Archive for November, 2010

The naked years: the end of privacy

By Razib Khan | November 30, 2010 2:59 am

I do talk periodically on this weblog about the coming ‘transparent society.’ The main reason I bring up the issue is that I think it is probably inevitable, and, I think we’re sliding toward it without even reflecting on it too much. Many people are very surprised at how little time it takes to find information on them in Spokeo and Pipl. Curious about where someone you lost touch with from high school has lived? Go to Intelius.

Rereading David Brin’s original 1996 essay introducing the idea in Wired I’m struck by the fixation on old-fashioned cameras. To me, what people do is almost less interesting than what they’ve done. How much did they buy their house for? Where did they go to university? Did they graduate? Who did they marry? Interestingly, much of this information is offered up freely by the individuals themselves.

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CATEGORIZED UNDER: Technology

Of interest around the web & elsewhere – November 29th, 2010

By Razib Khan | November 29, 2010 2:02 am

Goodbye November.

Male Reproductive Problems May Add to Falling Fertility Rates. There’s an implication that there may be epigenetic and developmental reasons for this phenomenon. But check out this quote: “Today, at least one in five 18-25 year old men in Europe have semen quality in the subfertile range.” I’m starting to wonder about genetic load W. D. Hamilton style. If death doesn’t prune the deleterious alleles, perhaps PGD is going to be necessary in the face of rising infertility. Or somatic genetic engineering.

Now a Giant, Google Works to Retain Nimble Minds. I, like every nerd, have friends who work at Google. Great food. Awesome company. Smart people. But I do wonder if the cycle of institutional sclerosis is speeding up. IBM maintained hegemony for decades. Microsoft’s time in the sun really didn’t make it to the 20th year (I think 1990 is a good compromise year to peg the age of Microsoft, though it really got going with Windows 95 and had some juice in the days of MS-DOS. Facebook is already breathing down Google’s neck. This doesn’t mean that Google won’t be profitable, Microsoft is still making bank, and will do so for years to come. But It companies may be more and more ephemeral.

Information overload, the early years. In some ways the internet is, I believe, qualitatively different from previous information revolutions. But the critics really do repeat old & tired arguments, which pre-date the printing press, and go back to alphabetic script in ancient Greece. I assume that cuneiform and hieroglyph elicited the same concerns, but we don’t have records of that.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Blog

No Romans needed to explain Chinese blondes

By Razib Khan | November 29, 2010 12:08 am

uyghurboy
Uyghur boy from Kashgar

Every few years a story crops up about “European-looking” people in northwest China who claim to be of Roman origin. A “lost legion” so to speak. I’ll admit that I found the stories interesting, amusing, if  implausible, years ago. But now it’s just getting ridiculous. This is almost like the “vanishing blonde” meme which always pops right back up. First, let’s quote from The Daily Mail,* DNA tests show Chinese villagers with green eyes could be descendants of lost Roman legion:

For years the residents of the remote north western Chinese village of Liqian have believed they were special.

Many of the villagers have Western characteristics including green eyes and blonde hair leading some experts to suggest that they may be the descendants of a lost Roman legion that settled in the area.

Now DNA testing of the villagers has shown that almost two thirds of them are of Caucasian origin.

The results lend weigh to the theory that the founding of Liqian may be linked to the legend of the missing army of Roman general Marcus Crassus.
Enlarge

In 53BC, after Crassus was defeated by the Parthians and beheaded near what is now Iran, stories persisted that 145 Romans were captured and wandered the region for years.

As part of their strategy Romans also hired troops wherever they had conquered and so many Roman legions were made up not of native Romans, but of conquered men from the local area who were then given training.

