Relevant excerpts from “Spillover”

In light of the current COVID-19 pandemic, I’ve been reading “Spillover: Animal Infections and the Next Human Pandemic” by David Quammen, published in 2012 (!!).  It takes a look into various zoonotic viruses that make the jump from animal to human. There have been a number of passages that have just jumped out and resonated with me as I’ve been reading.

One further factor, possibly the most crucial, was inherent to the way SARS-CoV affects the human body: Symptoms tend to appear in a person before, rather than after, that person becomes highly infectious. The headache, the fever, and the chills—maybe even the cough—precede the major discharge of virus toward other people. […] That order of events allowed many SARS cases to be recognized, hospitalized, and placed in isolation before they hit their peak of infectivity.

And a few paragraphs later:

“That probably helped account for the scale of worldwide misery and death during the 1918–1919 influenza: high infectivity among cases before they experienced the most obvious and debilitating stages of illness. The bug traveled ahead of the sense of alarm. And that infamous global pandemic, remember, occurred in the era before globalization. Everything nowadays moves around the planet faster, including viruses. If SARS had conformed to the perverse pattern of presymptomatic infectivity, its 2003 emergence wouldn’t be a case history in good luck and effective outbreak response. It would be a much darker story. The much darker story remains to be told, probably not about this virus but about another.”

One section of the book that was especially chilling involved the monkeys that inhabited the sacred monkey temples on Bali. In 2014, Kerry and I took our honeymoon there and I had even posted about the crazy monkeys: “While cute looking, the monkeys here are ridiculously aggressive. It was a bit scary!

Anyway, the monkeys on the island are all apparently infected with herpes B, which kills nearly everyone.

The monkeys aren’t shy about accepting, even demanding, those handouts. They have lost their wild instincts about personal space. Enterprising local photographers run a brisk trade in photos of tourists posed with macaques. “And here’s me in Bali, with a monkey on my head. Cute little guy, just wanted that Snickers bar. But the cute little guys sometimes bite and scratch.”

Engel, Jones-Engel, and their colleagues gathered two interesting sets of data from this place. They surveyed the monkey population, by way of blood samples; and they surveyed the human workforce at Sangeh, by way of interviews and also blood samples. What they found says a lot about the scope of opportunity for virus spillover between Asian monkeys and people.

The team drew blood from thirty-eight macaques, of which twenty-eight were adults, the rest youngsters. They screened the blood serum for evidence of antibodies to herpes B, the same virus that killed William Brebner and most of the other people ever infected with it. The results of the lab work were chilling: Among adult long-tailed macaques at Sangeh, the prevalence of herpes B antibodies was 100 percent. Every mature animal had been infected.

But, there is good news!

The researchers merely estimated that there must be thousands of monkey-bitten tourists walking away from Sangeh each year—and Sangeh is just one such Balinese monkey temple among a handful. The odds of a human contracting herpes B under these circumstances seem vast.

But it hasn’t happened, so far as anyone knows.

I recommended the book to my dad and he asked if it had a happy ending. I shared this passage toward to end of the book with him.

“These scientists are on alert. They are our sentries. They watch the boundaries across which pathogens spill. And they are productively interconnected with one another. When the next novel virus makes its way from a chimpanzee, a bat, a mouse, a duck, or a macaque into a human, and maybe from that human into another human, and thereupon begins causing a small cluster of lethal illnesses, they will see it—we hope they will, anyway—and raise the alarm.

Whatever happens after that will depend on science, politics, social mores, public opinion, public will, and other forms of human behavior. It will depend on how we citizens respond.”

He replied simply, “so much for the happy ending.”

I ended up rating this book 5 stars on Goodreads. I probably wouldn’t have discovered it if not for the current global pandemic, but it is something I think I’d have enjoyed before everything changed. David Quammen looks at a number of zoonotic diseases (SARS, Lyme, and AIDS among them) and their fascinating histories.

See a satellite tonight (maybe)

I’ll admit, it’s been awhile since I’ve seen the International Space Station pass overhead (it’s something I loved to do in the past).

