Showing posts with label mad scientist. Show all posts
Showing posts with label mad scientist. Show all posts

Saturday, January 23, 2021

Reflections on a Postman Presidency

Well. Thank goodness that's over.

If the 1960 Nixon-Kennedy debate was the beginning of our barbarian invasion, as Neil Postman suggests in Amusing Ourselves to Death, then electing a TV game show host president was surely the end. The American equivalent to Odoacer chasing Romulus Augustulus out of Rome. If Postman were alive to write a sequel to AOtD, he would probably title it something like: I Hate It When I'm Right.

Postman warned of the damage television is doing to America's social fabric. His argument is not hurr durr teevee dum, but rather that television is harmful because it pretends to be serious. The medium is inherently incapable of presenting material in any meaningful way. When its producers claim otherwise, and the audience believes otherwise, television poisons every institution it touches: education, religion, news, and -- most of all -- politics. Always a dirty business, yes, but there once was a possibility bad behavior would be checked by an electorate interested in solutions not spectacle. Television turned politics into burlesque, and politicians became entertainment. Any failing or lie or crime can be overlooked; the only sin is looking bad on TV.

Postman feared a terrible end was coming, but he did not know what form the end would take or whether disaster could be averted.

Today, we can see the answer to both of those questions is Donald Trump.

The Trump administration may be gone, but it is far from over.

Thursday, December 31, 2020

Fitting an SIR Model to COVID-19 Data

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The US has one of the highest COVID-19 per capita infection rates in the world. Many factors have contributed to this unfortunate honor, including the Trump administration's bungled response to the pandemic, the Trump administration's bungled response to the pandemic, and also the Trump administration's bungled response to the pandemic. I'm here reminded of Richard Clarke's testimony at the 9/11 commission which he opened with an apology: Your government failed you. Those entrusted with protecting you failed you. I failed you. I suspect we'll get no such apology from The Donald.

The good news -- if we can call it that -- is because of Trump's stunning malfeasance, the humble SIR model is a better description of the COVID pandemic than it otherwise would be. Intervention complicates disease dynamics, adding terms to the equations and expanding the search space of parameters we need to fit. In the absence of a public health response, we're left with only three classifications -- susceptible (S), infected (I), and removed (R) -- and two parameters -- the transmission (β) and recovery (γ) rates -- which describe both our model and our fate.

Additionally, the longer COVID drags on the more data we have to test. Of course, none of the numbers can be trusted as long as Trump lackeys have opportunity to spike the CDC spreadsheets. Videre quam esse, and all that. However, that, too, can be good thing, for it allows us to check if model parameters match what healthcare workers are reporting from the trenches. Any discrepancy indicates malarkey may be afoot, kinda like how Neptune was discovered by analyzing the discrepancies of Uranus.

So, let's fire up Matlab and fit a COVID model. We're all sequestered at home this happy holiday, so what else is there to do?

Tuesday, October 6, 2020

The Superspreader

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As a result of recent events, the internet is simply full-to-bursting with words like "karma" and phrases like "everything Trump touches dies." But to be honest, it's impossible to get any kind of an accurate read on the situation.

We're told the president tested positive for COVID, as did his fluffer Hope Hicks, truth scarecrow Kellyanne Conway, administration eye candy Kayleigh McEnany, Senators Mike Lee, Thom Tillis, and Ron Johnson, RNC person Ronna McDaniel, professional hanger-on Chris Christie, three WH reporters, and a WH staffer. Also the president of Notre Dame, this significant as he introduced the guest of honor at Mitch McConnell's SCOTUS coming out party for jurist and Octomom wannabe Amy Coney Barrett.

Which sounds kinda bad, but who can say. It's possible all of these people have tested positive, or some of them have, or none of them have. Because nothing claimed by this administration can be trusted. Nothing. Trump has been nothing but a perjury firehose since the day he took office. Even Charlie Brown would have stopped kicking at this particular football by now. As far as we know, every single elected Republican is dead and the country is being run by Bill Barr in a Trump mask. Or perhaps they all spent a week lounging 'round the pool at Mar-a-Lago sipping Mai Tais from an infant's skull and having a larf. Either scenario is equally likely. This is what four years of chaos has wrought.

But a tale need not be true in order for it to be a cautionary tale. There is an epidemiology lesson hiding in this story, and that lesson is titled The Superspreader.

