They’re looking for additional support from past and current journal editors. I am, obviously, not even close to a journal editor (and neither are most of this blog’s readers, I’d wager.) But I’ve passed it along to a bunch of my former professors and PIs. And I’m posting it here. Which I guess is as much as I can do.

If I were to name a holy trinity for improving scientific research, it would be open access, study preregistration, and machine-and-human-readable sharing of the raw data behind experiments.

Open access facilitates review and critique by peers while also increasing the diversity and clarity of the literature itself, by allowing anyone – regardless of affiliation or socioeconomic status – to read, comment upon, translate, and even extend research.

Study preregistration holds researchers accountable for their experimental decisions and sharply decreases degrees of freedom, while also encouraging journals to focus on the quality of the methods rather than the sexiness of the results.

Sharing of raw data allows for more and better meta-analysis, which is an utterly vital part of research, especially in medicine. There are tens of millions of articles in the research literature, yet only a small percentage report enough information to enable meta-analysis. I’ve read studies – recent studies – that report null results with the simple phrase “was not significant”. The loss of this data is a tragedy.

We’re making small steps on each of these points, but we still have a long way to go.

I did not enjoy winning. I did not enjoy losing. And those were the only two options. When we won and knocked a team out of a tournament I’d see disappointment and tears on the other teams’ faces and feel sick to my stomach.

Now I play in the MIT league, which has no walks or strikeouts, where you give the other team some players if they’re short. This is how not-competitive the league is: once I pitched for another team who didn’t have enough players. They ordered pizza in the middle of the game, and walked out onto the field with gloves on one hand and slices in the other. “Do you want me to wait to pitch until you’re done?” I asked. They shook their heads and told me to go ahead.

We played that team again yesterday. At one point, they were up by ten runs. By the end, they were down by twelve. At no point did anyone really care.

This is my favorite team I’ve ever played on.

*

There are a lot of critiques to make about hackathons. They’re too developer-focused. They don’t address real needs. The projects created are often abandoned at the end of the weekend.

Those are reasonable critiques. But the one that bothers me the most is: they’re too competitive.

I had a lot of fun at the PyCon sprints. They were like hackathons in many ways – a bunch of developers sitting around tables working on projects for three days straight. But there were no “winners”, no prizes, and no two teams working separately on the same problem. If you had similar goals, you worked together and helped each other.

I’ve participated in exactly one actual hackathon. I drank some beer, met some people, and worked with a friend of mine on a small project that had nothing to do with the theme of the event. I don’t think anyone was particularly motivated by the prizes, but the organizers kept talking about them.

I left at about ten a.m. the next morning, right before the judging started.

*

I understand, intellectually, that competition can be a good thing. That for some people, it’s an incredible motivator – that it drives production and innovation and creativity.

Competition is the pulsing heart of capitalism – real capitalism, not the world of regulatory capture and corporate oligarchy we now inhabit – and yeah, I’m not the biggest cheerleader for any kind of capitalism, but I do see its value. I do think competition can be a healthy part of society.

But it can warp and corrode. In a competition, there must be a set of “win conditions” and those conditions are often different from the true goals of the competitors.

The goal of improving collective knowledge becomes the win condition of publishing papers in prestigious journals, and you get papers filled with errors, a research literature no one quite trusts.

The goal of tackling social problems and improving society becomes the win condition of securing funding, and you get activists focusing more on the needs of donors than the needs of their communities.

The goal of governing wisely and well becomes the win condition of amassing enough money to outspend your opponents, and you get politicians beholden to the rich.

I’m not saying we ought get rid of competition in these circumstances. Perhaps it’s enough to re-evaluate the win conditions, to re-align them with our goals. I don’t want to discount dynamics that have worked in major ways, just because the thought of participating in these systems – taking the spot of another promising researcher in a graduate school program, using funds that could have gone to another project or non-profit, defeating someone who sincerely wanted to serve their country – makes my heart ache.

But it’s at least worth considering that none of these things have to be a competition.

*

I play a lot of board games.

I like the cooperative games better than the competitive ones, of course, but I still enjoy the latter. The key for me is finding a group to play with who don’t take it too seriously. There was a guy in my old board game group who used to swear and get upset when he was losing. I felt bad every time I beat him. I felt bad every time I played him – because he made winning and losing a thing.

I think that games are good for me. I get to practice being competitive. But when they get too competitive, and I find myself reacting, I think – if a board game does this to me, how am I supposed to handle the real world? I think, Jesus Christ, Shauna, you are too damn soft-hearted.

