04 September 2010

Daily Digest, 1 and 2 September 2010

Wednesday & Thursday: Hauser's scapegoat?; what would scholarly publishing look like if it were invented today?; two new science blog networks; a reminder that you don't "own" the e-books that you thought you "bought"; a new journal on the "scientific" (i.e. empirical) study of literature; nope, no God, says Hawking; Coyne and Dawkins attack the eusociality paper; the phylogeny of culture; pack up your troubles in your old kit bag (or an envelope, or something); Dye vs. the nativists; an odd (and unnecessary) gender-neutral pronoun; it would be a really really bad idea to urinate on this fence; Here & Now reports on the Savory Collection; Ross's "audio guide" on the chaconne/lament/walking bass; Georg Friedrich Haas; a new fire curtain at the Staatsoper; Thompson & Bordwell on film; "I Survived Earl" T-shirts, On Sale, Cheap!

Because I've been running a bit behind on these digests all week, and because Wednesday and Thursday individually were a bit thin, I've decided to combine then in order to try to catch up. (Which, since I'm posting this on Saturday night, I obviously haven't...)


Neuroskeptic summarizes some of the recent developments in the Marc Hauser affair, and speculates whether Hauser has attempted to use as a scapegoat David Glynn, a former research assistant in his lab (and a likely source for the document from the Harvard investigation that was leaked to The Chronicle of Higher Education).  Which (as Neuroskeptic points out) doesn't make much sense, since the research for the retracted paper in Cognition (the one for which it looks likely that Hauser fabricated data) was done before Glynn was in Hauser's lab.

There have now been so many stories on Hauser and I've mentioned the case so many times that I'm giving up providing links to my earlier reports.  Use the "Search"!

Scholarly Publishing

Cameron Neylon at Science in the Open has a thought-provoking posts, "What would scholarly communications look like if we invented it today?"

Neylon suggests that the four principal functions that need to be filled by a system of scholarly publishing are filtering, archiving, re-usability, and registration (where "registration" means "Registration of ideas, data or other outputs for the purpose of assigning credit and priority to the right people").  He thinks that the current system deals reasonably well with filtering, archiving, and registration. He writes:
It is on re-usability and replication where our current system really falls down. Access and rights are a big issue here, but ones that we are gradually pushing back. The real issues are much more fundamental. It is essentially assumed, in my experience, by most researchers that a paper will not contain sufficient information to replicate an experiment or analysis. Just consider that. Our primary means of communication, in a philosophical system that rests almost entirely on reproducibility, does not enable even simple replication of results. A lot of this is down to the boundaries created by the mindset of a printed multi-page article. Mechanisms to publish methods, detailed laboratory records, or software are limited, often leading to a lack of care in keeping and annotating such records. After all if it isn’t going in the paper why bother looking after it?
Here here.

Neylon doesn't mention the Hauser case here; one naturally wonders whether a more open system might have helped catch that train wreck before it happened.

Neylon goes on to suggest that in the long run, the aims of scholarly publishing might be best served if we "move away from considering the paper as the only form of valid research output," and that we publish research "objects" online as soon as they come into existence.  An interesting idea, although it is not immediately obvious to me how this approach would work for, say, archival research in the humanities or interpreted videos in psychology or cognitive science (think Hauser case again). 

Which isn't to say it wouldn't work.

Neylon's post is highly recommended for anyone thinking about the future of scholarly publishing.

The reconfiguration of the science blogosphere continues.  Two new science blogging networks have just been announced:
The PLoS Blogosphere, to which Neuroanthropology, one of my long-time favorites, has moved. Daniel Lende and Greg Downey, the co-bloggers at Neuroanthropology have a great introductory post inaugurating their new home, explaining (among other things) why PLoS is so great....which it is.

And Guardian Science Blogs, about which I haven't got any particular reason to be excited yet.  But that may change.

As a reminder that you don't own your Amazon e-books in the same way that you own, say, a paperback book, Mike Masnick Techdirt reports the story of a woman who was locked out for a month from the e-books that she had legitimately purchased for her Kindle; and Amazon couldn't be bothered to help.

The extensive comments section on this post is also enlightening: many of Masnick's readers chime in with their own experiences.  This one particularly caught my eye.
chester, Sep 2nd, 2010 @ 8:26am

My wife is in grad school. Her last class required her to purchase three e-books for $80 each. They were locked pdf files that required her to be logged in to her school account to open them. So after graduation, she can't open them anymore. Worst part is the $240 is automatically added to her tuition. We had no choice but to rent the books for $240 when I could have bought the paper version for the same price or less.
This is appalling.

