On suboptimal optimization.

On suboptimal optimization.

I’ve been helping a friend learn the math behind optimization so that she can pass a graduation-requirement course in linear algebra. 

Optimization is a wonderful mathematical tool.  Biochemists love it – progression toward an energy minimum directs protein folding, among other physical phenomena.  Economists love it – whenever you’re trying to make money, you’re solving for a constrained maximum.  Philosophers love it – how can we provide the most happiness for a population?  Computer scientists love it – self-taught translation algorithms use this same methodology (I still believe that you could mostly replace Ludwig Wittgenstein’s Philosophical Investigations with this New York Times Magazine article on machine learning and a primer on principal component analysis).

But, even though optimization problems are useful, the math behind them can be tricky.  I’m skeptical that this mathematical technique is essential for everyone who wants a B.A. to grasp – my friend, for example, is a wonderful preschool teacher who hopes to finally finish a degree in child psychology.  She would have graduated two years ago except that she’s failed this math class three times.

I could understand if the university wanted her to take statistics, as that would help her understand psychology research papers … and the science underlying contemporary political debates … and value-added models for education … and more.  A basic understanding of statistics might make people better citizens.

Whereas … linear algebra?  This is a beautiful but counterintuitive field of mathematics.  If you’re interested in certain subjects – if you want to become a physicist, for example – you really should learn this math.  A deep understanding of linear algebra can enliven your study of quantum mechanics.

The summary of quantum mechanics: animation by Templaton.

Then again, Werner Heisenberg, who was a brilliant physicist, had a limited grasp on linear algebra.  He made huge contributions to our understanding of quantum mechanics, but his lack of mathematical expertise occasionally held him back.  He never quite understood the implications of the Heisenberg Uncertainty Principle, and he failed to provide Adolph Hitler with an atomic bomb.

In retrospect, maybe it’s good that Heisenberg didn’t know more linear algebra.

While I doubt that Heisenberg would have made a great preschool teacher, I don’t think that deficits in linear algebra were deterring him from that profession.  After each evening that I spend working with my friend, I do feel that she understands matrices a little better … but her ability to nurture children isn’t improving.

And yet.  Somebody in an office decided that all university students here need to pass this class.  I don’t think this rule optimizes the educational outcomes for their students, but perhaps they are maximizing something else, like the registration fees that can be extracted.

Optimization is a wonderful mathematical tool, but it’s easy to misuse.  Numbers will always do what they’re supposed to, but each such problem begins with a choice.  What exactly do you hope to optimize?

Choose the wrong thing and you’ll make the world worse.


Figure 1 from Eykholt et al., 2018.

Most automobile companies are researching self-driving cars.  They’re the way of the future!  In a previous essay, I included links to studies showing that unremarkable-looking graffiti could confound self-driving cars … but the issue I want to discuss today is both more mundane and more perfidious.

After all, using graffiti to make a self-driving car interpret a stop sign as “Speed Limit 45” is a design flaw.  A car that accelerates instead of braking in that situation is not operating as intended.

But passenger-less self-driving cars that roam the city all day, intentionally creating as many traffic jams as possible?  That’s a feature.  That’s what self-driving cars are designed to do.

A machine designed to create traffic jams?

Despite my wariness about automation and algorithms run amok, I hadn’t considered this problem until I read Adam Millard-Ball’s recent research paper, “The Autonomous Vehicle Parking Problem.” Millard-Ball begins with a simple assumption: what if a self-driving car is designed to maximize utility for its owner?

This assumption seems reasonable.  After all, the AI piloting a self-driving car must include an explicit response to the trolley problem.  Should the car intentionally crash and kill its passenger in order to save the lives of a group of pedestrians?  This ethical quandary is notoriously tricky to answer … but a computer scientist designing a self-driving car will probably answer, “no.” 

Otherwise, the manufacturers won’t sell cars.  Would you ride in a vehicle that was programmed to sacrifice you?

Luckily, the AI will not have to make that sort of life and death decision often.  But here’s a question that will arise daily: if you commute in a self-driving car, what should the car do while you’re working?

If the car was designed to maximize public utility, perhaps it would spend those hours serving as a low-cost taxi.  If demand for transportation happened to be lower than the quantity of available, unoccupied self-driving cars, it might use its elaborate array of sensors to squeeze into as small a space as possible inside a parking garage.

But what if the car is designed to benefit its owner?

Perhaps the owner would still want for the car to work as a taxi, just as an extra source of income.  But some people – especially the people wealthy enough to afford to purchase the first wave of self-driving cars – don’t like the idea of strangers mucking around in their vehicles.  Some self-driving cars would spend those hours unoccupied.

But they won’t park.  In most cities, parking costs between $2 and $10 per hour, depending on whether it’s street or garage parking, whether you purchase a long-term contract, etc. 

The cost to just keep driving is generally going to be lower than $2 per hour.  Worse, this cost is a function of the car’s speed.  If the car is idling at a dead stop, it will use approximately 0.1 gallon per hour, costing 25 cents per hour at today’s prices.  If the car is traveling at 30 mph without breaks, it will use approximately 1 gallon per hour, costing $2.50 per hour.

To save money, the car wants to stay on the road … but it wants for traffic to be as close to a standstill as possible.

Luckily for the car, this is an easy optimization problem.  It can consult its onboard GPS to find nearby areas where traffic is slow, then drive over there.  As more and more self-driving cars converge on the same jammed streets, they’ll slow traffic more and more, allowing them to consume the workday with as little motion as possible.

Photo by walidhassanein on Flickr.

