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I’d like to teach scientists how to program, but that would be a lot easier to do if we had better software tools to offer them.

I’d like to teach undergraduates how to design better software tools, but that would be a lot easier to do if they knew more about software engineering.

I’d like to teach undergraduates an evidence-based introduction to software engineering, but that would be a lot easier to do if more people knew how to teach well.

I’d like to teach everyone how to teach well, but that would be a lot easier to do if people in power actually valued and rewarded good teaching.

I’d like to teach people who don’t have power where it comes from and how to take it, but—ah. OK, I guess I’ve found the yak I need to shave.

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17 days ago
Lansing, MI
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Davis, CA
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The Gospel According to Monty Python

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Easter looms on the holiday horizon! And as it falls on April Fool’s Day this year, my thoughts naturally turned to history’s greatest meeting point of religion and humor: Monty Python’s Life of Brian. But as I looked at the movie, and the controversy around it, I came to a startling realization.

Life of Brian can teach us how to live.

Unfortunately, a lot of the controversy around the film’s original release overshadowed its message. Because, unlike most Python movies, or most great comedies, it does have a message.

First, a caveat. I’m not in any way here to disparage the actual Gospels, Psalms, Shewings of Julian of Norwich, Ramayana, Hadith, or Deuteronomy, simply to point out a couple of valuable morals hidden within one of the greatest comedies of all time.


A Brief Historical Interlude

I assume, if you’re on this site, that you know plenty about Monty Python, but I will give you an incredibly quick recap in case you need it. Life of Brian was the Python’s third film. Their second film, Monty Python and the Holy Grail, was a huge hit. (Like, an enormous hit, and an incredibly important cultural moment, which always feels weird to me since I grew up later with Monty Python as a cult thing that nerds quoted instead of having actual conversations with each other.) The Pythons went on a world tour to promote Holy Grail, and at some point during a layover at an airport someone asked what their next project should be. Eric Idle said: “Jesus Christ: Lust for Glory”—either to the other Pythons or to the press, and after they stopped laughing they thought about it and decided to go ahead with it.

Life of Brian follows Brian, an unassuming young man growing up in 1st Century Judea, who tries to join an anti-Roman movement before accidentally becoming a messianic figure. After months of research they created what may be the single most accurate film about the 1st Century C.E. It leaves both The Last Temptation of Christ and The Passion of the Christ in the dust (which it promptly shakes it from its feet as it leaves town)—from the tense relationship with the Romans to the proliferation of philosophers and self-proclaimed messiahs to the fractured ideas of how to oppose occupation. The Pythons decided that Jesus himself was not really a good target for satire (they all liked his teachings too much) but the structures of religion were fair game, as were the various political factions that had sprung up and could mirror the ever-more-ridiculous splinter groups of the 1960s.


A Note On Jesus

Brian Colle as Jesus in The Life of Brian

Life of Brian is really explicitly not about Jesus. That gentleman does have two cameos, and the film is completely, almost weirdly reverent during each of them. I say weirdly because “reverence” isn’t a word that comes up much when discussing the Pythons. First, it’s made quite clear that the stable down the street from Brian’s—you know, the one with Jesus in it—is bathed in holy light, surrounded by angels and adoring shepherds, the whole shmear. The second cameo comes when Brian attends The Sermon on the Mount. Not only is the Sermon well-attended, but everyone approves of the few snatches of the speech they’re able to hear. He’s also referred to as a “bloody do-gooder” by a former leper who lost his revenue stream when Jesus healed him. If you somehow only learned about Jesus from Brian, you’d have an image of an objectively divine person who was a hugely popular public speaker, and who could actually heal people. This is a more orthodox version of Jesus than the one presented in Last Temptation.

Predictably, however, the film caused a firestorm of controversy when it came out.


