26 August 2010

Daily Digest, 2010.08.25

Wednesday: Akst on peer review; Nigel Hawkes on peer review; experiments in peer review; organizing an open science project; the NYT comes out in favor of tweaking copyright; Stevie Nicks says Internet killed rock; a project to record symphonies for the public domain; the psychology of possibility; Grayling on neurophilosophy; autism at The Browser; inclusive fitness overturned?; the world's smallest frogs; Esperanza Spalding hits Europe; an interview with Klaus Heymann on the future of classical music recording; Ansel Adams Publishing Trust files suit; happy 80th birthday, Sean Connery.


Several links today on peer review (see also my separate post on the latest entry in Melody Dye's series on the "politics of ideas," which also deals with peer review).

Jef Akst wrote earlier this month at The Scientist on peer review: on why some think it is broken, and on attempts by some journals to fix it ("I Hate Your Paper").  Here are the main points in Akst's piece (I've omitted his lengthy but very interesting elaborations of each point, which anyone interested in the topic should read in full):
Problem #1

Reviewers are biased by personal motives

Solution: Eliminate anonymous peer review ( Biology Direct, BMJ, BMC); run open peer review alongside traditional review (Atmospheric Chemistry and Physics); judge a paper based only on scientific soundness, not impact or scope (PLoS ONE)


Problem #2

Peer review is too slow, affecting public health, grants, and credit for ideas

Solution: Shorten publication time to a few days (PLoS Currents Influenza); bypass subsequent reviews (Journal of Biology); publish first drafts (European Geosciences Union journals)

[Akst's discussion of this point refers to Google Knol, with which I'm not familiar, but need to investigate]


Problem #3

Too many papers to review

Solution: Recycle reviews from journals that have rejected the manuscript (Neuroscience Peer Review Consortium); wait for volunteers (Chemical Physics Letters); reward reviewer efforts (Biology Direct, BMC, Frontiers, ACP)
This is an excellent article: thoughtful and well-researched. Highly recommended.

This past Saturday (21 August), Nigel Hawkes published an opinion piece on peer review in The Independent: "Peer-reviewed journals aren't worth the paper they're written on." Considerably less thoughtful than Akst's piece, considerably more contentious, and full of overheated rhetoric.  Hawkes writes that peer review is "largely hokum," because rejected articles end up being published by journals "further down the pecking order," and peer review "seldom detects fraud." (But then, how could it be expected to? Even only moderately clever fraud may be very difficult to detect, especially if the raw data is not made available.) He writes, without citing any evidence, that peer review "is biased against women and against less famous institutions, and that its "benefits are statistically insignificant." And more in this vein.

His anger seems to spring particularly from two recent instances of gratuitous arrogance on the part of academic researchers and an academic journal. The first involved Professors Kate Picket and Richard Wilkinson, authors of The Spirit Level, who claimed that because the research behind their book was all peer-reviewed, debate about their book should only take place in peer-reviewed publications. This was just downright silly (and very unlikely to happen in any case).  But it does seem indicative of a certain kind of blinkered arrogance that one not infrequently finds in academics.

The second incident involved an article published in The Lancet about mortality from Casearean operations.  The Lancet high-handedly dismissed criticism of the methodology and conclusions of this article from outside the academic community. This was short-sighted, unwise, and stupid, but it does not by any means justify calling the entire enterprise of peer review "hokum."

On Monday (23 August), Patricia Cohen at The New York Times published an article (oddly, it's in the Arts section) on an experiment with an open web alternative to traditional peer review.  Shakespeare Quarterly undertook the experiment for its fall issue.  As Cohen explains:
Mixing traditional and new methods, the journal posted online four essays not yet accepted for publication, and a core group of experts ... were invited to post their signed comments on the Web site MediaCommons, a scholarly digital network. Others could add their thoughts as well, after registering with their own names. In the end 41 people made more than 350 comments, many of which elicited responses from the authors. The revised essays were then reviewed by the quarterly’s editors, who made the final decision to include them in the printed journal, due out Sept. 17.
Dan Cohen, director of the Center for History and New Media at George Mason University (and whose Digital Humanities Blog is a must read) is quoted in the NYT article as saying:  “Serious scholars are asking whether the institutions of the academy — as they have existed for decades, even centuries — aren’t becoming obsolete."