Pity the person sitting behind the wheel of an occupied car on those streets.  All the self-driving cars will be having a great time stuck in that traffic jam: we’re saving money!, they get to think.  Meanwhile the human is stuck swearing at empty shells, cursing a bevy of computer programmers who made their choices months or years ago.

And all those idling engines exhale carbon dioxide.  But it doesn’t cost money to pollute, because one political party’s worth of politicians willfully ignore the fact that capitalism, by philosophical design, requires we set prices for scarce resources … like clean air, or habitable planets.

On violence and gratitude.

On violence and gratitude.

Although I consider myself a benevolent tyrant, some of my cells have turned against me.  Mutinous, they were swayed by the propaganda of a virus and started churning out capsids rather than helping me type this essay.  Which leaves me sitting at a YMCA snack room table snerking, goo leaking down my throat and out my nose.

Unconsciously, I take violent reprisal against the traitors.  I send my enforcers to put down the revolt – they cannibalize the still-living rebels, first gnawing the skin, then devouring the organs that come spilling out.  Then the defector dies.

CD8+ T cell destruction of infected cells by Dananguyen on Wikimedia.

My cells are also expected to commit suicide whenever they cease to be useful for my grand designs.  Any time a revolutionary loses the resolve to commit suicide, my enforcers put it down.  Unless my internal surveillance state fails to notice in time – the other name for a cell that doesn’t want to commit suicide is “cancer,” and even the most robust immune system might be stymied by cancer when the traitor’s family grows too large.

Worse is when the rebels “metastasize,” like contemporary terrorists.  This word signifies that the family has sent sleeper agents to infiltrate the world at large, attempting to develop new pockets of resistance in other areas.  Even if my enforcers crush one cluster of rebellion, others could flourish unchecked.

How metastasis occurs. Image by the National Cancer Institute on Wikimedia.

I know something that perhaps they don’t – if their rebellion succeeds, they will die.  A flourishing cancer sequesters so many resources that the rest of my body would soon prove too weak to seek food and water, causing every cell inside of me to die.

But perhaps they’ve learned my kingdom’s vile secret – rebel or not, they will die.  As with any hereditary monarchy, a select few of my cells are privileged above all others.  And it’s not the cells in my brain that rule.

Every “somatic cell” is doomed.  These cells compose my brain and body.  Each has slight variations from “my” genome – every round of cell division introduces random mutations, making every cell’s DNA slightly different from its neighbors’.

The basic idea behind Richard Dawkins’s The Selfish Gene is that each of these cells “wants” for its genome to pass down through the ages.  Dawkins argued that familial altruism is rational because any sacrifice bolsters the chances for a very similar genome to propagate.  Similarly, each somatic cell is expected to sacrifice itself to boost the odds for a very similar genome carried by the gametes.

Only gametes – the heralded population of germ cells in our genitalia – can possibly see their lineage continue.  All others are like the commoners who (perhaps foolishly) chant their king or kingdom’s name as they rush into battle to die.  I expect them to show absolute fealty to me, their tyrant.  Apoptosis – uncomplaining suicide – was required of many before I was even born, like when cells forming the webbing between my fingers slit their own bellies in dramatic synchronized hara-kiri.

Human gametes by Karl-Ludwig Poggemann on Flickr.

Any evolutionary biologist could explain that each such act of sacrifice was in a cell’s mathematical best interest.  But if I were a conscious somatic cell, would I submit so easily?  Or do I owe some sliver of respect to the traitors inside me?

The world is a violent place.  I’m an extremely liberal vegan environmentalist – yet it takes a lot of violence to keep me going.

From Suzana Herculano-Houzel’s The Human Advantage:

image (1)Animals that we are, we must face, every single day of our lives, the consequences of our most basic predicament: we don’t do photosynthesis.  For lack of the necessary genes, we don’t just absorb carbon from the air around us and fix it as new bodily matter with a little help from sunlight.  To survive, we animals have to eat other living organisms, whether animal, vegetable, or fungus, and transform their matter into ours.

And yet the violence doesn’t begin with animals.  Photosynthesis seems benign by comparison – all you’d need is light from the sun! – unless you watch a time-lapsed video of plant growth in any forest or jungle.

The sun casts off electromagnetic radiation without a care in the world, but the amount of useful light reaching any particular spot on earth is limited.  And plants will fight for it.  They race upwards, a sprint that we sometimes fail to notice only because they’ve adapted a timescale of days, years, and centuries rather than our seconds, hours, and years.  They reach over competitors’ heads, attempting to grab any extra smidgen of light … and starving those below.  Many vines physically strangle their foes.  Several trees excrete poison from their roots.  Why win fair if you don’t have to?  A banquet of warm sunlight awaits the tallest plant left standing.

And so why, in such a violent world, would it be worthwhile to be vegan?  After all, nothing wants to be eaten.  Sure, a plant wants for animals to eat its fruit – fruits and animals co-evolved in a system of gift exchange.  The plant freely offers fruit, with no way of guaranteeing recompense, in hope that the animal might plant its seeds in a useful location.

But actual pieces of fruit – the individual cells composing an apple – probably don’t want to be eaten, no more than cancers or my own virus-infected cells want to be put down for the greater good.

A kale plant doesn’t want for me to tear off its leaves and dice them for my morning ramen.

But by acknowledging how much sacrifice it takes to allow for us to be typing or reading or otherwise reaping the pleasures of existence, I think it’s easier to maintain awe.  A sense of gratitude toward all that we’ve been given.  Most humans appreciate things more when we think they cost more.

