Medley’s right.

Posted on April 28, 2007 by Bill Hooker

I haven’t said anything about the Kathy Sierra fiasco for the same reason I don’t say much about politics any more: my blogroll does a much better job than I ever could. But that assumes that you are reading my blogroll pretty extensively, and some things simply warrant more effort than such a blithe assumption. Medley is right, the Sierra incident is one such case:

I wrote briefly about the Kathy Sierra situation earlier. I resent the hell out of the fact that these despicable behaviors are out there and must be addressed — not only is the harassment and threatening vile in and of itself, but the fact of it takes time and energy and spirit away from all of us who are compelled to speak out against it. It’s a double-win for the misogynists and hatemongers of the world.
But, we must speak.
This kind of crap must not go unanswered. It’s why, if you scan my del.icio.us feed, I’m always ranting that MEN WHO DON’T HATE WOMEN MUST SPEAK against this crap as well.

I still think my blogroll is a better source of information and insight than I am, though, so for such times as this I’ve built a custom Google search engine that will emphasize the results from sites in my blogroll:

Try searching for combinations of “Kathy Sierra”, Markos, sexism, misogyny, “death threat”. And for the record: what happened to Sierra was vile, the perps are wastes of oxygen who should be doing serious jail time, and Kos is an idiot who long ago made himself irrelevant to progressive politics.
This “point to my custom search” approach isn’t perfect, but I simply don’t have time to cover all the things I find important, even just the ones I find compelling. But I do have great faith in the ability of my blogroll to cover any topic — after all, if they don’t cover it, I won’t know about it anyway. I don’t get news anywhere else. So, we’ll see if I can’t get the most important issues at least a little coverage here.

Update: yet another woman is being targeted by filth on the internet. Deviousdiva is a British expat living in Greece and writing about the plight of the Roma in Athens. Her meatspace ID has been revealed and she’s been threatened. (Hat-tip: Lindsay.)
There’s a real pattern developing here, a pattern of online abuse of women. My guess is that as outright misogyny becomes less and less acceptable in public discourse, the online world provides a kind of outlet for mouth-breathing cowards who would not dare say these kinds of things to anyone’s face.
The answer, pace idiots on the right, is not to abolish online anonymity; nor, pace idiots on the left, is the answer to establish some kind of Code of Conduct.
The answer is to SPEAK UP and make cyberspace as unwelcoming as meatspace for these degenerates. So if you have a blog, please consider joining the “Take Back the Blog” virtual march on April 28th (I’ve messed with the date to keep this post on top until then). Even if, like me, you are no expert on such issues and probably won’t have anything more substative to say than [this is good], say that — stand up and be counted.

Every time a traditional publisher puts their foot in it, an angel gets its wings.

Posted on April 25, 2007 by Bill Hooker

Zuska alerted me to Shelley’s recent run-in with Wiley, one of the big 7 — or is it 6 now? — science/tech/med publishers. Shelley reviewed a recent article in the Journal of the Science of Food and Agriculture (no link — what would be the point, they won’t let you read most of it), and in doing so reproduced a chart and one panel from one of more than 10 figures. Rather than see this as fair use and damn good publicity, Wiley sent a nastygram:

Re: Antioxidants in Berries Increased by Ethanol (but Are Daiquiris Healthy?) by Shelly Bats
http://scienceblogs.com/retrospectacle/2007/04/antioxidants_in_berries_increa.php
The above article contains copyrighted material in the form of a table and graphs taken from a recently published paper in the Journal of the Science of Food and Agriculture. If these figures are not removed immediately, lawyers from John Wiley & Sons will contact you with further action.
Regards,
[redacted]
Editorial Assistant
Journal of the Science of Food and Agriculture
Society of Chemical Industry
14-15 Belgrave Square
London UK
SW1X 8PS
T: [redacted]
F: [redacted]
E: [redacted]
W: www.soci.org
SCI – where science meets business
Register with Wiley Interscience to sign up for free contents alerts to SCI journals (Journal of the Science of Food and Agriculture, Journal of Chemical Technology and Biotechnology, Pest Management Science and Polymer International) by email. Visit http://www.interscience.wiley .com/alerts

