Journalist/developer. Interactive editor @frontlinepbs. Builder of @HomicideWatch. Sinophile for fun. Past: @WBUR, @NPR, @NewsHour.
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The three kinds of code you write in the newsroom

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Journalists have been writing code, in one form or another, for several decades. Yet coding is still considered a speciality skill in the journalism profession.

Thus, if you're a journalist who codes, you probably work alone or on a small team of colleagues with similar technical skills. This divide can breed tension between coders and non-coders in the newsroom, especially when it comes to the rhythms and speed of the news production process.

Journalist and developer Chris Amico knows this struggle all too well. Drawing on a decade of experience slinging code in newsrooms big and small, he tackled this topic in a lightning talk at the National Institute for Computer-Assisted Reporting conference (aka, NICAR) in early March.

"Moving at different speeds is something I've seen every newsroom I've worked in struggle with," Amico said.

In his six-minute talk, Amico outlined how technical work, like data analysis and web development, should sync with three general newsroom objectives: reporting, storytelling or product.

Amico's remarks were pre-recorded and delivered in absentia. At the last minute, he cancelled plans to travel to New Orleans, La., for NICAR due to rising concerns about exposure to Covid-19. In retrospect, this was a smart move.

Amico also published the script of his talk.

Amico's definition of product is particularly striking. Note how he recasts technical debt and on-going maintenance costs—topics everyone prefers to avoid—as the central underpinning of the newsroom's enterprise.

The NICAR conference is best known for the dozens of sessions that introduce journalists to computer languages, software packages and other technical tools.

For the fourth consecutive year, I co-led First Python Notebook. This year, Andrea Suozzo of Seven Days in Burlington, Vt., joined our coaching team and re-vamped our data viz course materials.

I wasn't just at NICAR to teach. I was a student in First Graphics App, I learned more about how news app developers produce custom interactive content using Node.js.

Here are a few highlights from this year.

Big Local News is data sharing and collaboration platform that launched just in time to demo at NICAR and, as fate would have it, to help journalists cover the Covid-19 crisis.

The Big Local News initiative is led by Stanford computational journalist Cheryl Phillips. Based on previous success with The Stanford Open Policing Project, Phillips believes that, by gathering together disparate data from smaller jurisdictions, journalists and social scientists can identify larger regional and national patterns that yield more impactful research and journalism.

Datasette is a growing ecosystem for exploring and publishing data that fits neatly into the workflows of computer-assisted reporters. Datasette started as a hobby project of Simon Willison (co-creator of the Python's Django framework), who is now working on the project exclusively as a Stanford John S. Knight fellow at Stanford. Check out Willison's tipsheet.

DataShare is a secure document research platform that has become the tool of choice of the International Consortium of Investigative Journalism (ICIJ) when managing projects based on big document leaks. ICIJ researcher editor Margot Williams and Quartz machine-learning journalist Jeremy Merrill explained how Datashare was instrumental in ICIJ's recent Luanda Leaks project.

VisiData is a slick command-line tool for exploring, summarizing and analyzing spreadsheets. It's kind of like a hacker version of Microsoft Excel. Not only is VisiData free and open-source, it's also faster and can handle much larger datasets. Buzzfeed's Jeremy Singer-Vine, who publishes the Data is Plural newsletter, lead a hands-on introduction to VisiData.

James Gordon  
   
Senior Editor

James Gordon researches and develops new platforms for journalism, drawing on his background in coding, data analysis and product management.





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chrisamico
5 days ago
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Summary of my #NICAR20 lightning talk
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When will the coronavirus pandemic end? What scientists can say about life returning to normal

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“That’s one of the hardest questions to answer in epidemiology, and it’s one of the things that everybody is most interested in,” said Samuel Scarpino, an epidemiologist at Northeastern University. “We’re going to have to be very cautious because we don’t want to waste all the sacrifices that we’ve already made.”

The first sign that the tide has started to turn, scientists say, will be a decline in new cases over several consecutive weeks, even as testing expands. In Boston, that peak is likely at least a few weeks away, Scarpino said. New coronavirus-related hospitalizations should fall a week or two after the number of new cases declines, in light of the time it takes for the disease to progress.

That would indicate that the economically devastating social distancing measures are working. Even then, it will be too soon to fully return to normal, specialists say. Just because there was a peak doesn’t mean it was the peak.