It's clear to me that many of them are already obsolete.

The article is well worth reading in full.  Among other things it has pointed me to two sites that I wasn't previously aware of:
Media Commons (which conducted the open peer review experiment for Shakespeare Quarterly), which describes itself (in part) as follows:
"MediaCommons, a project-in-development with support from the Institute for the Future of the Book (part of the Annenberg Center for Communication at USC) and the National Endowment for the Humanities, is a network in which scholars, students, and other interested members of the public can help to shift the focus of scholarship back to the circulation of discourse."
Sociologica, the Italian Journal of Sociology online, which describes itself thus:
Sociologica aims at debating sociologically relevant issues in an open but rigorous way; at promoting sound intellectual exchange between different approaches within the social sciences and between different theoretical and methodological traditions; and at exploiting the potential of online web 2.0 tools to advance active scientific exchange.

Meanwhile, Cameron Neylon at Science in the Open has a very interesting post about the nuts and bolts of organizing a major scientific project that aspires to be "as open as possible."  Read his "Separating the aspirations and the instruments of Open Research."

Creative rights (Music division)

Responding to the possibility that public availability of the newly discovered Savory collection of jazz recordings (see my previous posts on the collection here, here, and here) may be hindered by current copyright law, The New York Times has published an editorial supporting fixes to that law that would ease the process of making recordings like these accessible.

The Times suggests first that sound recordings be brought under purview of federal copyright law (which does not currently cover sound recordings made before 1972), and second that the copyright term on "ophan works" should be shortened.

Mike Masnick at Techdirt appreciates the sentiment, but writes:
While it's nice to see the NY Times editorial board concerned about this, it seems like if they were really serious about fixing copyright law, they wouldn't just focus on this one situation, but the overall issues associated with current copyright law. But, of course, since the newspaper mistakenly thinks it needs strong copyright laws to survive, that seems unlikely.

Masnick also points to a semi-coherent rant by Stevie Nicks, who claims that the Internet has destroyed rock.

I'm guessing she doesn't get out much? 

And as Masnick points out, she touchingly seems to think that a musician today still needs the backing of a major label in order to be successful.  Those were the good old days....

Richard Esguerra at the Electronic Frontier Foundation writes on the effort by Musopen to raise money in order to hire a world-class orchestra to create a body of digital recordings of great symphonies that can then be placed in the public domain. 

A worthy sentiment, but I'm skeptical about its prospects....


Deric Bownds points to an article by Cara Feinberg in Harvard Magazine on the work of Ellen Langer, "The Mindfulness Chronicles: On 'the psychology of possibility'."  I haven't had time to read this yet, but it sounds like a must read on the basis of Bownds' description:
An interesting article in the Harvard Magazine describes the life work of Ellen Langer, her demonstrations that our social self image (old versus young, for example) strongly patterns our actual vitality and physiology, her work on Mindfulness, unconscious processing, etc.

Sean Roberts at a replicated typo has posted parts 8 and 9 of his series on the evolution of color terms, "Embodied Relationships" and "Niche Construction."

A. C. Grayling has an essay in the series "Ideas of the century" at The Philosophers' Magazine on "Neurophilosophy," dealing with the contributions of empirical neuroscience to the study of philosophy, and the limitations of this approach.

Some quotes:
For when one thinks about persons, their characters, what they know and believe, the frameworks of concepts that organise their view of the world and their attitudes and responses to it, and the way they give weight to competing reasons for action, the neurophilosophical approach is only going to be part of the story, because in principle it cannot be the whole story. The reason is that minds have to be understood “broadly” as opposed to “narrowly”, in the same sense that we speak of “broad content” and “narrow content” in relation to mental content generally.