250px-Statue-AugustusLet’s start from the end. The last paragraph indicates a total ignorance of the nature of military recruitment during the late Republic. In the year 110 BC the Roman army was composed of propertied peasants. These were men of moderate means, but means nonetheless. They fought for the Republic because it was their duty as citizens. They were the Republic. Due to a series of catastrophes the Roman army had to institute the Marian reforms in 107 BC. Men with no means, and who had to be supplied with arms by the Republic, joined the military. This was the first step toward the professionalization of the Roman legions, which naturally resulted in a greater loyalty of these men to their leaders and their unit than the Republic. Without the Marian reforms Sulla may never have marched on Rome. By 400 AD the legions were predominantly German in origin, and supplemented with “federates,” who were barbarian allies (though alliances were always subject to change). But in 53 BC this had not happened yet. The legions who marched with Crassus would have been Roman, with newly citizen Italian allies in the wake of the Social War. The legions of the Julio-Claudians were probably still mostly Italian, a century after Crassus (service in the legions, as opposed to the auxiliaries, was limited to citizens, who were concentrated among Italians). So that objection does not hold.

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CATEGORIZED UNDER: Genetics, Genomics, History

Slouching toward transparency

By Razib Khan | November 28, 2010 5:28 pm

In regards to the WikiLeaks story, it seems that:

- The explosive stuff is really a shift from assumed understanding to explicit acknowledgment. For example, that Arab nations are just as terrified of Iran’s nuclear program as Israel.

- The surprising stuff is more funny or strange. More like gossip you wouldn’t have guessed, but isn’t really that significant in the broad canvas of diplomatic history.

Strangely, I sort of think this is of a piece with the recent “Teacher’s Union Gone Wild” videos. Basically, the expectation of privacy is disappearing, on the grandest and most mundane scales. In the latter case, a woman was chatted up at a bar, and recorded for hours on end. Unfortunately for her, she used to the N-word, though not even in a offensive context (follow the link). Who hasn’t run their mouth off at a bar? Make sure you don’t have enemies! Imagine how someone could utilize damaging conversations in office politics. On the grand scale you have problems of coordination across agencies where secrecy and confidentiality are of the essence.

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CATEGORIZED UNDER: Technology

Internet usage by country

By Razib Khan | November 28, 2010 1:14 pm

In my post below on the rise of China, I ran into the data on internet usage by country again. I was online regularly by the spring of 1995, and it’s amazing to think that there are hundreds of millions of Chinese on the internet now! The World Bank estimates that both China and India have exhibited an increase of internet usage by an order of magnitude from 2000-2010, though from different bases. So while there are ~300 million Chinese users of the internet, there are ~50 million Indians. But who would have guessed that Nigeria has more per capita internet users than India? See below.

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CATEGORIZED UNDER: Culture, Data Analysis, Technology
MORE ABOUT: Data, Internet

Latitudes and continents

By Razib Khan | November 28, 2010 11:04 am

Thanksgiving in the tropics:

Finally, here are some pictures I took today. It was way too hot and humid when we first got to Taiwan, but now we’re getting some lovely winter weather – Taiwan is about the same latitude as Hawaii :-) It sure doesn’t feel like Thanksgiving or Xmas around here!

One aspect of the East Eurasian temperate zones is that they are far to the south of the West Eurasian temperate zones. Cork, Ireland, at about the same latitude as Petropavlovsk, Kamchatka, and eight degrees further north than Vladivostok!

But since Steve brought up Hawaii, let’s compare highs and lows in Honolulu, and Hanoi, two cities at 21 degrees north. On the literal margins of the tropics:

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CATEGORIZED UNDER: Science
MORE ABOUT: Climate

Taking the end of the age seriously

By Razib Khan | November 28, 2010 2:19 am

I am about two-thirds of the way through Why the West Rules-for Now: The Patterns of History, and What They Reveal About the Future, and I have to agree with Tyler Cowen’s assessment so far. The author is an archaeologist, and though a little less shy in regards to general theory than most in his profession, he still seems to exhibit the tendency to focus on thick-detail without any elegant theoretical scaffolding. In some ways it is an inversion of Gregory Clark’s A Farewell to Alms: A Brief Economic History of the World, which manifests an economist’s preference for stylized system-building at the expense of the messy residual. Why the West Rules has added almost no broad-brush theoretical returns beyond what you could find in Guns, Germs and Steel and The Wealth and Poverty of Nations. Though the author has a lot of scrupulously footnoted detail which probably makes Why the West Rules a worthy read.