Personally, I don't understand why anyone would freely choose to buy an e-book (or a musical track, for that matter) in a proprietary format with any form of DRM, and I will resist doing so myself as long as I possibly can.

But when universities and teachers collude with corporations to require students to buy (errr, let's say "license" or "rent") e-books of this sort, they are forcing students to act against their own best interests.

And (as several of Masnick's commentators point out), this kind of behavior by publishers strongly increasing the incentive to "steal."

A new journal has been announced:  Scientific Study of Literature (from John Benjamin Publishing), edited by Willie van Peer of the University of Munich. The first issue will appear next year, and there will be two issues per year.  The pricing is stupid and short-sighted:  print + online is €145.00, and online is €141.00.

Here is the blurb from the journal's website:
Literature has an important role in human culture. Broadly interpreted, literature is defined as all cultural artefacts that make use of literary devices, such as narrativity, metaphoricity, symbolism. Its manifestations include novels, short stories, poetry, theatre, film, television, and, more recently, digital forms such as hypertext storytelling. This new journal, Scientific Study of Literature (SSOL), will publish empirical studies that apply scientific stringency to cast light on the structure and function of literary phenomena. The journal welcomes contributions from many disciplinary perspectives (psychological, developmental, cross-cultural, cognitive, neuroscience, computational, and educational) to deepen our understanding of literature, literary processes, and literary applications.

Scientific Study of Literature (SSOL) is the official journal of IGEL (the International Society for the Empirical Study of Literature). IGEL membership includes a subscription to SSOL.
(via OnFiction)

The Universe and Everything

Stephen Hawking's new book, The Grand Design (with Leonard Mlodinow) will be published next week, and is currently being serialized in the The Times (where, of course, it is behind a paywall, hence no link). An excerpt published in The Times has created a minor furore, because Hawking explicitly rejects the need for God in explaining the existence of the universe. 

Among the many reports, I've read Andrew Moseman at 80beats and Roger Highfield at New Scientist. Moseman provides the two quotes that have kicked up the fuss. Hawking writes:
Spontaneous creation is the reason why there is something rather than nothing, why the universe exists, why we exist. It is not necessary to invoke God to light the blue touch paper [fuse] and set the universe going.


Some would claim the answer to these questions is that there is a God who chose to create the universe that way. It is reasonable to ask who or what created the universe, but if the answer is God, then the question has merely been deflected to that of who created God. In this view it is accepted that some entity exists that needs no creator, and that entity is called God. This is known as the first-cause argument for the existence of God. We claim, however, that it is possible to answer these questions purely within the realm of science, and without invoking any divine beings.

[Saturday addendum: John Wilkins at Evolving Thoughts has posted a commentary.]


Some of the big guns have now weighed in on the "eusociaity" paper (Novak, Tarnita & Wilson 2010). John Hawks ("Inclusive fitness works") links to and cites from strongly critical responses by Jerry Coyne and Richard Dawkins.

Coyne's response, posted at Why Evolution is True, is "A misguided attack on kin selection."  A couple of quotes (but you should read the whole thing):
I’m baffled not only by Nowak et al.’s apparent and willful ignorance of the literature, but by statements that are just wrong.  They flatly assert, for instance, that “inclusive fitness theory” is something different from “standard natural selection theory.”  But it’s not: it’s simply a natural extension of population genetics to the situation in which one’s behavior affects related individuals.


I can’t fathom any motive, either psychological or scientific, for Wilson and Company to repeatedly denigrate the importance of inclusive-fitness theory.  It’s just a shame that, this late in his career, Wilson has chosen to fight the wrong battle.


Finally, a big raspberry to the folks at Nature who decided to publish such a strange paper in the interest of stirring up controversy.  If they’d gotten decent reviewers, and followed their advice, it never would have seen print.
So we can perhaps also file this story under the ongoing debate on peer review.

On the eusociality article see also Susan Milius's story at Wired Science, which provides some clarification of what the article is actually claiming. Milius quotes Martin Nowak:
Nowak clarifies that the team isn’t arguing that kinship is irrelevant in biology. “Relatedness does matter,” he says. What he and Tarnita are challenging is the accounting method of inclusive fitness, which he contends is overly complicated.
One has the impression from the Wired story that Nowak et al. are actually making an argument mainly about the math involved in theories of the evolution of cooperation and altruism.  Although I confess that so far I haven't tried to grapple with the article directly, previous experience has led me to think that evolutionary biologists (who are...let's put this charitably...not generally stellar mathematicians) play rather fast and loose with the notions of "cost" and "benefit," which are central to kin selection theory, but seem to me to be ill defined.