Sunday, August 23, 2020

Exploring Herd Immunity

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Herd immunity is in the news these days, and, no, it has nothing to do with Devin Nunes. (Because cow. And cows come in herds. And Devin Nunes (R-CA) keeps suing a talking cow on Twitter. Because Congress doesn't have more pressing problems at the moment. Just a little joke to help soften the pain of watching the Republic die. But I digress.)

The idea is straightforward. To halt an epidemic, you don't need everyone immune, just enough people to break the chain of transmission. COVID isn't immortal. Think of infection as starting a clock. The virus has a finite window of opportunity to infect another host before its current host becomes inhospitable, either because the host's immune system has come on-line or the host has died. If it doesn't jump to a new host by the time the clock runs out, it goes down with the ship.

It's like The Hidden, except without Ferraris and strippers.

Now for the bad news.

Sunday, August 2, 2020

iCOVID: Individual Based Epidemic Modeling

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Previously on LabKitty, we attempted COVID simulation in the large, using what a professional epidemiologist would call mass action modeling. There it was assumed the variability and vagaries of individual actors can be glossed over, condensing all behavior into a mythical average behavior that is captured by a few numbers. In the SIR mass action model, the few numbers are the number of susceptible, infected, and recovered in the population plus the transmission and recovery parameters.

However, an alternate approach exists in which we literally follow each individual individually, a bottom-up attack that constructs the evolution of an epidemic as the sum of its parts. This goes by the name individual-based modeling. We generate a history for each individual in the population, then assemble the population response by mashing together everybody's story.

Which brings us, once again, to COVID.

Thursday, July 2, 2020

Politics and Exponential Growth

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The greatest shortcoming of the human race is our inability to understand the exponential function. This was Al Bartlett's mantra. His catchphrase. The alpha and omega of the lectures he gave on overpopulation before his death in 2013.

Bartlett was a physics professor. He understood natural phenomena often outstrip our brain's gronkulatory machinery. The very small (quantum mechanics). The very fast (relativity). But also exponential growth. So he spent his emeritus years educating the public. Breaking it down for the layperson. You may know some of his examples. Wheat and chessboards. The bacteria bottle. Doubling rates. If you don't, you should (Bartlett's lectures are available on YouTube).

The crux of our misunderstanding is the power of the exponential. If a process grows exponentially and its constraint does not, exponential growth will win every time. What kind of process? Human population growth, yes. But also the adoption of technology. The spread of rumors. Compound interest. Nuclear reactions. The transmission of disease. Tolian Soren notwithstanding, exponential growth is the fire in which we burn.

Which brings us to COVID.

Monday, June 29, 2020

The Consequences of an Asymptomatic Infectious Period on COVID-19 Spatiotemporal Dynamics

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Many years ago, a Dan O'Bannon script rumored to be in consideration for Alien^3 circulated on the Interwebs. O'Bannon's tale had teh Alien arriving on Earth in a form of a virus, one that converts the host directly sans a facehugger instar. In what was sure to have become an infamous scene, a Weyland-Yutani bean counter is PowerPointing to a crowded boardroom, coughs once or twice, then a fully-formed adult Alien bursts from his shuffled mortal coil as it splats to the carpet in a bloody heap.

Until that moment, the bean counter had no idea something was amiss. It's a strategem designed to achieve the viral gold standard of success: transmission. That is what a virus lives for (or doesn't live for, as it were).

Perfect organism, Ash called it.

Which brings us to COVID-19.

Friday, March 20, 2020

The Circus has Arrived

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Now that the Trump administration's spectacular incompetence* is literally getting people killed, one naturally wonders what calamity tomorrow will bring. Poetic justice would be if Trump himself and his ring of enablers were culled by COVID-19, but I'm not holding my breath (I mean I am, but that's only because you're standing too close). If you think any comeuppance whatsoever will ever inconvenience these guys, you are practicing for your coma. As Jessie observed of Walter White, Donald Trump is the devil.

Which brings us to sequesterfying.

In Part I LINK of LabKitty's Plague Song Trilogy, we examined the spatiotemporal properties of infectious disease to model the global spread of COVID-19, from its humble beginnings in a Pangolin's alveoli to a pervasive plague rivaling the Black Death, rap, or Facebook. In Part II, we examined the rationale of the response, which the Internetigensia has taken to calling "flattening the curve." Now here in Part III we examine the mechanics of that response.