The Pythons vs. the World

EMI, the film’s original producer, pulled out about two days before the Pythons were set to go to Tunisia to begin filming. Eric Idle mentioned this disaster to his friend George Harrison, who mortgaged his house to found Handmade Films, which would later produce such British classics as Mona LisaWithnail and I, and Lock, Stock and Two Smoking Barrels. They decided to premiere it in America first (give yourself  few minutes to laugh at the idea of America welcoming a religious satire with open arms) because, well, we have freedom of speech enshrined in the Constitution. What they didn’t expect was that, first, they had to make out wills before they came to New York just in case someone took a shot at them, and second, the people who protested the most vociferously were The New York Association of Rabbis, who were angry at the use of a prayer shawl in the stoning scene (seen above).

It’s worth noting that the film caused its own miracle, because members of different stripes of Judaism, Catholicism, Orthodoxy, and Protestantism all came together to picket film screenings. Despite Life of Brian being banned in some areas of the Bible Belt, the film ultimately benefited from the controversy, opening on 600 screens across the U.S. instead of the original 200, and earning more than expected.

The reason the Pythons were seriously worried comes down to a single person: Mary Whitehouse. She was a teacher who, during the 1950s, became obsessed with the idea that Britain’s moral character was failing, and that the only way to help was to send piles and piles of letters to the BBC to tell them not to allow people to use the word “bloody” on air. She developed two large groups, the “Clean Up TV Campaign,” which became the National Viewers’ And Listeners’ Association, and the Nationwide Festival of Light, which managed to wield some influence with high-level politicians, who in turn pressured the executives at the BBC to listen to her demands. Amongst these demands were: less war footage shown on TV, lest the British public become too pacifistic, less sex in general (surprise), and… less violence on Doctor Who?

Wait, Doctor Who?

Huh. Yes, she was angry about the “strangulation—by hand, by claw, by obscene vegetable matter” in “The Seeds of Doom.”


Whitehouse’s highest profile success came just two years before Brian’s premiere, when she sued the publishers of Gay News (exactly what it sounds like) over a poem called “The Love That Dares To Speak its Name.” The poem, a play on the phrase ‘the love that dare not speak its name’ from Oscar Wilde’s boyfriend’s poem “Two Loves,” upped the homoerotic stakes by centering on a Centurion who has pretty unholy feelings for Jesus. Whitehouse later told a reporter that “I simply had to protect Our Lord.” The specific thing they sued for was “blasphemous libel” (also exactly what it sounds like) and, in a trial where the prosecuting attorney told the court: “It may be said that this is a love poem—it is not, it is a poem about buggery,” and which only allowed two character witnesses for the defense rather than any experts on pornography or theology, the jury found for Whitehouse (10-2!) and Gay News was fined £1,000, while publisher Denis Lemon was fined £500 and received a nine-month suspended prison sentence. This was for a crime that had not been prosecuted since 1922.

So when someone in Brian’s crew leaked 16 pages of the script to the Festival of Light, the Pythons became considerably more nervous about their movie.

At first the group only encouraged Christians to pray for the failure of the film, but that soon turned into the usual letter writing campaigns and pressure on local councils. The Pythons decided to get out ahead of any backlash by agreeing to a televised debate with two prominent Christians on the chat show Friday Night, Saturday Morning.

The debate (embedded below) manages to be more painful than you might reasonably expect, and I urge everyone to watch it. Historically speaking, it’s an extraordinary document of a cultural moment that could have only happened in the 1970s. A pair of young-ish satirists speak earnestly about their intentions for the movie, telling the interviewer that, after devoting themselves to studying the Gospels, they all came to the conclusion that they couldn’t make fun of Jesus. It’s heartbreakingly sweet, given what comes next: Mervyn Stockwood, then Bishop of Southwark, clad in purple robes and fondling the largest crucifix I’ve ever seen anyone wear (and my great-aunt was an old-school nun) and Malcolm Muggeridge, a former editor of Punch who converted to Christianity in his late 60s—after a life of public debauchery (and who, along with Mary Whitehouse and a pair of British missionaries, was a cofounder of the Festival of Light)—proceed to badger and heckle the two Pythons, talking over them, insulting them, and refusing to engage in any true debate beyond wagging their fingers, while their moderator, Jesus Christ Superstar lyricist Tim Rice, sits back and watches rather than adding any points from his own experience working on a theologically thorny project.

