Denisovan DNA East of Wallace's Line

As naturally and inevitably as gators eat the dogs of careless owners in Florida, the one time I carelessly leave town for personal reasons--to attend the wedding of Honduran friends in Louisiana--Science ejaculates a gob of interesting articles. There are too many of them to review in one post, so I will tackle them one at a time and hope to finish one day.

First up is this discussion in the "Perspectives" section:

Cooper, A. and C. B. Stringer (2013). Did the Denisovans Cross Wallace's Line? Science 342: 321-323.

Wallace's Line is the imaginary boundary that winds north to south through the islands of modern Indonesia marking the frontier between the mainland Asian fauna to the west and the Austronesian ecosystems to the east. Cooper and Stringer attempt to explain why small "remnant" Denisovan DNA is only found in modern human populations east of the Wallace line when the only known Denisovan lived far away in southwest Siberia. The characteristics of the Denisovan DNA sequence imply a large and diverse population in Asia. The authors, however, reject the obvious idea that most east and southeast Asian peoples once had Denisovan DNA that was later "overwritten" by subsequent gene flows. Their evidence for rejecting this interpretation is pretty strong: the DNA of isolated, remote, and evidently "indigenous" Asian populations thought to predate later migrations, such as that of the Andaman Islanders, lacks Denisovan DNA, precisely where one might most confidently expect it to be found. Moreover, recent analysis of the ancient DNA from a Chinese specimen dating from ca. 40,000 ya shows no trace of Denisovan introgression. They therefore suggest that the Denisovans who crossed the Wallace Line encountered the ancestors of Homo floresiensis, the hobbits, who were there at least 800,000 ya if not 1 mya. Perhaps, they conjecture, the Denisovan DNA signal was better preserved east of the Wallace Line because of the small size of the populations involved, which might have encouraged interbreeding, or because of selective advantages conferred by some of the genes upon rapidly advancing human populations. I didn't find their final answer to be very satisfying, but their control of the data was impressive and their discussion thought-provoking.

Impact Factors, Again

On The Big Bang Theory, Sheldon says something like, "That might well appear to be serendipitous to someone unfamiliar with the law of large numbers." Well, I have a passing familiarity with the law of large numbers, but I still find it serendipitous that a major paper on impact factors and citation patterns should come out in Science the day after my little blog post on journal impact factors in archaeology. Moreover, the paper comes from the laboratory of my favorite physicist, Albert-Lázló Barabasí, who in my opinion is producing some of the finest research in the current wave of social physics. His research has focused on power law distributions and scale free and fractal patterns in social phenomena, such as networks and human movement. He is also an alarmingly talented writer, as I have said before in this blog (see my August 21, 2010 post on his book Bursts).

The article that came out on Friday is

Wang, Dashun, Chaoming Song, and Albert-Lázló Barabasí (2013). Quantifying Long-Term Scientific Impact. Science Vol. 342, pp. 127-132. 10.1126/science.1237825.

The authors present a model that purports to predict the long-term impact of scientific articles. The model incorporates three factors: 1) preferential attachment--a positive feedback dynamic in which the increase in a quantity, such as wealth, citations, or social connections, grows for each individual in proportion to its already existing value, so that the rich get richer, highly cited papers accumulate even more citations, and the well-connected develop more associations. Preferential attachment is important because it is often invoked to explain the spontaneous emergence of power law distributions and scale free patterns. The distribution of citations has often been modeled as a power law, hence the logic of including preferential attachment as a process. 2) "Aging," which accounts for the decline in citations to an article over time. The authors show that when preferential attachment is controlled for by only considering papers with the same number of citation, the subsequent citations decay over time following a log-normal distribution. 3) "Fitness" is the third factor, defined as the "inherent differences between papers, accounting for the perceived novelty and importance of a discovery." This, of course, is difficult to measure because it is complex, intangible, and subjective, and it ultimately depends on the collective views of the scientific community.

The model seems to do a good job of describing citation patterns over time, both for individual papers and for journals. For example, given the first five years of citation data for a paper, the model predicts with considerable precision the next 25 years' of citations. If the first 10 years of data are used, the prediction improves markedly. A major novelty of the model is the incorporation of preferential attachment, which seems to account for its greater success compared to previously proposed models, which do not include a preferential attachment dynamic.

Removing preferential attachment from Barabasí's model yields a simpler, "lognormal" model that, like other existing models, works well for papers with small numbers of citations, but seriously under-predicts the long-term accumulation of citations. Another way of thinking of this might be that the dynamical process has two regimes. The first few (7 or 8) citations that a paper receives are subject to random effects, but after that preferential attachment kicks in and dominates the process of securing additional citations. This is not to say that the initial citations are truly random, but merely that the cumulative effects of the processes in total yield a match to a lognormally distributed random variable. Beyond the threshold, the citation process is dominated by different factors. For example, hypothetically, the first few citations to an article might come predominantly from articles in the same journal or closely allied ones, read by one community, but as citations accumulate the probability rises of being cited in journals with different audiences, which would exponentially increase the visibility of the article, thereby setting in motion the preferential attachment regime. This kind of explanation might even be tested.