The Human

James Winters at a replicated typo points to two new papers by Simon Greenhill on the application of phylogenetic technique (basically, the making of genealogical trees) to human culture.  (I'm strongly interested in this, although in a skeptical sort of way, partly because of the potential applications to the analysis of textual sources in the prepartion of scholarly editions.)  The articles are apparently "in press" at Philosophical Transactions of the Royal Society, B, and are not (so far as I can see) posted yet at the journal's website.

Winters posts the abstracts for both, which are needlessly opaque and badly written. An example, from the abstract for "On the shape and fabric of human history." (With a title like that, this is either a seminal must-read or simply a paper with an overblown title):
Instead of a priori dichotomous disputes about the validity of cultural phylogenetics phylogenies, we suggest that the debate is better conceptualized as involving positions along continuous dimensions. The challenge for empirical research is therefore to determine where particular aspects of culture lie on these dimensions.
Based on that, my bet is on "overblown title."

Which doesn't necessarily mean the article is bad or uninteresting.

As regular readers of this blog know, I'm an atheist.  I'm also an active member of Theodore Parker Unitarian Universalist Church in West Roxbury. Even though I don't find the concept of God necessary (or coherent), I feel strongly that the impulses that lead human beings to religion are ones that we ignore at our peril. 

As a member of the Music & Worship Committee at Theodore Parker Church, I'm particularly interested in the role of ritual in giving shape and meaning to the lives of human communities.  I am currently helping prepare (along with minister Lilli Nye and my friend Avi Davis) our third annual High Holy Days/Yom Kippur service (to be held on Sunday, 19 September, the day after Yom Kippur; you'll be hearing more about that service here), in which we will again incorporate a version of the Tashlikh ceremony for symbolically casting off the "sins" of the previous year. 

This is not our only service that deals with "casting off." As long as I have been member, the church has also celebrated a ritual on the Sunday closest to 1 January in which the members of the congregation write on a piece of flash paper a wish for the New Year (either something to leave behind or to hope for), and place the paper into a brass bowl with a candle, where it vanishes in a quick blaze of fire.  I've found both ceremonies among the most personally and emotionally meaningful ones in which I've participated.

Thus the following study linked by Deric Bownds caught my eye:
Xiuping Li, et al. (2010), "Sealing the Emotions Genie: The Effects of Physical Enclosure on Psychological Closure," Psychological Science.  The article is behind a paywall at Sage Publicaitons, and costs $35.00
Here is the abstract:
This research investigated whether the physical act of enclosing an emotionally laden stimulus can help alleviate the associated negative emotions. Four experiments found support for this claim. In Experiments 1a and 1b, emotional negativity was reduced for participants who placed a written recollection of a regretted past decision or unsatisfied strong desire inside an envelope. However, enclosing a stimulus unrelated to the emotional experience did not have the same effect (Experiment 2). In Experiment 3, we showed that the effect was not driven by participants simply doing something extra with the materials, and that the effect of physical enclosure was mediated by the psychological closure that participants felt toward the event.
Frankly, my intuition counsels skepticism on the article, but I'd like to read it before writing my reflection for the Yom Kippur service.  So an "angel" would be appreciated.

Interesting, though, that someone is doing research on a behavior that has so much symbolic and ritualistic resonance.


Melody Dye at Child's Play continues her series of posts on the nativist vs. empiricist debate over language learning, with a strong critique of a classic (or at least old) article by Miller and Chomsky from 1963 that formalizes (or at least pretends to) the "poverty of the stimulus" argument, which any of you who have taken courses in cognitive science or linguistics in the last 30 or 40 years will undoubtedly have run into. 

Oddly, Dye doesn't, so far as I can see, list Miller and Chomsky's article in her References or link to it.  My best guess is that she's referring to George A. Miller and Noam Chomsky (1963), "Finitary models of language users," in R. Duncan Luce, et al., Handbook of mathematical psychology, vol. 2, 419-491. At any rate, the title seems to correspond to what she's critiquing.  I don't have the Handbook handy, unfortunately, and the chapter does not seem to be readily available on the Web (at least I didn't find it in a quick search).  Dye does, however, cite and link to several more recent articles that I'm looking forward to reading.

