Is the Open Science Revolution For Real?

Monty Python’s rebels ponder all they must replace if they kill the Romans

The researcher rebellion against the closed research-and-publishing system, tallied most explicitly in a petition boycotting publisher Elsevier, continues to expand. (The Economist covers it here, and I covered the complaints last year in a feature.) The big question, of course, is whether this noisy riot will engender something like a real revolution. Will it replace the old regime with a new?

That will be depend on many things, but a key will be the construction of a replacement model for the traditional academic publishing system that so frustrates open-science advocates. As studious rebels know, a key part of a successful revolution is building an alternate set of institutions and services  — an alternate infrastructure — to offer people as and after you topple the regime: Give the oppressed good schools, healthcare, and clean water, the thinking goes, and you win their hearts and minds even as you learn to govern.How well are the open-science revolutionaries doing on that front? To replace the traditional publishing system, they need to provide alternatives to its main functions. Those functions, as I described in my feature Free Science, One Paper at a Time, are:

Editing  & review —  making sure a paper is logical and intelligible; also assessing its value and significance. Review has traditionally been formal peer review.

publication/distribution — getting the thing out there so people can read it

credit/reputation — ensuring that the author or authors get credit for the work

archiving – making the work available to future researchers.

In the current system, the journal system bundles all these functions into the paper: The journal edits the paper and puts it through peer review; publishes it in print and online (usually requiring payment, a key complaint); provides a formalized citation that the authors can put on their resumes and wave around at tenure or job application time; and keeps the work available in print and online so future scholars can hopefully find and use it.

This system’s strength lies partly in its convenience and familiarity: everyone knows how this works, and knows where to go to try to publish or find things or see how many papers a research has produced. Major downsides include inefficiency and  the fact that paywalls prevent more thorough distribution and availability to future scholars. (See my feature for more detail on that.)

What are the rebels offering to replace that system? By casting around the last couple days, I’ve assembled a list of tools created by the open-science community that seek to replace or amend the various parts of the conventional journal system. You can skip the indented text here if you don’t want the details. In any case,  together they show that the rebels (to indulge my metaphor) have gone a long way to creating the alternate infrastructure.

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Tortoises Hump & Fingers Freeze As Open Science Catches Fire – January’s Best at Neuron Culture

Galapagos making more Galapagos, by JupiterSSJ4

Open science stole the show in January, with evolution, frostbite, and PTSD hysteria following. I’m throwing in tortoise sex for feel-good factor.

Congress Considers Paywalling Science You Already Paid For

Should you be able to read research you’ve helped to fund? A few years ago, Congress decided this was a good idea, and approved an access policy that makes most taxpayer-funded research freely available online within 12 months of publication. This modest step toward open access — which, as I’vewritten before, is vital to healthy science and science policy — has proven a huge boon to researchers and also to those of us who write about science, while leaving most publisher profits quite healthy.

 Congress didn’t think so, though; at the behest of campaign contributors, they sought to kill this policy. It backfired.

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Of Mothers, Lovers, & Strangers: Valentine’s Day Drinks & Book Talk, NYC

Want to talk of books, lovers, and mothers? Of course you do.

On February 14, at 6:30 p.m., at Melville House in Brooklyn, fellow Atavist author Cris Beam, Wired and New York Times Magazine contributor Clive Thompson and I will be talking about memoir in the digital age — and Cris Beam’s Atavist hit Mother, Stranger and my own My Mother’s Lover. From the program:

What is the future for memoir in the digital age? Kids are replacing parents as the true family archivists, posting photos, drawings, diaries, and video: the narratives of the young are dominating those of the rest of the family online everyday.

As more people tell their own stories through Facebook, YouTube and other social media, is the memoir an obsolete medium? Can “e-memoirs” mark a rebirth of the form? What does this new kind of personal storytelling mean for how families are conceived and our histories remembered? Is the digital space not the end of memory, but the end of forgetting? The Atavist is bringing together two of its own memoirists, Cris Beam and David Dobbs, along with New York Times Magazine and Wired contributor Clive Thompson, for a night of discussion and drinks, moderated by Alissa Quart, senior editor of The Atavist.