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CATEGORIZED UNDER: Culture, History

Open Thread – November 27th, 2010

By Razib Khan | November 27, 2010 2:16 pm

Hope Thanksgiving went well for Americans. I didn’t gain weight at all, 142lbs as of Friday morning!

Out of curiosity, what fiction do you read?

Also, check out Dienekes post on the ability to generate disjoint clusters in the DODECAD sample set. He asserts that one may now be able to generate extreme fine-scale assessments of likely population assignment from genetic material now. Check out this table; each column after the first two are the number of individuals in a given cluser. The rows are populations. The second column are the N individuals.

Last week’s This American Life had a segment on dog feces DNA fingerprinting. I think this is a good idea.

CATEGORIZED UNDER: Blog
MORE ABOUT: Blog

Assorted links related to this weblog

By Razib Khan | November 26, 2010 11:04 am

23andMe kits are discounted to $99 from $499 today.

My twitter account: http://twitter.com/#!/razibkhan

My total content feed: http://www.razib.com/wordpress (rss: http://www.razib.com/wordpress/?feed=rss2)

The blog’s Facebook page: http://www.facebook.com/GeneExpression (content gets fed onto this page via Networked Blogs)

My ResearchBlogging page: http://researchblogging.org/blogger/home/id/1604 (65 posts)

The original Gene Expression: http://www.gnxp.com

And finally, my “personal home page”: http://razib.com

If you have a blog/website of interest to readers of this weblog, feel free to leave it in the comments

CATEGORIZED UNDER: Administration, Blog
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Friday Fluff – November 26th, 2010

By Razib Khan | November 26, 2010 12:09 am

FF3

1. First, a post from the past: Innate social aptitudes of man.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Eating, and eating well

By Razib Khan | November 25, 2010 12:33 am

turk
Credit: tuchodi

Happy Thanksgiving Day to all the Americans out there. This is a day to loosen the belt a bit, but after the Holidays you probably want to think about slimming back. So, ScienceDaily, Obesity Riddle Finally ‘Solved’, and, Diets with High or Low Protein Content and Glycemic Index for Weight-Loss Maintenance. The upshot seems to be that a high protein-low (refined) carb diet worked best in a large sample of Europeans.

Myself, I was in the 155-165 pound range between 2000 and 2007. 2008-2010 I’ve been in the 140-150 range, and usually closer to the low end than the high. I went from a waist size in the 31-33 inch range to 28-30 range (I wear 28s regularly now). I’m moderately active in that I walk a lot, but I have totally turned away from refined carbs. I am not a religious ‘Paleo’, but I do track glycemic indices and glycemic loads for various foods rather closely. That being said, different people have different biologies. I think that’s important to remember. As a South Asian I have a higher risk for type 2 diabetes, so I’m particularly vigilant about sugar and other variables which increase my probabilities for chronic diseases. If I was a Northern European I might have different priorities, and chill out a little bit about dessert. Life is about trade-offs, and pleasures do often have costs. I am not much of a sweet-tooth, and I’m genetically predisposed to type 2, so my aversion toward sweets is a rather simple calculation. Others may have different outcomes performing the same operations because of different inputs. The answer to a riddle may vary depending on who is asking.

CATEGORIZED UNDER: Blog
MORE ABOUT: Diet

We were all Africans…before the intermission

By Razib Khan | November 24, 2010 4:35 pm

modelhumanQuick review. In the 19th century once the idea that humans were derived from non-human ancestral species was injected into the bloodstream of the intellectual classes there was an immediate debate as to the location of the proto-human homeland; the Urheimat of us all. Charles Darwin favored Africa, but in many ways this ran against the cultural grain. The theory of evolution was birthed before the highest tide of the age of white supremacy and European hegemony, and Darwin’s model had to swim against the conviction that Africans were the most primitive of the colored races. After the waning of the ideological edifice of white supremacy, and the shock it received during and after World War II, the debates as to the origin of humanity still remained contentious and followed the same outlines (though without the charged normative inferences). But as the decades wore on many more researchers began to believe that Darwin was correct, and that the origin of humanity lay in the African continent. First, the deep origin of the human lineage in Africa was accepted, but eventually a more recent expansion out of Africa was argued for by one school. The turning point in these academic disputes was the popularization of the “mitochondrial Eve” theory of the 1980s.

