Anthropology.net

Yesterday, my father emailed me a link to the Iranian Genome Project that caught my eye. Ironically, Razib over at Gene Expression also highlighted this project in a recent post. Much like the intentions Harappa & Dodecad ancestry projects, of which I’ve participated in by submitting my 23andme data, the Iranian Genome Project aims to enlighten Iranian heritage and health. As an Iranian American who follows population genetics regularly, I am very keen on intersection of these two topics.

I’ll be following the project, but honestly I don’t have high hopes. I would love to be proven wrong. It seems lofty, using a lot of high yield buzzwords. My first impression was if this nothing more than a CV booster … Especially since it hasn’t been updated since last September. I guess it can’t be completely an empty shell because they have an impressive member on research team, Pardis Sabeti.

You can learn more about this project by checking out their site, watching the following video and following them on Twitter: @irangenes. If you want, you can participate in the project by filling out this survey.

We’ve covered the mitochondrial genome of the Denisova individual 2 years ago, back in March 2010. For those not familiar with the Denisova hominin, this specimen represents an archaic human species present at least 41,000 years ago – coexisting with Neandertals and modern humans in the Altai Mountains of Siberia. The species is represented by a tooth and phalange.

A draft of the genome was released shortly afterwards in December, 2010. Today, after 30-fold coverage of the genome using Illumina GAIIx sequencing platform, the complete genome was released. It is free to download and use on Amazon Web Services… weighing in at 160gb.  I can imagine a lot of interesting comparisons can be made with this dataset and am happy the researchers made it available to the public.  There’s a caveat though, you can use the data but however agree that you cannot publish your findings until the researchers at Max Planck first get a stab at it.

I am now two-thirds done with my psychiatry rotation. It has been a fascinating experience so far. I’ve seen the gamut of psychiatric cases, depressed people who cut their necks through and through, to florid schizophrenics worried that the Hiroshima bomb will go off any moment. The treatment of psychiatric conditions like depression or schizophrenia often revolves around regulating monoamine neurotransmitters like serotonin, norepinephrine and dopamine.

Dopamine is an important neurotransmitter that functions in a lot of behaviors and reactions, such as movement, lactation, aggression, fear, etc. In diseases like Parkinson, dopamine levels lower and movement becomes uncontrolled. In other diseases like schizophrenia, either dopamine levels are high or response to dopamine is higher, and paranoia & hallucinations manifest. Treating schizophrenia involves blocking dopamine receptors. As you can imagine, a common side effect of antipsychotics is movement disorders — or Parkinsonism.

So why am I on this neuropsychiatric kick on an anthropology blog? Our cultural and behavioral predisopostions ultimately boil down to chemicals in our brain interacting and stimulating other areas. One of the most important functions of dopamine is in the reward system of the brain, an area called the nucleus accumbens that primes pleasurable behavior to repeat, such as sex, eating, and drugs.

In this video, Robert Sapolsky of Stanford Neurology makes the distinction between how dopamine levels rise in the anticipation of pleasure and not as a response to pleasure. I especially like that comment he made regarding reward and religion, “There’s no monkey out there willing to lever press because St. Peter is down the line.”

Anonymous is not a force to be reckoned with. Scientologists have felt their wrath for sometime, Sarah Palin did as well, as have MasterCard & Visa post-Wikileaks fiasco. I’m sure Aaron Barr is now realizing the impact Anon has. Aaron Barr is head of an internet security company, HBGary Federal. His company was contracted by Bank of America as a counter Wikileaks impending release of cables that will incriminate BofA.

Anon vs. Scientology

Ars Technica has written up a 3 page account of the situation, which is absolutely fascinating. The tl;dr seems like its comes straight out of a B movie. Aaron’s ingenious plan was to ‘infiltrate’ Anon…He joined IRC channels in an attempt to sabotage Anon and get names of those in the organization.

His problems started here. Aaron failed to realize Anon is not a true organization. At its core, Anon is an anti-organization, as anarchist as you can be, with no leadership and an ever-changing membership. Aside from infiltrating the chat groups, Aaron attempted to flesh out members of Anon via a guilt-by-association method using something akin to 6-degrees-of-separation and social media. He revealed himself to the group, claiming to research them.

What ended up completely backfired on Aaron. Anon was pissed. In traditional hacking manner, they hacked his company’s site and replaced the front page. They also managed to get a hold of at least 44,000 of his emails and release them via torrents. They deleted 1 TB of his backups, wiped his devices and to top it all of, got a hold of his Twitter and LinkedIn accounts where they posted messages as him. For a company that was in the midst of a sale, Anon effectively ruined that.