The nativists and empiricists really do not get along; each camp tends to act as if everyone in the opposing one is a feeble-minded pseudo-scientist.  So anyone interested in what a scientific brawl looks like should read the very extensive comments section on Dye's post.  (To give the flavor, in her main post, Dye compares Miller and Chomsky's argument to the arguments of Intelligent Design.)

games with words, whose posts I sometimes cite here has contributed to the commentary on Dye's post, and has also posted a not very friendly response, "When is the logically impossible possible?"

Some thoughts occur to me about all this, but as a non-specialist (if strongly interested) outsider with no allegiances, I'd be nuts to say anything.

They seem to be enjoying themselves, though.

A few days ago I posted on the history of attempts to find gender-neutral pronouns.  In a recent post, Geoffrey Pullum at Language Log discusses an example of a strikingly unnecessary (and to him, "startling") example of the singular use of "their."  The context is a request from a university for a reference for a job applicant who is clearly male. (Pullum has changed the details, including the name, in order to protect identities, but the point is still clear):
Dr Gerald Black has applied for a position of Lecturer in the Department of Criminology at the University of Penzance. I would be grateful if you could provide a reference on their suitability for this post.
I find it particularly striking that most of the comments (which are quite extensive on this post) seem to have no trouble with this, or even defend it.

Victor Mair at Language Log passes on this unambiguous sign in the language Visayan from the central Philippines:

As Mair explains:
Transcription:  Guinadili ang pag-pangihi dinhi. Ang silot [bang!]
This can be roughly analyzed as:
forbidden TOPIC act.of-urination here. TOPIC penalty [bang!]
More freely: "It is forbidden to urinate here. The penalty is [bang]"


On Thursday, the NPR program Here & Now had a segment on the Savory Collection of live jazz recordings from the late 1930s and early 1940s.  You can listen to the segment here.  Lots of brief and tantalizing sound clips.

Alex Ross of The Rest is Noise is back from vacation, with a vengeance.

His next book, Listen to This, will be published at the end of September, and Ross has already made the framework for the "Audio Guide" for the book available at his blog The Rest is Noise (the existence of the guide suggests that Ross and the publisher are grooming the book for classroom use, perhaps for music appreciation classes?). 

I have not yet thoroughly investigated, but the framework for the Audio Guide to Chapter 2, "Chacona, Lamento, Walking Blues," with many many audio clips, will certainly be of interest to some of my readers.  The examples posted so far (which are keyed to pages in the book) range from eastern European folk music to the Play of Daniel to Monteverdi (of course) to Ligeti to Mamie Smith to "My Funny Valentine" (of course) and Led Zeppelin.

Ross also writes on Moving Sounds, a series of concerts taking place right now (2-5 September), a co-production of The Austrian Cultural Forum New York, The Argento New Music Project, MICA Music Austria, and The Czech Center.  The featured composer in the series is the Austrian Georg Friedrich Haas.  I'd never heard of Haas until reading Ross's post (I'm admittedly a bit out of the loop these days when it comes to contemporary "classical" music), but Ross raves about Haas, mentioning that at the conclusion of his book The Rest is Noise, he referred to Haas's in vain as "one of the great pieces of the new century." 

There is a sample sound clip embedded in Ross's post (apparently from in vain, although it's not clearly labeled), and it is certainly striking enough that I'm going to look for more recordings.

The stage at the Staatsoper in Vienna is fronted buy a protective iron fire curtain. I attended many performances (probably over 100) at the Staatsoper during the years I lived in Vienna, almost always in standing room, which meant that I almost always arrived before the fire curtain was raised. Through all my years in Vienna, this was the fire curtain I saw (depiction of Orpheus leading Eurydice out of Hades, by Rudolf Eisenmenger):

This curtain has now been replaced.  The new fire curtain is by American artist Cy Twombly; the title (which may not be evident from its appearance) is "Bacchus" (which has no clear reference in opera):

Read the story Der Standard (auf Deustch).

I hope they saved the old curtain.


Kristin Thompson and David Bordwell, the proprietors of my favorite film blog, Observations on film art, are also the authors of a popular introductory textbook on film, Film Art: An Introduction (on my Amazon wishlist).

At the beginning of the school year for the past few years, Thompson and Bordwell have posted a list keying some of their blog posts from the preceding year to the relevant chapters in the textbook, as an aid to anyone who wish to draw on their blog posts for teaching.  This year's list is here.  Worth perusing even if you aren't teaching or taking a class.


[Saturday morning:]

So what am I going to do the 500 "I Survived Earl" T-shirts that I had printed up??

I have an idea.  I'll take them back to the printer and have this photo added underneath:

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