There’s irony in that sentence, though. And there are worse things than compassion.

*

To compete is to possibly lose. To potentially fail.

My dislike of competition is more than just aversion to beating others. It’s also a fear of failure. I’ll admit to that.

So I admire competitors. I admire their bravery, their vulnerability.

But there is a bravery and vulnerability in cooperating, too. In working with others to find critique constructively, to find compromises. In trusting that others are committed to your shared project. In acquiescing to someone else’s choices, someone else’s vision, and hoping that they’re right, that your work won’t come tumbling down around you. You can definitely fail when cooperating.

But when you fail, you fail together. And when you succeed, you succeed together. You don’t have to shut off your empathy in order to enjoy your successes.

That’s how I want to work, to play, to live. Never shutting off my empathy. It’s hard, because competition is so much of our culture, so rooted in our heritage, our biology. But so is cooperation. And that’s the part that I choose to embrace.

Ever since I first heard of Victoria Woodhull about a year ago, I’ve been meaning to read the weekly newspaper that she put out with her sister, Tennessee Claflin, from 1870 to 1877. I found a library that claimed to have the complete collection in microform, so I made my way over there this week.

Unfortunately, they only had three of the 7-8 years of issues. I also, rather naively, though that the microform would be in good enough shape to apply OCR once I digitized it. I have yet to find an OCR tool that recognizes any words at all from these files.

Although I had hoped to scan, digitize, and post the entirety of the collection, I was only able to copy five full issues. The poor quality of the microform meant I had to scan and re-scan the individual pages, and even then some pages are only marginally readable. At a certain point I switched to skimming, and made copies of nine excerpts of varying sizes.

Still, what I accomplished was better than nothing. I’m throwing what I’ve got up on github – anyone who wants to can upload copies of additional issues, try their hand at more sophisticated OCR techniques, or do some transcription. I plan on adding to the repository over time.

In the mean time, here are some pieces that I’ve transcribed.

In the May 23rd, 1874 issue, from an excerpt titled ‘The Financial Problem’:

But what, at bottom, is really the underlying question involved in the present controversy? We hear a great deal said and a great deal written about the “well known” and “well established principles of finance.” We deny that there are any principles involved in any part of the financial question as it is now being discussed. The questions that are agitated are purely matters of policy. There is no principle in the proposition that the gold dollar is the true monetary standard. It is, on the contrary, the most arbitrary assumption possible to think of, having no conceivable basis in principle. It is a financial dogma as unsupported by any natural reason of fact as the now long since exploded dogma of theology. And it was invented for the same purposes that these dogmas were instituted for – to enslave the masses of the people, and it has succeeded industrially even more completely than they ever did religiously.

A short note, titled ‘What is a free paper?’, from April 25th, 1874:

There seems to be a queer idea among a queer set of people as to what constitutes a free paper. This class imagines that is can send in manuscript enough every week to fill two papers, and if it is not published, then the paper loses its character of freedom. It also pretends to think it can write articles fillwed with personal abuse, having no relation whatever to principle, but merely a vent of personal spleen, and if they are not inserted, then the freedom of the paper falls. We publish such an article this week, in order to illustrate what we mean; we refer to the communication on page 6 relative to Spiritual matters in Springfield, Mass. In the article to which this pretends to be a reply, there wasn’t a line to warrant the personal language of this. We utterly deprecate all such discussion, and permit this to be published to give formal notice to all whom it may concern, that from this time hence, we shall refuse to permit such articles to appear in the WEEKLY. This constitutes no part of the meaning of a free paper as understood by us.

This relates specifically and only to the publication of articles which principles, ideas and methods are discussed. Such articles will always be regarded as entitled to publication, but we cannot promise to insert everybody’s writings. From what we receive we must select such a variety as will, in our judgment, conduce most to the advance of reform, and from such as are treated in the most concise and forcible manner. Others may pretend to know more about our motives in making selections than we do, but until we are convinced that they do, we shall continue to act as heretofore, even if there must be another paper started to accomodate their injured dignity and immense importance. It’s our opinion that a soldier who will attempt to blow up the arsenal because his plan of conducting the campaign is ignored, is a traitor at heart to the cause.

