Anthropology.net

The current issue of the Journal of Neurodevelopmental Disorders has published an open access paper announcing the discovery of a new candidate gene linked to language, KIAA0319. The paper is titled, “Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment.”

The gene sits on short arm of Chromosome 6. Through linkage analysis, it was found to be associated with variability in language abilities in a study of children with Specific Language Impairment (SLI) and their family members, as well as with variability in speech and reading abilities. Specific alleles were confirmed with association analysis.

“A total of 322 participants, including 86 probands, 134 siblings, and 102 parents and other relatives were tested from an ongoing longitudinal study of Specific Language Impairment… The significant results cluster in the 5’ region of KIAA0319… In particular, we replicate the associated alleles for rs4504469 (allele C); rs761100 (allele G); rs6935076 (allele T) and rs3756821 (allele A).”

It should be noted that KIAA0319 was already linked to dyslexia in previous studies. But, in this paper, the pleiotropic effects of KIAA0318 alleles on language ability, speech impairments, and text comprehension were correlated.

Rice, M., Smith, S., & Gayán, J. (2009). Convergent genetic linkage and associations to language, speech and reading measures in families of probands with Specific Language Impairment Journal of Neurodevelopmental Disorders DOI: 10.1007/s11689-009-9031-x

FOXP2 is one of my favorite genes. I studied it extensively while getting my Master’s degree and wrote about it several times on Anthropology.net. For those that do not know much about it, I’ll quickly introduce it. FOXP2 is a transcription factor gene, which means it controls the expression and regulation of many other genes. It is significant in that it is implicated in human language.

I caught news of a new study on FOXP2 today while reading Nicholas Wade’s article in the New York Times about a hot-off-the-press Max Planck study published in Cell on FOXP2. The study comes from Svante Pääbo‘s lab, who created a strain of transgenic mice with the human FOXP2 variant and noted that these mutant mice made whistles that had a slightly lower pitch than ones with the wild-type FOXP2 gene.

The study has been published as an open access paper under the title, “A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice.” There are more findings tucked inside the paper that indicate the impact of the human FOXP2. Aside from the changes in dopamine levels, the most interesting one is the increased axonal and dendritic length of medium spiny neurons in the basal ganglia by 80% when compared to FOXP2^wt. These neurons coordinate the movement and timing of multiple organ systems. Check out the differences for yourself:

Foxp2(hum) Increases the Length of Dendritic Trees

The authors hypothesize on the meaning behind this change in these neurons,

“Currently, one can only speculate about the role these effects may have played during human evolution. However, since patients that carry one nonfunctional FOXP2 allele show impairments in the timing and sequencing of orofacial movements (Alcock etal., 2000,Watkins etal., 2002a), one possibility is that the amino acid substitutions in FOXP2 contributed to an increased fine-tuning of motor control necessary for articulation, i.e., the unique human capacity to learn and coordinate the muscle movements in lungs, larynx, tongue and lips that are necessary for speech (Lieberman, 2006). We are confident that concerted studies of mice, humans and other primates will eventually clarify if this is the case.”

What’s also curious is that the mutant FOXP2 mice don’t seem to have any other effects on other organs, despite the fact that FOXP2 is pretty much ubiquitously expressed all over. It seems like the only manifestations of a human variant showed up in the neuron length and dopamine levels of the brain and ultimately vocalization behaviors. This is an excellent paper which investigates the functional differences of FOXP2, and I recommend you downloading a copy and reading it for yourself.

Today’s issue of Nature has a brief essay on the role of language in cultural evolution. The authors touch up on a lot basics, such as anatomical localization of brain activity related to language and tool making, FOXP2, and how language has helped humans pass on cultural information more effectively than any other form of communication. Overall, it is a well written review that I want to pass on.

Related, Erin from the Spitton, shared news of the identification of a new language related SNP on the gene CNTNAP2. The paper which reports this is titled, “A Functional Genetic Link between Distinct Developmental Language Disorders,” and was published in the New England Journal of Medicine. I believe it is open access, I got to the full text with no problem. The authors hypothesized that neural pathways downstream of FOXP2 can also affect language impairment.

To identify possible downstream candidates that might be involved in typical SLI, the authors transfected a human brain cancer cell line (SH-SY5Y) to continually express FOXP2. FOXP2 is a transcription factor, meaning it is a controller of the expression of other genes. If it is mutated, it can’t regulate its targets properly and leads to different, sometimes mutant, phenotype. The used a type of test called the chromatin immunoprecipitation (ChIP) assay which identifies how and often where proteins, like the FOXP2 transcription factor, bind to specific regions of the genome. This is done by using specific antibodies that recognize a specific protein or a specific modification of a protein, in this situation anti-FOXP2 antibodies.

