09 July 2010

Daily Digest, 2010.07.08

Thursday: filtering the flood of scholarly publication; update on the ScienceBlogs fiasco; why software patents are a bad idea; Nicholas Wade on the "Hazebura" flints; a neutral model of language evolution?; protons smaller than everyone thought? (physics in a tizzy); Anne Midgette's Siepi obit; Pletnev says it was all a misundertanding (oh sure); Berg and Schönberg at Klimt's funeral; game theory and opera; a new Velázquez?; German lawsuit against Facebook; cats eat man's foot.

Scholarly Publishing &c.

Kent Anderson at Scholarly Kitchen writes on the flood of scholarly publishing. Main points:
Most papers (his data seems to be mainly from scientific papers) eventually get published: "[T]he rate of non-publication across all papers [that is, submitted papers that end up not being published at all] is somewhere between 10% and 53%, with most studies showing it to be between 10% and 45%."

So much for the filtering function of peer review.

Thus "impact factor" becomes the "filter" by which one decides what is important (and worth reading) and what isn't. (You're much more likely to read and to want to cite an article from Nature than one from the Lower Slobovian Journal of Industry-Funded Research.)

But impact factor is broken.

So how are we going to filter the flood of published research, especially now that Google Scholar and similar methods of searching basically allow us to treat all published research as a single pool?
He does not mention (so far as I have seen, the authors at Scholarly Kitchen never mention) the ways in which journal and article pricing, and other for-profit and proprietary aspects, contribute to the brokenness of the current system. (They do occasionally discuss open access, but not, in my experience, "closed access.")

I was amazed to find out, for example, just now, as I was looking for a contrastive example of a high impact journal in (say) evolutionary biology vs a low impact one, that I apparently do not have access to an up-to-date public version of such a list.  Journal Citation Reports, perhaps the most widely used, is a commercial product of Thomson Reuters, and I have seen at least one site that reports having received a takedown notice for having posted a comprehensive list of the sort I was looking for. (This is why I made up my example.)

I would say (and I will be writing more about this) that the entire scholarly publishing system is broken, not just the "Impact Factor" system, and it is broken, in part, because of the central role of commercial and for-profit interests.

As for filtration systems:  Hi.  We're part of your new and improved filtration system.

And speaking of filtration systems, an update on the ScienceBlogs fiasco.  Not surprisingly, the PepsiCo blog is history (via PZ Myers). I would think, though, that the damage to ScienceBlogs may be deeper and more long-lasting than this quick fix can repair.

In the meantime, inspired by the fiasco, John Wilkins has set up a new Opinionated Bastards blog for ranting.

Glyn Moody at open ... passes on the story of an egregious example showing why software patents are a (very very) bad idea, because they amount to patenting math.


Nicholas Wade at the NYT has a typically excellent article on the 800,000-year-old Happisburgh flints, well worth reading even if you've already read previous summaries of the discovery. Among other useful bits of information, he tells us that the name of the town is pronounced "HAZE-bura."  Well of course. 

Bayes at Gene Expression has an interesting post on a new study that proposes a possible "neutral model" for language evolution. The article is:
Florencia Reali and Thomas L. Griffiths (2010), "Words as alleles: connecting language evolution with Bayesian learners to model genetic drift," Proceedings of the Royal Society B. This is one of the articles that is available for free download through the end of July.

80beats has great summary of a new article in Nature claiming that protons are 4% smaller than had been thought. This doesn't sound like a lot, but if borne out, the discovery has the potential to shake the foundations of physics.

See also Alasdair Wilkins's post on this story at io9, which quotes Ingo Sick, a physicist at the University of Basel:
"It's a very serious discrepancy. There is really something seriously wrong someplace."
The article is:
Randolf Pohl, et al. (2010), "The size of the proton," Nature. The article is behind a paywall, and costs $32.00.
A quick glance at the institutional affiliations of the authors shows that all of them are employed by publicly-funded institutions.


Anne Midgette's obituary of Cesare Siepi, in The Washington Post.

An article by Thomas Fuller in Wednesday's NYT with more on the arrest of Mikhail Pletnev in Thailand for pedophilia. 

Pletnev claims "This whole thing is a misunderstanding."

And I suppose that Pletnev "owns several houses and businesses" in the seaside resort of Pattaya purely because he likes the climate, and it's simply a coincidence that Pattaya is known for its "freewheeling nightlife" (it grew from fishing village into city because of U.S. servicemen using it for R&R) and that it has a section call Boyztown.


Alex Ross at The Rest is Noise writes on this year's Bard Music Festival, which is devoted to Alban Berg and his context.  Ross also links to a collection of photographs of Berg at gettyimages, including one from Klimt's funeral that shows (among many other well-known people) Berg in uniform and Schönberg.

