28 August 2010

Daily Digest, 2010.08.27

Friday: editor of Cognition says fabrication of evidence the only "plausible" explanation in Hauser case; would open online peer review become merely a popularity contest?; JSTOR riles the librarians; a new series on meaning in language; Williams Syndrome and synaesthesia; homology and analogy; genetics of the Ashkenazim; genetics of the Tut family; the evolution of music, at ICMPC; the sociology of religion in Death Metal; Best(Worst) Pun in a Science Book Title; a pig's whisper.


On Friday, Gerry Altmann, editor of the journal Cognition—which has retracted an article that Marc Hauser published in the journal in 2002—published a post on his blog based on his analysis of evidence relevant to that paper from Harvard's investigation of Hauser .

Altmann states bluntly that the only "plausible" conclusion, in his view, is that Hauser fabricated some of the data in the paper.  Altmann's statement, which is quite damning, is worth quoting in full:
As Editor of the journal Cognition, I was given access to the results of the investigation into the allegations of misconduct against Marc Hauser as they pertained to the paper published in Cognition in 2002 which has now been retracted. My understanding from those results is the following: the monkeys were trained on what we might call two different grammars (i.e. underlying patterns of sequences of syllables). One group of monkeys were trained on Grammar A, and another group on Grammar B. At test, they were given, according to the published paper, one sequence from Grammar A, and another sequence from Grammar B - so for each monkey, one sequence was drawn from the "same" grammar as it had been trained on, and the other sequence was drawn from the "different" grammar. The critical test was whether their response to the "different" sequence was different to their response to the "same" sequence (this would then allow the conclusion, as reported in the paper, that the monkeys were able to discriminate between the two underlying grammars). On investigation of the original videotapes, it was found that the monkeys had only been tested on sequences from the "different" grammar  - that is, the different underlying grammatical patterns to those they had been trained on.  There was no evidence they had been tested on sequences from the "same" grammar (that is, with the same underlying grammatical patterns). Why is this important? Because if you just tested the monkeys on one underlying pattern, and you record how many times they turn around to look towards the hidden loudspeaker (this is how it was done), perhaps they would turn round as often if they heard **anything** coming from that speaker. So you'd need to include the "same" condition - that is, the sequence of syllables that had the same underlying pattern as the monkey had been trained on, to show that the monkeys *discriminated* between (i.e. turned a different number of times in response to) the different grammars.

It would therefore appear that the description of the study in the Cognition paper was incorrect (because the stimuli used during testing were not as described), and that the experiment *as run* did not allow any conclusions to be drawn regarding monkeys' ability to distinguish between different grammatical patterns. Given that there is no evidence that the data, as reported, were in fact collected (it is not plausible to suppose, for example, that each of the two test trials were recorded onto different videotapes, or that somehow all the videotapes from the same condition were lost or mislaid), and given that the reported data were subjected to statistical analyses to show how they supported the paper's conclusions, I am forced to conclude that there was most likely an intention here, using data that appear to have been fabricated, to deceive the field into believing something for which there was in fact no evidence at all. This is, to my mind, the worst form of academic misconduct. However, this is just conjecture; I note that the investigation found no explanation for the discrepancy between what was found on the videotapes and what was reported in the paper. Perhaps, therefore, the data were not fabricated, and there is some hitherto undiscovered or undisclosed explanation. But I do assume that if the investigation had uncovered a more plausible alternative explanation (and I know that the investigation was rigorous to the extreme), it would not have found Hauser guilty of scientific misconduct.
Altmann's reaction is covered by Carolyn Johnson at the Boston Globe (which first broke the Hauser story); Mark Liberman at Language Log has additional links and reproduces a graph and a passage from Hauser's 2002 paper that seem to be based on the allegedly fabricated data.  Jerry Coyne at Why Evolution is True also reports on Altmann's post (quoting Johnson's story), and adds his own scathing comment:
It’s absolutely unbelievable that, as a sanction for this kind of crime against science, Hauser was given just a year’s suspension without pay. (There may also have been sanctions about his future ability to mentor graduate students and postdocs.)  Although funding agencies like the NIH and NSF may impose further sanctions, he’ll nevertheless get to keep his job—forever.  I’m deeply ashamed of my alma mater.
I wonder, though, whether Hauser will actually "get to keep his job." Harvard very much dislikes bad publicity, as Larry Summers discovered. So if things keep looking as bad for Hauser as they have been, I would guess that the pressure on him to resign will grow.  Harvard protects its image above everything.