The ChIP assay showed that the FOXP2 transcription factor binds to a particular, novel region of interest, the first intron of gene CNTNAP2. When transcribed and translated, CNTNAP2 normally encodes for the protein CASPR2 — a protein that is localized and understood to function in the nodes of Ranvier on myelinated neurons. Of further interest, CNTNAP2 is expressed in the human cerebral cortex, specifically the orbital gyrus and superior frontal anlage, spanning the inferior and middle frontal gyri — all regions know to related to language cognition.

To make sure that FOXP2 was for sure targeting this region, and wasn’t mislead due to any conformational changes that came from the antibody it was complexed with, the authors did some PCR and sequencing and saw that this region of interest, intron 1, does have matching known consensus, binding sequence for FOXP2. They did some other tests that shows that this sequence is highly specific to FOXP2… all of which suggests that this site on CNTNAP2 is definitively a binding site for FOXP2 (CAAATT).

The authors next varied the amount of FOXP2 expression and tried to see if it affects the ultimate expression of CNTNAP2. They were able to show there is a correlation — CNTNAP2 transcript levels were lowest where there are higher levels of FOXP2, suggesting that FOXP2 down regulates CNTNAP2. We haven’t know about FOXP2-CNTNAP2 interactions before, because FOXP2-bound fragment of CNTNAP2 is outside of the classically defined regulatory regions that promoter based microarrays identify… So identifying this pathway is very commendable.

With this downstream candidate gene isolated the authors moved to see how polymorphisms in CNTNAP2 manifest language phenotypes. Their population sample was made up from children from 184 different families where at least one child had a specific language impairment (SLI). The children had wildtype FOXP2, but children who carried the guanine nucleotide at rs17236239 SNP on CNTNAP2 had worse scores on a test that measures their ability to reproduce nonsense words like “brufid” and “contramponist.”

Now don’t get me wrong, this SNP, rs17236239, ain’t on intron 1 — where FOXP2 binds. FOXP2 was used as bait to fish out what gene bites to it. When CNTNAP2 was figured out to be a new novel target of FOXP2, the authors tried to see if CNTNAP2 variations also affect language. And they do. What’s also of interest is that other SNPs in the same regaion that rs17236239 is found also have CNTNAP2 as been linked to delayed speech in children with autism.

I’m really impressed with this paper. It’s a gem. Well written and straight forward. I don’t regularly read papers of such caliber, to be honest… So I really appreciate when I do. The new language related gene is also very important as we begin to piece together the complex network of genes and proteins, anatomy and behaviors that have allowed us to have language and use it.

Eörs Szathmáry, Szabolcs Számadó (2008). Being Human: Language: a social history of words Nature, 456 (7218), 40-41 DOI: 10.1038/456040a

S. C. Vernes, D. F. Newbury, B. S. Abrahams, L. Winchester, J. Nicod, M. Groszer, M. Alarcon, P. L. Oliver, K. E. Davies, D. H. Geschwind, A. P. Monaco, S. E. Fisher (2008). A Functional Genetic Link between Distinct Developmental Language Disorders New England Journal of Medicine DOI: 10.1056/NEJMoa0802828

Pinpointing when language became a prevalent trait during human evolution has been tricky. Last fall we read a paper which documented that Neandertals have the same FOXP2 sequence as modern humans. FOXP2 is a transcription factor associated with language. Two recent papers have shown that chimpanzees and humans have very similar structures in the brain that function in processing and producing sound. And despite the fact that several non-human apes have well known, documented histories of comprehending and communicating in sign language or with language boards, there has not been a consensus on when language definitively arose.

Rolf Quam, of the American Natural History Museum, along with several other colleagues have been investigating this issue. He’s been looking at the ear bones of Homo heidelbergensis, and he thinks they were capable of hearing sounds similar to how people do today. In other words, their ear bone anatomy is remarkably similar to modern Homo sapiens, despite the fact that Homo heidelbergensis is not directly related. The team reported their findings July 3 in Paris during the Acoustics ’08 conference.

From the press release,

“The skulls are from a site in Atapuerca, Spain called Sima de los Huesos, or “pit of the bones.” The Atapuerca research team, which includes members from many disciplines and universities, used CT scanning of the skulls to reconstruct the size and shape of the ear canals, Quam says.