This leads me to a open up a discussion regarding the Anthropology of Hackers, a timely piece that appeared in the Atlantic yesterday by NYU’s Gabriella Coleman. In her write up she outlines her 13 week curriculum on the culture of hacking, covering topics like open source, privacy & anonymity, and the dawn of the nerds. Ironically, almost all are relavent to HBGary Federal, given Aaron’s troubles. I wonder how they’d benefit from a crash course in Coleman’s class. Looking at Coleman’s course topics, there’s a lot to consider regarding hacking. The most relevant to this topic is the material covered in Weeks 11 & 12,

Week Eleven: Anarchism and the Politically Minded Hacker

Many hackers express some degree of ambivalence over the politics of hacking as Patrice Riemens has argued and as hackers themselves have raised. This is not the case with a small but well organized cadre of hackers located primarily in Latin America, Europe, and North America who havecharted collectives, many of them influenced by the political philosophy of anarchism. To grapple with anarchism as a political philosophy (which, similar to hacking, is plagued with a parade of misconceptions), we turn to David Graeber‘s fantastic pamphlet, Fragments of an Anarchist Anthropology. We also read Jeff Juris’s ethnographic work about technology activists during the counter-globalization era Networking Futures.

Week Twelve: Trolls and the Politics of Spectacle

If anyone has been paying attention to the Internet in recent years, it has been impossible to miss a class of provocateur and saboteur: the Internet troll, whose raison d’être is to be as offensive as humanely possible via raunchy (but often humorous and quite esoteric) language, images, pranks, and tricks, basically, doing it for what they call the “lulz.” To get a sense of the cultural logic and exploits of trolls we read “The Trolls Among Us” by Mattathias Schwartz. To help us grapple with the nature of spectacle, we read a couple of chapters of Dream: Re-imagining Progressive Politics in an Age of Fantasy by Stephen Duncombe. We read excerpts from Lewis Hyde’s magnificent book on tricksters to consider whether the troll might be an example of these mythical creatures that have dazzled countless societies with their trickery. We watch a talk on a protest movement against the Church of Scientology whose roots lie in the act of trolling buteventually turned into a morally serious protest movement, which nonetheless retained the tactics of spectacle as part of its political arsenal.

This is a very interesting time to be looking at the intersection of technology and culture. There are anthropologists doing some fascinating work researching the sense of identity in online communities like World of Warcraft and Facebook… These groups share an online space, often with avatars and complex long-lasting interactions.

But with Anon there’s no identity.

Anon remains behind ever-changing screen names and masked localities behind proxies. I’m sure if you’ve ever taken an Intro to Cultural Anthropology course you would have touched on Erik Erikson’s theories of personality, We know what defines identity is a loose association of markers like behavior, language, dress, shared spaces, etc. Anon is disparate to any modern definition of identity. They do not share the same space, language, or any other measure of similarity except for behavior and ideology…

“We are Anonymous.  We are Legion.  We do not forgive.  We do not forget.  Expect us.”

I’d really like to get to hear Coleman’s take on this current event, or any cultural anthropologist for the matter. So if you’re interested, please chime in on your take on this all — What do you understand on Anon and how are they similar/dissimilar to other groups?

Carol Ward1, William Kimbel, and Donald Johanson have published a paper in Science on the arch seen in a newly discovered fourth metatarsal of Australopithecus afarensis (AL 333-160). A lot of the popular press are publishing misleading headlines that this proves bipedalism in australopithecines. No, we’ve known they were bipedal — we just didn’t have a true idea as to what extent they were bipedal. So a find like this helps investigate the degree of bipedalism.

AL 333-160 left fourth metatarsal in dorsal, lateral, medial, plantar, and proximal views.

How does this tell us how bipedal A. afarensis were?

) Box plots of angular relations of the proximal and distal metatarsal ends to the diaphysis in chimpanzees, gorillas, humans, and AL 333-160.

If you’ve ever had the pleasure of visiting a podiatrist, you’d know flat feet are not conducive to bipedalism. The two-way arch helps support upright walking and distribute recoil force. Other great apes like, chimps and gorillas have flatter feet than us. The authors of this paper confirmed this by comparing the fourth metatarsal of chimps, gorillas, and humans to AL 333-160.