The two older men vacillate wildly between mugging for the audience and talking over Cleese and Palin in horrifyingly condescending tones. It isn’t a debate, because the Bishop and Muggeridge aren’t listening, they’re simply pontificating on the state of the world and treating their opponents like naughty schoolboys who need to have their knuckles rapped (I’ll remind you that Cleese and Palin were pushing 40 at this point).¹ The Pythons did manage to get some excellent points in, with Cleese saying, “Four hundred years ago, we would have been burnt for this film. Now, I’m suggesting that we’ve made an advance”—but it became clear that the two Christian leaders were not there for either the five-minute argument, nor the full half-hour—they were just there to berate the Pythons.

The men’s biggest concern was with the ending–the musical chorus line that happens during Brian’s crucifixion. (Can I admit something? Just typing that line made me grin uncontrollably. Perhaps I’m not the best person to write about this, maybe my position is already too clear.) When I re-watched the debate and documentary for this post, I was reminded that both of them are really hung up on the crucifixion. They keep returning to that moment above all others in the film, with Muggeridge in particular expressing outrage that anyone could make a joke out of moment that has inspired the greatest works of Western art in the last 2,000 years. Stockwood further asks, “Why lampoon death? That sort of worried me. I don’t think one would make a farce about Auschwitz or of death … it was a shattering thing what happened to [Jesus]–crucifixion.”

Which, hm. First, what the Pythons are doing in their crucifixion scene is stripping the uniqueness from Brian.

He’s the one we’ve followed through the story, so even if he isn’t the Messiah, we’re still on his side, empathizing with him, rooting for him, so that when he’s captured and sentenced to crucifixion it’s legitimately terrible, but the way the Pythons deal with it is to show us a long line of condemned people all being processed with ruthless efficiency by Romans. It shows crucifixion as it most likely actually was: just another day in the Roman machine, exacting obedience through public torture. I have to wonder if that’s part of what the two men are objecting to. Because generally in the West, when you think of crucifixion there’s really only one Guy who comes to mind. Even when Kubrick made Spartacus, about a Roman pagan who was crucified about 40 years before Jesus’ most likely birthdate, he plays with imagery that was used in Christian art to evoke a sense of holy martyrdom around his character. (The “I am Spartacus” line is also played with in Life of Brian.) It became so iconic a part of Jesus’ story that according to Catholic lore, Peter specifically asked to be crucified upside down so as to not exactly replicate his Master’s execution.

So for Life of Brian to take that moment and turn it into a song-and-dance number isn’t just the usual Python silliness, but something much deeper… but I’ll come back to it in a minute.

The debate finally came to an end with the Bishop and Muggeridge shouting down all of the Pythons’ points. Tim Rice thanked the men for their time, but the Bishop managed to get the last word by snapping, “You’ll get your thirty pieces of silver, I’m quite sure,” while Rice murmured, “I hope that the film won’t shake anybody’s faith.” Then, in what is possibly the most whiplash-inducing moment of the decade, Rice cut to Paul Jones performing “Boom Boom (Out Go the Lights)” in which the singer announces his intent to stalk his ex-girlfriend and beat her into unconsciousness as soon as he finds her. Neither religious leader—still onstage for the performance—saw fit to decry this celebration of violence in the media. Not “shattering” enough, presumably.