Note that the flack doesn’t even bother to spell Shelley’s name properly; and can you believe that marketing boilerplate bullshit at the bottom there?
Shelley got around this hassle by re-creating the necessary figures for herself, but as she rightly notes, the point of science publishing is to disseminate information, not to threaten grad students who happen to be interested in a particular paper. Except that for Wiley, the point is profit, and apparently you do make that by threatening grad students. (Cue more flacks in my comments squealing about how Wiley is “your partner in research” or somesuch. Save your breath, weasels.)
Here’s the bottom line: if you’re a researcher, publish only in Open Access journals whenever possible, and if you absolutely have to publish with a toll-access journal then use an Author Addendum to retain copyright in your paper and in your data and deposit your article in an OA repository just as fast as you can find one to take it. Until the research community stands up and says “enough”, we will continue to be held hostage in this fashion by greedy, oversized corporations — but the good news is, we need only reach out and take that power back. In the Gutenberg era, publishers had leverage; in the Google age, they have none.
If this kerfluffle is the first you’ve heard of, or really thought about, Open Access publishing, please read Peter Suber’s brief introduction or more detailed overview. If you have serious stamina/interest/masochistic tendencies, you could also read my 3QuarksDaily series on Open Access/Open Science (part 1, part2, part 3).
Update: Shelley got a pretty standard-issue non-apology apology from further up the foodchain, and (having neither the time nor the money to waste on pursuing this further) is content to let it rest there. So, Shelley now has permission to reproduce the figures in question and no threat of attack lawyers, and Wiley has a public black eye; seems about right to me. Per Shelley’s request, and because apparently some of the letters she received were less than polite, I’ve redacted the original flack’s name and contact details above. (Obdisclosure: I wrote, but I was polite — although I included a link to this entry, which isn’t.)

“Thinking bloggers”.

Posted on April 13, 2007 by Bill Hooker

Abel of Terra Sigillata kindly tagged me with a recent blog trope, naming me one of the bloggers who makes him think. This, it goes without saying, is undeserved, but that never stopped me grabbing for good things before. So without further ado, here are five blogs (in no particular order) whose authors make me think, challenge my preconceptions, and generally give my grey matter a workout on a regular basis:
The Bell by Jared Dunn. In his own words:

Content, likely to be a mish-mash of politics, culture, media, sports, and tech, with emphasis probably on politics. I’m a rather incorrigible generalist / dilettante and a serial digressionist…

He’s also smart as hell, and never stops trying to figure out why people do the stupid shit they do. Obdisclaimer: he’s a pal.
One Foot In, by Alice Domurat Dreger. The title refers to one foot in the academy, one foot in the real world. In her own words:

Most of my professional energies have gone to improving the medical and social treatment of people born with socially-challenging bodies, including people with intersex, conjoinment, dwarfism, and cleft lip. I work with affected adults, parents, and clinicians to make things better in the social and medical worlds. The question that motivates me is this: Why not change minds instead of bodies?