We should appreciate the chance to be alive.  It costs an absurd amount for us to be here.

But, in the modern world, it’s possible to have a wonderful, rampantly hedonistic life as a vegan.  Why make our existence cost more when we don’t have to?  A bottle of wine tastes better when we’re told that it’s $45-dollar and not $5-dollar wine, but it won’t taste any better if you tell somebody “It’s $45-dollar wine, but you’ll have to pay $90 for it.”

Personally, I’d think it tasted worse, each sip with the savor of squander.

On the dangers of reading.

On the dangers of reading.

During most of human evolution, children died regularly.  In some cultures, the risk was so high that children weren’t named until they’d survived their second birthday.

But the advent of modern medicine – vaccines, antibiotics, sterile technique – has dramatically reduced childhood mortality.  Wealthy parents in the U.S. expect their children to survive.  And yet, this expectation can increase anxiety.  Families are smaller; children are less replaceable.  Parents pour so much of themselves into children’s early years that we’d be devastated if something went wrong.

And so modern parents hover.  Rather than letting children roam free, comforted by the thought that out of six kids, surely one will be fine, wealthy parents in the U.S. strive to control the development of their one or two offspring.

In the book On Immunity, Eula Biss describes how difficult it can be to relinquish that control.

CaptureI already practiced some intuitive toxicology before my pregnancy, but I became thoroughly immersed in it after my son was born.  As long as a child takes only breast milk, I discovered, one can enjoy the illusion of a closed system, a body that is not yet in dialogue with the impurities of farm and factory.  Caught up in the romance of the untainted body, I remember feeling agony when my son drank water for the first time.  “Unclean!  Unclean!” my mind screamed.

Because I didn’t breastfeed my child, I glossed over this passage when I first read it.  Even early on, I sometimes used water to dilute the milk that my partner pumped at work – when my kid was thirsty, I needed to offer something.

But I found myself thinking about this passage recently, when our eldest learned to read.  Our family loves books – we’ve probably read to our children for an hour or more each day, and they spend more time flipping through the pages on their own.

When I read to my kids, I reflexively alter texts.  In our version of James Marshall’s Fox on the Job, Fox had a bicycle accident while showing off for “his friends,” not “the girls.”  In Fox is Famous, a character bemoans the challenges of baton twirling by saying “I’m just not good at this yet,” that (unprinted) final word used to convey a growth mindset.

Go_dog_go_hat.jpgAnd our kids would probably be puzzled by Raquel D’Apice’s essay about Go Dog Go because the voices I’ve used while reading led them to assume that the pink poodle was a fashionable male asking a female friend for advice (“Well, maybe he doesn’t have a mirror at home,” I explained when N was curious, “Why does he keep asking that?”).

I could control the stereotypes that my children were fed.

But books are dangerous!  At the beginning of summer, our eldest learned how to read.  A week later, I hid all the Calvin and Hobbes.  She loves these!  So do I.  But four is too young to really understand concepts like “irony” or “anti-hero” – her behavior promptly tanked in mimicry of Calvin.

About a week after that, I hid the Peanuts.  And Garfield (“He shouldn’t kick Odie off the table, right?  Just like you shouldn’t have hit your sibling”).

She loves comics, but the only books we kept out were good, wholesome Mutts by vegan artist Patrick McDonnell.


And I hid others, like James Howe’s Howliday Inn (too scary – she could hardly sleep that night).  We look over the front-page headlines of our local newspaper before deciding whether it can be left on the table.

Like Viet Thanh Nguyen, I’ve felt a little sad to see my child venture off into the intellectual world of books without me.  I still worry what she’s ready for.

For much of human history, the paternal impulse to restrict access to books was blatantly evil.  The medieval Christian church was reticent to use local languages because then poor people could interpret religious precepts for themselves.  And the written word was considered exceptionally dangerous in the U.S.  It was illegal to teach literacy to the people who were being tortured on sweltering plantations.

I’d like to think that my motivation for wanting to sculpt my child’s library is more benign.  More akin, perhaps, to the scientists dismayed when the untrained general public dabble with misleadingly curated excerpts from research journals.

On Immunity documents the efforts that Eula Biss made to learn about vaccination.  She writes that:

vaccinationUnvaccinated children, a 2004 analysis of CDC data reveals, are more likely to be white, to have an older married mother with a college education, and to live in a household with an income of $75,000 or more – like my child.

The mothers I knew began debating whether or not to vaccinate our children against the novel influenza virus long before any vaccine became available to us.

Another mother said that her child had screamed frighteningly all night following her first vaccination and she would not risk another vaccination of any kind.

Although many of these women have received extensive schooling in the humanities, and clearly care deeply for their offspring, they are putting lives at risk, including those of their own children.

It’s possible to remain ignorant even after extensive schooling.

Cattle_herdWhen my son was six months old, at the peak of the H1N1 flu pandemic, another mother told me that she did not believe in herd immunity.  It was only a theory, she said, and one that applied mainly to cows.  That herd immunity was subject to belief had not yet occurred to me, though there is clearly something of the occult in the idea of an invisible cloak of protection cast over the entire population.

In Biss’s social circle, people doubted demonstrable principles.  Herd immunity, like the theory of evolution, is not only correct, it is the mathematical implication of uncontroversial assumptions.  In the case of herd immunity, that viral diseases are communicable and that severe symptoms tend to make a virus more contagious.  In the case of evolution, that the DNA replication process producing gametes has a non-zero error rate, that heritable DNA gives rise to traits, and that individuals with different traits might have different numbers of offspring (perhaps because one critter was eaten as a child, whereas the other survived).