A Brief History of Jesus on Film

Life of Brian was coming out of a very specific social milieu that has since shifted in ways that would make the film impossible to make now. In order to get that, allow me to give you an EXTREMELY abbreviated history of The Jesus Movie:

In the beginning was spectacle. The Silent era produced a couple of brief films of the Nativity, and some giant Cecil B. DeMille epics. In the fifties, we got Greatest Story Ever Told and King of Kings, both huge films with casts of thousands that used a syncretic approach to the New Testament. By cherry-picking some of the most famous scenes and quotes from each of the Gospels, and shoving them all into one film, they try to give you an idea of Jesus’ life, and an extremely sanitized retelling of the beginnings of Christianity. In the 1960s we got a stellar Jesus movie, Pier Paolo Pasolini’s Gospel According to St. Matthew, which does exactly what it says on the tin – the words and events of Matthew are depicted in black and white via a very tight, constantly moving shot. This film, with its minimalism and aggressively revolutionary Jesus, is often seen as a reaction to the big budget spectacles of Hollywood.

The 1970s created a perfect storm of liberalism, social awareness, musical theater, and the Jesus Freak movement, giving us Godspell and Jesus Christ Superstar, both of which were adapted into films in 1973. (Full disclosure: I am inordinately fond of both of these films.) JCS features a long-haired hippie Jesus, Black revolutionary Judas (who’s actually kind of the hero), and Native American Earth-mama Magdalene (who’s a main character rather than a hanger-on.) They sing, at length, about revolutionary movements, selling out, and megalomania. In Godspell we get a colorful troupe of hippies running amok in Manhattan and acting out a stripped-down version of Matthew and Luke like an evangelical Sesame Street gang. (Victor Garber, in a nod to the Christianization of the Jewish historical Jesus, wears a skintight Superman t-shirt throughout the film.) And even Franco Zeffirelli’s far more traditional Jesus of Nazareth (the one that used to get shown on TV at Easter each year) features a complicated, politically-motivated Judas.

In 1979, as people were becoming increasingly disillusioned with most of the revolutionary movements, Life of Brian arrives, able to use the Jesus story as a jumping-off point for their character Brian, and a wide-ranging satire that mocks organized religion, political movements, and Latin teachers with equal glee. Hilariously (?) Martin Scorsese ran into even more controversy, death threats, and low earnings when he made The Last Temptation of Christ (1988)—which, again, is based on a novel by Nikos Kazantzakis and at no point claims to be any kind of canonical gospel—while Mel Gibson’s The Passion of the Christ (2004) was released to praise from religious groups and boffo box office, despite drawing on the Book of Revelation, traditional Passion art, and, most notably, The Dolorous Passion of Our Lord Jesus Christ, a book describing the visions of 18th century nun Anne Catherine Emmerich, rather than sticking to Gospel-era canon.


But What About the New Testament?

So glad you asked. Talking about what sort of life the gospels want you to lead is fairly difficult. Since there are four of them, and they all have slightly different takes on the teachings that evolved into early Christianity, it can get overwhelming.

Here’s my best attempt:

  • Mark = put all of your moral affairs in order, as the end is nigh.
  • Matthew = are you poor, but good? Wretched, blighted, suffering, oppressed, but trying your best every day to be decent person? You’re probably going to be okay, kid. Wait, you want me to tell you how? I’m not going to tell you how, that would be cheating.
  • Luke = the same as above, but with slightly more flowery language.
  • John = put all your moral affairs in order – oh, neat, a miracle! Now keep putting them in order, because the end? Super nigh.

Depending on which gospel you’re reading, you’re supposed to be meek, compassionate, or radically empathetic—like, Betazoid level empathetic. In Matthewyou’re told to be perfect; throughout Mark, you’re told that there were people living then who would see “the kingdom of God come with power,” and in Luke that even the most prodigal of sons would be forgiven.

If you’ll allow me to delicately sidestep the non-canonical stuff because it would take too long, I’ll make my first point: even if you’re trying to align your life with those gospels (or with the more formal teaching of Catholicism, Orthodoxy, or most Protestantisms) Life of Brian actually adds an exciting addendum to those teachings. Because what is the true message of Brian? Be an individual. Be creative, think for yourself, don’t blindly follow people who claim to be in power—for won’t you both fall into the pit?