 We’ll also talk about the ebook and longform innovation that is The Atavist — a small guerilla outfit that has figured out how to let writers write short books they couldn’t likely publish otherwise and, with luck, create some hits. My Mother’s Lover, which describes my excavation of my mother’s secret WWII affair, shot into the top 20 of all Kindle books when it launched last May and has remained in the top 25 Kindle Singles ever since. Stranger, Mother debuted this week in the top 10 Kindle Singles. We’ll discuss these tales and the stories behind writing, producing, and presenting them on the Atavist’s innovative platform. Atavist co-founder and editor Evan Ratliff  will also be on hand to discuss the e-publishing system the company has created, which the company will soon release for general use.

Drinks and chatter begin at 630; at 7 we’ll begin an hour or so of more structured conversation, then return to informal hobbing, nodding, and gobbling. We’d love to see you. Tell your friends.  Location and directions below. If you would, please quickly RSVP, so they’ll be all ready for you.

Hope to see you there.

145 Plymouth St, Brooklyn, NY 11201

Melville House Books » The Melville House Bookstore

145 Plymouth St

Brooklyn, NY 11201

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Subway: High St


Why Open Science? Michael Nielsen ‘Splains It To Ya

In the wake of my post yesterday on the sudden surge of the open-science movement, I thought a primer on the subject would be useful for those lacking time to read my feature about why so many scientists want to ditch the traditional academic research and publishing model for something more open and decentralized. I started to write a primer — then realized that this short TED talk from Michael Nielsen would serve beautifully. Nielsen does brilliant work on quantum computation, a subject I find daunting (in fact, I don’t even know what it is), but he’s utterly clear and accessible in this story about the promise of the huge gains to be made from open science. He brings the same lucidity to his book Reinventing Discovery, which is a smart and inspiring longer read on the subject.

Testify: The Open-Science Movement Catches Fire

For years, the open science movement has sought to light a fire about the “closed” journal-publication system. In the last few weeks their efforts seemed to have ignited a broader flame, driven mainly, it seems, by the revelation that one of the most resented publishers, Elsevier, was backing the Research Works Act — some tomfoolery I noted in Congress Considers Paywalling Science You Already Paid For, on Jan 6. Now, 24 days later, scientists are pledging by the hundreds to not cooperate with Elsevier in any way — refusing to publish in its journals, referee its papers, or do the editorial work that researchers have been supplying to journals without charge for decades — and the rebellion is repeatedly reaching the pages of the New York Times and Forbes. This is easily the biggest surge the open-science movement has ever put on. At The Cost of Knowledge, the site created for the roster, there were 1,400 signatories last night, and when I woke today at 5 a.m., over 1,600. The thing seems to be snowballing. Some have ached to take action for years. Others are newly radicalized. In my feature I speculated whether librarians would eventually lead the charge. But Jason Hoyt, then of Mendeley and now of OpenRePub, seemed to have it closer: The revolution awaited only the researchers. A skim through their testimony (below the jump here) is an education in why the call for open science is going mainstream:

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Glowing Maps of Scientific Collaboration

Science research collaboration

This lovely map of scientific collaboration is done by research analyst Olivier Beauchesne at Science-Metrixm who examined scientific collaboration around the world from 2005 to 2009.  I love the way the patterns in the EU, so dense and flaring, look like the center of an explosion. Here’s the same EU pattern up close:

I would bet good money that similar patterns hold for literary pursuits, especially science writing. You can see why I so loved living in London (the brightest spot in the cluster at upper left), where you’re in the midst of immense international traffic both virtual and real — though there were many other reasons as well.

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Neuron Culture to SOPA: Drop Dead

I’m stealing this direct from my colleague Maryn McKenna, who keeps the fabulous SuperBug blog here at Wired. Much of the Internet is dark today, to protest the ludicrous law known as SOPA. Here are some links, from McKenna, with which to eduficate yourself about his awful proposed legislation:

Constant readers: Today, Wikipedia is locked, Boing Boing is dark, and I join with many bloggers much more important than me to protest legislation that would destroy the Internet as we know it. Superbug is dark today to protest the ill-conceived Stop Online Piracy Act (SOPA) in the House of Representatives and the Protect IP Act (PIPA) in the Senate.