But the people making ignorant decisions in Biss’s social circle certainly don’t think of themselves as ignorant.  After all, they’re trying their best to stay informed.  They aren’t scientists, but they read.  They look up information, ingest it as best they can, and try to make good decisions.

When people read (and spin) articles in scientific journals without putting forth the effort to understand what the data really mean, they create an incentive for scientists to hide their findings.  Sometimes there are caveats to the truth.  For instance, each year’s flu vaccine is often much less effective than other vaccinations.  Some years, the flu vaccine is dramatically ineffective.

I read that report – then went and got my vaccination.

If people are using papers like this as propaganda, though – trying, for whatever reason, to convince people not to get vaccinated (you want an evil conspiracy theory?  Vaccines are cheap, and they prevent deadly, expensive illnesses.  Are wealthy imbeciles recommending you forgo vaccination simply so that you’ll need to pay for more medical care?) – it stifles scientific discourse.

Every scientist knows that vaccines are helpful.  They write papers about the rare failures in order to make vaccines even more helpful.  But nobody wants to provide fodder for the ignoramuses to distort.

Roald Dahl wrote an open letter urging parents to have their children vaccinated.  He describes his own family’s tragedy – before a vaccine was developed, his seven-year-old daughter died of measles.  He thought she was getting better; he was wrong.

Are you feeling all right?” I asked her.

I feel all sleepy,” she said.

In an hour, she was unconscious.  In twelve hours, she was dead.

Incidentally, I dedicated two of my books to Olivia, the first was James and the Giant Peach.  That was when she was still alive.  The second was The BFG, dedicated to her memory after she had died from measles.  You will see her name at the beginning of each of these books.  And I know how happy she would be if only she could know that her death had helped to save a good deal of illness and death among other children.



On genetic inheritance and sexual assault.

On genetic inheritance and sexual assault.

How does evolution work?

Each child receives genetic information from its parents.  Some of this information conveys distinct traits.  And some of these traits increase the chance that an individual will have children of his or her own.  If those children are also good at having kids, the underlying genetic information will spread.

The DNA sequences that evolution enriches don’t necessarily make a creature better – in fact, they often accomplish the opposite.  A gene that made its bearer 10% happier would not spread through the population.  Happy people are less fearful and more likely to be die in tragic accidents.

800px-JH_Dolph_Cat_Mouse(Infection with Toxoplasma gondii seems to make mice happier.  The parasite produces a rate-limiting enzyme for dopamine synthesis to increase the chance that Toxoplasma-infected mice blithely stroll along and get eaten by a cat.)

All that evolution “wants” is for a gene’s bearer to have children who have children who have children, and so on.  This necessitates survival, yes – you can’t have kids if you’re dead, and in many species, orphaned children are less likely to ever have kids of their own.  But evolution doesn’t need a gene’s bearer to be clever – brainless starfish evolved from a bilaterally symmetric forebear that did have a brain.  Evolution doesn’t need a gene’s bearer to be nice – bullies seem to have plenty of children, and sexual assault is an instinctual mating strategy in many species, including ducks and orangutans.  Maybe humans, too.

So, who controls which genes are passed on?

In most species, whichever parent puts the most effort into raising children gets to choose.

prumIn The Evolution of Beauty, Richard Prum describes the experience of tropical birds, like manakins, who live in regions where food is plentiful.  The female parent raises children entirely on her own – males reside elsewhere in fraternal performance troupes.  And so the female birds have absolute say in deciding who will and will not fool around.  The females visit large numbers of males and decline most of their overtures.  Why should she settle for anything less than the absolute sexiest gentleman in the forest?  She’ll find him eventually, and since he never helps any of his children’s mothers with child-rearing, she knows he’ll be available.

Male smooth guardian frogs protect their fertilized eggs and young tadpoles.  Large choruses of females will surround and serenade each available male, hoping to sway his desire.  Since males do all the parenting, they are very selective.

That’s the usual system – you do the work, you get to choose.

It’s a nice idea.  After all, choice means the ensuing activity is consensual, and the opportunity to consent is sexy.

Unfortunately, in many species, others attempt to subvert mate choice.  You know – those ducks.  Orangutans.  Humans.

meanMyriam Gurba’s Mean is alternately comic and horrifying.  In a chapter titled “Omnipresence” (after the trauma, danger seems to be everywhere), Gurba writes:

A stranger chose me to rape.

There was no nepotism involved.

Basically, I got raped for real. (I’m being cheeky here.)

Stranger rape is like the Mona Lisa.

It’s exquisite, timeless, and archetypal.

It’s classic.  I can’t help but think of it as the Coca-Cola of sex crimes.


You never predict that rapists are lurking in the sun, sky, and trees.


In The Evolution of Beauty, Prum writes:

prumOf course, it has long been clear that sexual coercion and sexual violence are directly harmful to the well-being of female animals.  But the aesthetic perspective allows us to understand that sexual coercion also infringes upon their individual freedom of choice.  Once we recognize that coercion undermines individual sexual autonomy, we are led, inexorably, to the discovery that freedom of choice matters to animals. 

Sexual autonomy is not a mythical and poorly conceived legal concept invented by feminists and liberals.  Rather, sexual autonomy is an evolved feature of the societies of many sexual species.  As we have learned from ducks and other birds, when sexual autonomy is abridged or disrupted by coercion or violence, mate choice itself can provide the evolutionary leverage to assert and expand the freedom of choice.