In fact, once new infections fall to a level that hospitals can manage, experts predict different regions will still experience a series of peaks and valleys in virus caseloads until a vaccine can be developed, something that will likely take at least 12 to 18 months. If social distancing restrictions are relaxed, governments will have to weigh economic against public health consequences in determining when, or whether, to reimpose them.

“What we’re doing right now is definitely worth it,” said Alex Perkins, an epidemiologist at the University of Notre Dame studying the trajectory of the pandemic. “Hopefully we’ll start to see some benefits, but we also have to recognize that we’re going to have to continue to adapt to this situation for the foreseeable future."

To reduce deaths by at least hundreds of thousands, top infectious disease specialists at Imperial College London recently projected that the United States should expect to have rolling periods of social distancing and school closures through late 2021. In each period, the measures would last about two months, relax for one month, then resume for two more. The specialists suggested using the number of coronavirus patients in intensive-care unit beds, based on the country’s peak intensive care unit capacity, as a trigger for restarting the restrictions.

For example, the Imperial College model projected that 510,000 people would die in two years in Great Britain without action. But the death toll would fall to 39,000 if the social distancing measures restarted every time the patient count in ICUs hit 400, or could shrink to 8,700 deaths if the trigger were 60 ICU patients.

The United States would see proportionally similar results, the specialists said, projecting that if the US did nothing, at least 2.2 million Americans would die.

Complicating projections is how much there is still to learn about the virus. For example, scientists aren’t sure how long immunity from the virus lasts in people who recover.

During the Spanish flu epidemic in 1918-1919, the last time the world confronted a pandemic of this scale, the impact of social distancing was clear. Philadelphia held a World War I victory parade and saw 10,000 deaths in the following month, while in St. Louis, which had canceled its parade, the death toll did not exceed 700, according to the US Centers for Disease Control and Prevention.

Another important milestone would be for America’s testing capacity to advance to the point of being able to quickly identify and isolate coronavirus patients and their contacts, including household members. That may require bolstering local health departments, Perkins said.

“We’d like to get to where it’s a more manageable thing,” Perkins said. “We’re not anywhere near that right now.”

Through extremely restrictive social distancing measures and far more testing, other countries have shown it’s possible to control the virus.

On Thursday, China announced its first day with no new locally transmitted cases. That was a bright spot for many epidemiologists who have watched Italy’s hospitals become overwhelmed and deaths in that country surpass China’s roughly 3,200.

But getting the virus under control in China took draconian measures that tanked both the economy and civil liberties, as many non-infected citizens weren’t allowed to leave their homes and coronavirus patients were required to be hospitalized despite not needing hospital care. Now, China is reopening factories and businesses but has implemented thermometer scans at the entrances to many buildings. Many schools are still closed.

It’s unclear whether democratic societies would tolerate such measures.

“China’s response was extreme by US standards, but it seems to have worked" at least in the short term, said Nadia Abuelezam, a Boston College epidemiologist.

In Singapore, Taiwan, Hong Kong, and South Korea, governments managed to keep case numbers relatively low through large-scale testing that allowed for people with infections to be identified and quarantined.

Epidemiologists would welcome any news about increased testing capabilities to ensure that anyone with symptoms could receive a test. Currently, many sick people have complained that they were denied tests due to a shortage and strict rules that have limited tests except for those with links to a confirmed case or foreign travel.

Until testing capacity is up, epidemiologists said, the numbers do not offer a true measure of the outbreak because they’re just showing that more people are being tested. Researchers believe the state’s confirmed case count — 525 on Saturday — represents a fraction of the actual number of infections.

“We don’t have enough data now to know where we are on the epidemic curve because we simply aren’t testing enough," Abuelezam said.

Elizabeth Halloran, a senior researcher at the Fred Hutchinson Cancer Research Center in Seattle, said it’s crucial that the US boost its testing capacity even for people with mild or no symptoms. Studies show that undetected cases drive the growth in epidemics as people who don’t feel severely ill often continue to go about life, infecting those they interact with.

Experts would also celebrate any innovations that can increase the availability of ventilators or hospital capacity. But true long-term progress won’t come until either drugs or a vaccine are developed and mass-produced.

Vaccines are ideal because they prevent infections and establish immunity among a large population of people, Perkins said, but they’re also extremely difficult to create. Many infectious diseases still lack a vaccine. Clinical trials are underway for coronavirus vaccines.