While reading about Elon Musk’s ambitious plan to build a constellation of over 40,000 satellites for providing Internet coverage, I discovered a pretty awesome website for tracking viewing opportunities for his Starlink constellation, as well as other notable objects in orbit (such as the ISS):

See a Satellite Tonight is a project put together by James Darpinian, that shows you which satellites will be visible in your location per the next few days. As an added bonus, you can view where in the sky the satellites will pass overhead using Google Streetview. It’s pretty neat!

On the off chance that the SpaceX Starlink constellation is passing overhead, check it out — you’ll see a train of (as of this writing) 60 satellites appear overhead.

Due to weather and lighting condition in Oakland, I haven’t been able to see it yet, but my dad sent me the following message after using the same website:

Made a point to get up early this AM to watch for Elon’s Starlink. Wow, what a sight! 60 satellites in a row. Just thinking about all the implications of this. Definitely a visual I’ve never seen in my lifetime! Kind of surreal, actually.

Next level code review skills

I’m always searching for better ways to improve my workflow, increase productivity, and just generally learn new and exciting things. (Besides, it’s part of having a healthy growth mindset.)

We’ve had some big changes on our team during the past year and I’ve felt like I’ve needed to step up when it comes to reviewing code that my fellow colleagues write. While searching for some ideas on how to improve my code review skills, I discovered a blog post from 2018, entitled “Code Review from the Command Line“.

This blew my mind and really helped reframe how we engineers should approach code reviews:

When I ask that other people review my code, it’s an opportunity for me to teach them about the change I’ve just made. When I review someone else’s code, it’s to learn something from them.

Jake, the author of the above post, goes on to describe his setup and custom tooling for conducting an interactive code review.

He uses custom git alias to see which files have changed and how many changes there are, a custom script that visualizes how often the files within the pull request have changed over time, and another custom script that can visualize the relationship between changed files.

All of these go above and beyond the call of duty for reviewing code, but it’s stuff that decreases friction and can make a sometimes tedious process much more enjoyable.

I’ll be implementing some of these ideas into my own workflow in the near future.

Book Review: “Talking to Strangers” by Malcom Gladwell

Talking to Strangers” examines how our internal and cultural biases affect our interactions and perceptions of the people around us.

Early in the book, Gladwell mentions a study that gets right to the heart of the book and was really eye opening for me.

It’s a study into the “illusion of asymmetric insight” and shows us how we think we’re good an interpreting what a stranger is thinking or their intentions (spoiler: we’re actually really horrible at it).

Participants were required to complete a set of words with missing letters and then asked what the results say about them.

For example, someone was given “TOU _ _”. Some people would fill in the blanks as “TOUGH” and others would put “TOUCH”.

Afterward, the participant was asked if they think these results reflect their beliefs and core values. Nearly every participant said their word choices were random and had no relation on how they view the world.

Then they were given a random set of words from other people and asked the same question: What do you think these word choices say about these strangers?

Everyone had a strong opinion within literally minutes of being asked the same question about themselves! “Whoever wrote these sounds pretty vain“, or “this person sounds very obsessed with money and power.

Crazy, right?

The book is full of studies like this, as well as specific examples from real life interactions like this (some with very tragic consequences) and takes a deeper look into why things might have played out the way they did — from a traffic stop in Texas that went very wrong, broken diplomatic promises before World War II, a high-profile sexual assault that occurred at Stanford, and even looking into the motivations of people who try to commit suicide and our collective misunderstanding as to why and where these things happen.

I went into this book not knowing exactly what it was about. I thought, “Oh! New Malcom Gladwell book and it seems to be getting some good reviews, let’s go for it”. It took around a chapter or two for me to really get into the book and see where it was going, but when things finally clicked for me, this was fascinating and enlightening look at every day interactions.

Book Review: “You Look Like a Thing and I Love You” by Janelle Shane

You Look Like a Thing and I Love You is a great, quick read for anyone who is even remotely curious about what things like AI, machine learning or neural networks actually mean and how it affects your day-to-day life.

Whether it’s facial recognition, to self-driving cars, to the search results you get from Google, this book describes the different types of machine learning algorithms, often in a humorous way (the first few pages deal with the author trying to generate pick-up lines using a neural network — hence the title of this book).