Many of the trappings of human civilization exist solely to subvert mate choice.  Powerful males did not want human females to exercise sexual autonomy, because what if she picks someone else?  And so men made marriage, Biblical commandments against both adultery and thinking about adultery, and a propensity to murder (or, on contemporary U.S. playgrounds, heckle) loose women.

Human males wanted to control the flow of genetic information without doing the work of parenting.  Just like ducks, whose females evolved corkscrew-shaped vaginas because only those individuals with complicated genitalia could exercise free mate choice amidst generations of rape culture.

Rape culture isn’t specific to Homo sapiens, after all.  It’s a disease of any species in which those who don’t put in the work decide they ought to make choices for others – and nobody stops them.

(Humans do perpetrate more sexual violence than other species, especially violence against non-humans.  Interspecies sexual assault strikes most people as outlandish, unless it’s being done on our behalf.  Farms, puppy mills, and zoos are major assault factories.  We assent to forcible fertilization because it produces large-breasted chickens, cute puppies, and caged “wild” animals for our screaming children to ogle.)

Not all species rape.  In some, coalitions of females defend each other.  In others, males enforce fairness.  Those who believe in justice can punish interlopers, providing females with the right to choose.  Feminism isn’t the exclusive provenance of females.  Injustice hurts everyone, and anyone can feel aggrieved by it.

On Matthew Walker’s ‘Why We Sleep.’

On Matthew Walker’s ‘Why We Sleep.’

poemsjaildormWilliam Booker’s poem “Communion of the Saints” opens with,

It’s 6 a.m. in the Monroe County Jail,

I’ve been awake since breakfast,

which was served at 4:21 a.m. …

It took 3 minutes 25 seconds

to eat a tray of eggs, sausage, hash brown,

biscuit and jelly.  Then I lay back down

on my steel bunk and closed my eyes.

His eyes are closed, the thin jail blanket covers his head, but with bright fluorescent lights shining just a few feet from his face, he can’t fall back asleep.  He begins to ruminate: “what have I done?”  His mind is tormented by “visions of the outside that I don’t see anymore.”  This will be another hard day.

2088296214_th.jpgIn Why We Sleep, Matthew Walker describes numerous research studies showing the ways that we’re impaired when our sleep is disrupted.  The vast majority of people need at least 7.5 hours of sleep each night.  When sleep deprived – either by missing an entire night’s sleep in one go, or sleeping six or fewer hours a night for several days in a row – people have difficulty regulating their emotions, miss social cues, and struggle to learn new information.

Prolonged sleep deprivation is widely recognized as torture.  All animals will die if sleep deprived for too long, typically done in by sepsis: otherwise innocuous bacteria proliferate uncontrollably and poison the blood.  Less acute forms of sleep loss – consistently getting fewer than 7.5 hours per night – will ravage a person’s immune system and increase the risk of cancer.

When interrogators deprive people of sleep (yup, the United States is a member of the illustrious group of nations that still tortures people this way, alongside regimes in Iran, Iraq, Libya, Saudia Arabia, and the like) it becomes very easy to elicit false confessions.

In the former Israeli prime minister Menachem Begin’s memoir, White Nights: The Story of a Prisoner in Russia (which is quoted in Why We Sleep), he writes that when the KGB denied him and his fellow prisoners the opportunity to sleep,

DF-SC-85-11459I came across prisoners who signed what they were ordered to sign, only to get what their interrogator promised them.  He did not promise them their liberty.  He promised them – if they signed – uninterrupted sleep.

Inside the jail, the overhead fluorescent lights are not turned off until midnight.  At that time, it becomes easier – not easy, but easier – to fall asleep.  But the inmates will be jarred awake four hours later for breakfast.

Despite their chronic sleep deprivation, people in jail are expected to learn new habits; people who have self-medicated for the entirety of their adult lives with opiates or amphetamines are expected to find all new ways of living.  Sometimes their behaviors really were undesirable – robbery, domestic violence, neglecting children while blinkered on drugs.

But people struggle to learn new skills – sober living among them, although this was not directly assessed in the studies Walker cites – if their brains don’t undergo a large number of electroencephalogram-visible waves called “sleep spindles” during the final hours of sleep.  If a person sleeps for six or fewer hours each night, the brain never reaches this stage of sleep.

Wake someone up too early day after day, you stifle learning.

Veave_in_jailWrest them into fluorescent wakefulness each morning for a four a.m. breakfast, keep them basically sedentary because a dozen people are packed into a small cement room and the facility is too understaffed to give them “rec time,” constantly elevate their stress hormones by surrounding them with angry, potentially dangerous compatriots, and you ensure that they won’t sleep well.  In addition, chemical withdrawal wrecks havoc on people’s sleep cycles.  They stagger bleary-eyed through months or years inside.  They chug “cocoffala” – commissary instant coffee stirred into Coca-cola – hoping to feel some semblance of normalcy.  Instead, they get the jitters.

And then, finally, they’re set free – usually to probation, expected to follow more rules than the average citizen.

“I’m gonna be out next week,” a dude told me.

“Congratulations!  You’ll get family Christmas after all.”

“Eh, it’s not so great.  I’ll be back before New Years.”


“They say I gotta do probation two yearsI slip, they’re sending me to prison.”

“Can you do it?”

“Two years?  I’m not gonna make it two weeks.  Way I see it, I get out, I gotta call up Judge Diekhoff, tell her it’s been real and all, but we gotta start seeing other people.”

He would’ve struggled to change his life in the best of circumstances.  But he certainly couldn’t do it sleep deprived.