The length of the ear canal determines what frequencies of sound waves resonate, and are therefore heard more easily, says Sunil Puria of Stanford University, who models hearing patterns from ear structure.The geometry of the ear canal reveals that the hearing patterns of H. heidelbergensis overlapped with those of modern-day humans. Both modern people and the ancient hominids have especially sharp hearing in the 2 kilohertz to 4 kilohertz frequency range, where much of the sound energy of spoken language is transmitted….

…The results don’t necessarily show that the ancient humans could speak, Quam says. “We’re saying that the ear changed for some reason and that those changes facilitated the possibility of language development,” he says.”

Like in modern humans (shown in solid blue), the ear canal of H. heidelbergensis (shown in red and magenta lines) had a peak in auditory sensitivity in the frequency range from 2 kilohertz to 4 kilohertz, where much spoken information is transmitted. Chimpanzees (shown in solid green) have a dip in sensitivity in that range.

All this really shows is that H. heidelbergensis could hear in the frequency range as modern humans. While I think it is very possible H. heidelbergensisis communicated, this research can not indicate that they used their ‘modern ear anatomy’ for anything special.

I’ve been extremely busy this last week. Busy with finals and organizing my graduation ceremonies to keep up with blogging. I finally got some time to catch up, take a deep breath and dive into the backlog of anthropology news. I’ve found some interesting things and will blog about it now that my life isn’t in overdrive.

For those interested in Mesoamerican linguistics, is this interactive exercise in learning how to read and speak in Mayan. I found it off of Digg and it comes from the “Cracking the Code” initiative which I mentioned in April. This exercise is based off of Stela 3, which is currently on found on a pyramid at the Maya site of Piedras Negras in northwestern Guatemala, more information about Stela 3 can be found here. In this excercise, you’ll see ancient Maya glyphs from Stela 3 on the left and to the right are the phonetic transcriptions of the glyph and sound bite (spoken by Barbara MacLeod). Accompanying notes help translate each glyph’s meaning. You’ll get a good taste of how the language sounds and flows, as well as some insight into hieroglyphic languages.

Here’s a screenshot of the interactive Flash application:

About 9 months ago, I shared some news of language extinction and the conservation efforts of K. David Harrison and David Anderson. My coverage was far from a thorough treatment of the subject, partially because I know little about the problem and the ways to remedy it. Fast forward to today, where I come across this video posted by Simon Greenhill on his blog HENRY.

The video is an interview of well spoken linguistic anthropologist K. David Harrison, by host Mark Molaro. In the video, David touches on many aspects, such as ownership of a language and what he considers ‘the greatest conservation challenge’ of humans. For anyone interested in the subject, I recommend you check out this 26 minute interview. Harrison integrates cultural issues as well as the importance of knowledge locked in unknown languages that can be useful to other disciplines such as botanists and zoologists.

Ownership of a language is a critical concept to understand. Speakers of widely spoken languages such as English, French, Chinese, Spanish, may not consider much ownership to their language. But to those who are one of the few speakers of a dying language, such as Chulym where only 30 or so speakers are alive, feel more attached to their language — it is something they identify with.

Harrison also outlines ‘the greatest conservation challenge’ of humans. See, every 2 weeks or so a language dies off. In contrast, species are going extinct at a much slower rate and yet a monumental conservation effort is put into saving this from happening. But studying, saving and/or curating languages aren’t given the same dedication as ecological or archaeological conservation. It is ironic that language, perhaps the most complex monument to human genius, has been ignored in our efforts to conserve the rest of the world.

Support is required from outside to conserve language, and with that a change in the ways we approach language is needed. Harrison suggests that while curating a language is critical to the conservation, understanding the folk taxonomy, a.k.a. the folksonomy, is also imperative. He brings up examples of different single word terms to refer to different reindeer in some Siberian languages. When translated, these single words unravel into elaborate, information packed phrases. He uses that to explain how often times there is a lot of local knowledge hidden lesser spoken language, that can span millennia. Harrison advocates that other researchers entertain the possibility that languages are an untapped resource for knowledge.

But to do that, a restructuring of how we consider discovery is needed. We, as academics, are largely stuck in this colonial paradigm of how discovery is approached. Many zoologists, botanists, even anthropologists and archaeologists discover new things without absorbing native knowledge. It is an awfully imperial way of looking about it, if Western culture doesn’t know about it the rest of the world never know about it! But who’s to say local peoples didn’t know about a certain plant or animal for ages prior to the “Western discovery”? We need people to acknowledge the vast body of knowledge out there, locked in indigenous, endangered languages.

Harrison wraps up his talk emphasizing how language is an infinite system, and I couldn’t agree with him more. He’s put particular consideration on local knowledge, but there is also a lot of knowledge that can be extracted from language — such as human migrations, which will have gaping holes if languages are allowed to erode at the rates they are now.