And finally, from a September 27th, 1873 article called ‘The Scare-crows of Sexual Slavery’:

A single question will, however, show the absurdity of the theory of ownership. If parents own their children, how does it come that they ever lose their title, as they do at adult age; or again, and still more forcibly, if the title of children is in their parents, how is it that society, by its laws, claims them when, before adult age, the commit some crime, or still again, to whom is this ownership transferred when the parents die, and again, how is it that society compels the education of children? if they belong to their parents, what right has society to meddle? Answer these and then say if you can that children do not belong to society.

It is well known that, as civilization progresses and education becomes more a question of public interest, society demands more and more the conduct of the instruction of children. Public schools are now imperative, where, but a hundred years ago, there was no such system. Compulsory education is already adopted in some States and is being seriously considered as a national measure. It is but one step beyond compulsory education to the complete charge of children. If society have the right to say how and how much a child shall be educated mentally, it certainly has the right, also, to say what the other processes of education shall be.

Indeed, it is more than a right. It is a duty that society owes to those whom it is to make amenable to its regulations, that they shall have the best possible preparation to assume the insticts and the responsibilities of citizenship and equals, and still more a duty, that all children should become citizens, having received equal opportunities of preparation, so that no man, by his superior culture, shall be able to enslave others of less acquirements, either industrially, intellectually, or in any other manner whatever. Who shall dare say, if all children should be reared according to the theory of M Godin’s Industrial Palace, at Guise, France, that they would not be better men and woman than those who have been reared under our present theory of parental ownership?

What will become of the children? Again, what does become of them? One half of all children cut off by death before the age of five years – a commentary on the pretended anxiety for children that seems more like a horrible tragedy. Think of it, mothers! fathers! reformers! One half of all children dying before they reach five years of age – victims of our present social system, f the prevailing ignorance of the science of sexuality and the needs of the houng, and of the theory of parental ownership! The world cannot afford this terrible loss. When a ship founders at sea, with the loss of a few hundred lives, the whole country is aroused over the horror, but it sleeps quietly over the fact double that number of children – babes, almost – fall victim daily to the fell destroyers, ignorance and superstition and false social customs.

It’s been a little while since I’ve updated here. I’ve been posting regularly at the OpenHatch blog, and on my MetaScience tumblr, and I’ve been busy with a pack of things. Probably the most useful to mention is the Boston Civic Expo, which I’m co-organizing. It’s on Friday, May 31st. If you’re interested in government transparency and in using technology to improve government and communities, you should come.

& Recommendations

A friend asked me the other day for my top science fiction recommendations, and I realized I’d never posted them here. Let’s rectify that.

1.

photo by Daniel Wabyick, courtesy Wikimedia Commons, cc-by-2.0

Contact, by Carl Sagan, is probably my favorite science fiction novel, and one of my favorite books period. Many authors get so caught up describing future tech or alien civilization that they forget to write compelling main characters, but Contact’s Ellie Arroway is the heart of the story: brilliant, stubborn, kind, self-righteous, lonely, and deeply curious. She elevates the plot – a well-told, innovative take on first contact – into something unforgettable.

2.

photo by Christopher Michel, courtesy Wikimedia Commons, cc-by-2.0

Hyperion, and its sequels Fall of Hyperion, Endymion, and Rise of Endymion, by Dan Simmons, are gorgeous, ambitious novels. The first book, which is my favorite, tells six intertwined short stories – the tales of six pilgrims on their way to the Time Tombs, on the planet Hyperion. The Time Tombs are guarded by the Shrike, an enigmatic, half-mechanical being, and legend says that it kills all pilgrims save one, to whom it will grant a single wish. If that premise doesn’t hook you, I’m not sure what will. Simmons is endlessly inventive, and a beautiful craftsman of worlds, characters, and sentences.

3.

a picture of the book cover, courtesy of the New Yorker

On any given day I will list a different story of Ursula le Guin’s as her best. Sometimes it’s the more fantastical Lathe of Heaven, or the more political The Dispossessed, and one can make strong arguments for many of her short story collections. (I’ve written about The Ones Who Walk Away From Omelas on this blog before.) But today, I’m going with The Left Hand of Darkness, a book told by an envoy to a world without seasons or genders. It’s an exploration of a culture without duality, and the title comes from a poem/proverb of that culture: “Light is the left hand of darkness / and darkness the right hand of light.”

Honorable mentions: Do Androids Dream of Electric Sheep? by Philip K Dick; Flatland: a Romance of Many Dimensions by Edwin Abbott; The Handmaid’s Tale by Margaret Atwood; and Sum: Forty Tales from the Afterlives by David Eagleman.

