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Category Archives: Transparency

After attending the annual ScienceOnline meetings in North Carolina for many years, this time around, I won’t be going. The primary reason has nothing to do with the upsets in that community of late (oh, yes, I have thoughts, but they’re not for the sharing today). Oh, sure, not seeing the people I’d hoped to see because ongoing problems drove them away—that’s a fine secondary reason. Before and above all that, though, is the fact that I’m mid-PhD. I realized I could no longer justify the time, the stress and, indeed, the carbon footprint of traveling to attend #scio14.

What can one do? I revile air travel more every year. I don’t have time/energy to prepare for the conference beforehand, or to follow up on anything discussed there after. My proposal for the session I was to moderate was, to summarize only slightly, “hey let’s build this website”. Must I travel for that??
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You know what I’d like to see? I’d like to have all the course materials necessary for a good, solid undergraduate physics degree available online, free to access and licensed in a way which permits reuse and remixing. I’d like it all in one place, curated, with paths through it mapped out to define a curriculum. When I say all the course materials, I mean that this webzone should have online textbooks; copies of, or at least pointers to, relevant primary literature; video lectures; simulation codes; sample datasets on which to practice analysis; homework and exam problems with worked-out solutions; interactive quizzes, so we can be trendy; and ways to order affordable experimental equipment where that is possible, e.g., yes on diffraction gratings, but probably no on radioactive sources. I’m talking about physics, because that’s what I nominally know about, but I’d like this to encompass the topics which I got sent to other departments to learn about, like the Mathematics Department’s courses in single- and multivariable calculus, differential equations, linear algebra, group theory, etc.

One way to think about it is this: suppose you had to teach a physics class to first- or second-year undergraduates. Could you get all the textual materials you need from Open-Access sources on the Web? Would you know where to look?

What with Wikipedia, OpenCourseWare, review articles on the arXiv, science blogs, the Khaaaaaan! Academy and so forth, we probably already have a fair portion of this in various places. But the operative word there is various. I, at least, would like it gathered together so we can know what’s yet to be done. With a project like, say, Wikipedia, stuff gets filled in based on what people feel like writing about in their free time. So articles grow by the cumulative addition of small bits, and “boring” content — parts of the curriculum which need to be covered, but are seldom if ever “topical” — doesn’t get much attention.

I honestly don’t know how close we are to this ideal. And, I don’t know what would be the best infrastructure for bringing it about and maintaining it. Idle fantasies and pipe dreams!

I’d like to have this kind of resource, not just for the obvious practical reasons, but also because it would soothe my conscience. I’d like to be able to tell people, “Yes, physics and mathematics are difficult, technical subjects. The stuff we say often sounds like mystical arcana. But, if you want to know what we know, all we ask is time and thinking — we’ve removed every obstacle to your understanding which we possibly can.”

I don’t think this would really impact the physics cranks and crackpots that much, but that’s not the problem I’m aiming to (dreaming that we will) solve. Disdain for mathematics is one warning sign of a fractured ceramic, yes: I’ve lost count of the number of times I’ve seen websites claiming to debunk Einstein “using only high-school algebra!” We could make learning the mathematical meat of physics easier, but that won’t significantly affect the people whose crankishness is due to personality and temperament. Free calculus lessons, no matter how engaging, won’t help those who’ve dedicated themselves to fighting under the banner of Douche Physik.

Alchemists work for the people. —Edward Elric

Lyrics and original music by Neil Gaiman (for Peri Lyons), performed with extra chordification by Amanda Palmer. No, not the one who works for Al Jazeera, the other one.
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A couple noteworthy items:

Tim Farley, who spoke at TAM 6 about Internet tools which skeptics can use, has put the transcript for his talk online. There’s a great deal of stuff in there to geek over; we can at least have a lot of fun while we’re failing to save the world. Farley makes me feel shame at the weakness of my RSS-fu.

Via the diligent Peter Suber comes word of Open Education News, an aggregator site for open-education developments (new teaching tools, textbooks which are free as in speech or as in beer, etc.). It’s interesting to see how much younger OE looks and feels than OA, with none of the crotchety arguments about definitions and fireballs hurled at traditional enemies.

Gary Schwitzer asks,

Is the news media doing a good job of reporting on new treatments, tests, products, and procedures? Ray Moynihan and colleagues analyzed how often news stories quantified the costs, benefits, and harms of the interventions being discussed, and how often they reported potential conflicts of interest in story sources [1]. Of the 207 newspaper and television stories that they studied, 83 did not report the benefits of medications quantitatively, and of the 124 stories that did quantify the benefits of medications, only 18 presented both relative and absolute benefits. Of all the stories, 53% had no information about potential harms of the treatment, and 70% made no mention of treatment costs. Of 170 stories that cited an expert or a scientific study, 85 (50%) cited at least one with a financial tie to the manufacturer of the drug, a tie that was disclosed in only 33 of the 85 stories.

Moynihan et al. (2000) inspired some Australians to do a similar survey in 2004, which found after six months that Australian print and online news coverage of medical advances was “poor.” Now, Schwitzer has done a more extensive survey of United States media. The punchline is as follows:

In our evaluation of 500 US health news stories over 22 months, between 62%–77% of stories failed to adequately address costs, harms, benefits, the quality of the evidence, and the existence of other options when covering health care products and procedures. This high rate of inadequate reporting raises important questions about the quality of the information US consumers receive from the news media on these health news topics.

Details are available at PLoS Medicine. Now, we just need somebody to pay for a similar survey of non-medical science reporting.

