Anthropology.net

Rachel Mackelprang and Edward Rubin have written up a short review of current state of paleo-DNA in today’s issue of Science. They pay particular attention to the Neandertal sequencing project and the recent research, such as the melanocortin 1 receptor (Mc1r) and forkhead box P2 (Foxp2) studies we read about last fall. They also outline some of the challenges facing extracting, amplifying, and sequencing ancient DNA, as well as future prospects.

Mackelprang, R., Rubin, E.M. (2008). PALEONTOLOGY: New Tricks with Old Bones. Science, 321(5886), 211-212. DOI: 10.1126/science.1161890

Ajit Varki from University of California, San Diego believes to have found out what it means to be human. He’s been investigating a molecule called Neu5Gc, a variant of sialic acid, and his progress has been summarized in this news article. Neu5Gc functions as a marker or tag which identifies cells and helps them stick together. It also helps regulate immune response.

Chimpanzees, bonobos, gorillas, orangutans are able to produce Neu5Gc, but curiously humans do not produce Neu5Gc. Humans do produce Neu5Ac, a precursor to Neu5Gc. But we do not have the enzyme that helps tack on an extra oxygen atom to make Neu5Ac to Neu5Gc. Neandertals, also, do not have the enzyme to convert Neu5Ac. Clearly there was potentially a strong human lineage specific loss of function mutation somewhere during human evolution. The Neu5Gc that is found in us is found from red meat and milk products.

Varki believes that this difference, potentially explains some of the more unusual differences between humans and apes,

“Chimpanzees do not seem to suffer from heart disease, cancers, rheumatoid arthritis or bronchial asthma – common conditions in humans. Nor do they get sick from the human malaria parasite, which uses sialic acid to latch on to our blood cells.”

He’s found that some people produce antibodies that react to Neu5Gc. When an antibody targets a foreign molecule, it triggers inflammation. This observation, seeing how Neu5Gc elicits an immune reaction to create anti-Neu5Gc antibodies, further points to some strong selection against Neu5Gc. Varki believes that the mutation that prevents processing Neu5Ac into Neu5Gc helped shrug off a particular disease.

There’s one glarring thing that this news article gets wrong. It quotes that, Varki and team,

“estimates that the genetic change first appeared up to three million years ago, which coincides with the emergence of Homo erectus, the first of our ancestors to venture out of Africa.”

Uhh, there were no Homo erectus around 3 million years ago. There were ausrtalopithecines then… but the genus Homo didn’t emerge until 500,000 years later. Regardless, there was most definately a mutation that occurred after our last common ancestor with great apes. The irony is that what may have protected our ancestors, is now partially responsible for many diseases, such as malaria and even cancer.

Tangvoranuntakul, P. (2003). Human uptake and incorporation of an immunogenic nonhuman dietary sialic acid. Proceedings of the National Academy of Sciences, 100(21), 12045-12050. DOI: 10.1073/pnas.2131556100

Zeresenay Alemseged is no stranger to this blog. I mentioned his new position as the chairman of anthropology at the California Academy of Sciences several weeks ago. John Hawks caught this profile of him in the San Francisco Chronicle which gives an overview of his accomplishments, accolades and his own outlook on his future fieldwork and role at the Cal Academy.

Two articles in the Journal of Human Evolution reanalyze the geochronology of the Kibish Formation, in the Omo Valley, Ethiopia. One is titled, “Microstratigraphy of the Kibish hominin sites KHS and PHS, Lower Omo Valley, Ethiopia,” and the other is titled, “Sapropels and the age of hominins Omo I and II, Kibish, Ethiopia.”

Excavations of Kibish Formation between 1967–1974, yielded two very important Homo sapiens calvariae, each from different localities — Omo I which resembles modern humans and Omo II which has more primitive features. Omo I’s site was called Kamoya’s Hominid Site (KHS) after the discoverer, and about 2.6 km northwest of KHS, Omo II’s site, Paul’s Hominid Site (PHS) is located. These two were first indirectly dated to be 130,000 years old by a U-series disequilibrium analysis (a measurement of the decay of uranium into thorium over time) from layer near the Omo I site. Why Omo II wasn’t dated? I don’t know… later on I quote how Omo II’s exact location is kinda uncertain. Regardless, this date wasn’t well accepted. Richard Klein raised the possibility, in his book “The Human Career,” that Omo I and Omo II effectively sank into a older sediment layer (Member I) because the site was once a prehistoric delta.

About 40 years later, Frank Brown and Ian McDougall along with John Feagle returned to the Omo Valley and re-dated mineral crystals from volcanic tuffs where Omo I and II came from. Why? One reason is that the 160,000 year old Homo sapiens idaltu crania (BOU-VP-16/1, BOU-VP-16/2 and BOU-VP-16/5) from Herto, Ethiopia dethroned their claim to the oldest known Homo sapiens specimens. The team dated the ⁴⁰Ar/³⁹Ar feldspar crystals from pumice clasts above (Member III) and below layers (Member I) of river sediments that contained the early human bones. The argon-argon dates yielded a 195,000 year old age. They published their results in Nature, “Stratigraphic placement and age of modern humans from Kibish, Ethiopia.”