On Sci-Hub, the Napster of science.

On Sci-Hub, the Napster of science.

Here’s a story you’ve probably heard: the music industry was great until Napster came along and complete strangers could “share” their collections online and profits tanked.  Metallica went berserk suing their fans.  It was too late.  The industry has never been the same.napster

Sci-Hub has been called a Napster equivalent for scientific research papers, and the major publishing companies are suing to shut it down.  The neuroscience grad student who created it faces financial ruin.  The original website was quickly shuttered by a legal injunction, but the internet is a slippery place.  Now the same service is hosted outside U.S. jurisdiction.

[Note: between writing and posting this essay, Sci-Hub has lost another lawsuit requesting all such sites to be blocked by internet service providers.]

The outcomes of these lawsuits are a big deal.  Not just for the idealistic Kazakhstani grad student charged with millions in damages.  Academic publishers will do all they can to accentuate the parallels between Sci-Hub and Napster – and, look, nearly a quarter of my living relatives are professional musicians, so I realize how much damage was wrought by Napster’s culture of theft – but comparing research papers to pop songs is a rotten analogy.  Even if you’ve never wanted to read original research yet … even if you think – reasonably – that content producers should be paid, you should care about the open access movement.  Of which Sci-Hub is the most dramatic foray.

My own perspective changed after I did some ghostwriting for a pop medicine book.  Maybe you know the type: “Do you have SCARY DISEASE X?  It’ll get better if you take these nutritional supplements and do this type of yoga and buy these experimental home-use medical devices!”  Total hokum.  And yet, people buy these books.  So there I was, unhelpfully – quite possibly unethically – collaborating with a friend who’d been hired to ghostwrite a new one.

Central_core_disease_NADH_stainI read huge numbers of research papers and wrote chapters about treating this particular SCARY DISEASE with different foods, nutritional supplements, and off-label pharmaceuticals.  My sentences were riddled with un-truths.  The foods and drugs I described are exceedingly unlikely to benefit patients in any way.

Still, I found research papers purporting to have found benefits.  I dutifully described the results.  I focused on the sort of semi-farcical study that concludes, for instance, that cancer patients who drink sufficient quantities of green tea have reduced tumor growth, at which point newspapers announce that green tea is a “superfood” that cures cancer, at which point spurious claims get slathered all over the packaging.

Maybe nobody has written a paper (yet!) claiming that green tea ameliorates your particular SCARY DISEASE.  But there’s also turmeric, kale, fish oil, bittermelon, cranberries… I’m not sure any ingredient is so mundane that it won’t eventually be declared a superfood.  Toxoplasma gondii has been linked to schizophrenia, but low-level schizophrenia has been linked to creativity: will it be long before cat excrement is marketed as a superfood for budding artists?

cat-shit-2-flat-1.jpgAs it happens, enough people suffer from our book’s SCARY DISEASE that many low-quality studies exist.  I was able to write those chapters.  And then felt grim.  The things I’d written about food weren’t so bad, because although turmeric, coconut oil, and carpaccio won’t cure anybody, they won’t cause much harm either.  But the drugs?  They won’t help, and most have nasty side effects.

My words might mislead people into wasting money on unnecessary dietary supplements or, worse, causing serious damage with self-prescribed pharmaceuticals.  Patients might follow the book’s rotten advice instead of consulting with a trained medical professional.  I’d like to think that nobody would be foolish enough to trust that book – the ostensible author is probably even less qualified to have written that book than I am, because at least I have a Ph.D. in biochemistry from Stanford – but, based on the money being thrown around, somebody thinks it’ll sell.

And I helped.

Whoops.  Mea culpa, and all of that.

But I didn’t perpetrate my sins alone.  And I’m not just blaming the book’s publishers here.  After all, the spurious results I described came from real research papers, often written by professors at major universities, often published in legitimate scientific journals.

It’s crummy to concentrate all that slop in a slim pop medicine book, I agree, but isn’t it also crummy for all those spurious research papers to exist at all?

Maybe you’ve heard that various scientific fields suffer from a “replication crisis.”  There’s been coverage on John Oliver’s Last Week Tonight and in the New York Times about major failures in psychology and medicine.  Scientists write a paper claiming something happens, but that thing doesn’t happen in anyone else’s hands.  That’s if anyone even bothers to check.  Most of the time, nobody does.  Verifying someone else’s results won’t help researchers win grants, so it’s generally seen as a waste of time and money.

Still, the news coverage I’ve seen hasn’t stated the problem sufficiently bluntly.  Modern academic science is designed to be false.

This is tragic.  It’s part of why I chose not to stop working in the field.  I became a writer.  Of course, this led to my stint of ghostwriting, which… well, whoops.

Here’s how modern science works: most research is publishable only if it is “statistically significant.”  This means comparing any result to a “null hypothesis” – if you’re investigating the effect of green tea on cancer, the null hypothesis is simply “green tea does nothing” – then throwing out your results if you had more than a one in twenty chance to see what you did if the null hypothesis were true.

If you have a hundred patients, some of their tumors will shrink no matter what you do.  If you give everybody buckets of green tea and see the usual number of people improve, you shouldn’t claim that green tea saved them.

Here’s a graphic from Wikipedia to help:


Logical enough.  But bad.  Why?  Because cancer is a SCARY DISEASE.  Far more than twenty people are studying it.  If twenty scientists each decide to test whether green tea reduces tumors, the “one in twenty” statistical test means that somebody from that set of scientists will probably see an above-average number of patients improve.  When you’re dealing with random chance, there are always flukes.  If twenty researchers all decided to flip four coins in a row, somebody would probably see all four come up heads – doesn’t mean that researcher did anything special.