What some paleontologists had long argued, that anatomically modern humans have their locus of origin in Africa, was supported now by research from genetics which indicated that Africans were the most basal clade of humans on a continental scale, so that non-Africans could be conceived of as a subset of Africans. From this originates the chestnut of wisdom that Africans have more genetic diversity than all other human populations combined. By the year 2000 one could say that the “Out of Africa” triumphalism had proceeded to the point where an almost exterminationist model had taken hold when it came to the relationships of anatomically modern H. sapiens, and other groups which had evolved outside of Africa over the past million or so years, such as the Neandertals.

ResearchBlogging.orgBut the theoretical dichotomies were too coarse and absolute as it turns out. A division between multiregionalist phyletic gradualism, where H. sapiens evolved out of its hominin ancestors concurrently on a world wide scale, and a model of rapid expansion of one tribe in Africa to replace all others in totality, may have been warranted in the age of classical genetics and a morphometric analysis, but now we can look at the raw genomic material in a more fine-grained fashion. In fact, we can now look at the genomic patterns of variation among extinct hominins! Though there have long been hints that the expansion-and-replacement paradigm was too extreme from the genetic and morphological data, with the publication last spring in Science of a paper which made the claim for admixture between Neandertals and non-Africans in the range of 1-4% in all non-African groups based on a comparison of Neandertal and modern human genetic variation, one can dismiss absolutist expansion-and-replacement as self-evidently true orthodoxy. But one orthodoxy has no given way to another, and the shock to the old models presented by the data has not resulted in the coalescence of new robust paradigms. We live in a time of scientific troubles, so to speak.

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North Korea vs. South Korea

By Razib Khan | November 24, 2010 1:13 am

There isn’t a lot of good data coming out of North Korea, but I thought the following charts would be of interest. USA and Mexico included for comparison. In case you don’t know, the South Korea = Republic of Korea, North Korea = Democratic People’s Republic of Korea.

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: Korea

The inevitable social brain

By Razib Khan | November 24, 2010 12:35 am

ResearchBlogging.orgOne of the most persistent debates about the process of evolution is whether it exhibits directionality or inevitability. This is not limited to a biological context; Marxist thinkers long promoted a model of long-term social determinism whereby human groups progressed through a sequence of modes of production. Such an assumption is not limited to Marxists. William H. McNeill observes the trend toward greater complexity and robusticity of civilization in The Human Web, while Ray Huang documents the same on a smaller scale in China: A Macrohistory. A superficial familiarity with the dynastic cycles which recurred over the history of Imperial China immediately yields the observation that the interregnums between distinct Mandates of Heaven became progressively less chaotic and lengthy. But set against this larger trend are the small cycles of rise and fall and rise. Consider the complexity and economies of scale of the late Roman Empire, whose crash in material terms is copiously documented in The Fall of Rome: And the End of Civilization. It is arguable that it took nearly eight centuries for European civilization to match the vigor and sophistication of the Roman Empire after its collapse as a unitary entity in the 5th century (though some claim that Europeans did not match Roman civilization until the early modern period, after the Renaissance).

It is natural and unsurprising that the same sort of disputes which have plagued the scholarship of human history are also endemic to a historical science like evolutionary biology. Stephen Jay Gould famously asserted that evolutionary outcomes are highly contingent. Richard Dawkins disagrees. Here is a passage from The Ancestor’s Tale:

…I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould’s Full House (reprinted in A Devil’s Chaplain) defended the popular notion of progress in evolution: not progress towards humanity – Darwin forend! – but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of compelx adaptations like eyes strongly suggest a version of progress – especially when coupled in imagination with of the wonderful products of convergent evolution.