(I would link to the photograph and include it here, but even the preview is blighted by an obtrusive Getty Images watermark.  But it's worth looking at in any case for the Vienna-obsessed.)

We all just missed a conference at University College London, "Game Theory, Drama, and Opera"

From the conference blurb:
While [Game Theory] has been universally applied to the study of conflicts between real human agents there have been only few attempts to employ it for the understanding of fictional characters in drama or opera. This appears surprising as many plays have structures that can be naturally captured through game theoretic modeling (sequences of actions, information that can be hidden or public, common or conflicting interests, and so on).

This workshop will investigate whether there is indeed scope for game theory as an interpretative toolbox for drama and opera, drawing on examples from the repertoire and illuminating matters like belief and betrayal, or escalation and revenge.
Well sure, guys, this is obvious (and no, you're not the first to think of it), and it's not just drama, but also fiction in general, including, perhaps most importantly, film. (In fact, I did some preliminary work on this a couple of years ago in regard to a classic film that I won't mention here because who's going to pay me if someone steals the idea? The film is such a good example in this case that it could be used in classroom discussions of the evolution of reciprocal altruism.) 

And so far as I can see from the program, no one actually addressed exactly why we should be especially interested in looking at opera from this point of view.  Is there really anything in the music that can be explained or elucidated by game theory, as opposed to just the plots?  How, exactly, would one apply game theory to music anyway?  And if game theory doesn't have anything to do with the music, then why was this conference devoted to opera?  Just to give some of the usual suspects a chance to show off how smart and interdisciplinary they are?

And call me a cynic, but I wonder just how much sophisticated understanding of the mathematics of game theory was in evidence at that conference.  It isn't all just cute little four-box charts and simple integers.  I mean, really:  go look at the foundational texts by von Neumann and Morgenstern and Nash. Or take a look at this, which I had out of the library about a year ago, and realized was over my mathematical head (and my mathematical chops are considerably more advanced than your average ex-musicologist, or even your average music theorist).

And in this regard, it is interesting to note that the tree diagram used as one of the two illustrations on the home page of the conference is actually taken from Wikipedia and has nothing whatsoever explicitly to do with music, opera, or even fictional plots. It serves at Wikipedia as an illustration of an Extensive form game, which is just a way of representing (in this case a two-player) game as a tree.  Not to say that this type of diagram might not be used to outline some (very simple) fictional situations, just that this particular diagram does not illustrate a case taken from fiction.

And as long as we're in a cynical mood: what are the chances, do you suppose, that the papers from the UCL conference, when sent out for peer review (they will be sent out for peer review, of course?), will be reviewed by anyone with actual expertise in game theory or its many well-established applications?


John Marciari of the San Diego Museum of Art, and formerly a junior curator at the Yale University Art Gallery, has proposed that a painting in storage at the Yale gallery is an unrecognized early work of Velázquez. Jori Finkel has a good summary at the Los Angeles Times.

Marciari has published an article making his case in Ars Magazine. (Finkel's article mentions the Ars publication, but has no direct links.  Come on guys, this is the age of digital publishing, get with the program.)  Ars has its own story (in English) here (with several illustrations). The actual article is:
John Marciari, "Redescubriendo a Velázquez," Ars, No.7, July-September 2010, available only in the print version of the magazine (if I'm reading the Spanish correctly), but illustrated on the magazine's site with tantalizing (but illegible) thumbnails of all the pages in the article. A print copy of the magazine costs 35 € (I'm assuming that doesn't include shipping).
Here is the blurb on the article from the magazine's site:
Durante su estancia en la Universidad de Yale, John Marciari se encontró con un singular lienzo en los almacenes del museo. Su belleza cautivó al conservador. La restauración de la pieza, aún en curso, y sus características le han llevado a situar la obra en el periodo sevillano de Diego Velázquez. Publicamos por primera vez esta pintura, que podría ser la incorporación más significativa a la obra del maestro en el último siglo.
To be honest, the painting doesn't make a much of a first impression, and my "blink" reaction (which of course, could be wrong) is to remain skeptical.

Johannes Caspar of the Hamburg data protection office has filed suit against Facebook for privacy violations.

Department of Gross and Disgusting Stories (Proceed beyond this point at your own risk)

Cats found eating the foot of a 74-year old man found dead in his home in Pennsylvania.  The man probably died of a heart attack, and his 94-year-old mother probably died of dehydration when her son was no longer able to care for her (the "trash-filled home didn't have running water"). Story from The Tribune-Democrat, via BoingBoing.

I'm taking care of kitties this weekend.  I think I'll wear boots and carry a baseball bat for protection.

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  1. The caption of the picture of Berg as soldier mistakenly gives Berg as "3rd from the left".

  2. In the photo of the Klimt funeral, Berg seems to be fifth from left in the back row, and Schönberg second from left.

    The direct link to this photo, by the way, is:


    But perhaps that isn't the one you mean?