It started with this beauty:

It makes the link between sine waves, the interior angles of triangles, and the unit circle so intuitive it’s hypnotic.

My favorite source for these is the tumblr of a physics undergraduate named Lucas who frequently uploads his creations to wikipedia:

A visualization of how Eigenvectors are transformed, yet keep their direction.

A visualization of Reimann integration, showing progressively better estimations of area under the curve.

(Also delightful, but not a math gif, is his series of videos visualizing pitch class in classical music as a spiral.)

From elsewhere:

Outtakes from the game of life.

A visualization of the tautochrone problem.

And finally, the gif a friend posted to facebook, which reminded me how much I love these:

If you know of others, please share!

More low quality cell phone pictures below the fold.

Many oreos were sacrificed to make this cake.

May helped decorate *and* helped eat. She’s a giver.

People actually working.

Raised beds? Oh, I thought you said ‘raise the dead’!

We were talking about the documentary when a man sitting next to Adelaida interrupted us. Sorry for eavesdropping, he said, but he was curious – his son had recently gotten accepted into MIT, but he couldn’t get his daughter interested in computer science. How could he encourage her?

The only response that seemed reasonable was: well, maybe your daughter’s just not into computing.

He then asked a much more answerable question. He ran a software startup, and he’d just hired his second female engineer. How could he make his company more welcoming to women?

Afterwards, Adelaida complimented my response. She asked if she could use it when asked similar questions, to which I said, of course.

So. In case anyone else finds it useful, here is how I answer the “Women In Tech” question – Three Minutes Before The Next Stop Edition.

Are you familiar with the concept of the leaky pipeline?

The answer is almost always no, so I explain:

The leaky pipeline is a way of viewing the path that people take to success in their field. The idea is that women experience many ‘leaks’ along the way, and each leak decreases the amount of women who ultimately succeed. These leaks happen everywhere, and so there’s no one solution – instead, there’s a lot of individual patches to be made.

What I like about the leaky pipeline metaphor is that it allows me to pick and choose a few things to talk about without suggesting that I’m providing a comprehensive answer. Also, I think it’s pretty accurate, for a metaphor.

Because this man was the head of a startup, I focused on the leaks he could most directly impact.

Here are some things you can think about.

Also, make sure you respect all of your employees’ work/life balance. Because women on average spend twice as much time doing housework and twice as much time doing childcare as men, women have less ability to sacrifice their weekends and evenings for your company. Creating a company culture with constant pressure to work hurts everyone – but especially women.

Obviously I wasn’t able to cite individual studies – my ability to speak on the fly isn’t that good! – but that’s the gist of it.

I wouldn’t say I have a phobia of flying, because a phobia is supposed to impair your functioning, and while some people might say that taking a twelve hour greyhound bus down the eastern seaboard when you can afford to fly is dysfunctional, I prefer to think of it as character building. And when there’s no way to avoid flying, I do it. Like this past month, when I flew to California and then to Florida. I took four flights – six, if you count connecting flights.

To calm my anxiety, I do two things. I eat outrageous amounts of gummy bears, which are my favorite comfort food. And I read novels. I try to find the most engrossing, pulpy novels I can. I read five novels over my four flights, but unfortunately, none were as compelling as I hoped.

Stars In My Pocket Like Grains of Sand was a beautiful book – full of deep world building and casual lyricism – but the wrong kind of book to read in flight. Delaney, the author, does some very interesting things with gender and sexuality, as well as with family structures. But the central narrative is rambling, detached, and not particularly moving. It’s a good book, but not a good story, if that makes sense.

The Forever War I found unremarkable. The writing is tight, the scene-setting is well done though not especially original, and the main character is sympathetic even as he does some pretty unsympathetic things. But I think that in the end, this is more of a war novel with a science fiction aesthetic than the reverse. And I’m not a huge fan of war novels. Though I’m a pretty voracious reader of non-fiction accounts of war – I prefer my stories of horrific violence to be as non-narrative and non-romanticized as possible. So this book didn’t work for me, but for a different kind of reader I imagine it very much would.

At this point, I switched out of the sci-fi genre and into contemporary fiction, in the hope that it would be more satisfying.

Saturday takes place over the course of a single day – a Saturday, of course. Almost necessarily, the book is full of digressions – memories and self-reflections and daydreams of the main character. It was an interesting way to approach a story, and it resonated very well with the events of the book, during which the main character’s intellectualism and remoteness is a source of conflict. But it was hard to get into. There are only a few moments throughout the day in which anything is at stake, and even those moments are dragged down by the continual focus on the main character’s interior world.