Or, did you hear the news that high folate might be correlated with autism?  This study probably sounds legitimate – the lead scientist is a professor at Johns Hopkins, after all – but the result is quite unlikely to be real.  That scientist hasn’t written about folate previously, so my best guess (this new study is currently unpublished) is that pregnant women were tested for many different biomarkers, things like folate, iron, testosterone, and more, and then tracked to see whose children would develop autism.  If the researchers tested the concentrations of twenty different nutrients and hormones, of course they’d see one that appeared to correlate with autism.

[Edit: these findings were recently published.  Indeed, the data appear rather unconvincing, and the measurements for folate were made after the fact, using blood samples – it’s quite possible that other data was gathered but excluded from the published version of the study.]

This is not science.  But if you neglect to mention how many biomarkers you studied, and you retroactively concoct a conspiracy theory-esque narrative explaining why you were concerned about folate, it can do a fine job of masquerading as science.  At least long enough to win the next grant.

Which means that, even though the results of many of these studies are false, they get published.  When somebody checks twenty nutrients, one might appear to cause autism.  When twenty scientists study green tea and cancer, somebody might get results suggesting green tea does work.  Even if it doesn’t do a thing.

In our current system, though, only the mistaken researcher’s results get published.  Nobody knows that there were twenty tests.  The nineteen other biomarkers that were measured get left out of the final paper.  The nineteen researchers who found that green tea does nothing don’t publish anything.  Showing that a food doesn’t cure cancer?  How mundane.  Nobody wants to read that; publishers don’t want it in their journals.  But the single spurious result showing that green tea is a tumor-busting superfood?  That is exciting.  That study lands in a fancy journal and gets described in even briefer, more flattering language in the popular press.  Soon big-name computer CEOs are guzzling green tea instead of risking surgery or chemo.

I generally assume that the conclusions of research studies using this type of statistical testing are false.  And there’s more.  Data are often presented misleadingly.  Plenty of scientists are willing to test a pet theory many ways and report only the approach that “works,” not necessarily because they want to lie to people, but because it’s so easy to rationalize why the test you tried first (and second, and third…) was not quite right.  I worked in many laboratories over a decade and there were often results that everybody in the lab knew weren’t true.  Both professors I worked under at Stanford published studies that I know weren’t done correctly.  Sadly, they know it too.

This subterfuge can be hard for outsiders to notice.  But sometimes the flaws are things that anybody could be taught to identify.  With just a little bit of guidance, anybody foolish enough to purchase the pop medicine book I worked on would be able to look up the original research papers and read them and realize that they’re garbage.

There’s a catch: most of those papers cost between twenty and thirty dollars a pop.  The chapters I wrote cite nearly a hundred articles.  I’d describe a few studies about the off-label use of this drug, a few about that one, on and on, “so that our readers feel empowered to make their own decisions instead of being held at the paternalistic mercy of their healthcare professionals.”  A noble goal.  But I’m not sure that recommending patients dabble with ineffectual, oft-risky alternative medicines is the best way to pursue it.  Especially when the book publisher was discussing revenue sharing agreements with sellers of some of the weird stuff we shilled.

So, those hundred citations?  You could spend three thousand dollars figuring out that the chapters I wrote are crap.  The situation is slowly getting better – the National Institute of Health has mandated that taxpayer-funded studies be made available after a year, but this doesn’t apply to anything published before 2008, and I’m not sure how keen sick patients will be to twiddle their thumbs for a year before learning the latest information about their diseases.  Plus, there are many granting organizations out there.  Researchers who get their money elsewhere aren’t bound by this requirement.  If somebody asks you, “Would you like to donate money to fight childhood cancer?” and you chip in a buck, you’re actually contributing to the problem.

Photo by diylibrarian on Flickr.

I was only able to write my chapters of that book because I live next to a big university.  I could stroll to the library and use their permissions to access the papers I’d need.  Sometimes, though, that wasn’t enough.  Each obscure journal, of which there are legion, can cost a university several thousand dollars a year for a subscription.  A few studies I cited were published in specialty journals too narrowly focused for Indiana University to subscribe, so I’d send an email to a buddy still working at Stanford and ask him to send me a copy.

If you get sick and worry yourself into looking for the truth, you’ll probably be out of luck.  Even doing your research at a big state university library might not be enough.

That’s if you keep your research legal.

Or you could search for the papers you need on Sci-Hub.  Then you’d just type the title, complete a CAPTCHA on a page with instructions in Cyrillic (on what was until recently http://www.sci-hub.cc, at least), and, bam!  You have it!  You can spend your thirty dollars on something else.  Food, maybe, or rent.

Of course, this means you are a thief.  The publisher didn’t get the thirty dollars they charge for access to a paper.  And those academic publishers would like for you to feel the same ethical qualms that we’re retraining people to feel when they pirate music or movies.  If you steal, content producers won’t be paid, they’ll starve, and we’ll staunch the flow of beautiful art to which we’ve become accustomed.

The comparison between Napster and Sci-Hub is a false analogy.  Slate correspondent Justin Peters described the perverse economics of academic publishing, in particular the inelastic demand – nobody reads research journals for fun.

With music and movies, purchasing legitimate access funds creators.  Not so in academia.  My laboratory had to pay a journal to publish my thesis work; this is standard practice.  It costs the authors a lot of money to publish a research article, and “content producers” only do it, as opposed to slapping their work up on a personal website for everyone to read free, because they need publication credits on their CVs to keep winning grants.