And above all, don’t be afraid to laugh at authority, especially when its name is Biggus Dickus.


Face the Curtain with a Bow

So, we must come, inevitably, to death. As I said, this seemed to be the sticking point for much of the controversy in the 1970s – far more than any lampooning of the origins of Christianity, it seemed to be the fact that anyone made a joke about crucifixion that was the issue.

Here’s why it’s important. At a certain point in an interview, Palin says that if they focused on the pain and torture of crucifixion it would have ruined the film, because making light of suffering wouldn’t work. But. They do give us the close-up of Graham Chapman’s face, in pain. They give us his hope when the Crack Suicide Squad shows up, and then how crushed and defeated he is when they just stab themselves. They do give us the moment of Mandy and Judith visiting him, and his utter desolation as they leave him. Is it the physical torture of Mel Gibson’s Jesus Chainsaw Massacre? No. Is it a hallucination of happiness that is then cruelly taken away, as in Last Temptation? No. It is a gradual breaking down of every scrap of hope that Brian has. Brian, who is not the Messiah (he’s a very naughty boy), who does not have a seat at Anyone’s right hand awaiting him. Brian, who, weirdly, expresses no religious beliefs of his own at all. Brian isn’t a grand historical figure, he’s just an everyday guy who wants to stand up to an oppressive regime. He could be anybody, he could be us, and we watch his life and hope be stripped away from him. And then Eric Idle leads him in a song. A death-defying, life-affirming, gleeful Fuck You of a song.

I still remember the first time I watched Holy Grail, but I don’t remember much of the first time I saw Life of Brian. What I remember of it is the ending. I remember watching that chorus line for the first time, and I remember feeling my mouth fall open as everyone began to sing. The idea that you could do that, that you could make something silly and joyful out of a tragedy—that tragedy, the axis mundi of the Western Canon—and just giggle. All bets are off if you can make fun of that. There are no limits to laughter, not even death. For me, this is the moment when Life of Brian joins that lineage of “greatest works of Western art.”


1. Interesting Side Notes: The televised debate between the Pythons and the Festival of Light was mocked to hilarious effect in a Not the Nine-O’Clock News sketch that aired a week later, ultimately asserting that Britain is a nation of Pythonists. You can watch the skit hereIn 2014 the BBC revisited the controversy with a surprisingly emotionally-resonant biopic called Holy Flying Circus that highlights the Pythons as decent men men trying to helm a fight for free speech without losing their senses of humor. I recommend it to all the Pythonists reading this.

Leah Schnelbach asks herself at least once a day: “WWBD?” Come call her a blasphemer on Twitter!

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24 days ago
Davis, CA
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Harry Potter and the Battle For Gun Control

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Emma Gonzalez, March for Our Lives

Voldemort shouts the Killing Curse over and over, and every time he expects that he will win.

And every time, Harry moves to disarm.

The March For Our Lives was this weekend. I didn’t bring a sign, just a body that could be counted in a tally. This isn’t for me, I thought to myself. It’s for the children around me. Children who are standing with parents and friends and doing their best to still smile and laugh and make the day triumphant. That’s what we expect of children. That they must continue to be children in spite of everything. They must maintain some semblance of innocence, no matter how callous the world has become.

These children were raised on dystopia, we are told. They are growing up with Resistance fighters in Star Wars and superheroes who avenge. With Katniss Everdeen’s love for her little sister. With Maze Runner and Divergent and Uglies and The Giver and Shatter Me and Unwind and… That quote from G.K. Chesterton comes up now and again: “Fairy tales do not tell children the dragons exist. Children already know that dragons exist. Fairy tales tell children the dragons can be killed.”

But sometimes the parallels are so exact that they’re not comforting in the least.