Call it what you will -- sheltering in place, avoiding public spaces, social distancing, that thing we nerds have been doing since Gymboree -- paramount is one question: Will it work?

You're not going to like the answer.

Sunday, March 15, 2020

Flattening the Curve

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Now that amateur epidemiology is all the rage, what with the White House's official COVID-19 response consisting of whatever Jerry Kushner can find on Facebook (not kidding), it falls to the Interwebs to help us make sense of the world. It seems like only yesterday all was snips and snails and puppy dog tails, and today we're chained to the front of Furiosa's minivan. Except instead of a heavy metal guitar player shooting fire, the soundtrack is just an endless loop of Yakety Sax. If you don't understand God sent this as punishment for electing Donald Trump, you're not paying attention.

On a related note, I hate it when I'm right.

Which brings us to "flattening the curve." The pandemic lingo de jure, which to the uninitiated means not much. Who curve? Where flat? What it do, and when it be?

Well LabKitty is here to help. Since we can't go to the pub anymore, or the liquor store, or the pub, there's more time for illustrative Javascript. Let's dive into a little epidemiology modeling and decipher why medicos don't want us going to the pub anymore. Or the liquor store. Or anywhere, really. As it happens, the idea is almost a century old, emerging from the seminal work of Scottish biochemist Anderson Kermack and Scottish physician William McKendrick, published in 1927.

Read on.

Tuesday, March 3, 2020

LabKitty Pandemic Simulator

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Recent events have rekindled my long-standing interest in epidemiology, as yet another emergent virus currently does a slow burn across the globe. COVID-19 arrives against a backdrop of influenza currently doing a slow burn across the globe, not to mention reduced herd immunity, declining antibiotic efficacy, and an incoherent public health response. Experts call this "instability in the disease dynamical manifold" but what they really mean is "asking for it."

We may never know how coronavirus came to be, although packing eleventy billion humans into an ecosystem seems to my way of thinking relevant. In any event, it didn't take long for politicians to exploit the situation. Republicans declared the virus was clearly designed in a Chinese weapons laboratory, because China has coronavirus and weapons laboratories. Yes, the logic is as airtight as the rationale. Are there votes to be had by gloating over dead Chinese? Apparently so in the red states of our waning republic.

Which got me thinking about designing a virus. Suppose you wanted to create a pandemic. How would you go about it? What would be the ideal virus? What parameters would you select? Where would you release the thing? How long would it take? What could anyone do to stop it?

There are CDC scientists studying such questions on supercomputers as we speak. One hopes. For the rest of us -- and perhaps for the CDC too, what with their recent budget cuts (thank you Donald Trump) -- there is Javascript.

I give you: jPandemic.

Thursday, July 12, 2018

Pascal's Climate Wager

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Perhaps you have heard of Pascal's Wager, second only to if we came from monkeys why are there still monkeys in the pantheon of flawed arguments my relatives roll out each Thanksgiving dinner in hopes of saving my soul from eternal damnation wrought by a sinful life of fancy book lernin. In return, I attempt steer the conversation back to less contentious topics like 'nana pudding and sweet tea. I resist the urge to ask why Jonah didn't get digested, why they say Jesus rose after three days since (Good) Friday to (Easter) Sunday is only two, and why the First Commandment mentions other gods if there aren't any. Checkmate atheists.

For you heathenskins tuning in today in need of a refresher, Pascal's Wager goes as follows: If there is a God and I don't believe in Him, then I go to hell, whereas if there is no God and I believe in Him then I have lost nothing. The take home is you may as well believe, for there is nothing to lose.

What nobody seems to have noticed in the 500 years since Blaise put forth his wager is it's not a wager at all. A wager requires risk -- that's the very definition of the thing. And in Pascal's "wager" there is none. There is nothing ventured, nothing proffered. No outcome results in loss. Ergo, it's not a wager. (Technically, it's a Nash Equilibrium. Pascal's Nash Equilibrium sounds like the house band at a Poetry Slam.)

Thursday, January 7, 2016

/etc/su Brute?

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Dante stuck Brutus down in the lowest circle of hell, or so Wikipedia tells me (yeah, like I have time to read 700 pages of iambic pentameter). Judas is down there too, the transgression being trusted friend who stabs you in the back. In Brutus' case, the back-stabbing was literal (I'm talking about the Ides of March, ya bunch of savages). Judas paints a rather more complicated picture what with divine pre-determination and whatnot that shan't concern us here, for we have bigger fish and loaves to fry.