It’s a quick read and dives into some of the limitations that machine learning algorithms are bound by and how machine learning algorithms can be tricked, return results outside the parameters of a problem, or even cheat (e.g., when one AI agent was given an objective to minimize the number of times a character died in a video game, it found out how to simply pause the game).

One particular section of the book talks about the recently released GPT-2 data model by OpenAI, which can be used to generate fairly intelligent and coherent sounding blocks of text. It prompted me to try and run the model on my own machine.

After giving the model a prompt of “machine learning can be scary,” the computer responded with the following block of text:

“The problem is, it’s easy to forget that we can’t avoid the problem with software. It’s often hard to avoid the problem, but knowing how to avoid it is not the same as knowing how to avoid it. The problem is, the problem is easy to avoid, but the problem is hard to avoid.”

Do we need to worry about robot overlords any time soon? Probably not.

This is a book that I’d recommend to both people who are tech savvy and to parents who might still call you with questions on how to turn on a computer… or at least anyone curious to how machine learning affects various aspects of our lives.

We are all just algorithms…

I’ve long joked that “we’re all just algorithms in some engineer’s machine.”

But it’s kind of true.

I recently finished reading Homo Deus: A Brief History of Tomorrow by Yuval Noah Harari, which imagines what the lives of our children, grandchildren, and beyond will be like and how technology will affect them.

We generate copious amounts of data each day and give our personal electronic devices and social networks almost unfettered access to all of it. Everything from how long we sleep, how often we exercise, where we go each day to the types of songs, movies and books we like.

There was one passage from the book that I found both amazing and frightening:

A recent study commissioned by Google’s nemesis – Facebook – has indicated that already today the Facebook algorithm is a better judge of human personalities and dispositions than even people’s friends, parents and spouses. The study was conducted on 86,220 volunteers who have a Facebook account and who completed a hundred-item personality questionnaire.

The Facebook algorithm predicted the volunteers’ answers based on monitoring their Facebook Likes – which webpages, images and clips they tagged with the Like button. The more Likes, the more accurate the predictions. The algorithm’s predictions were compared with those of work colleagues, friends, family members and spouses.

Amazingly, the algorithm needed a set of only ten Likes in order to outperform the predictions of work colleagues. It needed seventy Likes to outperform friends, 150 Likes to outperform family members and 300 Likes to outperform spouses. In other words, if you happen to have clicked 300 Likes on your Facebook account, the Facebook algorithm can predict your opinions and desires better than your husband or wife!

This is one of the main reasons why both Google and Facebook have some of the largest (and most effective) advertising networks on the internet.

They fundamentally know who you are and what you like and know us better than we know ourselves.

Indeed, in some fields the Facebook algorithm did better than the person themself. Participants were asked to evaluate things such as their level of substance use or the size of their social networks. Their judgements were less accurate than those of the algorithm.

Excerpts from “Homo Deus: A Brief History of Tomorrow” by Yuval Noah Harari.

National Novel Generation Month, 2017 Edition

November is traditionally “National Novel Writing Month.” The goal is to write a short novel that is 50,000 words in length. I always have grand plans to attempt it and have started a number of times over the years but have never actually finished. (One day, I swear!)

Recently, I stumbled across a geekier take on it, called National Novel Generation Month. The goal of this particular project is to write code that can generate a 50,000 word novel instead. Hey, why not?

I published my code at the beginning of November for my project: The Complete Encyclopedia on 1,449.5 Random Ways to Make a Sandwich.

This book of 1,449.5 random sandwich recipes was created for NaNoGenMo (National Novel Generation Month) 2017. You can view the source code for this project on GitHub.

It uses data parsed from a 1909 book, entitled “The Up-To-Date Sandwich Book: 400 Ways to Make a Sandwich”, written by Eva Greene Fuller and now available for free in the public domain.

For this particular book, new sandwich recipes were generated using Markov chains created from the above text.

Please don’t try to actually make any of the sandwich recipes created with this process. However, if you do, please contact me and show me pictures.

Disclaimer: I cannot be held responsible for any health issues that may arise from eating any of these sandwiches.

There are definitely some interesting ones…

BUTTERED CHEESE AND OLIVE SANDWICH NO. 3

Use three slices of Swiss cheese, spread fresh butter and two tablespoonfuls of olive oil, the juice of two oranges and knead the mixture.