On science blogs this week: Evolution

OPEN ACCESS IS SOMETIMES NOT SO OPEN AFTER ALL. The very high-profile journal Nature keeps most of its content behind a pay wall. But it claims to make an exception for genome sequence data. Papers reporting on genome sequences are supposed to be freely available.

Unfortunately for Nature, the equally high-profile evolutionary biologist Jonathan Eisen discovered otherwise. Wanting to link to the Arabidopsis sequence paper where he is a co-author, he discovered that access to the paper requires a subscription. And, he found after more searches, so do many other sequence papers in the journal.

"Am getting really pissed off right now," Eisen writes at Tree of Life. He points out that the only reason he even noticed the lapse is that he was doing the search from his home, where he does not have full-text access, rather than from his office, where he does. (I should point out that Eisen has a dog in this fight. He's a top editor at PLoS Biology, the flagship of the family of journals that has pioneered open access.)

Eisen would like to cut Nature some slack, but is not sure he should:

This is probably just some glitch in their system. They really do seem committed to trying to make these available. But clearly, the system either does not work well. Or they are not committed to it. Either way this is really annoying. In some cases, the papers were sold to communities of scientists in part with the "These will be freely available to all forever" line as part of the sell.

The post is followed by comments from Nature folk promising immediate attention, but there's no resolution reported on the blog as I write this. UPDATE: Now there is, according to a second comment by Nature spokesperson Grace Baynes. But not for me: I still get this message:

To read this story in full you will need to login or make a payment.

Given that Eisen is as well-known in his realm of evolutionary biology as Nature is in the realm of journals, his annoyance is a pretty big deal. It will cause Talk. Expect a quickish fix.

YET ANOTHER UPDATE: Indeed. I now have full-text access to the Arabidopsis paper--and so, probably, do you.

And it serves as a reminder to all of us who publish: you gotta keep an eye on those guys.

WHEN JOURNALISM BECOMES CHURNALISM. "Churnalism" is not a term yet in use on this side of the Atlantic. But it describes a phenomenon familiar to us all and now firmly institutionalized at sites like Science Daily and the National Science Foundation's Science360 "news service". It's the practice of presenting pre-prepared material, often press releases, as original reporting. (NSF muddles these things deeply, featuring the news releases most prominently but also linking to real news stories and blogs. The latter are themselves a mixed bag; some of the chosen blogs promote institutions and their research, which in my book makes them press releases. Not that there's anything wrong with that.)

Sometimes churnalism means running press releases verbatim as if they were news stories — and even, breathtakingly, topping them with a local reporter's byline. Sometimes that means the reporter may or may not do some original reporting, but draws on the press release, rewritten or not, for part of the piece. Not infrequently a big part.

In the UK, the Media Standards Trust has set up a site, called Churnalism.com, that permits easy detection of material lifted whole from one source and slotted into the news. Unfortunately, the site checks only UK news sources, including the BBC.

There is some curiosity in the US, however, about what the Media Standards Trust is up to. After I started writing this item, I came across a just-published explanatory piece about churnalism.com in the Columbia Journalism Review. It's written by Martin Moore, who heads the Trust. The churnalism.com site itself also provides an FAQ page that lays out Churnalism.com's goals and methods. Can a US version be far behind?

She said hopefully.

COMING TO A CENTURY NEAR YOU: THE SIXTH MASS EXTINCTION. Not much blog commentary yet on the new Nature paper arguing that we are heading into Earth's sixth major extinction event — defined as the disappearance of at least 75% of species — in the past 540 million years. That would be the first since the dinosaur demise some 65 million years ago.

Discover's 80Beats describes the paper and some of its coverage. An unusual additional analysis comes from Nick Matzke at The Panda's Thumb, who describes how the paper grew out of a Berkeley seminar he attended on mass extinctions.

Matzke tells how the grad students wrestled with the difficulty of making apples-to-oranges comparisons between extinction evidence in the fossil record and the pace of contemporary extinctions. He provides a modicum of hope too:

Obviously, given the study we made of how extinction rates can be variable, we are not so naive as to predict that a mass extinction will come for sure in a few hundred or a few thousand years. ..Rather, what we say is that we are currently on that path. Taking a different course will require that humans recognize the problem and make decisions to avoid it.

