Category Archives: Transparency

Warda/Han and Well-Hung Tongues

The story so far:

As January gave way to February, several bloggers called attention to a puzzling review article in the journal Proteomics, available online and slated for publication in the paper version. Mohamad Warda and Jin Han’s paper was entitled, “Mitochondria, the missing link between body and soul: Proteomic prospective evidence.” As PubMed and Proteomics now note, that paper has been retracted, but not, surprisingly, because it offered no actual evidence for its stated claim — that some grandfalutin’ higher power had been at work inside mitochondria, designing the ways their proteins worked together. Instead, the paper was retracted due to “substantial overlap of the content of this article with previously published articles in other journals” — in plain language, plagiarism.

The story is still unfolding. What concerns the scientific community now is not so much the transparently flawed allegations of Warda and Han themselves, but the sloppy practice of the journal Proteomics in letting those claims get through peer review into publication. Now, nobody expects peer review to be perfect — like any human institution, it’s not going to be — it’s just a procedure for telling, as Cosma Shalizi says, that “a paper is not obviously wrong, not obviously redundant and not obviously boring.” Still, this incident is rather beyond the pale.

While the Warda and Han paper was itself obviously wrong, the developments from it have been far from boring. The Korean newspaper The Hankyoreh picked up the story, and in consequence machine translation gave us the delightful phrase, “OK, the power of science blog!” More recently, Fabienne Gallaire wrote it up in the French publication Rue89. Gallaire’s piece describes how these shenanigans have played out, from the beginning until now. Of particular interest is its accurate description of how the plagiarism was first discovered:
Continue reading Warda/Han and Well-Hung Tongues

Commies Conquer Publishing Industry!

Yesterday morning, an omnibus spending bill was signed into law, a bill among whose provisions lurked the mandate that the National Institutes of Health require Open Access for all research funded under its auspices. The language in question states,

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

And it ain’t just a good idea no more.

John Gordan has had the best rimshot so far:

I’d also like to thank the biomedical publishing industry. This could never have happened without the transformation of a cottage industry into short-sighted publicly traded corporations dedicated to maximizing near term revenue. Publishers pushed journal subscription and archive access prices to stratospheric levels, knowing their subscribers had no real options. It was a great short term strategy …

This is what happens when those slinky, no good Reds are “both elusive and in possession of a better message“.

Physics from Open Yale Courses

Yale has started putting course material online in a systematic way, following in the grand tradition of MIT’s OpenCourseWare. Among the handful they’ve uploaded so far, the two which catch my eye the most strongly are Fundamentals of Physics and Frontiers and Controversies in Astrophysics. These classes come with Quicktime video of the lectures, and all material is licensed under Creative Commons BY-NC-SA.

Hat tip: Peter Suber.

Wikipedia and Creative Commons

This is pretty big news: Wikipedia, which has so far been licensed under the GFDL, is moving towards integration with the Creative Commons system. Two days ago, the Wikimedia Foundation requested that the GNU folks modify the GFDL to allow “mass collaborative projects” developed under the GFDL to migrate to the Creative Commons Attribution-Share Alike 3.0 license.

A time of troubles awaits in the near future, when Wikipedians will be asked to decide: relicense the encyclopedia under CC-BY-SA 3.0, or not? Even if the community says no, the new version of the GFDL will allow other content developers to mix material from Wikipedia and CC sources much more easily than was possible before.

(Via Peter Suber.)

Sleep Tight!

All things considered, the antics of my government are still higher on my list of oh-god-we’re-all-gonna-die than quantum Zeno effects with dark energy. To illustrate why, I quote David Leppard in the Sunday Times:

A senior lawyer for the American government has told the Court of Appeal in London that kidnapping foreign citizens is permissible under American law because the US Supreme Court has sanctioned it. […] Until now it was commonly assumed that US law permitted kidnapping only in the “extraordinary rendition” of terrorist suspects.

The American government has for the first time made it clear in a British court that the law applies to anyone, British or otherwise, suspected of a crime by Washington.

Yep. This is all gonna end well.

Via Warren Ellis.

Rejecta Mathematica

Walt and Isabel are talking about the newest oddity in mathematics publishing: a forthcoming journal called Rejecta Mathematica. This will be an online journal dedicated to mathematical papers which have been rejected from peer-reviewed publications.

Such a journal could be a useful publication venue: papers which show that a promising technique fails or which reprove a known theorem in a not-quite-snazzy way might be worth collecting. Furthermore, it would be neat to look at a probability argument or some “entropy” bafflegab from a cdesign proponentsist and say, “This couldn’t even be published in Rejecta!

Open Access: Get the Story Right

Dear Nature News,

Get your facts straight. The new National Institutes of Health policy currently up for a vote on Capitol Hill will not require researchers “to publish only in journals that make their research papers freely available within one year of publication.” This is false. Such a requirement is nowhere present in S.1710 or H.R.3043. The new policy will require research funded by the NIH to be placed in an open-access repository within 12 months of publication. Really:

The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine’s PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law.