The implication is that the character and content of one’s mind is the result of its interaction with the social and physical settings in which it became functional and increasingly mature. Any individual mind is accordingly the manufacture of a community of minds and of input from the world; it grows by continuous feedback in interaction with parents, teachers, the community, and the physical environment. Therefore to identify what a person knows and believes, and to describe how he thinks, is to see him as a node in a complex of relationships with other minds and a manifold of accompanying external stimuli.
Which, of course, sounds like Neuroanthropology (which Grayling doesn't mention; in fact, he gives the impression of seeing empirical work in this area as being limited so far to fMRI studies).

The current topic at The Browser is autism, and includes links to interviews with Simon Baron-Cohen and Temple Grandin, a review of Tim Page's Asperger's memoir, an article at Wired on the alleged connection between autism and vaccination (for which there is no scientific evidence), and an article in CHE by Tyler Cowen on "Autism as Academic Paradigm."  I haven't had time to read these yet, but it looks like a good collection.


One of the great conundrums of evolutionary theory has been the existence of "eusocial" species, like ants and bees, in which some individuals sacrifice their own reproduction in support of the reproduction of another individual (a "queen," for example). To oversimplify: how could evolution by natural selection produce a sterile cast?

For the past four decades or so, the most widely accepted explanation to that problem has been the concept of kin selection, developed by William D. Hamilton in classic papers in 1963 and 1964 ("Hamilton's rule" has been referred to previously on this blog), and later elaborated into the theory of inclusive fitness.  Eusocial species can be considered the extreme case that led to the development of the theory, but the concepts of kin selection and inclusive fitness have been brought to bear on the problem of the evolution of altruistic or cooperative behavior in general across a broad range of species, including humans.

A new paper in Nature now claims to have overturned the theory of inclusive fitness, and to have shown that ordinary natural selection is sufficient to explain the evolution of eusociality.  This is, as we used to say in high school, a BFD.

The article is:
Martin A. Nowak, Corina E. Tarnita, and Edward O. Wilson (2010), "The evolution of eusociaity," Nature 466, 1057-1062 (26 August 2010).  It is unfortunately behind a paywall, and costs $32.00. (An angel would be appreciated here.)
Here is the abstract:
Eusociality, in which some individuals reduce their own lifetime reproductive potential to raise the offspring of others, underlies the most advanced forms of social organization and the ecologically dominant role of social insects and humans. For the past four decades kin selection theory, based on the concept of inclusive fitness, has been the major theoretical attempt to explain the evolution of eusociality. Here we show the limitations of this approach. We argue that standard natural selection theory in the context of precise models of population structure represents a simpler and superior approach, allows the evaluation of multiple competing hypotheses, and provides an exact framework for interpreting empirical observations.
Natasha Gilbert's summary at Nature News is a good place to start. Nowak is quoted there as saying:
"We show that inclusive fitness is not a general theory of evolution as its proponents had claimed .... In the limited domain where inclusive fitness theory does work, it is identical to standard natural selection. Hence there is no need for inclusive fitness. It has no explanatory power."
See also Dienekes and Razib Khan.

Marc West at the Mr Science Show has an audio interview with Professor Louis Ptáček, head of the Laboratoires of Neurogenetics at UC San Francisco, on the Photic Sneeze Reflex, "an autosomal dominant hereditary trait which causes sneezing...when suddenly exposed to bright light, possibly many times consecutively. The condition affects 18-35% of the human population. [Wikipedia]" 

I haven't listened to the interview yet, but West also has a good short textual introduction here, as well as some useful bibliography. I've long believed that I suffer from PSR (although one doesn't suffer much), and think it likely that my Dad does too (although he may disagree!).