Emma Gonzalez, standing at the center of this movement with her friends, is reading Harry Potter. She has said that the fight between Dumbledore’s Army and Death Eaters at the Ministry of Magic is what they are going through right now. Their teachers are on their side, but the government isn’t interested. Their primary goal is to keep themselves and others safe, just as Harry taught his classmates do in the Room of Requirement.

We take solace in these cues, despite the terror in the source material. We shore each other up by casting ourselves as the heroes we love and recognize. Sometimes this is the only way to make nightmares bearable. I can see the lines, the broad strokes that get to these particular connections. But there are subtler ones, too. The subtler ones dig deeper, they hurt more. And when I see felt tip marker signs at these marches and rallies that invoke Dumbledore’s Army or Voldemort, these are the thoughts that preoccupy me:

When Harry is in the cemetery at Little Hangleton with Death Eaters surrounding him, Voldemort shouts “Avada Kedavra!” and he shouts “Expelliarmus!”

Harry lives.

Though I was the same age as Harry when the books were first published, my generation is not Harry’s anymore. In fact, I am the same age as Snape, as Lupin, as Sirius Black would have been when Harry started school. We didn’t have to contend with Grindelwald or a world of unrelenting global conflict—my parents’ generation were the ones who hid beneath their desks in preparation for nuclear devastation after fascism threatened civilization. My generation didn’t have to worry about that.

Instead, my generation remembers the fight over gun control as its ever-present reality. We were sitting at our desks as the Columbine massacre happened in 1999. We watched adults convince one another that it was an anomaly, that it could never happen a second time. We watched them blame video games and mental health. We saw the ridiculous and inadequate measures put in place that were meant to make us “safe.” Any attempt to speak up about it resulted in more blaming of video games, or sometimes music. White suburban parents really loved to chalk things up to Marilyn Manson back then.

None of the Parkland kids are mollified the way we were. And they aren’t content to be the only ones talking either. They invited a survivor of the Pulse Night Club Shooting to speak beside them. At the march, they had eleven-year-old Naomi Wadler talk to the crowd in D.C. in an attempt to recenter the conversation on those who need the platform most. Because this isn’t just a problem for students. As a part of the framework of our society, it goes far deeper than one school, or even every school. It is about communities going unaided and ignored while friends and children and loved ones are taken from them.

Wizarding society has much the same lesson to learn. From the “Mudbloods” and Muggles who can’t expect aid during Death Eater attacks, to the house-elves and werewolves and centaurs and goblins and giants and countless more who are meant to hold with the status quo and let things continue as they always have. Harry Potter is, in part, about giving voices to your allies, about knowing that you’re stronger together. It is about assuring a better future for everyone, not just the lucky few.


When Harry is being chased by Voldemort’s supporters as he escapes to the Tonks household, and comes across Stan Shunpike under the Imperius Curse, Harry shouts “Expelliarmus!”

Stan lives.


When I was nine years old, my fourth grade class went on a short field trip to visit some local business owners—to learn a little about entrepreneurship, I guess. We went to a flower shop and the chocolate shop next door to it. I bought a carnation with some pocket change, and the chocolates were heart-shaped and delicious. The woman who owned the flower shop loved her storefront and her neighborhood. It was her passion, the shop a perfect manifestation of that “American dream” I was always hearing about.

A month later, that same woman was dead; she and her daughter and sister had been gunned down in her store. Her daughter was a year younger than I was. Their shop was one block away from my apartment building.

No one really knew what to say, except “how depressing” or “how shocking.” I suppose it was, but I didn’t have the emotional vocabulary for that kind of tragedy. I buried my terror and did my best not to think about it—there was no better option presented. And the strange thing is, I think of that flower shop owner and her daughter often… yet I never say so out loud. What the hell does that even mean, that over two decades later it still seems forbidden to remember them?