The point being, whether you have read The Divine Comedy or not, it's still possible to find Brutus' ranking unjust. What Dante appears to have forgotten is Julius Caesar was gunning to usurp the Republic. He was trying to set himself up as dictator, as surely as Walt Disney or Al Haig. Heck, Julius Caesar wasn't even the first to get the point; that dubious honor goes to Tiberius Gracchus, who got got by his fellow senators back when Caesar's grandfather was still in short pants. And yet, you don't see Dante getting his pantaloons in a blossom over that, do you? (Answer: No, you do not.)

For his trouble, Brutus and coconspirators would eventually get an ass-kicking at Philippi, before Octavian and Antony turned on each other. The Republic fell anyway. Then, to add insult to injury, some cheap hack comes along and drags his family name through the lowest circle of hell.

Well, I dare say this Brutus bashing has gone on long enough. I say it's time we find a new occupant for the lowest circle of hell.

I know just the guy.

Friday, August 21, 2015

Grandaddy was a Biochemist

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Grandaddy LabKitty always said there's three kinds of people you shouldn't cross: (1) people who handle your food, (2) people who have a key to your house, and (3) people who know how to weaponize a virus.

Walked the walk, grandaddy did. He was unfailingly polite to the waitstaff when he'd take me to Denny's for a grand slam. He kept on good terms with the neighbors, even welcoming the Kerebotsos into our clan by way of matrimony. And he got a generous severance package when the local Monsanto factory closed up shop, but I like to think that was just a coincidence. It's what a just society does, right? Rewards faithful service? People shouldn't require a threat of total annihilation just to hold up their end of the social contract.

Wednesday, April 1, 2015

Calculus is like a Crazy Stripper Girlfriend

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Neil Postman is the patron saint of LabKitty, whether he likes it or not. The parallels are uncanny. Academic -- check. Social critic -- check. Nobody listened to him -- check. Dead -- um, give it time. For my part, I have droned on at length about Postman's dread concerns over broadcast media and the damage it is doing to the Republic. Forget redistricting, forget gerrymandering, forget Citizens United and campaign finance reform; Postman identified the real political disease of America. Everything else is just a symptom.

However, there is a dark side to Postman. A skeleton in the closet, bodies buried in the garden, schoolchildren caged in the basement. A shameful past people having only a passing familiarity with his work miss entirely and those who know it well prefer to forget. Because Postman committed one of the few unforgivable sins left in America. No, he didn't appeal to reason in a political debate or show his boobies at the Superbowl.

The dude harshed on the Muppets.

Friday, February 6, 2015

The Prospect of Ken Doll Genitalia

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It was the '50s, a time when men were men. They smoked at the office, dressed in Brooks Brothers suits, and had three-martini lunches. One day, logic demands, a group of these men got together in a boardroom at Mattel and had a discussion about baby doll penises.

"Say, boss. The boys down in plastic injection want to know what to do about Ken."

"Do?" the boss asks.

"You know," the junior exec shifts in his chair, "unit or no unit."

"More like Ken or Kant," Thompson quips while swirling his Glenlivet. The men chuckle. Thompson was always a card.

In the pre-CAD era, 5-axis NC was done by hand. Old-world artisans sculpted block aluminum water-cooled precast molds that would soon be stamping out an army of Ken dolls like the Truman administration battling the Reds in Korea. They had to get it right the first time.

"Well, what did we do with Barbie?" the boss asks.

The junior exec is puzzled. "What did we do with Barbie what?"

"You know," the boss motions, "down there."

The men look to each other nervously. Some pull out gold Dunhill lighters and begin to smoke.

It was the '50s. The only people who knew female anatomy were communists and jazz musicians. As far as polite society was concerned, it was pure Indian country. The Bermuda triangle.

One of the execs finally dares to breach the awkward silence. "So, lunch?"

Wednesday, September 10, 2014

Edited for Television

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Having recently spent a week in paradise (read: hotel with cable), I've had opportunity to update my mental scrapbook of the American psyche as revealed by that most perfect of metrics: Nielsen ratings. My occasional opportunity to check in on the crazy kids next door, my periodic eavesdropping on the neighbors when the planets align and I start picking up their baby monitor on my dental work.