The Wang et al. article set me to wondering whether we are nearing the day when one could engineer an article to be highly cited. I think the answer is still "no" because the critical part of the model is fitness, which remains a hot mess of imponderables. To address this, one could, hypothetically, pick the research topic of one's article through a social psychological analysis designed to identify a subject of optimal interest to the scientific community. I don’t know whether that is really possible, but I doubt it would be desirable. I fear it would preempt the element of serendipity that typifies most of the really significant and interesting scientific discoveries. 

Archaeology Journal Impact Factors

An obscure little Internet start-up named Google provides journal impact factors in its Google Scholar Metrics pages. The impact factors for the Top 20 archaeology journals are interesting. (They report the h5-index impact factor. Here is an explanation of it.)

The journal with the highest impact factor is the Journal of Archaeological Science. I wasn't surprised by this when I saw it yesterday because I had previously looked up its impact factor when I applied for tenure. I do remember, however, being very surprised when I first learned that it was the most impactful journal. Perhaps the popularity or significance of the journal is driven by the fundamental nature of archaeological science to our scholarly enterprise. Or, it might relate to the journal's truly worldwide focus--in contrast to most archaeological journals which have a geographic or regional focus--as well as to its high frequency of publication--it's the only monthly archaeological journal I know of.The latter is relevant because the formula for the h-index takes into account numbers of papers, and so a journal that publishes more articles seems likely to have an advantage.

For me, the big surprise was the second journal on the list: Vegetation History and Archaeobotany. I've never heard of it. As recently as last week, I asked a paleoethnobotantist whether there was a journal dedicated to paleobotany, and I was unequivocally told "no." Like JAS, this journal seems to be truly international in focus and is now being published 5 or 6 times a year, while most archaeology journals come out quarterly or semi-annually.

The placement of Numbers 3 and 4 on the list, Anitquity and Archaeometry respectively, are no surprise, but I would not have guessed that The Journal of Cultural Heritage would come in at No. 5. Maybe I shouldn't be so surprised: public archaeology and heritage management are world-wide concerns, and even though I'm involved in them, it's still easy for me to underestimate their impact. Also, the journal covers conservation and other museum issues, which draw in a somewhat different and perhaps larger audience than pure archaeology.

Finally, I was a bit taken aback by American Antiquity's rank: No. 9. I would have it expected it to be higher.

Take a look at the full list. It might influence what you read and where you choose to submit manuscripts, especially since some universities are looking at journal impact factors in evaluating researchers for productivity, pay, and promotion.

PS. Note that by some weird coincidence Michael Smith recently wrote a very interesting related blog post that looks at the impact factors as calculated by Thomsen Reuters Web of Knowledge, which are very different because they use a different article and citation database.

Dear NASA, Happy Birthday!

Dear NASA, Happy Birthday! To Celebrate, We're Shutting You Down. Love, Congress

From The Atlantic....

I won't be submitting any grant proposals today or tomorrow. The NSF grant proposal submission site, Fastlane, is turned off.

Online Archaeology Job Hunting Seminar

The Society for American Archaeology (SAA) is sponsoring a FREE online seminar for students about how to get a job. In an e-mail, they write,

"Get Hired!" is a one-hour online seminar that will help both graduate and undergraduate archaeology students and recent graduates in their transition from student to a career. It’s led by Ms. Carol J. Ellick, Director of Archaeological and Cultural Education Consultants, one of the leading experts in archaeological education and the development of public programs.  The seminar is free to SAA members only.

For more information about these seminars and to learn about future offerings in the SAA Online Seminar Series, visit http://www.saa.org/AbouttheSociety/OnlineSeminars/tabid/1503/Default.aspx.

 Sounds great! Please share with your students.

Cave research in Nicaragua

This should be a short post because there has been very little archaeological research on caves in Nicaragua. One probable reason for the dearth of research is the paucity of caves in Nicaragua, which is mostly volcanic. There are a few caves of volcanic origin, but they are not common. The only limestone area of the country, where caves should be (and may be) more common, is a small expanse of karst in a remote and inaccessible stretch along the northern border. There, Suzanne Baker recently discovered a significant cave with paintings that she named Cueva la Conga. There's a fine article on it in the new number of Latin American Antiquity that just came in the mail.

Baker, Suzanne M. and Ruth Ann Armitage (2013). Cueva La Conga: First Karst Cave Archaeology in Nicaragua. Latin American Antiquity Vol. 24, No. 3, pp. 302-329.