On all their comparisons, AL 333-160 fell within range of humans. There were some occasions where there’s a lot of gray area which I’ll address later. Nonetheless, to the right you can see the best comparison, in my opinion, which the comparison of the arch of the diaphysis of the bone between the two species. You can have a look at the rest of the figures here.

The problem I am seeing here is that this metatarsal is not Lucy’s (AL 288-1). AL 333 is designated to fossils from the site where the “First Family” came from and not the same  locality as AL 288. Nonetheless, they are not the same individual. Kimbel is quoted in the BBC News, saying,

“Lucy’s spine has the double curve that our own spine does,” Professor Kimbel said.

“Her hips functioned much as human hips do in providing balance to the body with each step, which in a biped of course means that you’re actually standing on only one leg at a time during striding.

“The knees likewise in Lucy’s species are drawn underneath the body such that the thighbone, or femur, angles inwards to the knees from the hip-joints – as in humans.

“And now we can say that the foot, too, joins these other anatomical regions in pointing towards a fundamentally human-like form of locomotion in this ancient human ancestor.”

This is a flawed association to make; a form of what I would call confounding bias. We don’t have Lucy’s 4th metatarsal to see what it looks like and unfortunately we don’t have the rest of the this specimens skeleton to say it looked like Lucy’s. In fact, we have very little australopithecine appendicular and skeletons other than AL 288-1 (most notable are AL 129-1 and STS 14). So how can Kimbel say that the foot joins other anatomical regions when we don’t know what the other regions really looked like?

See, the n of this sample is 1. Looking at the intervals in the figures, especially Fig 3 & 4, there a a significant amount of variation in humans and chimpanzees that overlap. Chimps aren’t bipedal but we are. So imagine you are a paleoanthropologist way in the future looking at one metatarsal of a now-current then-ancient chimpanzee way and comparing it to a humans — surely you could make the same conclusion as these three have. And herein lies the big issue with sensationalism… as is the problem often in paleoanthropology, we just don’t have many comparative samples but people want definitive conclusions.

Ward, C., Kimbel, W., & Johanson, D. (2011). Complete Fourth Metatarsal and Arches in the Foot of Australopithecus afarensis Science, 331 (6018), 750-753 DOI: 10.1126/science.1201463

Anyone remember 2 years ago, when Survival International released some photos of an uncontacted tribe at the border of Brazil and Peru? Well an update came out, a remarkable video showing the tribe and describing what’s being done to protect them. Oh and by the way, this is part of BBC’s Human Planet.

Check out the video here.

Image by Omar A. via Flickr

I stumbled upon this news piece in The Times regarding archaeology in Saudia Arabia. I wanted to share it with you all because of last week’s discussion of handaxes from the neighboring UAE. The article describes how archaeologists have been using Google Earth to survey for sites and have identified possibly 2,000 or so potential ones in Saudia Arabia. Now using Google Earth to do some armchair archaeology is nothing new really, there are examples from 2005, 2006, 2008 and 2010.

But we all know how strict Saudia Arabia is. One of their many impositions has traditionally been against archaeology — fearing that discoveries may disrupt the foundation of it being a cradle for Islam. From the article,

David Kennedy, a professor of classics and ancient history at the University of Western Australia, used Google Earth satellite maps to pinpoint 1,977 potential archaeological sites, including 1,082 teardrop shaped stone tombs…

…But few archaeologists have been given access to Saudi Arabia, which has long been hostile to the discipline. Hardline clerics in the kingdom fear that it might focus attention on the civilisations which flourished there before the rise of Islam – and thus, in the long term, undermine the state religion.

In 1994, a council of Saudi clerics was reported to have issued an edict asserting that preserving historical sites “could lead to polytheism and idolatry” – both punishable, under the Kingdom’s laws, by death.

This is not surprising to many. What is surprising was this tid bit:

Saudi Arabia’s rulers have, in recent years, allowed archaeologists to excavate some sites, including the spectacular but little-known ruins of Maidan Saleh (Correction its really Mada’in Saleh), a 2,000 old city which marked the southern limits of the powerful Nabataean civilisation.

For the most part, though, access to ancient sites has been severely restricted.

There are a lot of examples where traditions, governments, etc. get in the way of phenomenal discoveries. However, there are few where objection relaxed. I’m hopeful we’ll see more archaeology conducted on the Arabian peninsula, but I’ll think we’ll be seeing more from the more liberal areas like the Emirates.