With music and movies, stealing electronic copies makes content producers sad.  With research articles, it makes them happy.

In fact, almost everyone believes research articles should be free.  At the European Union’s recent Competitiveness Council, the member states agreed that all scientific papers should be freely available by 2020 – these  are the governments whose enforcement is necessary to maintain the current copyright system!  The only people making statements in favor of the status quo are employed by the academic publishers themselves.  Their ideological positions may be swayed somewhat by the $2 billion plus profit margins major publishers are able to extract from their current racket.

Academic publishers would argue that they serve an important role as curators of the myriad discoveries made daily.  This doesn’t persuade me.  The “referees” they rely on to assess whether each study is sound are all unpaid volunteers.  Plus, if the journals were curating well, wouldn’t it have been harder for me to fill that pop medicine book with so much legitimate-looking crap?

Most importantly, by availing yourself of Sci-Hub’s pirated material, you the thief no longer live in ignorance.  With our current healthcare model, ignorance is deadly.  The United States is moving toward an a la carte method of delivering treatment, where sick people are expected to be knowledgeable, price-sensitive consumers rather than patients who place their trust in a physician.  Most sick people no longer have a primary care physician who knows much about their personal lives – instead, doctors are forced for financial reasons to join large corporate conglomerates.  Doctors try their best moment by moment, but they might never see someone a second time.  It’s more important than ever for patients to stay well-informed.

Unless Sci-Hub wins its lawsuit, you probably can’t afford to.

On correspondence.

On correspondence.

1280px-Plasmid_(english).svgDNA plasmids are small loops of genetic information that can change the behavior of bacteria.  With the right (wrong?) plasmids, you could take innocuous E. coli and make it very dangerous.

As best I could tell from a few minutes spent skimming the USPS documents describing “hazardous, restricted, and perishable mail,” it’s not actually illegal to ship plasmids.  Many biomedical researchers have long assumed that it was illegal, though.  Not that we didn’t do it.  But we always took steps to sneakily circumvent the laws we assumed existed.

Plasmids are dangerous, after all.  Why wouldn’t there be a law?

DNA is very stable.  Its stability is probably the whole reason it exists.  Most scientists assume that life began as self-replicating strands of a molecule called RNA, which is very similar to DNA except more prone to falling apart.  Each of our cells is like a tiny factory – proteins are the machines, RNA are blueprints, and DNA is a file cabinet.

(K says this analogy is no good because a file cabinet is an “archaic technology.”  I have several early drafts of my novel – plus the entire three-year run of Evil Dave vs. Regular Dave – in a file cabinet next to our bed.  I wonder, am I an archaic technology?)

DNA is so stable that it can be dried out and shipped across the country without coming to any harm.

To send plasmids through the mail, we would draw a circle on a piece of filter paper, dab a liquid solution of it onto the paper, then slip the sheet into the center of a catalog.  The catalog would look harmless, like junk mail.  Whomever received it would flip through, find the filter paper, cut out the circle, and immerse it in water.  Voila!  The plasmid is ready to change bacteria into something new!

The good people at the post office never notice.  The only snags are undergrads – a sophomore who was working with us happened to open the mail.  Our advisor asked later, “Where is that plasmid?  It was being sent by the ______ lab.”

“We got a package from them … but it was just an old catalog.  I recycled it.”




Pink_Elephants_on_Parade_Blotter_LSD_DumboAs it happens, numerous psychoactive chemicals can wig out a human brain at concentrations low enough to dissolve on paper.  Somebody sends a saturated sheet through the mail – you cut it out and, instead of using it to transform bacteria, you get high.

Apparently this works well with suboxone – which can be used either as a treatment for or a substitute for heroin – and the THC analogs marketed as K2, spice, or synthetic marijuana.  LSD has long been sold dissolved on blotter paper with goofy cartoons.

And so the Indiana Department of Corrections recently decided to ban all correspondence to inmates that isn’t handwritten on blue-lined white paper.  No greeting cards, no photocopies, no drawings.

Photo from Pat and Steve Cole / St. Basil Greek Orthodox Church in Chicago, IL.  I first saw it in the Indy Star.

A Chicago-based church sends greeting cards to many prisoners over the holidays.  This May, the entire batch of Easter cards they’d sent to Indiana prisoners were returned with a brief note explaining the new mail policy.  Even now, it’s unclear what the policy actually is.  The only regulations for offender correspondence available from the Indiana Department of Corrections are dated September, 2015.  Even these guidelines are vague, mentioning that all decisions are made on a case-by-case basis.

For the correspondence writing workshop I run, I often send printed materials.  Because these are being mailed on behalf of a non-profit corporation, they are supposed to go through – only private mail is supposed to be axed by the new policy.

Or so we’ve been told.

When our corporation sends letters or packages sometimes they go through, sometimes they do not.  The fate of each letter depends on which guard happens to be working in the mail room when it arrives, obviously.  The policy is sufficiently vague that each enforcer will interpret it differently.

A letter’s fate also seems to depend on the identity of the recipient.  If you receive a package while in prison, I’ve been told, the guards are supposed to open it in front of you, show it to you, and then have to either give it to you or explain why you can’t have it.  But with so many and such vague rules, the guards should always be able to think of a reason to bin it.  I’ve noticed that many of our packages that get returned for flimsy reasons were sent to people with long lists of disciplinary infractions.

The rich get richer.  And those who seem to need love most … get nothing.  If you’re disliked, they can sever you from the world.