Matthew Nisbet at Big Think passes on the reactions of Wendy Melillo Farrill of American University to the recent article in the NYT about Shakespeare Quarterly's experiment with open online peer review, and Nisbet's subsequent post about open review at Big Think.

Farrill cites research done by James Evans, published in Science in 2008 (she cites Evans via Nicholas Carr's recent book The Shallows); according to Farrill, Evans found that:
Since journals moved online, scholars cited fewer journals than they had previously. Scholars also cited more recent articles with increasing frequency. The broadening of information led to a "narrowing of science and scholarship," Evans found. When Evans discussed his findings in a 2008 article in Science, he explained his counter-intuitive results by suggesting that search engines, which emphasize popular search findings, quickly establish and reinforce a consensus about what information is important and what isn't. The ease of clicking on hyperlinks leads online researchers to "bypass many of the marginally related articles that print researchers" would routinely skim as they browsed through journal articles and books in a library.
She wonders whether a similar effect might occur with online peer review:  basically, she worries that online peer review might become a popularity contest.

I guess we won't know until we actually try it.


As I frequently complain in this blog, I currently do not have access to the resources of a research library, and I have to rely on the kindness of strangers (and occasionally friends) in acquiring copies of recent research articles that are trapped behind paywalls at extortionate prices.  Because my recent interests have largely been focused on the current literature in cognitive science, evolutionary biology, and the like, I haven't lately been using JSTOR (which has not been a go-to source for the sciences), although I do have access to it, of a sort.

So I nearly missed the recent minor tempest caused by JSTOR's recent changes to its interface; see Steve Kolowich's story at Inside Higher Education

In a nutshell: librarians were appalled that JSTOR changed its interface in such a way that search results included by default articles that the user could not access through the JSTOR site without additional payment, and the JSTOR interface did not allow the local library to add an OpenURL that could alert the user when the item was otherwise available at that particular library (through, say, a different subscription).  JSTOR, like a cheating lover, quickly said it was all a mistake and a misunderstanding, and began to try to address the librarians' concerns.

Still, Barbara Fister at BlogU at Inside Higher Education wonders how JSTOR managed to persuade themselves that the original interface changes were a good idea, and she especially takes them to task for the omission of OpenURL.  Worth reading, if you care about access (and you should).


Melody Dye at Child's Play has begun what promises to be a fascinating new series on "the workings of human languages." Her first post examines the question "What is the relationship between words and the world?"

Or, more colloquially: How the hell is that we understand each other when we talk, anyway?

Kevin Mitchell at Wiring the Brain has an interesting post on Williams Syndrome and synaesthesia.  A quote:
One of the most remarkable features of Williams syndrome is the strong attraction of patients for music. Many show a strong interest in music from an early age and greater emotional responses to music. They are also more likely to play a musical instrument, some using music to reduce anxiety. A recent study from Elisabeth Dykens and colleagues adds a new twist to this story. They found in a neuroimaging experiment that in addition to activating the auditory cortex, music also stimulates visual activity and perceptions in Williams patients. In fact, this is not specific to music – non-musical sounds had the same or even stronger effects.