At that march on Saturday I realized—I am not a member of Dumbledore’s Army. My generation, we’re the Order of the Phoenix, at best. Faces on a picture waving up at them. Some of us are gone and some of us remain. The most I can hope for is Remus Lupin status: Here are a few spells to combat evil. Here are the fights we tried and failed to win. Here is my unflagging support. Here is some chocolate; eat it, it helps, it really helps. Forgive me for not doing more, for not ending this before you had to lose your friends and hide in a dark room and listen to adults tell you how to feel instead of telling you how they will stop this from ever happening again.


During the Skirmish at Malfoy Manor, Hermione Granger is being tortured by Bellatrix Lestrange. Ron Weasley bursts into the room and shouts “Expelliarmus!” Harry physically disarms Draco. Dobby snaps Narcissa Malfoy’s wand from her grip with a flick of his hand.

Hermione lives.


These teenagers stand up and they hold rallies and they speak about what happened and they encourage others to do the same. A new narrative emerges; Parkland was staged, and these children are “paid crisis actors.” Perhaps the people who buy and perpetuate this narrative expect that all children should be too frightened to put their grief into words and actions. They share obviously photoshopped pictures of Gonzalez tearing up the Constitution, and the kids begin receiving threats for speaking out. These kids survived a massacre and are receiving death threats for asking for help. These brave young people are berated for standing up to their state senator in a town hall, for asking him if he will continue to take money from the nation’s most powerful gun lobby, if he will continue to side with the people trying to delegitimize the death of school kids, to delegitimize the fury that their friends and classmates righteously feel. Their detractors try to gaslight a nation into ignoring the very real danger that exists in the United States, not everywhere, but potentially anywhere.

Harry Potter tells Cornelius Fudge that Voldemort is back after the Triwizard Tournament, and the government and frightened adults make moves to discredit him. The Daily Prophet becomes a newspaper full of propaganda. The Boy Who Lived is framed as unstable and dishonest. He craves attention, or something much worse.

Harry takes Defense Against the Dark Arts with Dolores Umbridge in his fifth year, and he is done with keeping truth to himself. He speaks out in the middle of the class and refuses to be gaslit by a Ministry-appointed teacher. He tells everyone that he saw Cedric Diggory die and that he saw Voldemort return. Umbridge puts him in detention and forces him to carve out words on the back of his hand with the help of a sadistic magical tool, the same words over and over each evening:

I must not tell lies.

Harry isn’t lying, and nothing that Umbridge forces him to do will change that. But the scars from that quill are the only scars that Harry carries out of the war aside from the trademark lightning bolt assigned to him by Voldemort. To put it more succinctly: Aside from the initial attack enacted on Harry by the Dark Lord, the only other physical scars he bears for the rest of his life come at the behest of someone who wants to silence him.

Imagine that.

More guns, some say. That will solve the problem. A good guy with a gun can stop a bad one, they say. More smart gun owners will outweigh the ones who aren’t so great. Arm security guards. Arm teachers. Arm anyone who will remember to put the safety on. That will keep us safe.

We know this isn’t true. And more importantly, it’s incomprehensibly inhumane to expect others to meet violence with more violence when something so simple and sensible could prevent it all.

Just don’t give people an easy means of murder.

Harry gets dressed down in the final book for being easy to spot due to his signature move, the Disarming Charm. It’s not the first time Harry’s is given flak for it either; there are members of Dumbledore’s Army who are initially disbelieving about its usefulness. Remus Lupin eventually tries to tell Harry that it’s too dangerous to keep using the spell as his default because it makes him easy to spot. Effectively, calling to disarm makes him more of a target. Harry refuses to alter his preference: “I won’t blast people out of my way just because they’re there. That’s Voldemort’s job.”


Harry’s disarmament of Draco accidentally makes him master of the Elder Wand. When he fights Voldemort for the final time, he tells the Dark Lord that this has come to pass. But Voldemort believes he’s invulnerable and he shouts “Avada Kedavra!” and Harry shouts “Expelliarmus!”

Voldemort’s Killing Curse rebounds on him and he dies.

And everyone else lives.

And everyone here could, too.

