No Funding, No Cures

No funding, no cures
by LabKitty

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.

Fitting an SIR Model to COVID-19 Data

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?

The Superspreader

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.

Exploring Herd Immunity

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.

iCOVID: Individual Based Epidemic Modeling

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.

Politics and Exponential Growth

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.

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

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.

The Circus has Arrived

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.

Flattening the Curve

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.

LabKitty Pandemic Simulator

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.

Pascal's Climate Wager

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.)

Bring back the Ostraka!

Of all the indicators that American democracy is broken -- and there are plenty -- perhaps the most striking is the chasm between congressional approval and congressional reelection rates. Congress is currently less popular than a root canal. That is, most Americans would rather their dentist plunge a high-speed burr into a decaying tooth and pneumatically extract its nerve-engorged stinking pulp than shake hands with a randomly-selected congressperson. And deal with their insurance company after. (A little health insurance joke I added there. Topical!)

On the other hand, congressional incumbent reelection is like 90%, which seems odd given that the vast majority of Americans hate every fiber of their being with every fiber of ours.

This queer arithmetic is of course the result of our election process, such as it is. People who loathe an incumbent (read: practically everybody) lie outside the Venn diagram of the people responsible for electing them (read: the 15% of constituents who bother to vote). As such, it's not difficult to renew your contract on America: you need only bribe the people back home with porks.

On the face of it, there's nothing wrong with this. A congressperson's first obligation is to their state or district. Opinions elsewhere don't matter. Nobody in Grundle county gives a hoot what them city slickers have to say about Votey McVoteface, 'cause ole Votey is bringing back the coal mining jobs and making sure the wimmen and nigras lern their place because guns. Conversely, nary a constituent in Upper Chardonnay offers one fig whether the wall-eared flapjacks residing outside their groomed enclaves disapprove of Reginald T. Legislator, Esq. championing quadgender inclusiveness and forcing churches to purchase bibles written in Esperanto by Chinese lesbians, and if so they may place it right in their bottoms.

You ain't the boss of my congressperson, is what I'm sayin'. It's in the Constitution, somewhere, though I'd bet not one in a million Americans could name the chapter and verse. No matter. We have bigger fish to batter this fine day.

Death by Navier-Stokes

A time traveller visits Washington DC in the year 2100. He arrives in January, naked because that is a rule of time travel stories, and shivering but not from any cold. The air is a summer swelter, absent any breeze and thick with the buzz of insects. After his head clears the disorientation, there is only a sense of oppressive heat. A cruel reminder of days past when you would step outside your crisp air conditioned life and be knocked back, every crevice under your clothes immediately filling with sweat.

The sky is a constant canopy of grey, the visible sun unseen. It seems to promise a shower that might relieve the tropical punishment, but relief never comes. It's probably for the best. Storms are hateful in this place, nail-hard rain driven by howling winds and lightning prodigal and ceaseless. As if the Earth were returning to its primordial form and scrubbing the works of man from its skin was the first order of business. Poets used to take inspiration from Nature and Nature's God. Anymore they just take shelter.

Octavian's Son

Family lore has it we are descended from royalty on my mother's side. French royalty to be precise, albeit the claim now impossible to prove. Our filthy peasants turned uppity back in the 18th century and burned all the government records (Jacobins, amirite? Talk about a pain in the neck). Although come to think of it, I am inordinately fond of cake.

Funny how nobody's unverifiable family tree ever takes root in the village drunk or Earl the insurance adjuster. Of course we're royalty. It has an irresistible appeal. Even if you commoners long ago stopped believing we were anointed by God to lord over you, there's still the money and the fancy clothes and a nice place to live. For most of recorded history, the corridors of power offered about the only lives that weren't nasty, brutish, and short. (Yes, the clergy did too, but it isn't exactly known for the things that keep a young man alive, as Rod Stewart sang. A sentiment oft contradicted by popular account, be it The Canterbury Tales or a grand jury indictment. Plus ça change, plus c'est la même chose.)

Yet, take away the trappings of power and the people running the show aren't exactly BFF material. Sure, Cleopatra was a hoot, and Aurelius seemed like a decent guy (although he writes like a Rubik's cube. Marcus should have meditated on hiring an editor), but a lifetime of privilege ferments a stink attitude more often than not. When you're born on third base, every free throw looks like a touchdown. If Downton Abbey were a documentary, Lord Grantham would be rogering the help in every episode. They'd have to run it on HBO.

As with most troubles in life, I blame Octavian.

Michael Savage [sic] for NIH head

LabKitty generally steers clear of politics. Sure, I'm happy to help folks understand the sorcery of polling, and I have some strong opinions on the state of democracy in America. And, yes, I'm currently running for president. I mean besides all that.

Specifically, you won't find LabKitty bad-mouthing any particular candidate here on the blog. It would be unfair, given the awesome power of the Internet to sway impressionable minds. I would like you to make your own choices, gentle reader, flawed though they may be.