“There’s so much of this across the world right now, it’s a disease that’s likely going to be with us for the foreseeable future,” Perkins said, noting that smallpox is the only infectious disease that has been successfully eradicated. “Getting all the way to zero is incredibly difficult.”

Drugs could likely come along sooner and would be hugely important in saving lives. Massachusetts General Hospital and Brigham and Women’s Hospital are enrolling patients in studies of the experimental drug remdesivir. Scientists hope that a drug could be used to prevent new infections as well as treat them.

Abuelezam said she did see two potential bright spots. She hopes this terrifying episode will lead nations to prioritize epidemic preparedness in the future. Many deaths from the pandemic could have been prevented with better monitoring and action, she said.

She also hopes the tragedy will unify people in common cause by showing how our fates are intertwined.

“A sign of progress that comes out of this," she said, could be "that our society is able to better support those who are vulnerable.”

Naomi Martin can be reached at naomi.martin@globe.com.

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chrisamico
9 days ago
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When will the coronavirus pandemic end? What scientists can say about life returning to normal - The Boston Globe
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Some People

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Some people feel helpless & anxious.

Some people are bored.

Some people are self-quarantined alone and are lonely.

Some people are realizing that After will be very different from Before.

Some people are really enjoying this extra time with their kids and will miss it when it’s over.

Some people just got off their 12th double shift in a row at the hospital and can’t hug their family.

Some people visited their favorite restaurant for the last time and didn’t realize it.

Some people have died from COVID-19.

Some people can’t stop reading the news.

Some people cannot afford soap.

Some people are learning how to bake bread.

Some people are working from home while simultaneously trying to homeschool their kids.

Some people are single parents trying to work from home while simultaneously trying to homeschool their kids.

Some people are living paycheck to paycheck and the next one will not arrive.

Some people are unfit to be President.

Some people left the city for their home in the country.

Some people can’t go to the grocery store because they’re at risk.

Some people lost their jobs.

Some people can’t sleep.

Some people are watching free opera online.

Some people have been quarantined for weeks.

Some people can’t work remotely.

Some people have contracted COVID-19 and don’t know it yet.

Some people can’t concentrate on their work because of anxiety.

Some people can’t afford their rent next month.

Some people are still gathering in large groups.

Some people are keeping the rest of us alive at significant personal risk.

Some people didn’t buy enough hand sanitizer.

Some people bought too much hand sanitizer.

Some people are missing their therapist.

Some people can’t go to work but are still being paid by their employers. For now.

Some people are mainly concerned about what to watch next on Netflix.

Some people are volunteering.

Some people are going to lose their business.

Some people are realizing that teachers are amazing.

Some people are ordering takeout from local restaurants.

Some people would really just like a hug.

Some people can’t convince their elderly parents to take this seriously.

Some people are worried about their 401K.

Some people have never had a 401K.

Some people will face increased abuse at home.

Some people are going to get sick or injured and will have a harder time getting medical care.

Some people can’t buy the food they need because the WIC-eligible stuff is sold out.

Some people won’t stop partying.

Some people lost their childcare.

Some people are doing everything they can to remain calm and hopeful and it’s not working.

Some people are watching Outbreak & Contagion and playing Pandemic.

Some people don’t know what they’re going to do.

Some people are overwhelmed with advice on how to work from home.

Some people are drinking or eating too much.

Some people are thinking about after.

Some people are upset because they can’t travel.

Some people are horny.

Some people are planning for a larger garden this year.

Some people won’t see their families for months.

Some people are logging off to stay grounded.

Some people can’t see the light at the end of the tunnel.

Some people will realize they need to split with their partner.

Some people are singing Imagine.

Some people aren’t on this list.

These are all based on the experiences of real people drawn from news stories, social media, and friends. Take heart: you are not the only person experiencing what you are going through. But be mindful: not everyone is having the same experience you are. Ultimately though, we are all in this together.

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chrisamico
9 days ago
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One Simple Idea That Explains Why the Economy Is in Great Danger

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An empty restaurant near Grand Central Terminal in New York on Monday. Eating out is one type of spending sure to drop sharply as communities struggle to reduce the spread of coronavirus.