Notice how there’s no Index of Prohibited Journals? In the industry jargon, the NIH policy will mandate “green OA,” not “gold OA.” This mistake is old enough and tiresome enough that we have a name for it: Journal-Archive Mixup, or JAM.

I’m cynical enough to expect the Washington Post to get this wrong, but Nature News should do better. The truly unfortunate part is that Slashdot picked up the error, so now a legion of science geeks will be completely misinformed.

Eric “Dr. Evil” Dezenhall must be pleased: his strategy for misinforming the public works so much better when all the reportage is sloppy anyway.

(Tip o’ the fedora to Peter Suber.)

Today’s History Lesson

Bear in mind, I got just about the best public-school education an American youngster could reasonably hope for. My high school was in the well-to-do end of town, and in fact ours was the only school district which did not include a low-income housing project. (This made for an interesting social dynamic when our quiz-bowl team went to competitions outside of town. In Huntsville, we were the rich kids, but when we played against schools like Vestavia, we became the scrappy champions of the downtrodden.) Therefore, every time I notice something that my education should have covered but didn’t, I get a bad vibe. Wasting the few resources our society devotes to education — that’s not a pretty spectacle.

Despite a year of AP United States History and a semester of AP American Government, I actually didn’t know this:

When the Senate, of the very first Congress, was considering the wording of the religion clauses of what was to become the First Amendment, it rejected, on September 3, 1789, two proposed phrases that, if adopted, could have arguably only prevented government from favoring one religion over another. The first proposed wording, rejected by the Senate, read: “Congress shall make no law establishing one religious sect or society in preference to any other.” The Senate additionally rejected wording that read: “Congress shall make no law establishing any particular denomination or religion in preference to any other.” The Senate finally chose wording that read: “Congress shall make no law establishing articles of faith or a mode of worship, or prohibiting the free exercise of religion.”

So, thank you, Eddie Tabash, for writing your brief to the California Supreme Court!

Stuart Pivar: Man and Myth

First, an announcement: Brent Rasmussen has the sixty-ninth Skeptic’s Circle up at his place. Rasmussen taps into that deeply American mythos, the aquifer of imagery which we specialists call “the Western.” Science After Sunclipse is represented by my two entries on Stuart Pivar, the hapless businessman who wrote a silly book, tried to sue the professor who gave it a scathing review and earned the moniker “classic crackpot,” bestowed upon him by an unsympathetic Internet.

In and of itself, that sounds like a nice legend too, doesn’t it? “Businessman versus blogger,” a hero tale for the Wild West Web.

But myths have their underside, and the closer we poke at a myth, the more interesting the telling becomes. The story of Cain and Abel might be an adaptation of a Sumerian fable; all that business about Cain finding a wife and needing a mark to protect him from the other people — what other people, if his was the only family on Earth? — may be the residue of a polytheistic age, when Yahweh was only supreme thunder-bringer of one patch of land, and Genesis was the origin story of his people alone. (In ancient Ugarit, Yahweh was the son of Elyon, the Most High.)

And what of our modern story? The clash between Pivar and PZ Myers is such the perfect Slashdot item; could there be more to it than that?
Continue reading Stuart Pivar: Man and Myth

Irony, Noun

James Boyle writes in today’s Financial Times:

The world wide web was designed in a scientific laboratory to facilitate access to scientific knowledge. In every other area of life — commerce, social networking, pornography — it has been a smashing success. But in the world of science itself? With the virtues of an open web all around us, we have proceeded to build an endless set of walled gardens, something that looks a lot like Compuserv[e] or Minitel and very little like a world wide web for science.

Discuss: should science publishing be more like pornography?

(Via Open Access News.)

PR Flacks for Pivar!

Over at the SciAm blag, Chris Mims breaks the story that a public-relations flack was cheerleading for classic crackpot Stuart Pivar. Matthew Rich, a.k.a. Matt Richards, is a New York-based PR veteran of sixteen years whose PR agency issued the press release for Pivar’s new edition of LifeCode. This was, incidentally, the press release which prompted PZ Myers to repost his old debunking of Pivar’s crackpottery. This was also the press release which claimed that Neil deGrasse Tyson supported Pivar’s work, a claim which random folks on the Internet soon demolished, and which Tyson himself soon denied.


For some reason, Matthew Rich then went around the Web, saying good things about Pivar. At the page for LifeCode, he wrote under the name M. rich “open minded”, saying this:
Continue reading PR Flacks for Pivar!

Evil Is His One and Only Name

By now, you’ve probably heard of PRISM, the organization of publisher bigwigs fighting against open access. John Baez has just made a shocking discovery. Take a look at the brains of their outfit, Eric Dezenhall:

It’s Dr. Evil!

Well, what would you expect? This is, after all, the man who said that “it’s hard to fight an adversary that manages to be both elusive and in possession of a better message: Free information.”