I don't own a television. More accurately, I don't own the part of a television where the cable thingy plugs in. I took that out with a soldering iron. (The rest of the TV is needed to watch my Netflix DVDs. Sue me; I'm old school.) You should not conclude from such a lobotomy that I'm immune to the charms of cable TV. Quite the contrary: I'm powerless against them. When it's finals week and you find yourself watching a picture-in-picture marathon of Chefs who Taunt and Navy Crimes Patriotism Hour instead of studying, it's time for a fluxed-based intervention.

Friday, July 4, 2014

Where's my parade?

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Never was so much owed by so many to so few.
        -- Winston Churchill

Manhattan Project lore has it the codename "Fat Man" was chosen for the plutonium bomb because if an enemy agent happened across the moniker s/he would assume it was a reference to Winston Churchill. It was a simpler time back then, the pre-PC era, when you could call a head of state fat -- not "portly," not "big boned," but straight-up fat -- and they would shrug it off with a stiff upper lip (and we're talking name-calling in official U.S. spycraft, not from some blog monkey who these days writes worse things about heads of state before the morning call to Cheetos).

The Robert Baratheon of his day, Churchill was. Powdered sug-aaaar!

So it is we are granted license to also impugn Mr. Churchill's arithmetic. The "many" he is referring to in the the above quotation is the WW-II population of Great Britain, whose livelihoods if not very lives would have been put to the sword by the Nazis if given the opportunity. The "few" are the pilots of the Royal Air Force, who threw back Hitler's planned invasion by denying him air superiority. The Wikipedia page on the Battle of Britain states the RAF fielded 2,936 pilots in the conflict. At that time, the population of the British Isles was about 48 million (source: www.parliment.uk). This gives a so many to so few ratio of 16,348 or 16.3 kilothanks, to use the modern parlance.

Is this truly the apex of concentrated gratitude? Was there some other time in history when more was owed to fewer?

Yes there was.

And it's owed to my people.

Wednesday, June 25, 2014

Hate the obfuscation, love the obfuscator

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Mathematicians suffer much good-natured ribbing here at the LabKitty. From a perfunctory perusal of past posts, it would appear I have, on occasion: compared them to the mugwumps from Naked Lunch, accused them of taking in nutrients though a proboscis, offered to fight them in the parking lot, impugned their allegiance to the Pope, and referred to them as "mathozoids" on no less than a dozen occasions (and now some mathozoid will inform me it should be "no fewer than a dozen occasions." Make it a baker's dozen). I also recall accusing someone of drowning puppies in a bucket, but I'll need to check my notes -- that sounds like something that came up at Thanksgiving dinner.

As Syd Field teaches us, every good hero needs a good villain. Holmes had Moriarty. Kirk had Khan. Science has the GOP. And Kirk had Khan. Still, some of you may be wondering: Kitty, just what did math do to you?

Show us on Stimpy where math touched you.

Wednesday, March 26, 2014

Global Warming Jump Rope

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When LabKitty was a child -- insomuch as LabKitty was ever a child -- children played outside. Girls played jump rope , a sadistic ritual wherein two girls would suspend a catenary of rope between themselves, excite the rope's primary vibration mode via arm swinging doing, and then one or more additional participants would enter the system and attempt to make periodic jumping matched to its fundamental frequency so as not to disturb the standing wave formed by the rope. Ergo: "jump rope."

What I have left out of this charming tale is the songs the girls would sing as they made with the jumping. I vaguely remember them, the songs. Something about Ali Baba's thieves washing their face in gravy and worms playing pinochle on your snout. Harmless enough I suppose, crude stereotypes notwithstanding.

However, their songs frequently took a turn for the worse.

Monday, March 24, 2014

You there! Step away from yacc and nobody gets hurt.

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Once upon a time there was the perfect programming language. It was called C and it was good. Simple. Elegant. Easy to spell.

X3.159-1989 was a masterpiece, no less than the Aeneid or the Magna Carta. With it, ANSI created paradise on Earth, the capstone of a journey of 1024 steps that Charles Babbage had begun two centuries prior, his dreams of building a thinking machine out of wooden dowels and Ada Lovelace interrupted by love and death.

Then came the expulsion.

S---------- tempted us with the fruit of C++.