This is very reminiscent of what happens in a form of synaesthesia, called “coloured hearing”.
The new study to which Mitchell is referring is:
Tricia A. Thornton-Wells, et al. (2010), "Auditory Attraction: Activation of Visual Cortex by Music and Sound in Williams Syndrome," American Journal on Intellectual and Developmental Disabilities. The article is behind a paywall, but the price is not immediately accessible.
Here is the abstract:
Williams syndrome is a genetic neurodevelopmental disorder with a distinctive phenotype, including cognitive–linguistic features, nonsocial anxiety, and a strong attraction to music. We performed functional MRI studies examining brain responses to musical and other types of auditory stimuli in young adults with Williams syndrome and typically developing controls. In Study 1, the Williams syndrome group exhibited unforeseen activations of the visual cortex to musical stimuli, and it was this novel finding that became the focus of two subsequent studies. Using retinotopy, color localizers, and additional sound conditions, we identified specific visual areas in subjects with Williams syndrome that were activated by both musical and nonmusical auditory stimuli. The results, similar to synesthetic-like experiences, have implications for cross-modal sensory processing in typical and atypical neurodevelopment.

Philosophy of Biology

John Wilkins at Evolving Thoughts has a wonderful post on "Homology and analogy" in classification.

I say "wonderful" not because it is perfect, but rather because it isn't: it's an example of what blogs can be at their best in scholarship and research. His post shows a very smart and knowledgeable scholar "thinking in public," and allowing other smart and knowledgeable people to poke holes in his thoughts or even blow them out of the water. It takes courage to do that, and a true commitment to the search for knowledge in an era when all too many scholars are motivated mainly by the quest for prestige and professional advancement.

I've been hoping to find time to get to his other recent posts on classification, a subject of great interest to me, albeit coming from the quite different angle of my "first" dissertation (the unfinished one) on the concept of genre (in music and in general), as exemplified by the concerto in the 18th century.

John's post on "homology and analogy" (and the subsequent discussion of the problems in his presentation of the mathematical concepts of "isomorphism" and "homomorphism," which also takes me back to an earlier lifetime) may get my mental juices flowing on these topics again. It's been a long time.


Razib Khan at Gene Expression writes on a new study in PNAS on the genetic history of Ashkenazi Jews. This paper follows hot on the heels of two papers earlier this year that look at the genetics of Jewish populations more broadly (see the links in the first paragraph of Razib's post, or the links in my posts here and here).

The new article is:
Steven M. Bray, et al. (2010), "Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population," Proceedings of the National Academy of Sciences.
Here is the abstract:
The Ashkenazi Jewish (AJ) population has long been viewed as a genetic isolate, yet it is still unclear how population bottlenecks, admixture, or positive selection contribute to its genetic structure. Here we analyzed a large AJ cohort and found higher linkage disequilibrium (LD) and identity-by-descent relative to Europeans, as expected for an isolate. However, paradoxically we also found higher genetic diversity, a sign of an older or more admixed population but not of a long-term isolate. Recent reports have reaffirmed that the AJ population has a common Middle Eastern origin with other Jewish Diaspora populations, but also suggest that the AJ population, compared with other Jews, has had the most European admixture. Our analysis indeed revealed higher European admixture than predicted from previous Y-chromosome analyses. Moreover, we also show that admixture directly correlates with high LD, suggesting that admixture has increased both genetic diversity and LD in the AJ population. Additionally, we applied extended haplotype tests to determine whether positive selection can account for the level of AJ-prevalent diseases. We identified genomic regions under selection that account for lactose and alcohol tolerance, and although we found evidence for positive selection at some AJ-prevalent disease loci, the higher incidence of the majority of these diseases is likely the result of genetic drift following a bottleneck. Thus, the AJ population shows evidence of past founding events; however, admixture and selection have also strongly influenced its current genetic makeup.
Razib's excellent summary (which also provides added context and analysis) may be all you need. But the article itself is a free download, so don't hesitate: you have nothing to lose.

National Geographic has a fascinating feature article ("King Tut's Family Secrets") by Zahi Hawass on the recent DNA analysis of the mummy of King Tutankamun and several other mummies. The analysis clarifies Tut's family relationships, and provides persuasive identifications of several previously unidentified mummies.

