus on the principles that undergird the Clean Air Act - protection of public health, with standards set to protect the most vulnerable. This critical prerogative is undermined by these (and other) recent efforts to roll back regulations that have clear and demonstrable health benefits. This is yet another example of the Trump administration’s abnegation of responsibility to the health and welfare of the US population.

For more information, see Gretchen T. Goldman and Francesca Dominici’s discussion in Science and their claim-by-claim evidence base. See also a nice summary of the issue at NRDC and a letter from Professor John Samet to the EPA that comprehensively outlines issues with changes to the evidence review process for the National Ambient Air Quality Standards.

W.S. Merwin, predicting the future

W.S. Merwin died on March 15th at 91 at his home in Hawaii. He was prolific, thoughtful, and provocative as a poet and, I learned recently, an active and impactful conservationist in his later life. His death was a reminder of his work - work made suddenly accessible through the internet and the outpouring of his fans.

He wrote often in the New Yorker, and while bumbling through their archives, I found a prescient piece of his titled “The Remembering Machines of Tomorrow” from November 29, 1969, excerpted below:

The first of the remembering machines is immense, immobile, no one’s. It learns, that is true. But its learning is based on information fed into it by sophisticated procedures, consciously, voluntarily. It is constructed of fragments. Even though it can record anything about us that we can conceive of having recorded, it is still in the main a recorder rather than a memory. But its progeny is approaching us.

The machines will become, in time, more compact. They will become the pride of smaller and smaller institutions, the playthings of more and more of the privileged… When the machines become small enough so that every person can have - then must have - his own, the day will be celebrated as the beginning of a new age of the Individual…

Attached to every person like a tiny galaxy will be the whole of his past - or what he takes to be the whole of his past. His attachment to it will constitute the whole of his present-or of what he takes to be the present.

Read the whole piece here.

Air Pollution and Impact Analysis of a Pilot Stove Intervention: Report to the Ministry of Health and Inter-Ministerial Clean Stove Initiative of the Lao People's Democratic Republic

Hill LD, Pillarisetti A, Delapena S, Garland C, Jagoe K, Koetting P, Pelletreau A, Boatman MR, Pennise D, Smith KR. 2015. Air Pollution and Impact Analysis of a Pilot Stove Intervention: Report to the Ministry of Health and Inter-Ministerial Clean Stove Initiative of the Lao People’s Democratic Republic.