(Tip o’ the fedora to Steve Novella.)

Alun Salt, an archaeology PhD student and therefore a elitist expert by Internet standards, used to edit Wikipedia, but after five hundred-odd edits, he decided to give up and become Wikipedian Emeritus. In giving his reasons, he also made a prediction:

From the limited information available it looks like the combination of Knol [see here] and Wikipedia’s policies will be a Wikipedia-killer.

First off Knol will attract experts because of its emphasis on authorship. Additional features like collaborative authoring will attract people who can work together. You can also bet that Google will be marketing Knol as a tool to experts. Even without migration from Wikipedia that will be a blow. The material will be protected from plagiarism. If there’s one company that can find copies on the web, it’s Google.

I find the idea of having one company in charge of hosting content and providing search functionality a little, well, spooky — and yes, that already applies to YouTube and Blogger — but moving on:
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Peter Suber and Stevan Harnad have been trying to clarify the different meanings of the term “Open Access.” Recently, these two advocates of the OA cause issued a joint statement which began as follows:

The term “open access” is now widely used in at least two senses. For some, “OA” literature is digital, online, and free of charge. It removes price barriers but not permission barriers. For others, “OA” literature is digital, online, free of charge, and free of unnecessary copyright and licensing restrictions. It removes both price barriers and permission barriers. It allows reuse rights which exceed fair use.

Suber and Harnad proposed using “weak OA” to describe the former kind, literature which is “price-barrier-free,” and “strong OA” for the latter, “permission-barrier-free” variety. Shortly thereafter, however, people got flustered and pointed out that “weak OA” is unnecessarily pejorative. After all, even lowering price barriers is a good thing, and there’s no reason to make life harder for the people trying to do that. Better terminology is needed. This is a chance for all you aspiring wordanistas to lead your very own revolution! (Given the audience which finds OA issues of interest, your revolution will be well-blogged, but not televised.) Can you come up with a better alternative than the current options like “Basic OA” versus “Full OA”?

Hopefully, whatever terms we end up using to denote these gradations in scale will be more illuminating than the ones employed by the US Post Office. Every time I walk in to post something, I find myself befuddled by Express, Priority and First-Class designations: which one is actually the fastest and the most expensive? When each term is tarted up to sound as exciting as possible, their ability to indicate a scale of any kind is ruined.

Geologist Mark Wilson has an interesting opinion piece at Inside Higher Ed,Professors Should Embrace Wikipedia.” While it was published on April Fool’s Day, one can take it in full seriousness. I don’t agree with it fully, but I believe the points it raises are well worth discussing. Here’s the nub of his argument:

What Wikipedia too often lacks is academic authority, or at least the perception of it. Most of its thousands of editors are anonymous, sometimes known only by an IP address or a cryptic username. Every article has a “talk” page for discussions of content, bias, and organization. “Revert” wars can rage out of control as one faction battles another over a few words in an article. Sometimes administrators have to step in and lock a page down until tempers cool and the main protagonists lose interest. The very anonymity of the editors is often the source of the problem: how do we know who has an authoritative grasp of the topic?

That is what academics do best. We can quickly sort out scholarly authority into complex hierarchies with a quick glance at a vita and a sniff at a publication list. We make many mistakes doing this, of course, but at least our debates are supported with citations and a modicum of civility because we are identifiable and we have our reputations to maintain and friends to keep. Maybe this academic culture can be added to the Wild West of Wikipedia to make it more useful for everyone?

And here’s his proposal for action:

I propose that all academics with research specialties, no matter how arcane (and nothing is too obscure for Wikipedia), enroll as identifiable editors of Wikipedia. We then watch over a few wikipages of our choosing, adding to them when appropriate, stepping in to resolve disputes when we know something useful. We can add new articles on topics which should be covered, and argue that others should be removed or combined. This is not to displace anonymous editors, many of whom possess vast amounts of valuable information and innovative ideas, but to add our authority and hard-won knowledge to this growing universal library.

An old saying has it that of all kinds of politics, academic is the nastiest, because the stakes are the lowest. One might fret that legions of quarrelsome professors would trample all over the pages pertaining to the controversies in their own specialized fields, bringing all the fury of the Dawkins/Gould or Fodor/Dennett deathmatches to the world of Wikipedia. However, I know of no evidence suggesting that these arguments would really be any more vituperative than the ones which already occur. Furthermore, Wikipedians with advanced degrees already exist; Wilson’s proposal would only bring in a larger number of them, perhaps with a shared ethos or sense of common purpose.
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I managed to miss the first anniversary of my own blag! Well, there’s no celebration like a belated celebration, so let’s lay down some drum beats and groove to the funky sound of scholarly activism. A few of the lyrics in the songs sampled in this video are less than safe for work:

Here’s to another year of missing the important stuff.

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:
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To summarize the apparent attitude of MySpace honchos:

Spines are for wimps, and Terms of Service are for pansies. Let’s delete the Atheist and Agnostic Group and then go sacrifice a goat to Rupert Murdoch.

Noises are being made that a “secular humanism” group (ID 100130357) has also been vaporized. I get an “invalid group ID” message when I try to check that page. Anybody know more?

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“.

Anybody here remember “Citizendium”? You know, the collaborative encyclopedia project started by former Wikipedia honcho Larry Sanger, the project whose guiding motto became, basically, “We are not Wikipedia”?

Well, for all that I’ve never noticed them doing anything, they’re still around, and they’ve decided to use a Creative Commons license. Good for them.

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.

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.)

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.