He also uses the post as an opportunity to talk directly to creationists about how evolutionary scientists do their work:

...this is the kind of thing that is going on every day of every week in biology departments. It’s about the furthest possible thing from being some kind of conspiracy or plot against creationism, God, the Bible, morality, etc. It’s just us doing our day jobs, just like all of the other scientists on campus.

I wonder, though, whether a conviction that evolution in an anti-God conspiracy is what animates all creationism. For some creationists, perhaps. But the faithful who are creationists because they believe the Bible is a book of history may just shake their heads and dismiss evolutionary scientists as simply delusional.

BLOGGERS AS POST-PUBLICATION PEER REVIEWERS. NO PREMENSTRUAL DYSPHORIC DISORDER TO BE FOUND HERE You may remember the flap of a couple months ago surrounding that "arsenic bug" paper and the debate over whether it was legitimate for scientists to critique papers on their blogs. Instead, some argued, researchers ought to send their formal post-publication critical discussions to journals in the traditional way.

That argument was lost long before it was even made, of course. Scientist bloggers have always critiqued papers. This week brings us a particularly nice example. Nice because it's a topic that has long interested me: mood changes throughout the menstrual cycle. And nice because two well-known scientist bloggers have collaborated to critique a paper (and a news story about the paper), each bringing her special expertise to bear on the study.

The bloggers are endocrinology specialist Kate Clancy at Context and Variation and neuroscientist Scicurious at Neurotic Physiology. The paper is "Neuroimaging Evidence of Cerebellar Involvement in Premenstrual Dysphoric Disorder" by Andrea Rapkin et al in the Feb 11 Biological Psychiatry (which is, unfortunately, behind a pay wall.) The news story is "Why women get anxious at that 'time of the month' " by Wendy Zuckerman, New Scientist Feb 14, 2011, (which is, blessedly, not.)

My interest in this topic dates back to grad school, which was a Very Long Time Ago. So long ago, in fact, that the consensus about premenstrual mood swings back in the last century was that although they were indeed all in the head, they had nothing to do with the brain. They were figments of women's imaginations, poor dears. I ground my teeth as I wrote my paper about this debate, but fortunately my physiology prof was female and equally irritated by the sneering literature.

No trace of a sneer remains, of course. Now that the topic has actually been studied rather than ridiculed, the evidence that in many women mood varies with the cycle — and that some women suffer horribly — is irrefutable. The paper reports on neuroimaging studies that show that the cerebellum — a part of the brain only recently associated with mood — seems to be involved in women with the more extreme forms of debilitating premenstrual mood changes, known now as premenstrual dysphoric disorder (PMDD.)

Clancy notes the paper's small number of study subjects and critiques its statistical analyses. She also analyzes the hormone studies in the paper and suggests ways they could be better. Scicurious notes that the study's findings are limited.

ALL you can say here is that women with PMDD had higher cerebellar glucose utilization during the luteal phase than women without PMDD. and the increase in activity correlated with a worsening of mood. This study shows NOTHING ELSE. NOTHING.

Yet, she points out, the paper (and the press release and the New Scientist article) emphasize the potential role of GABA-A receptors.

But to go from “we see differences in glucose utilization in the cerebellum” to “GABA-A receptors are probably it” is to draw a lot out of a little. I don’t blame the authors for hypothesizing, but I feel like the GABA receptors here got a lot of focus.

Owing to running out of time and space, I'm giving this useful analysis short shrift. The bloggers' commentary is intricate and deserves careful reading. Both, for example, also have nice things to say about the paper and its findings.

I'm hoping we'll see more of what Clancy and Scicurious are calling tag-team research blogging. Bringing diverse expertise to bear on a paper is a real service to readers. Not least it's a service to science writers, who can learn a lot about how to read a paper, what to look for, what might be missing, and what kinds of questions to ask the authors and outside experts as follow-up.

Mar. 3, 2011

Drexel University online