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chrisamico
15 days ago
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COVID 19 and BJJ

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I’ve been getting a lot of questions about this so let’s talk about COVID 19 (coronavirus) and BJJ…

My approach to this comes from three perspectives…

  1. I’ve trained in the martial arts for 40 years and got my BJJ black belt 14 years ago…
  2. I have both a B.Sc. and an M.Sc. in biology and have been following the science around this virus fairly carefully…
  3. I’m also a first responder, having served with the fire department for 20 years and having responded to countless medical calls.

Bottomline: I think we’re in big trouble. Really. Big. Trouble.  

And I don’t think we should be training, at least not in the way that we normally do.

 Note: This article was published in first draft form on Thursday March 12th. Last updated March 13th, 9:17 am PST 

Below is what I said on Twitter on March 5th, before most people thought it was a big deal in North America. And I’ve gotten significantly more cautious since then…

Let me explain…

The Big Problem

One of the big problems with this virus is that it’s contagious BEFORE there are symptoms.

That means you could be rolling around with someone who seems perfectly fine, not the slightest cough or any indication of fever, and they can still give you the damn thing.

But maybe you’re 20 years old.  If so you might reasonably object that this virus mostly affects old people.

And that’s roughly true.  Based on early mortality studies coming out of places like China and Korea the older you get the more likely you are to die from it.

Let me rebut this a few different ways…

First of all, even if you don’t die getting COVID might really suck . Some people who have recovered from it have described it as being suffocated alive

But let’s say that you’re young, dumb, healthy and athletic.  You think that if you get it you might not suffer very much.  And you may even be right…

But even if you’re not badly affected you could still transmit it to your parents, the grocer, the little old lady sitting next to you on the bus and kill them.

And furthermore, the slower this thing spreads then the more time society and the medical system has to prepare.

It’s called ‘flattening the curve‘ and you’re going to hear a lot about it in the days and weeks to come…

Flattening the Curve

The Effects of Flattening the COVID 19 Curve

The basic idea of flattening the curve is this…

Let’s say that that no matter what we do the same number of people are ultimately going to be infected by COVID 19.

In that case it’s MUCH better if we slow things down so that if you or I or your grandmother needs a doctor and a respirator then one is available.

In the diagram above the blue shape and the yellow shape have the same number of people in them.  The blue shape is what happens when everyone gets the disease all at once.

Read this excellent article in the Atlantic about the situation in Italian hospitals to get a sense of what it looks like when the medical system is overrun. The doctors are literally having to decide who lives and who dies because they can’t treat everyone.

Flattening the curve is a reasonable approach at this point now that containment has failed, which is why you’re seeing universities, concerts and the NBA shut down.

I know you love to train.  I do too.  But don’t be a selfish douchebag and undermine one of the only things that’s going to help save lives.

A Crash Course on the Science

There’s a TON of information and misinformation out there about this virus – some of it politically motivated – and it’s hard to sort out fact from fiction.

Two really good podcast episodes that passed my biologist’s sniff test were the Joe Rogan talking with Michael Osterholm (JRE #1439) and Sam Harris talking with Nicholas Christakis (Making Sense #190).

Here’s Joe Rogan…

And here’s Sam Harris…

If you listen to both of those episodes you’ll be fairly well caught up on the present state of the science.

Now a lot of people are saying things like ‘the mortality rate of this thing is no worse than the flu.’  And then, if they cite a source at all, they quote some random doctor they know and/or Sean Hannitty

At this point I don’t think that any one doctor’s interpretation is to be trusted. I’m going to go with two sources: articles published in places like the Lancet, Science, and Nature, and the scientists and epidemiologists who work at the World Health Organisation and the Center for Disease Control.

(And yes, those scientists know that it’s hard to exactly know the mortality rate with the data we currently have.  The current estimates may be a little bit high but, then again, they may also be too low.  Read this article in The Lancet for a good discussion of how the mortality rate estimation process works.


You might ask, “But isn’t the infection rate going down in China?

Yes, it looks like the rates have mostly levelled off there, but China also took incredibly drastic measures in late January (after first lying about it of course) that are unlikely to be enacted anywhere else. And I guarantee you that BJJ clubs weren’t allowed to be operating after January 24th 2020 in Wuhan.

Ultimately we’ve probably got something that is very contagious and also reasonably deadly that is going to overwhelm the healthcare system.

Is Kickboxing Safer than BJJ

It’s too soon to say, but striking martial arts are probably not much safer than grappling arts.

Until a few days ago the prevailing wisdom was that COVID 19 was a droplet-borne disease and could only be transmitted by touch or by someone directly sneezing on you.

