Friday, August 28, 2015

The Incredible Correspondence Archive Of Kanesh

We know a lot about Kanesh, in what is now south central Turkey, which from 1890 BCE to 1860 BCE was a thriving trade colony of Mesopotamian merchants from the city-state of Assur in what is now Iraq.

The trade routes between Mesopotamia and Kanesh via the Journal Antiquity.

This is because they used cuniform imprints on clay tablets that preserve very well over time and are quite simple to decode because cuniform is a phonetic alphabet rather than an ideogram system (like the symbol based proto-language of seals that preceded it in cultures from the Vinca culture in the Balkans, to Egypt, to Mesopotamia in modern Iraq, to the Harappan culture in the general vicinity of modern Pakistan).

These records from Kanesh provide some of the most insightful information about the early days of the Hittite empire, because this empire originated in the immediate vicinity of Kanesh in a process retold by these Iraqi traders.  The Hittite people ruled just two cities at that time.

These historical accounts are one of the important reasons that I think that the Anatolian Indo-European language, of which Hittite is the most prominent, arrived in Anatolia from elsewhere around 2000 BCE, rather than having much deeper origins in the area.  The Anatolian Indo-European languages are among the most divergent of the Indo-European languages, but, in my view, this has more to do with the fact that its substrate non-Indo-European languages that influenced the way that the specific local daughter language of Proto-Indo-European in Anatolia developed differed greatly from the substrate languages in other places where the Indo-European languages spread at around the same time, rather than because it diverged from Proto-Indo-European earlier in time.

A comprehensive treatment of the very early historical treasure trove will be recounted in a new book by Morgens Trole Larsen called Ancient Kanesh to be published by the Cambridge University Press later this year.

These communications, which were mostly trade related after all, also provide a wealth of economic information from prehistory that an August 27, 2015 article in the New York Times summarizes.  The bottom line of this analysis is that the economic system in place almost 4,000 years ago was very similar in many respects to our own economy.
[Earlier this year] Gojko Barjamovic, of Harvard . . . joined some economists, as well as some other Assyriologists and archaeologists, on a team that analyzed Kanesh’s financial statistics. The picture that emerged of economic life is staggeringly advanced. The traders of Kanesh used financial tools that were remarkably similar to checks, bonds and joint-stock companies. They had something like venture-capital firms that created diversified portfolios of risky trades. And they even had structured financial products: People would buy outstanding debt, sell it to others and use it as collateral to finance new businesses. . . . 
It’s impossible not to see parallels with our own recent past. Over the 30 years covered by the archive, we see an economy built on trade in actual goods — silver, tin, textiles — transform into an economy built on financial speculation, fueling a bubble that then pops. After the financial collapse, there is a period of incessant lawsuits, as a central government in Assur desperately tries to come up with new regulations and ways of holding wrongdoers accountable (though there never seems to be agreement on who the wrongdoers are, exactly). The entire trading system enters a deep recession lasting more than a decade. The traders eventually adopt simpler, more stringent rules, and trade grows again.

In 1962 A.D., as our modern era of globalization was just beginning, the economist Jan Tinbergen — who would later share the first Nobel in economic science — noted something curious: Trade within and between countries followed a mathematical formula. He called it the Gravity Model, sort of an E=mc2 for global business. It comes with an imposing formula: Fij = G(Mi x Mj)/Dij. Which, simplified, means that trade between two markets will equal the size of the two markets multiplied together and then divided by their distance. (The model gets its name from its mathematical similarity to the equation in physics that describes gravitational pull.) . . . 
Economists were drawn to the Kanesh archive because it offered an unprecedented chance to see how well the Gravity Model applied in an economy entirely unlike our own. This was trade conducted via donkey, through a land of independent city-states whose legal and cultural systems were totally dissimilar to any we know. But still, the model held up: Ali Hortacsu, a University of Chicago economist on the Kanesh team, says that the trade figures between Assur and Kanesh matched the formula almost perfectly. ‘‘It was a very nice surprise,’’ he told me.
Another business dispute between a trader who entrusted his goods with another trader going the same way who then breached the contract could have come right out of my conference room as I listen to a client describing a new case (except for the nature of the goods traded and the fact that they were being delivered via donkey train).