While we’re on the subject of Neandertal language capabilities, I want to share with you news from last week’s annual meeting of the American Association of Physical Anthropologists. I wasn’t there, I know a couple people who went but they didn’t tell me about Robert McCarthy‘s research. Robert has used new reconstructions of Neanderthal vocal tracts to simulate the voice, and presented his findings.

He’s not the first to have done this. Phil Lieberman estimated the dimensions of the larynx based off of skull sizes of Neandertals in the 1970′s. His work showed that Neandertals did not have a larynx like humans to catch the subtlety of modern human speech. Lieberman worked with McCarthy to simulate Neanderthal speech based on new reconstructions of three Neandertal vocal tracts.

By modeling the sounds the Neanderthal pipes would have made, McCarthy’s team engineered the sound of a Neanderthal saying “E”. He plans to eventually simulate an entire Neanderthal sentence. I’ve uploaded the sound bites for you to listen to and to be really honest, I don’t hear an “E.” I hear a sheep or a goat, but you can try figure out what you hear.

Here’s the human voice:

And here’s the Neandertal voice:

Haha, I’m laughing as I type this. I find the sounds really hilarious, especially because I expected Neandertals to have a really low pitched voice. Neandertals were more robust and larger than modern humans, and in my experience, modern humans that are larger and more robust than average have deep voices on average. So to hear high pitched “E”‘s from this simulation, I find it comical.

Anyways, for the linguists out there, McCarthy, explained that the difference in vocalizations was because Neandertal cranio-facial anatomy lacked the ability to produce “quantal vowel” sounds that underlie modern speech. Quantal vowels are necessary in providing audible cues that help speakers with different size vocal tracts understand one another.

Like I said, I don’t know exactly how McCarthy reconstructed these vocalizations. Since Lieberman collaborated with McCarthy, I expect that he did similar work. Furthermore, since only fossils of Neandertals remain, McCarthy had to compare and contrast the anatomical similarities and differences of humans and Neandertals to the vocalization. Is that the right way to do this?

Well, in 1999, David DeGusta and crew slammed Kay et al. for concluding Neandertal’s hyoid morphology indicated they were capable of modern language in, “Hypoglossal canal size and hominid speech.” So, I’m a bit skeptical.

Daniel Tight at the University of Minnesota has announced the completion of his dissertation, “The Role of Perceptual Learning Style Preferences and Instructional Method in the Acquisition of L2 Spanish Vocabulary,” on Linguist List. The abstract details a study which measured the effectiveness of preferred learning styles (visual, auditory, kinesthetic) in 128 intermediate-level L2 college Spanish students. Each of the students’ first language was English. Students studied 36 vocabulary words: 12 in their preferred learning style, 12 in a less-preferred style, and 12 in mixed modality instruction. An additional 12 non-studied words were used as a control. The results showed that individual learning style preference bears minimal relevance to L2 vocabulary acquisition, particularly when compared to mixed modality instruction.

Results of a repeated-measures ANOVA indicated that subjects performed equally well on the vocabulary posttests, regardless of learning style preference. Overall, mixed-modality instruction was more beneficial than instruction in a more-preferred modality, which in turn stimulated greater learning than instruction in a less-preferred modality. Such differences were statistically significant on the 1-week and 1-month posttests. Further analysis revealed, however, that differences between the more- and less-preferred modalities were primarily an artifact of the large number of visual learners, combined with an overall effectiveness of visual instruction for all subjects, rather than a product of style matching in general.

Although these style preferences have for years allowed students to individualize learning experiences, it appears the most effective method is to combine visual, kinesthetic, and auditory media. At least, for L2 concrete noun acquisition. Sounds like a great way to keep Broca, Wernicke, and your occipital lobe busy before a Spanish midterm.

For those of you out there interested in Mayan archeology and culture, or even those out there interested in how linguists crack codes, tomorrow night PBS’s NOVA will be airing a special on how the Mayan language was deciphered. The show is called, “Cracking the Mayan Code.” It airs tomorrow night at 8 p.m. on most PBS stations, but to double check what time it plays on your local PBS channel use this little applet to find out. The about page for the program describes the documentary as an inside story of how the decoding was done.

The problem with figuring out Mayan language has been that there really isn’t anything to compare too. Unlike Egyptian hieroglyphics, the Mayan writing system does not really have an equivalent Rosetta stone to help compare and contrast meanings behind the symbolic hieroglyphs. Actually, that’s a bit misleading… most Mayan texts were destroyed by mandate from Bishop Diego de Landa. But the good bishop did leave some element of translating written Mayan language… when he was composing his Relación de las cosas de Yucatán, he included a very sketchy and rather erroneous “summary” of Maya hieroglyphics. That summary hasn’t been really by useful, because the Bishop assumed the symbols were used as an alphabet, and just documented the phonetic representation of some of the symbols. So in a way he unwillingly preserved for us a source to begin figuring out how the written language sounded when spoken.