Related Articles

• Archaeologists Find 1,082 Ancient Tombs in Google Earth [Science] (gawker.com)
• Archaeologists Find 1,082 Ancient Tombs in Google Earth [Science] (gawker.com)
• Google Earth finds Saudi Arabia’s forbidden archaeological secrets (telegraph.co.uk)

Hans-Peter Uerpmann of the University of Tubingen has lead a team excavating the Jebel Faya site in the United Arab Emirates, right near the Straits of Hormuz. They’ve found 125,000 year old stone tools that look like early modern human tools from East Africa around the same time. They’ve published their findings in today’s Science, under the title, “The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia.”

The current understanding is what we know as anatomically modern humans (AMH) originated in Africa about 250,000 years ago. The oldest Home sapiens, known as H. sapiens idaltu, was found to be 160,000 years old, found at the Middle Awash site in Ethiopia. Then between 80k-100k years ago, modern humans began appearing in the middle east, as remains from sites like the Qafzeh cave in Israel have yielded. Most agree that AMH stayed in Africa and about 140,000 years ago they began migrating out. There was an exception, a colonization remained or failed in Israel about 100,000 years ago.

One of the hand axes from Jebel Faya, UAE (Photograph courtesy Science/AAAS)

These hand axes, pictured above, show a pattern of flaking distinct from that made by Neandertals and also dissimilar to those by ~100,000 year old Israeli tools. They are two sided and very similar to stone tools seen only in early Africa.

What this means is early humans left Africa 20,000 years earlier than thought. Just how did they do it? 130,000 years ago, there was a window of climate change. They figured this out by using luminescence dating to determine the age of sand grains buried with the stone tools. Luminescence dating is a technique that measures naturally occurring radiation stored in the sand. The data showed that 130,000 years ago, the Arabian Peninsula was relatively more warm which caused more rainfall, turning it into a series of lush habitable land. During this period the southern Red Sea’s levels dropped and was only 2.5 miles or 4 km wide. This offered a brief window of time for humans to easily cross the sea and cross the Peninsula to opposing sites like Jebel Faya.

Does this study tell us that modern humans left Africa, into Arabia and out from there? It is most certainly a possibility. However, these axes could be of an abandoned migration like the site in Israel I’ve mentioned. I say that because no genetic clade, be it from mitochondrial, Y-chromosome, or somatic genome, shows an earlier divergence of modern humans from Africa earlier than 60,000 years ago. At the very minimum a find like this tells us humans left Africa a bit sooner than we thought, but does not really tell us that these were the humans that helped seed the Eurasia.

Armitage, S., Jasim, S., Marks, A., Parker, A., Usik, V., & Uerpmann, H. (2011). The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia Science, 331 (6016), 453-456 DOI: 10.1126/science.1199113

If you don’t follow or subscribe to our sister blog Primatology.net, I want to make you aware of an anthropological post I just put up on the newly published orangutan genome. Click here to read about some of the findings, but to wet your appetite, it involves the estimated divergence of the two orangutan species at 400,000 years ago, the relative stabilitiy of their genomes compared to human and chimpanzee, and lastly the shared similarities between human and orang, and not orang and chimp.

Sumatran Orangutan (Pongo abelii)

For quick access to the primary sources, the full citations to the papers discussed are below this read more link.

Read the rest of this entry »

Map of Grape Domestication

I got some archaeobotany for you to start your weekend off right with — a new open access study in PNAS announces a genome wide association of 8,000 years of grape domestication, spanning the Eastern Caucasus to Western Europe. Lead author Sean Myles of Cornell University wrote in the abstract,

“support a geographical origin of grape domestication in the Near East. Grape growing and winemaking then expanded westward toward Europe, but the degree to which local wild sylvestris from Western Europe contributed genetically to Western European viniferacultivars remains a contentious issue. Our results … all support a model in which modern Western European cultivars experienced introgression from local wildsylvestris.”

In related wine archaeology, earlier this week, UCLA archaeologist Hans Barnard published the findings of a 6,000 year old uncorked wine barrel in Armenia. The barrel was discovered in the Areni-1 cave near the Iranian border. The results were published in the Journal of Archaeological Science, but you can read a bit more about it here.

Hope you found these two tidbits as interesting as I did. Cheers to a good weekend!

Myles, S., Boyko, A., Owens, C., Brown, P., Grassi, F., Aradhya, M., Prins, B., Reynolds, A., Chia, J., Ware, D., Bustamante, C., & Buckler, E. (2011). Genetic structure and domestication history of the grape Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1009363108