Summerland is less experimental/speculative than the other novels, and I picked it off the shelves of an airport news stand precisely for this reason. The story revolves around a set of three families dealing with the aftermath of a car accident in which one child was killed and another permanently injured. While it’s easy to sympathize with the characters’ pain, I don’t think the author builds very interesting characters. The only two which stuck out for me – the teenage Demeter, who helped cause the accident, and depressed Ava, the mother of the boyfriend of the deceased character – were treated pretty poorly by the narrative. It didn’t help that Demeter, the only fat character, was portrayed as unpopular, self-loathing, and constantly eating. And the ending of the novel was a bit trite. This was probably my least favorite of the books I read.

Finally, The Shadow of the Wind, a book which I’ve heard good things about but which ultimately fell flat for me. I enjoy a murder mystery as much as anyone else, but there’s something self-consciously literary about this book that kept me constantly aware that I was reading a piece of fiction. It seemed, in its content and ambitions and historical setting, like an inferior version of The Name of the Rose (which I thought was incredible. See, I do like books!)

So, there you have it. Four half-recommendations and a non-recommendation. I think next time I fly, I’ll make sure to do my research and bring some better books with me.

Some sample output:

“Contraception” – Democrats

“Contraception” – Republicans

“Gun” – Democrats

“Gun” – Republicans

There are apparently other word cloud generators which can compare texts directly and emphasize differences, which might have been better for this exercise, but it’s still pretty cool.

Code is here. Non-coders (or lazy coders who don’t want to clone & try themselves) should feel free to request searches.

And thanks to the good folks on #bostonpython for their help debugging.

The conference itself was excellent, although more than a few of the talks went over my head. Thankfully PyCon puts all their videos online, so I’ll be able to re-watch at my own speed, looking up references and concepts I don’t understand. My favorite talk, Awesome Big Data Algorithms, is for some reason not there, but you can find it on the speaker’s website. While you’re there check out Software Carpentry, an organization the speaker helps run, which teaches programming skills to scientists. There’s a bootcamp in Boston coming up in a few months.

After the conference I sprinted with the Center for Open Science. I didn’t get very much accomplished, since I was also helping out with the OpenHatch sprint and since I spent a lot of time dealing with hardware issues. (Guess what? I’ve got a new computer!) But I was able to test out a few javascript frameworks for the site, and I wrote some demos showing the functionality of my favorite one. And now when someone asks me, “What did you do at PyCon?” I can answer, “Learned how to program in Javascript!”

Skipping back to Sunday, which had a job fair in the morning. At the encouragement of some friends, I decided to go to each of the booths and ask if they offered part time positions (the only type of position I’m currently interested in.) All but one company said they didn’t. The exception was a small, new start up that shrugged and said they’d never considered it. There were a variety of different reasons cited: the cost of health benefits; difficulty evaluating programmers’ work; company loyalty; company culture; difficulty maintaining good communication between part timers and their full-time coworkers and managers.

I had a long conversation with a representative from Twitter about how many of those reasons are valid and inherent and inescapable – and how many could be handled by good management. The representative – also a manager – said I’d given him a lot to think about, which was maybe bull, but he seemed sincere. On the flip side, one not-to-be-named company admitted that they were looking for people to work time and a half – not half time. Which is so frustrating to hear. I’d love to work as a developer but not at the price of the volunteer work and side projects that are so meaningful to me. Not to mention how difficult it would be to have a family. The casual expectation of time and a half (a friend referred to his 50-hour work week as “light”) can’t be helping to retain women developers – or male developers who want to buck the national trend and do more than half the amount of housework that women do.

And, speaking of sexism in the tech industry – and oh! How sad is it that I can segue with “speaking of sexism in the tech industry”…

I can’t post about PyCon and not say that I’m pretty furious on behalf of Adria Richards. I’m not mad at the PyCon organizers, who I think handled the situation pretty well, or at the original jokers. Their comments were tame and the response of the person who was fired was more empathetic and reasonable than I expected. No, I’m furious at the many members of the tech community who have decided to throw sexist and racist insults Adria’s way, including rape and death threats. Those are the people who deserve to have been fired – not Adria. The next time somebody asks, “Where are all the women in tech?” I hope they’ll at least consider the possible answers: “Fired for speaking out about an uncomfortable situation” or “Being told they should get raped on Hacker News and Facebook.”