I humbly request that you consider visiting these sites for more:

The Electronic Frontier Foundation’s explainer’s petition, which our parent has also bannered and linked

A letter from leading tech companies.

Why is a journalist taking a position on legislation, when we are bound by professional practice to be objective and fair? This letter from the Online News Association explains journalists’ opposition to SOPA.

I’ll see you back here tomorrow. If SOPA and PIPA passed, on the other hand, maybe I wouldn’t.

Tortoise Sex, Via the Eyes of Lucky Jack Aubrey

One of the many pleasures of Patrick O’Brian’s Aubrey-Maturin novels, which follow through 20.5 volumes the Napoleonic-era adventures of British Royal Navy Caption Jack Aubrey and his surgeon/spy/naturalist Stephen Maturin, are the closely observed and imagined encounters with wildlife. O’Brian, being the masterful novelist he is, never just shows us the wildlife; we see that clearly enough, but we also learn, always, something additional about whatever character is doing the watching. Usually naturalist Maturin gets that job. Here it’s Captain Jack Aubrey, whose combination of chivalry, sexual interest, and naivete both sharpen his eye and add an extra layer of pleasure — without dimming the clarity of what we see.

On a walk of this kind in the Mediterranean islands he usually saw tortoises, which he did not dislike at all — far from it — but they seemed rare on Gozo, and it was not until he had been going for some time that he heard a curious tock-tock-tock and saw a small one running, positively running across the road, perched high on its legs; it was being pursued by a larger tortoise, who, catching it up, butted it three times in quick succession: it was the clap of the shells that produced the tock-tock-tock. ‘Tyranny,’ said Jack, meaning to intervene: but either the last blows had subdued the smaller tortoise — a female — or she felt that she had shown all the reluctance that was called for; in any case she stopped. The male covered her, and maintaining himself precariously on her domed back with his ancient folded leathery legs he raised his face to the sun, stretched up his neck, opened his mouth wide and uttered the strangest dying cry.

‘Bless me, said Jack, ‘I had no notion…’

This is the sort of thing you can do when you’re writing 3000 pages.

From Patrick O’Brian, Treason’s Harbor, p 52.

They Froze for Science — and Got the Eggs

Bowers, Wilson, and Cherry-Garrard just before departure, June 27, 1911.

In winter I sometimes warm up by reading books with real cold. For a few years years I shuttled between Rick Bass’s Winter, about his first winter in Montana in the 1980s, and R.M. Patterson’s magnificent, shivering Dangerous River, of his days trapping the Yukon in the 1920s. Last week, partly to commemorate the centenary of Robert Scott’s ill-fated expedition to the South Pole, I re-read The Worst Journey in the World, Apsley Cherry-Garrard’s beautifully written account of that mission and of a strange mission within it. For six weeks in the darkness of polar winter, with temperatures running between -40F and -70F (-40C to -56C) — a hundred degrees of frost — Cherry-Garrard and two other men drag a heavy sledge of supplies across the Ross Ice Shelf. They hope to reach a bay on Cape Crozier so they can collect the eggs of the Emperor penguin, for science.

Nothing beats this trip for cold. No trip could deliver more misery, for even a gram more would have killed them and ended it. They expected such daily.

On 29 June the temperature was -50° all day.… Owing to the weight of our two sledges and the bad surface our pace was not more than a slow and very heavy plod.… That night was very cold, the temperature falling to -66°, and it was °-55 at breakfast on 30 June.

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Our Sickening Rush to See PTSD – and What It Costs Vets

When Iraq-war veteran Benjamin Colton Barnes shot park ranger Margaret Anderson dead last week, the speculation started almost as soon as the gun reports faded: Barnes must have PTSD. I first saw this speculation on Twitter, where I suggested it was a tad early to speculate, since police were still trying to track Barnes down in the mountains. They later found him dead; he had died of exposure. And as Alex Horton explains at his blog at the VA, Barnes’ crime and his troubles had little to do with his military service, and our collective rush to attribute the crime to PTSD made two enormous but horribly common mistakes: It indulged in a reflexive diagnosis of PTSD for any mental or behavioral problem in any vet; and it erroneously assumed PTSD led frequently to violent behavior.

Here’s Horton on Barnes:

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