The big problem with this re-dating has been the uncertainty of whether or not they were getting crystals exactly from where the fossils came from. A National Geographic article summarized how the team estimated where the fossils came from,

“They were able to do this using National Geographic Society video footage taken during the first excavation. They also used photographs taken by Karl Butzer, a geologist currently at the University of Texas, who did the original geological studies of the site. Also helpful were hand-drawn maps from the late Paul Abell, another member of the 1967 team.”

As you can imagine, a substantial amount of erosion and deformation can happen to geological formations during 40 years, that would alter the stratigraphic context. And looking at videos, and photos, and hand-drawn maps is an hardly exact science. Believe me, exactly 1 year ago I was trying to find a locality based off of hand-drawn maps and missed. Frank Brown was even quoted in this same National Geographic article saying that the original locations have been lost. But they were able to find more of Omo I, including part of the femur that fit a piece found in 1967.

In the two new papers, both sets of authors reanalyze the best available evidence to pinpoint where Omo I and II came from: Member 1 of the Kibish Formation. Craig Feibel reconstructs the microstratigraphy of the formation and writes that he cannot falsify Klein’s claim but reaffirms that,

“The documented abundance of vertebrate fossils deriving from restricted levels in upper Member I provides an accumulational/preservational context within which the hominins are not out of place. Intrusion during the short period of terminal delta-plain development in latest Member I times would be temporally insignificant in any case.”

McDougall, Brown and Fleagle return to the argon-argon dating. They turn to checking out alkali feldspar crystals in pumice clasts and figure out that Nakaa’kire Tuff in Member I, and directly below the hominin levels, is 198,000 years old — extending the age of Omo I and II by 3,000 years. I do not know why PHS was not dated, but in the new paper the authors do write that the site of Omo II was mislocated by Butzer in his maps. In their conclusion, they make a snarky/competitive comment to the Herto discoverers, saying,

“Thus, the hominin fossils from Kibish are about 40 ka older than those from Herto, making Omo I and Omo II the oldest well-dated anatomically modern human fossils yet recovered.”

FEIBEL, C. (2008). Microstratigraphy of the Kibish hominin sites KHS and PHS, Lower Omo Valley, Ethiopia. Journal of Human Evolution DOI: 10.1016/j.jhevol.2008.05.011

MCDOUGALL, I., BROWN, F., FLEAGLE, J. (2008). Sapropels and the age of hominins Omo I and II, Kibish, Ethiopia. Journal of Human Evolution DOI: 10.1016/j.jhevol.2008.05.012

McDougall, I., Brown, F.H., Fleagle, J.G. (2005). Stratigraphic placement and age of modern humans from Kibish, Ethiopia. Nature, 433(7027), 733-736. DOI: 10.1038/nature03258

The linguistic diversity of the Caucasus is a unique phenomenon, similar to that of New Guinea. There are approximately 6,000 languages spoken throughout the world currently and about 820 (~14%) of them are spoken in New Guinea. In the Caucasus, you can expect to find representative languages from the Kartvelian, Abkhaz-Adyghe, Lesgian, Nakh, Indo-European, Avar-Andi-Dido, Andi, Dido/Tsez, Lak-Dargwa, Turkic language families. This image to the right documents the ethnic and linguistic diversity of the Cacasus region:

Curiously, neighboring regions, such as the Middle East and Europe, do not exhibit such a diverse array of languages. In a review piece, Bernard Comrie writes about the, “Linguistic Diversity in the Caucasus.” Linguistically diverse regions are important in understanding cultural evolution. Comrie describes these regions to be critical accretion zones — areas where population growth has added new layers in geneology, societal structure, etc. which has all effected the variation in the languages of the Caucasus.

Comrie describes the languages and their affiliations along with their divergences and convergences. He’s also offered up some useful resources, such as this map of languages in the area. If you would like a copy of this paper for academic purposes, let me know and I’ll email you it.

Comrie, B. (2008). Linguistic Diversity in the Caucasus. Annual Review of Anthropology, 37, 131-143. DOI: 10.1146/annurev.anthro.35.081705.123248

Remember that sensational set of photos of the ‘uncontacted’ people from the Brazilian-Peruvian Border? Well a couple weeks ago, Simon from HENRY, shared link that I think some of you maybe interested in. The link I speak of is this news piece, “Secret of the ‘lost’ tribe that wasn’t.”

In the news piece, Peter Beaumont, the author clarifies somethings that the press didn’t quite cover thoroughly. Firstly, the tribe photographed hasn’t been completely unknown to outsiders. In fact, ‘the tribe’s existence has been noted since 1910.’ Al-Jazeera got a chance to interview one of the sertanistas behind those photographs, Carlos Meirelles. Meirelles works for FUNAI, the Brazilian Indian Protection Agency  dedicated to searching out remote tribes and protecting them,

“Meirelles described how he found the group, detailed how they lived and how he planned the publicity to protect them and other tribes in similar danger of losing the habitat in which they have flourished for hundreds of years.