Her essays are fascinating, and showed me a whole shadowy world I never even knew was there. For a quick intro, try When Medicine Goes Too Far in the Pursuit of Normality, Proof that I Like Penises or Separate Together. You will also find Dr Dreger blogging — more frequently than on her own site, in fact — at the Hastings Center Bioethics Forum.
Philosopher’s Playground, by Steve Gimbel — “an on-going game of intellectual tag concerning ethics, science, politics, and all topics philosophical”. Steve is smart and well-read and funny and personable (online, I mean; we’ve never met, although he likes beer which inclines me to think we’d get along). He recently triggered an excellent blogversation about teaching science with a provocative post about whether labs are a waste of time, he’s dead wrong about impeachment, let’s see… oh yes, he’s also a prophet, and as far as I know the inventor of the tragically underused phrase civil fucking discourse.
Update: dammit, someone got Steve before I did. I read that post, too, and forgot all about it. OK then:
Big Monkey, Helpy Chalk by Rob Loftis. I’m not entirely sure what it is that Rob does for a living, apart from the fact that he’s an academic (or, as I like to call it, a government thinkmonkey) — but how can you not love a man whose latest writing proposal is “Gaius Baltar and the Image of the Tyrant in Plato and Boethius”. If you need more than that, try the North County Academy for the Excruciatingly Fine Arts.
Majickthise, by Lindsay Beyerstein. You probably already read Lindsay, and if you don’t you should. You should also support her efforts to establish a truly independent reporting career, and, I dunno, maybe name one of your children after her. Some of her big stories include Hurricane Katrina, Scumbag DeLay’s perp walk and Ned Lamont whuppin’ Holy Joe. I hope she runs for President one day. (Oh yeah, “magic thighs” — it’s a Hitchhiker’s Guide reference.)
Adventures in Ethics and Science, by Janet Stemwedel. I’m surprised Janet hasn’t already been tagged (someone got to Zuska before me, dammit). Science is not like law and sausages: you are encouraged to watch it being made. Adventures is an excellent window onto that process; Janet is a PhD chemist and a PhD ethicist, and looks at science not only from the bench but as a human endeavour, a process carried out by a particular (and peculiar) tribe. If you are interested in how science works, read this blog.
I want explicitly to say that I don’t expect my tag-ees to play, but if you feel like doing so the original guidelines, from Ilker Yoldas who started this thing in February, are as follows:
1. If, and only if, you get tagged, write a post with links to 5 blogs that make you think,
2. Link to this post so that people can easily find the exact origin of the meme,
3. Optional: Proudly display this ‘Thinking Blogger Award’ graphic (in silver or gold) with a link to the post that you wrote.

Another early-career scientist goes on the public record intending to do open science.

Posted on April 7, 2007 by Bill Hooker

I forgot to blog about this article in The Scientist when Bora first linked it, but now Jean-Claude has reminded me. The main focus is on Reed Cartwright’s adventures in authorship (and do go read that link; it’s a nice example of how science should work, and Comai is a class act), but Bora and Jean-Claude also get a mention; they’ve posted the relevant excerpts on their blogs. The bit that really grabbed me, and that I meant to write about, was this quote about/from Bora:

Zivkovic concedes that he has had less luck in convincing people that he should post his dissertation on his blog before he publishes it [than in convincing them to publish orphan data]. “But if and when I get to having my own lab I’d like to be completely open,” he says, “having a live blog where everyone posts what happens in the lab every day.”

Bravo, Bora! I’ve said the same thing, here and elsewhere, and of course Jean-Claude is actually doing it. It makes me wonder, who else is out there, hoping and planning to do open science? In comments here, Propter Doc (I wish I’d thought of that nick!) wishes there was a way to publish orphan data in the open (and Jean-Claude points to a couple of possibilities, including blogging). I have previously pointed to some other examples: bioinformatics work from Sandra Porter and Pedro Beltrao, chemoinformatics software from Egon Willighagen, organic syntheses from Org Prep Daily and Rosie Redfield and her students blogging hypotheses, thinking-out-loud and even data. I recently noticed that Jonathan Eisen had started blogging his OA papers (reminding me that I must get my professional back catalog, such as it is, onto a repository somewhere).
There must be more. Who else is doing, or planning to do, open science? And further, how can we help each other?
My working hypothesis is that open, collaborative models should out-produce the current standard model of research, which involves a great deal of inefficiency in the form of secrecy and mistrust. Open science barely exists at the moment — infancy would be an overly optimistic term for its developmental state. Right now, one of the most important things open science advocates can do is find and support each other (and remember, openness is inclusive of a range of practices — there’s no purity test; we share a hypothesis not an ideology).
So talk to me, putative ally and colleague! Who are you, where are you, how can I help you? I sure would like to hear from you.

Open Reading Frame

Monthly Archives: April 2007

Every time a traditional publisher puts their foot in it, an angel gets its wings.

“Thinking bloggers”.

Another early-career scientist goes on the public record intending to do open science.