The results are encouraging to those who see the laws of economics as being "natural" subject to some rather weak conditions, in much the same way that common law judge made rules are described as "discovered" rather than made, as opposed to being purely "positivist" creations of decision makers writing the rules out of whole cloth.

This sophistication also brings home the notion that human beings, apart from having more advanced technology in the physical realm weren't less intelligent or less sophisticated that people are today, four thousand years later.

Thursday, August 27, 2015

Old Astronomy

The "dark ages" weren't dark everywhere. In its early centuries, right around the remarkable Y1K era globally, the Islamic empire was at the center of the world's science and culture.

For example, a recent paper has used a newly discovered and detailed reliable historic report of an astronomy report from Yemen, previously known only through secondary sources, by an individual known as al-Yamani, to pin down the date of what we now know to be a Supernova to 2 p.m. on April 17 in the year 1006 CE in the Julian Calendar (the evening of the 15th of Rajab in the year 396h by local reckoning at the time it was observed).

The paper is Wafi Rada and Ralph Neuhaeuser, Supernova SN 1006 in two historic Yemeni reports (pre-print posted August 25, 2015).

Tuesday, August 25, 2015

Still No Sign of Proton Decay

The Super-Kamiokande Experiment has used an independent method to exclude proton decay and related di-nucleon decays involving protons to charged leptons, neutrinos, photons and neutral and invisible to the experiment's detector's X particles, up to very large mean lifetimes on the order of 1031 to 1032 years. By comparison, the universe is about 1.3*1010 years old.

So, over the life of the universe, the fraction of protons that decay as measured by these methods is less than one per 1021 protons (in words, less than one hundred per gram of protons, and probably less than ten per gram of protons).

Previous studies using other methods have set a minimum proton lifetime on the order of 1033 to 1034 years, i.e. 1.0 to 0.1 such decays per gram of protons over the entire lifetime of the universe, or put another way, less than 1 such decay per 10 kilotons of protons per year (a measurement of truly stunningly great precision).  A kiloton of protons is pretty much indistinguishable in mass from a kiloton of hydrogen at this level of precision in measurement.

All of the decays searched for in this study would violate baryon number conservation (which is perfectly conserved in the Standard Model) and also B-L number conservation (a widely assumed alternative), unless the missing X particles had a baryon number of 2 (in which case lepton number is also violated by a factor of -1).  Violations of these conserved quantity could explain the matter-antimatter asymmetry of the universe in the right amounts and the right types, assuming that the baryon number and lepton number of the universe were zero at t=0 in the Big Bang scenario, something widely assumed on aesthetic grounds by theoretical physicists.

But, the di-nucleon decays would not violate lepton number conservation, and the proton decays would violate lepton number conservation only if the X particles in the interaction (e.g. a heavy sterile neutrino), which were indirectly detected using missing energy, did not have a positive lepton number to counterbalance the charged anti-leptons to which they would be hypothetically paired.

The decays searched for would also not violate conservation of electric charge.

The X particles searched for would also violate "R-parity" or the equivalent, which is a conservative or approximately conserved quantity in many supersymmetry (SUSY) models.

The result is consistent with the Standard Model physics expectation, which is zero.  But this experiment, while not improving the overall limit on proton decay very much, makes the findings from other experiments measuring the same thing in different ways more robust.

Many Grand Unified Theories a.k.a GUTs, that try to unify the three Standard Model forces, including the simplest of them that can include all three Standard Model forces and all of the Standard Model particles, which is an SU(5) GUT model, predict proton decay in some form at detectable levels, and can be experimentally excluded on that basis.  Many remaining GUT theories predict proton decay at rates just slightly slower than the current reach of experimental evidence.

The stunningly low experimentally measured rate (relative to the stability of any other kinds of composite particles in the universe) clearly establishes that proton decay has had inconsequential phenomenological impact on the history of the universe for the vast majority of the 13.8 billion year history of the universe.

But, if proton decay happened more readily at a threshold energy scale in the extremely early stage of the universe, it might produce some sort of thermal relic dark matter in large enough quantities to impact cosmology.  The tight bounds on proton decay, however, greatly limit any realistic versions of these scenarios.