Meirelles admitted that the tribe was first known about almost a century ago and that the apparently chance encounter that produced the now famous images was no accident. ‘When we think we might have found an isolated tribe,’ he told al-Jazeera, ‘a sertanista like me walks in the forest for two or three years to gather evidence and we mark it in our GPS. We then map the territory the Indians occupy and we draw that protected territory without making contact with them. And finally we set up a small outpost where we can monitor their protection.’”

So Meirelles is a conservator of indigenous peoples and interested in finding more about them. He further explained the motivation behind the photos,

“…the Brazilian state of Acre offered him the use of an aircraft for three days. ‘I had years of GPS co-ordinates,’ he said. Meirelles had another clue to the tribe’s precise location. ‘A friend of mine sent me some Google Earth co-ordinates and maps that showed a strange clearing in the middle of the forest and asked me what that was,’ he said. ‘I saw the co-ordinates and realized that it was close to the area I had been exploring with my son – so I needed to fly over it….’

When I saw them painted red, I was satisfied, I was happy,’ he said. ‘Because painted red means they are ready for war, which to me says they are happy and healthy defending their territory….’

…But the revelation that the existence of the tribe was already established will provoke awkward questions over why a decision was made to try to photograph them – a form of contact in itself – in order to make a political point.”

So what do you think? Was photographing these people ethical?

Several weeks ago, a public relations company contacted me to let me know about the release of the History Channel’s Journey 10,000 B.C. and if I’d like a review copy. I said sure, despite the fact that I viewed the original airing of the show in March and wrote up an unfavorable review of it. But I didn’t say anything.

I was kinda surprised that the P.R. person, who went thru the effort of contacting me, didn’t extend that effort on researching if I hadn’t already reviewed the show. Actually I’m kinda dumbfounded, given that my original review is currently the second hit on Google for the search string, “Journey to 10,000 B.C.” It takes a few seconds to do that search, and for a company that ‘cultivates word-of-mouth measurably… through authentic social media,’ I feel as if they failed massively.

Anyways, the person sent me a copy of the DVD to review. I checked out the DVD. Nothing has changed since the original airing of show. The production value is still as crappy as it was when it first aired, and the most interesting argument made in the show is the review of the Soluteran peopling of the Americas, albeit it is a very far fetched, unsubstantiated hypothesis. I do not recommend you shell out your time and money to see this documentary.

I really don’t know why I’m blogging about this, I kinda feel obligated to do since she recently reminded me that she sent the DVD and is looking forward to a review of it. If this individual did her homework before she pitched the product to me, I wouldn’t have continued to make this point… perhaps something can be learned from this, do a quick Google search!

I wonder if Pardis Sabeti is going to be releasing a book or announcing something big for all this recent press on her?

A couple days ago, we saw her short biography on Big Think and in April Science ran a prominent overview of her research and accomplishments. Last night, PBS’s NOVA scienceNOW ran a segment featuring her life and hobbies. The segment is available for viewing on PBS’ website in Quicktime or Windows Media format.

You should check this out to get some insight into her life as a first generation immigrant, rock star, professor at Harvard, and geneticist. If you can’t check out the video, the full transcript of her interview is up as well.

The Independent reports on some interesting archaeological news about Paris and how it may have been inhabited by humans much earlier than suspected. See the French government agency for rescue archaeology, the Institut National de Recherches Archéologiques Préventives or INRAP, have been excavating a site about 1 mile away from the Eiffel tower since 1995.

This season they found thousands of flint arrowheads and fragments of animal bones that date to 10,000 years ago. This rich Mesolithic site is 3,000 years earlier than previously thought… The oldest previous human settlement within Paris’ city boundaries, a fishing and hunting village beside the Seine at Bercy near the Gare de Lyon railway station, date back to about 4,500 B.C.

Why is this significant? Aside from the novelty of knowing people settled in what is now Paris much earlier, this site seems to be an important resource for human technology in between the Paleolithic or Old Stone Age and the Neolithic or New Stone Age. The microliths of this culture period differ greatly from the Aurignacian artifacts, and could tell us how these hunter-gatherers were living before the agricultural revolution.

Excavations will have to end later this month. The site will be turned into a recycling plant operated by Syctom that will sort the 15,000 tons of garbage generated by Parisians. The irony is that this site looks to have been some sort of finishing and processing station for stone tool makers and hunters — lots of debitage and cores accompany the arrowheads andzooarchaeological remains… and now it will turn into a recycling plant.

Given the fact that the INRAP has stumbled upon a rich Mesolithic site, I suspect they are pressed for time to excavate and rescue this important cultural heritage resource.

In this 3 minute 44 second video, Pardis Sabeti discusses the future of genomics, i.e. how sequencing will become so cheap that personal genome sequencing will be ubiquitous. She also talks about the impact of sequence information on medical and human variation research as well as the necessary ethical precautions we need to take with this information. Check it out.