This is not the first article published about the cave. You can also see

Li, Ran, Suzanne Baker, Cathy Selvius DeRoo, and Ruth Ann Armitage (2012). Characterization of the Binders and Pigments in the Rock Paintings of Cueva La Conga, Nicaragua. In Collaborative Endeavors in the Chemical Analysis of Art and Cultural Heritage Materials, edited Patricia L. Lang and Ruth A. Armitage, pp. 75-89. American Chemical Society. ACS Symposium Series, Vol. 1103. DOI: 10.1021/bk-2012-1103.ch004.

Here you can find a nice web site about the project too.

Continuing on the theme of Nicaraguan cave research, I'm in the process of translating (from Spanish to English) long excerpts from the reports of Fray Antonio Margil de Jesús and Fray Rodrigo Betancourt describing their attempt to evangelize the central highlands of Nicaragua in 1703. Transcriptions of the documents have been published by both Ruz and Van Broekhoven. The latter transcription appears to be more complete and is certainly easier to parse because of the highly creative but unconventional organization of Ruz's article. The two transcriptions also differ, at least slightly, because they come from two different copies of the reports. Ruz found his copies in the Franciscan archives in Rome, the Archivio Generale de la Ordine dei Fratri Minori, while Van Broekhoven's come from a conventual archive in Querétaro, México. What do these have to do with cave archaeology? They contain remarkable descriptions of cave worship and rites, so much so that the majority of the text concerns the religious use of caves in one way or another. It's great stuff! The cultural-religious patterns they describe sound very Mesoamerican, so it is relevant to all those Mayanist and Mexicanist cave archaeologists, though I have never seen it cited by them. I plan to include my translations in a book, the manuscript of which is nearing completion. Wish me luck in the proposal and submission process. Here are the full references for Ruz and Van Broekhoven:


Ruz, Mario Humberto (1994). Atajar los ríos, poner puertas al campo. Loa sacramental para los dioses de Nicaragua, 1703. Estudios de Cultura Novohispana, Vol. 14, pp. 61-115, México, UNAM: Instituto de Investigaciones Históricas.

Electronic copies of Ruz's article are available on the internet.

Van Broekhoven, Laura N. K. (2002) Conquistando Lo Invencible: Fuentes Históricas sobre las Culturas Indígenas de la Región Central de Nicaragua.Leiden (The Netherlands): CNWS Publications.

This book is out of print and difficult to obtain, except through InterLibrary Loan here in the United States.  It merits reprinting.

Request: Do you know of any archaeological research on the domestication of tea?

One of my graduate students has an interest in tea. I have not had much success in finding articles that offer primary archaeological data on the origin and domestication of tea. It is such an important crop that the apparent lack of literature seems odd. If you can share with me any references or articles, I'd be grateful. If the lack of research is not merely apparent but real, then perhaps the topic merits more study.

Thanks!

Video of Yucatec song: "My Culture Will Never Die"

Here is moving video of a young Yucatec Maya man singing his song "My Culture Will Never Die" in Yucatec.

You don't hear a lot of music performed in Yucatec.

The man who posted the video has a number of other Yucatec language videos on his YouTube channel.

Enjoy!

Flint knapping and language--follow-up

The best comment I've seen on this study (see the previous post): "More proof that flintknapping is the origin of swearing" by Peter Mills (on the university press release website).

Flint Knapping and the Evolution of Human Language

The idea that tool-making and the human capacity for language were linked has been floating around for a while, but a new article in PLoS ONE uses brain imaging to show they really are connected, through the activation of the same lateralized parts of the brain.

Citation:

Uomini, Natalie Thaïs and Georg Friedrich Meyer (2013) Shared Brain Lateralization Patterns in Language and Acheulean Stone Tool Production: A Functional Transcranial Doppler Ultrasound Study PLoS ONE 8(8): e72693. doi:10.1371/journal.pone.0072693.

They actually hooked flint knappers up to a functional transcranial Doppler Ultrasound machine while they made Acheulean handaxes and, alternately, produced words based on initial letter cues. The latter is evidently an established test for brain lateralization in linguistic production. The two tasks are reported to have produced very similar and highly correlated brain activity as measured by blood flow. If you're wondering why they didn't use one of the better known brain imaging techniques, such as functional MRI, think about the knapping. Most imaging techniques won't work properly if you're whacking away a big nodule of stone. They found some pretty handy knappers. The handaxes are pretty impressive (see Figure 2, but note that the captions of Figures 2 and 3 seem to have been swapped). Don't miss the video of one of the knappers.

The authors suggest that tool making by flint knapping may have played a role in the co-evolution of language, starting with the Acheuleans (Lower Paleolithic). This would be earlier than many of the chronological estimates for the emergence of language, which often rely upon analyses of anatomy and morphology. Overall, the PLoS ONE article is pretty interesting and clever research. I knew there had to be a reason I was studying those chips of stone.