It now appears that Tut was the son of Akhenaten, who is very likely the previously unidentified mummy known as KV55. What is more, Tut's mother was almost certainly one of Akhenaten's sisters:  in other words, Tut was the product of brother-sister incest.  Although it is less certain, there is also now genetic evidence to suggest that previously unidentified mummy KV21A is Ankhesenamun, Tut's wife and half sister (she was the daughter of Akenaten and Nefertiti, who was almost certainly not Tut's mother).

The article includes an interesting sidebar by David Dobbs (of Neuron Culture), "The Risks and Rewards of Royal Incest," a great interactive family tree showing some of the important genetic markers that were used in the analysis, and a photo gallery.


Victoria Williamson summarizes a session on the evolution of music on day 2 of the International Conference on Music Perception and Cognition. The session was organized by Aniruddh (Ani) Patel, of The Neuroscience Institute in San Diego, and author of Music, Language, and the Brain (2008).

The session consisted of an introduction to the topic, by Tecumseh Fitch; a talk by composer David Teie and Charles Snowden on music composed for Tamarin monkeys that takes into account the range of their own vocalizaitons (an obvious thing to do, from my point of view; but this kind of thing is often overlooked in animal studies); a talk which Williamson does not summarize by Hugo Merchent about the abilities of monkeys to reproduce timing intervals; and an update from Ani Patel on his work with Snowball the dancing cockatoo.

One of these days pretty soon, I'm going to make available the longish paper I wrote on Snowball for Irene Pepperberg's class in Animal Cognition at Harvard Extension in the spring 2008, before Patel had published any of his findings, as some of my readers may find it amusing.  I wrote the paper at Pepperberg's suggestion, but she never commented on it (I got an A in the class).  Patel's recent experiments investigating the social component of Snowball's drive to dance sound quite interesting. However, I think I know a key aspect of what's going on with Snowball that has, so far as I know, not yet been mentioned in the literature. Since I'm unemployed and have no standing in the field, I'm obviously not going to mention it here.

Greg Downey at Neuroanthropology has a fascinating post, "Death metal, religion and the socialization of emotion." Some of my readers will be skeptical of the positive reference to the work of Robert Walser. I have no opinion on that matter (I haven't read his work), but this is, in fact, the kind of question that the sociology or anthropology of music should be addressing.


Best (or, depending on your perspective, perhaps the worst) pun in the title of a recent book on science or math:
Alex Bellos, Here's Looking at Euclid: A Surprising Excursion through the Astonishing World of Math
The book is briefly reviewed by Elizabeth Quill at Science News.

language hat passes on (via Schott's Vocab) this recent (March 2009) draft revision for an entry in the OED:
pig's whisper, n.
Brit. /pɩgz wɩspə/, U.S. /pɩgz (h)wɩspər/ Forms: 17- pig's whisper, 18 pigs-whisper. [< the genitive of PIG n. + WHISPER n.]
1. A very short space of time, an instant.
1780 J. O'KEEFFE Tony Lumpkin in Town I. 4 I'll be with them in a pig's whisper. 1837 DICKENS Pickwick Papers xxxi. 333 You'll find yourself in bed, in something less than a pig's whisper. [...] 1918 P. B. KYNE Valley of Giants xxv. 218 'Thanks so much for the invitation', Ogilvy murmured gratefully. 'I'll be down in a pig's whisper'. 1991 R. COOVER Pinocchio in Venice xxi. 229 'Back in a crack, direttore!' 'In a pig's whisper, direttore!'
2. A whisper; a confidential tone of voice.
1846 Swell's Night Guide 110/1 Pig's Whisper.., a word 'twixt you and me. 1866 M. BANIM Peter of Castle 5 The eulogist may.. in what they call a pig's whisper (that is, in a confidential tone).. [relate] a few anecdotes of his prowess. 1922 J. JOYCE Ulysses II. 484 Virag (Prompts into his ear in a pig's whisper). 2001 Hindu (Nexis) 21 Jan., I heard Ata informing Mummy, in a pig's whisper, that plagiarism, too, was actionable.
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