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CATEGORIZED UNDER: Biology, Evolution, Genetics

The rise of men & the fall of the non-men

By Razib Khan | November 23, 2010 3:35 pm

Dienekes Pontikos ruminates on the changes in human genetic variation on a world-wide scale over the past 10,000 years based on an MDS plot of East Eurasian genetic variation which he generated. I’ve taken his plot and added geographical labels, so you can see the difference in scale between geography and genetics in terms of distance:

pcaeast

He argues:

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CATEGORIZED UNDER: Genetics, Genomics, History
MORE ABOUT: East Asian, History, Japan

The cult of Korea

By Razib Khan | November 23, 2010 2:11 pm

There are currently some scary goings-on in the Korean peninsula. If you have some time, I recommend Inside North Korea from National Geographic. Here’s the final scene. Jump to 5 minutes.

CATEGORIZED UNDER: Culture
MORE ABOUT: Korea, North Korea

Eurogenes 500K SNP BioGeographicAncestry Project

By Razib Khan | November 23, 2010 12:11 am

Since I have been promoting the Dodecad Ancestry Project, it seems only fair to bring to your attention Eurogenes 500K SNP BioGeographicAncestry Project. The sample populations are a bit different from Dodecad, but again ADMIXTURE is the primary tool. But the author also makes recourse to other methodologies to explore more than simply population level variation. For example, his most recent post is Locating and visualizing minority non-European admixtures across our genomes:

Imagine, for example, a white American carrying a couple of tiny segments of West African origin, from an ancestor who lived 250 years ago, and an eastern Finn with no Asian ancestors in the last 4000 years or more. If we run an inter-continental ADMIXTURE analysis with these two, it’s very likely the American will score 100% European, while the eastern Finn will probably come out around 9% North and East Asian due to really old Uralic influence.

That sort of thing isn’t a huge problem when comparing the genetic structure of populations. Obviously, overall, eastern Finns rather than white Americans are genetically closer to North Asians, and that’s basically what ADMIXTURE picks up. However, if the focus is also on individuals, this certainly can become an issue. Our hypothetical American might be aware of that African ancestor, with solid paperwork backing up their genealogical connection, but he’s pulling his hair out because nothing’s showing up via genetic tests.

So let’s take a look at a real life example of how RHHcounter can pick up segments of potentially recent Sub-Saharan African origin…

euras1
Olivia Munn & Uyghur woman

The basic issue here is that in terms of genomic variation old admixture looks different from new admixture. Someone who is a first generation Eurasian, with a Chinese and European parent, may be about the same ancestral mix proportionally as a Uyghur. They would resemble a Uyghur on STRUCTURE and be placed within that cluster on a PCA chart (this is what happens in 23andMe). But, the Uyghur “Eastern” and “Western” genetic heritage has been reshuffled to a great extent by recombination over the past 1,000-2,000 years. In contrast, a first generation Eurasian will have huge swaths of their genome which are Eastern or Western on alternating strands (from their respective parents). In population genetic language a group of first generations hybrids would be exhibit a lot of linkage disequilibrium (LD). In a panmictic hybrid population LD will decay due to recombination, which breaks apart the distinctive allelic associations inherited from the parental populations.

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CATEGORIZED UNDER: Genetics, Genomics

A positive rate of rate of change

By Razib Khan | November 22, 2010 8:12 pm

A Cheaper Plan at Netflix Offers Films for Online Only:

Netflix said Monday that it was introducing a subscription plan for customers who want to watch movies only online, underscoring yet another step away from its roots in DVD rentals by mail.

The new plan offers unlimited access to Netflix’s library of streaming movies and TV shows for $8 a month. That is cheaper than virtually all of the company’s DVD plans.

I of course immediately downgraded; I haven’t received a physical DVD from Netflix since circa 2007 (it took me a year to return it because I forgot where I’d left it, and never watched it). But when I’m not feeling so well and can’t focus on anything cognitively challenging Netflix is very convenient. There are plenty of free alternatives on the net, but I’ll pay sub-$10 fees to save some time and headache.

But it does make me reflect on the rapid changes in the area of home entertainment since World War II. Video displaced 8 mm in the 1980s, but VCR’s themselves totally evaporated in the first half of the 2000s. Now the DVD format itself is being superseded, but the internet is replacing the hard copy mode of distribution in general for home film viewing. Netflix is already supposedly 20 percent of peak US traffic.