Some critical breakthroughs were made by J. Eric Thompson and Yuri Knorosov in the mid 20th century. While their conclusions were largely opposing, they both made headway in explaining how the Mayan writing system used symbols to represent signs and concepts. Thompson thought that the glyphs only related to astronomical affairs, while Knorosov contested that conclusion. She understood the written language as an amalgamation of signs for complete words and symbols for syllables. She believed the system was capable of conveying any word in the Maya language, and much more robust than Thompson’s understandings. Tatiana Proskouriakoff, also helped figure out commonalities in the Mayan language. She looked at stellae, and was able to figure out repeated symbols. To her, these repeated symbols were the names of rules.

In the early ’80′s, David Stuart made some monumental discoveries in deciphering Mayan written language. He currently runs a weblog called, Maya Decipherment, where he writes on deciphering the language. You should definitely check it out and add it to your RSS reader. He’s also announced the airing of this PBS show too. I’ll be interested to read what he thinks of it, since it seems as if his work will make a cameo on this show.

Oh yeah, Simon Martin, one of the coauthors of this book, “Courtly Art of the Ancient Maya,” is also gonna be commenting on Maya inscriptions. As will the late Linda Schele of the University of Texas at Austin, Peter Mathews of the University of Calgary, and Michael D. Coe of Yale University…. so it seems like there will be a thorough representation of all the great minds in Mayan linguistics. Unlike many History Channel and Discovery Channel specials, I trust NOVA ones… and I think this one will be a very complete and informative documentary to watch.

As always, if you do end up seeing it, please don’t hesitate to write a comment on this post’s thread about your thoughts and opinions.

National Geographic News has just published an article about the recent symposium in Alaska regarding a possible connection between Yeniseic languages in Siberia and Na-Dene languages in the Americas. John Roach’s article, Siberian, Native American Languages Linked — A First, highlights the recent work of Edward Vajda, who defended his connection during the February symposium. Vajda goes deeper than cognate lists in his parallels, providing several corresponding grammatical systems, particularly verb prefix structure. Ket, his primary Siberian source, is the only living Yeniseic language (which remains highly endangered) and bears some striking grammatical similarities to Navajo. Yeniseic languages have a unique verb prefix system: unique enough that Vajda could not find a corresponding system throughout Northern Asia. Na-Dene was the closest family geographically with a similar system. Johanna Nichols, a groundbreaking Historical Linguist and Linguistic Anthropologist, attended the symposium and made comment. Roach quotes:

With the exception of the Eskimo-Aleut family that straddles the Bering Strait and Aleutian Islands, this is “the first successful demonstration of any connection between a New World language and an Old World language,” Nichols said.

Vajda has not yet published his findings, so the extent of his linguistic claims is not yet clear. However, based on Roach’s summary of his discussion, there are two major points of controversy. First, Roach states that Vajda found “several dozen” cognates. Whether or not the comparative method for linguistic reconstruction was used remains to be seen. Regardless, a cognate list under 50 seems a bit thin to solidify a connection at all, let alone begin reconstruction. Furthermore, the public at this point has no access to the words to assess their status as true cognates. Without a doubt, a consistent and corresponding element of grammatical structure is a strong argument for a common ancestor, but we must consider the systems of linguistic change, particularly sound change (which requires cognates), as a central factor.

A second point of controversy is the matter of depth: how long ago does the proposed connection date back? Vajda makes no direct claims, but states that this would be the oldest known language link if it corresponds to the late Pleistocene migrations evident in the archaeological record. Unfortunately, the field of linguistics currently has no reliable absolute dating techniques, and relative dating such as glottochronology, has been widely discredited. In this case, it seems the lack of cognates would help secure this relationship as an old one. If that were indeed the case, a volume of cognates would become evident in the reconstructions of Proto-Yeniseic and Proto-Na-Dene. Whether or not Vajda has taken this into consideration remains to be seen. At any rate, Nichols is not convinced of a 10,000 year-old connection:

“I don’t think there is any reason to assume the connection is [10,000 years] old … this must surely be one late episode in a much longer and more complicated history of settlement,” she said.

At this point it is very difficult to make any generalizations. Vajda has not yet published his findings, but merely opened the door to discussion on the topic. Until he does, the foundation of our support or criticism is unknown.