Emily Asher-Perrin says #NeverAgain. You can read more of her work here and elsewhere.

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23 days ago
A deeper parallel - Voldemort is driven by a fear of death and the overarching moral of hp is you are going to die and you have to accept it or you'll turn into someone evil and ultimately very lonely and small. Much like those frantic and obsessive gun owners.
23 days ago
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24 days ago
Davis, CA
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That says it all about the new economy.

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25 days ago
Davis, CA
26 days ago
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Pydoit, snakemake, and workflows-as-applications

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Ever since Camille Scott, a grad student in the lab, developed the dammit transcriptome annotator, I've been intrigued by the design decision she made. Dammit runs a lot of other software, and Camille made the brilliant decision to avoid having dammit coordinate the execution of the dependent software itself - instead, she wrapped dammit around doit, a Python workflow library in Python.

doit, like other somewhat related systems such as make, makeflow, and snakemake, specifies workflows in a declarative manner: "to reach such and such a target result, you need these intermediate results", and so on - effectively laying out a directed acyclic graph of dependencies. As part of this, these systems coordinate the execution of the commands needed to produce all of the results. And, because they have insight into the structure of the dependencies, they can do clever things like execute them in parallel, on multiple nodes, restarting failed jobs, etc. etc.

By using doit, Camille was able to set up the dependency graph for the final annotated transcriptome and could then delegate the execution to the pydoit library. I myself have written many a spaghetti ball of shell commands in my time, and I was impressed with the separation of workflow logic from execution details achieved by dammit.

Now, I was all set to use doit myself for some projects, but in the meantime my lab fell under the sway of my other CS grad student, Luiz Irber, who had been slowly converting people in the lab over to snakemake without me really noticing.

It turns out that snakemake is much easier to dig into that doit, and between that and Luiz's wealth of knowledge (and inexorable persuasion), I ended up implementing the spacegraphcats application workflow in snakemake. And I've been pretty happy with that so far, after a few months of working with it. (More on spacegraphcats at some future point.)

Now, my lab does a lot of workflow-y stuff, because we're a bioinformatics group and bioinformatics is all about running other people's software on other people's data (which is about as much fun as it sounds, but we get by). So when yet another project, the dahak metagenomics project decided to use snakemake to specify its workflows, I requested a command-line interface in the same style as spacegraphcats - but with a few extra fun twists. I wrote up a quick example in 2018-snakemake-cli, which shows a simple way to combine workflow specification with parameter specification. From the 2018-snakemake-cli README, we use run to execute snakemake workflows:

./run <workflow_file> <parameters_file>


rm -f hello.txt
./run workflow-hello params-amy

creates hello.txt with "hello amy" in it, while

rm -f hello.txt
./run workflow-hello params-beth

creates hello.txt with "hello beth" in it.

Here, the workflow file workflow-hello.json specifies the target hello.txt, while the parameters file params-amy parameterizes the workflow with the name "amy".


rm -f goodbye.txt
./run workflow-goodbye params-beth

will put goodbye beth in goodbye.txt.

All workflows use the same set of Snakemake rules in Snakefile.

...and this is now being implemented for dahak in dahak-taco. (Warning: the dahak repos have become self aware and are replicating.)

Anyway, to bring this back around to the beginning:

I really like the idea of specifying workflows in a dedicated workflow engine, and then building an application around that. It means we don't have to worry about executing commands, we can tap into a large existing support community, we can make use of more powerful abstractions in our own code, and as the workflow system expands its functionality we can take advantage of it automatically. For example, snakemake seems to interface well with biocontainers and has support for Kubernetes which are both things we intend to make use of in the future. It also (in theory) makes the application much more extensible and hackable vs the traditional "I wrote my own shell command management foo" stuff I used to do.


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28 days ago
Davis, CA
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Olga Botvinnik - If you liked it, you should have put a Seq on it

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From: Lab for Data Intensive Biology
Duration: 55:22

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32 days ago
Davis, CA
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