Also, I just realized that I don’t think I’ve been inside of a specialty “video store” since the early 2000s (most definitely from when I first subscribed to Netflix in late 2004). I have looked in the windows, and from what I can tell these stores are all-DVD format now, and it’s rather strange that I’ve never been inside of a “DVD store” even though I’ve passed so many of them over the years. Have you? Do they still rent video games as well?

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CATEGORIZED UNDER: Technology
MORE ABOUT: Netflix

Of interest around the web & elsewhere – November 22nd, 2010

By Razib Khan | November 22, 2010 12:10 pm

Epilepsy’s Big, Fat Miracle. Two points to note: 1) modern medicine seems to have strongly resisted the ketogenic diet because of ideology, 2) this treatment works, but they don’t really understand why. It shows the importance of empiricism in medicine, but the reality that even an empirical discipline can be shifted by ideology.

Grumpy Kvetching of the Day. One of Sean Carroll’s readers complains about the content he’s posting up. If I ever get one of those blogs where my readers “sponsor” me, then I would listen to this sort of input. You paid for the privilege. Until then, shove it. Anyone who leaves a comment like that would be on my permanent “sh*t list.” I’m not really that disagreeable in person, but in person people rarely make demands on my own time as if such requests are the nature of things. Not so on the internet.

“Operation: Stop Palin” Gets Rolling. I was expecting this to happen some point soon, but my probability that the Republican establishment will be able to crush Sarah Palin is dropping from ~1.0, perhaps moving toward ~0.5. The main issue from what I tell is that the establishment is unlikely to be able to co-opt Mike Huckabee, who is the only other candidate on the horizon that could eat into her base.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Daily Data Dump

The flux of genes on the South Seas

By Razib Khan | November 22, 2010 12:29 am

poly1
Huli Wigman from the Southern Highlands, Painting of Tahitian Women on the Beach by Paul Gauguin

ResearchBlogging.orgMany demographic models utilized in genetics are rather simple. Yet the expansion and retreat of various demes in post-Ice Age Europe seems to be far more complex than had previously been assumed, though I suspect part of the rationale for the original simplicity was a preference for theoretical parsimony in the face of a paucity of data. The landscapes traversed by our species are rich and topographically convoluted. Not only does the land vary, from plains, to deserts, to mountains, but the climate shifts radically over time and space. In the pre-modern age when humans were more dependent on environmental exigencies these fluxes in ecological and climatic parameters were essential in sharping the arc of human demographic expansion and contraction.

Oceanias_RegionsThis is why a closer examination of the prehistory of Oceania is so appealing: here you have a physical geography which is radically constrained and so reduces the degrees of freedom of human movement and habitation. Unlike Europe, South Asia, or much of Africa, the time depth of the residence of the current indigenous inhabitants of Australia is on the order of 40 – 50,000 years. It seems likely that the indigenous people of the island of New Guinea to the north are from the same original settlement of Sahul, the ancient super-continent which consisted of New Guinea, Australia, and Tasmania. After the initial sweep out to the farthest reaches of what became Tasmania, there was a later push to the east of New Guinea, to the Solomon Islands,~30,000 years before the present. Then nothing for tens of thousands of years. The march of humanity seemed to stand still on the shores of the Solomons, just as the hominin lineage had once been cordoned off from Sahul by the forbidding seas between it and Sundaland, the Ice Age peninsula of Southeast Asia which was later submerged and became the western portion of Indonesia and Malaysia. The stasis was shocked by the Austronesians, a seafaring peoples who seem to have exploded out from somewhere between Borneo and Taiwan within the last 10,000 years, likely just on the margins of written history. The most famous of th Austronesian peoples are the Polynesians, who pushed across the Pacific, and likely even had some tentative contact with the New World. A less well known case is Madagascar, whose inhabitants speak an Austronesian language with clear affinities to a dialect of Borneo. The map below shows rough distribution of Austronesian peoples:

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CATEGORIZED UNDER: Genetics, Genomics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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