Annalee Newitz at io9 reports on the discovery of the world's tiniest frogs, Microhyla nepenthicola, on Borneo.  The frogs are only 10-12 mm long, but have relatively loud calls, which led to their discovery.

The article on the discovery, published in Zootaxa, is freely available here.


Volker Schmidt at Zeit Online has a profile (auf Deutsch) of jazz bassist and vocalist Esperanza Spalding, on the occasion of the release of her new album Chamber Music Society.

Gramophone interviews Naxos founder Klaus Heymann on the future of classical recording. Heymann believes that the market for physical CDs of classical music has stabilized, and that CDs will be around for "many more years to come." He does not believe that the future of classical music distribution is in downloads. A quote from Heymann:
Well, the growth in downloads has slowed down dramatically. There’s a bit of growth, but it’s not at the same rate. Again we’re talking about classical music, but I doubt it will go above 20 per cent of total sales. And 80 per cent physical. Possibly a little higher than 20 per cent in the States, and the speed of development is different in different markets. I think the future of listening will be an all-you-can-eat formula where people pay a flat rate, per month or per year, and they can listen to as much as they want. This is the model of our music library, and now our video library, of the Spotify premium model, or Rhapsody. It will happen on TV as well – I think we will not be interested in watching 150 channels and looking for what might be on at that moment. But if someone wants to watch Parsifal, they want to watch it now, and they can watch it. We’ll still see what we call linear channels, but more and more it will be an ‘on demand’ service. That will be the future. What form it will take – whether the service will be offered by broadband providers, ISPs, by telephone companies, by cable TV, electricity companies – nobody knows yet.
And speaking of the Naxos.com Music Library:
Well, it’s still universities and music schools which account for a large percentage of users. More and more professional musicians use it. If you talk to Marin Alsop or Leonard Slatkin, they say they can’t live without it any more. They use it for making programmes and listening when they travel. There’s an iPhone application now, and we’re working on Blackberry and Android applications – that’s more and more attractive to professional musicians. If a cellist is building a programme of French cello music, and they want a piece that is 11 minutes long, they can type in ‘10-12 minutes’, ‘France’, ‘cello’, click – and all the pieces come up.
Naxos started out as a budget label, and now we’re the major service provider to the industry – distribution service, logistics service, digital distribution for Chandos, Bis, for more than 60 labels, we supply the content to iTunes, to eMusic, we create metadata in Hong Kong and the Philippines. No label can do it on their own.


[W]e’re very good at [metadata]. I myself proof-read every entry – I don’t proof-read the whole listing, but I proof-read what appears on screen, as one line, and make sure that’s 100 per cent correct, and I sometimes look at others to check they’re consistent. Spelling consistency is an issue – is it C major: capital C, lower case major for example – iTunes has a formula which is not quite in line with musicology, so we basically keep two sets of data, our site which is [in the same style as] Grove and the RED catalogue, and another one which is the iTunes standard which they’ve set. Data creation is really very important – that’s why we employ 13 musicologists in Manila, and another two in Hong Kong.

We’re now working on an online music encyclopaedia, we’ve right now people who are copying up all of our music notes into the sections that belong to individual works.


David Ng at the Culture Monster blog at the Los Angeles Times reports (based on a story from the AP) that the Ansel Adams Publishing Trust has filed suit against Rick Norsigian and PRS Media Partners (the firm of the dubious David W. Streets) to block them from "using Adams' name, likeness and trademark to sell prints not authorized by the Trust."

For background on the story, see the links in Ng's post, and my posts here and here.


Sean Connery turned 80 today (co-latha breith sona dhut!).  Because of the perhaps unusual array of blogs and other new sources that I follow, I learned about his birthday not from English-language sources, but from two German papers:

Zeit Online has a wonderful gallery of 21 photos of Connery from throughout his career, including this one, from the Mr. Universe contest in 1952, in which he placed third.

And this article at FAZ.NET, with, apparently, exactly the same photo gallery, but a longer text (a nice short appreciation).
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