But then a study by Princeton and other universities came out showing that the virus particles can survive and remain infectious in the air for up to 3 hours.

Viruses are tiny.  Unbelieveably freaking tiny.  Way smaller than the smallest pollen particle in the history of pollen particles.

So think about how long pollen particles can stay in the air, then imagine how far and pervasively a virus particle a million times smaller could float around.

Now think of people breathing heavily, shouting, and spattering sweat all over the place.

So until we have further data I would assume that your kickboxing, karate and krav maga are essentially as dangerous as your BJJ class.  Don’t do them.

What I’m Going to Do

I’m personally washing and sanitizing my hands about 20 times a day.

I’m not shaking hands and am practising social distancing.

As of yesterday I’ve pulled my kids from school and am homeschooling them, and have cancelled extracurricular activities.

I had to take a flight for urgent family business last Monday.  I was the only person wearing an M95 mask on the plane.


I bet that I’m not the only one wearing a mask on the flight home tomorrow (although to be effective it really does need to be an M95 rated mask – those paper filter masks probably don’t do much).  And my clothing will also go directly into the wash as soon as I get home.

Unfortunately a more effective mode of transmission than rolling around on the ground with people who have also been rolling with other people cannot be imagined.

I wish it weren’t true.

But until this thing is under control I’m not training with anyone anymore.

Not grappling, not striking, not weapons.

I love training.  And I have a vested financial interest in the health of the sport.  And I have many friends who make their living teaching jiu-jitsu and martial arts.

Until we have more data about this whole thing I’m going to do strength and conditioning and work on my BJJ skills by watching videos. I’m just NOT willing to risk bringing an infection to my family and coworkers because of how much I enjoy training.

BJJ School Owners

And if you run a school then I think it’s irresponsible to keep it open at this point.

Follow the lead of Marcelo Garcia, Keenan Cornelius and others who have just announced 2 week closures.

Your school IS going to close at some point (I should add that hopefully this is just temporarily).

The only question is whether you close it before or after you allowed one person to transmit it to 10 new people and thus perpetuate the exponential growth of this infection.

Maybe ask your students to continue paying you for now, but offer them free classes in the future (at staggered intervals) to make up for it. So student A will get a free month of training in July, student B will get a free month in August, and so on…

And if you can’t make rent or pay your bills then the only good news is that you won’t be the only person negotiating with your landlord and your creditors for a temporary suspension of payments. Most landlords will need to do something to help you or risk losing most of their tenants.

Everyone will be in the same boat and eventually there might be some sort of government intervention on this front (I’m not sure about how it works, but Italy has suspended mortgage payments during it’s state of lockdown, so a precedent of sorts exists).

I really, truly wish it weren’t so. And maybe the science is wrong, but the smart money says otherwise.

A Plea to BJJ Students

Look, your instructor is about to go through some really fucking miserable times.

Right now he’s freaking out if the school and team that he’s spent years building is going to be undone by trillions of nanometer-scale virus particles.

Most schools I know simply can’t absorb the loss of a single month of student fees. They’re simply operating that close to the edge.

If you’d like a school to return to and train at after all this blows over then, if you can at all afford it, please don’t cancel your membership. Maybe work out a deal where you can pay him now but get a free month from him sometime in the future.

Let’s Panic in a Calm and Responsible Manner

This is pandemic, and maybe, hopefully, it will be brought under control.  But not without our participation and not without changing our behavior.

As training partners, as citizens, and as human beings there are things we can do to help out.

Martial arts is about discipline, and in this case it’s about the discipline NOT to train.

Don’t let your love of working out result in a single additional transmission or quite literally the death of an elderly or immunocompromised person.

It’s easy to rationalise things and go do what you want to do anyway. But one of my favorite quotes comes from Richard Feynman who said, “The first principle is that you must not fool yourself – and you are the easiest person to fool.

Let’s not fool ourselves on this one.

Stephan

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chrisamico
18 days ago
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My gym is closed for 10 days, and I wouldn't be surprised if that's extended. It's the right call right now.
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Coronavirus is a nightmare. These stories tell us how to survive — and rise above it.

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Fiction such as "Contagion," "World War Z" and "Year of Wonders" demonstrates the values we'll need to fight the pandemic and build a better world when it's over.
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chrisamico
19 days ago
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