However, it has recently come to my attention that (Republican frontrunner and presumptive nominee) Donald Trump made a statement which poops in LabKitty's wheelhouse, as the saying goes, and I feel it would be irresponsible not to respond.

The offense?

He agreed Michael Savage [sic] should head the National Institutes of Health.

Polling -- How do it Know?

Because we are currently living in the Season of the Bitch an election year, you can't swing a dead cat* without hitting a prediction of some sort. These predictions usually come in the form of a poll, or at least the respectable ones do (my Uncle Randall predicting Obama is going to cancel the election so lizard people can extract our vital juices is a different kind of prediction). For example, a recent poll on the CNN website claims Hillary Clinton and Bernie Sanders are tied in the lead-up to the Nevada primaries. Overall, 48% of likely caucus attendees say they support Clinton, 47% Sanders... the article reads (Source: CNN Digital Dashboard 2/17/2016). However, further down the page we find this:

The CNN/ORC Nevada Poll was conducted by telephone February 10-15 among a random sample of 1,006 adult residents of the state. Results among the 245 likely Republican caucusgoers [sic] have a margin of sampling error of plus or minus 6.5 percentage points. For results among the 282 likely Democratic primary voters, it is plus or minus 6 percentage points.

Such a caveat should give any thinking person pause. How can you possibly predict the behavior of millions of voters with just 1,006 phone calls? Isn't this just guesswork? (short answer: No, with a but). Can the result be totally wrong? (short answer: Yes, with a however). What is this voodoo? And what the heck is a margin of sampling error?

Put such questions to a mathozoid, and they will drone on about the null hypothesis and Type-I error and confidence intervals and the standard deviation.

Ask LabKitty and you will get enlightenment.

So, ask away.

The 2016 Voter Self-Disqualification Quiz

Voting is the lifeblood of government, as any high-school civics book will tell you. A homily that conveniently overlooks a long history of restrictions on just who got to donate. In Sparta, only the homoioi had a say. In ancient Rome, ordinary punters were excluded until the Licinian-Sextian laws were passed. For much of the Middle Ages, the monarchy answered to the aristocracy vis-a-vis Parliament or the Diet but only to the aristocracy. Even when America ended the Divine Right of Kings, property ownership was a de facto if not explicit voting requirement. And women voted pretty much nowhere until the 20th century.

Yet, against a background of hard-won suffrage, voter turnout in America remains notoriously low. As a result, election outcomes are increasingly determined by special interest groups and their money. Some have called for reform that might reverse this trend such as automatic registration or making election day a national holiday. Some have even called for making voting mandatory. Call me cynical, but recent election cycles lead me to question whether marching citizens to the polls at gunpoint is the solution. Is the issue really turnout? In 2000, half the electorate voted for the president they'd prefer to have a beer with. In 2008, half the electorate voted for a vice president who was dangerously incompetent. As of this writing, the frontrunner for the 2016 Republican nomination is a reality TV star. The frontrunner for the Democratic nomination is under FBI investigation. As of this writing, Congress somehow simultaneously manages a single-digit approval and a 90% reelection rate. It seems to me merely putting bodies in the voting booth is failing to grasp an essential dimension of the problem.

Something deeper is broken in American democracy.

LabKitty for President!

Now that the floodgates have been opened and every lunatic with a hankering for the launch codes is throwing his/her hat into the Oval Office ring, it's time for LabKitty to officially add my bonnet (which is ridiculous of course -- cats don't wear hats, they drive sports cars!).

Admittedly, I don't have any experience at politics or running the country or real life in general, although I once read one of those Dummy's books on the Constitution (fun quiz: guess how many delegates weren't wearing pants when they signed it). However, I bet I know more about the serotonin 5HT-6 receptor than almost any of the other candidates, and it would be nice to get a little mileage out of that tidbit seeing how much time, effort, and NRSA money went into it. But I promise this: I will never lie to you, except when it's expedient.

Ken Ham sleeps with the jawless fishes

LabKitty spent most of high school keeping a low profile, taking a page from Red Green on self-defense (Quando omni flunkus moritati). Being singled out with the other smart kids in grades K-6 for the gifted program did nothing if not ensure the wrath of the student body once teenage hormones kicked in. Yes, yes, it all sounds so very cliche: little nerd kid gets picked on. But on the mean streets of Circle Pines, the reality was not quite so Rockwellian. I recall one nerdling who got beat in the face so bad he went to the hospital.

Perhaps this explains that odd nerd archetype: the martial arts fanatic. I have lost count of the number of tech people I have met in my travels who lead a double life outside the lab honing themselves into a remorseless killing machine. There are few things more unnerving than pulling an all-nighter in the clean room all-the-while knowing the guy in the pink bunny suit one vacuum chamber over could at any moment blow a head gasket and demonstrate the five-finger exploding putamen technique. A smaller subset than the spindly asthmatic nerd archetype or the portly diabetic nerd archetype, but still. Joseph Campbell should consider looking into this.