Other Physics News

Meanwhile, the ATLAS experiment has once again ruled out "flavor changing neutral currents" also forbidden in the Standard Model, to an every greater level of precision, with branching ratios limited to less than one per one thousand decays in an interaction where FCNC's have been proposed to exist on a highly suppressed basis in some Beyond the Standard Model theories.

These core qualitative assumptions of the Standard Model have remained very robust.

Entropy Reconsidered

Sean Carroll has a very sophisticated discussion of the physics concept of entropy at his blog in connection with a new paper written by him and several collaborators.

He discusses two complementary but distinct ways to define entropy conventionally (one based on macrostates and microstates and the other based on information known about the system), notes that the Second Law of Thermodynamics is true only statistically, reviews the derivation of the Second Law from two antecedent corollaries of it, and then generalized an information based definition of entropy to allow increased information to decrease the entropy of a system in an information based measurement in a Baysean manner, after adjusting for heat loss from the system.

This is really quite a ground breaking paper conceptually.

A post on entropy is also as good a place as any to note the premature passing of Jacob Bekenstein last week, an astrophysicist best known for his work on the entropy of black holes.

Sunday, August 16, 2015

An Ancient Plague In A Collapsing Northern Chinese Civilization

In about 3000 BCE in ancient northeast China, 97 bodies, from juveniles to middle aged, were stacked up in a house that was just 210 square feet. Half were between age 19 and 35, and the rest were younger. None were older. Then the house was set on fire - burning some of the bodies more than others.
[The] Hamin Mangha site is the largest and best-preserved prehistoric settlement site found to date in northeast China[.]
The community also had at least 29 one room houses with doors and hearths. The village's population couldn't have been more than a few hundred, yet it lost almost a hundred souls in what must have been a matter of days or weeks at most.  An abstract of a 2011 paper on the site clarifies that it was located in Inner Mongolia.
The ages of the victims at Hamin Mangha are similar to those found in another prehistoric mass burial, which was previously unearthed in modern-day Miaozigou in northeast China, the researchers noted. . . . "This similarity may indicate that the cause of the Hamin Mangha site was similar to that of the Miaozigou sites. That is, they both possibly relate to an outbreak of an acute infectious disease," wrote Zhou and Zhu.
A poster abstract from an anthropology conference is here and indicates that there was a third similar site in the region as well. It is also similar to a northeast China site at Lajia, which is also the site were the oldest evidence of noodles in China (ca. 2000 BCE and made of millet) were discovered.

The researchers didn't offer speculation on what disease, if any, may have been involved in the two cases. But, any disease that killed so rapidly that this kind of mass grave and burning to prevent spread of the disease could have had powerful demographic effects and left traces behind in modern populations through selection on genes that confer resistance to it.


The Neolithic culture of that time period in Inner Mongolia was the late Hongshan culture (4700 BCE to 2900 BCE), which interacted with the larger contemporaneous but separate Yangshao culture.  Remains from the Hongshan culture are associated with Y-DNA N1 (xN1a, Nic), C and O3a (O3a3).  There is dispute over whether these people spoke a language in the same language family as Chinese.

Unlike almost all other historical Chinese cultures, they had an elaborate temple based goddess worship system, were known for jade artifacts depicting pregnant women, dragons, and tortoises, and are believed to be the original source of the Feng Shui mystical system.  They had small copper rings, although they were not necessarily a full fledged copper age civilization.

This would have happened long after the domestication of rice and millet, but not long before the rapid expansion of rice farming into mainland Southeast Asia, India and Nepal. It was before written records are available. A millet and pig based diet like the neighboring Yangshao culture seems likely, although hunting and fishing may have played a major part as well.

A warm period known as the Holocene Climate Optimum, from ca. 7000 BCE to 3000 BCE was just ending when this disaster struck, and it may have been harder to survive this climate transition in an inland relatively high altitude area like Inner Mongolia, than in places that stayed relatively warm like coastal China or Southern China.

During the Holocene Climate Optimum, "Current desert regions of Central Asia were extensively forested due to higher rainfall and the warm temperate forest bets in China and Japan were extended northwards."  It appears that this civilization collapsed due to rapid expansion of northern deserts into its territories possibly forcing its people to migrate to the south.
[R]ivers and lakes once dominated the region’s terrain, and that relatively deep water existed there between 5,000 and 9,000 years ago, along with vegetation including spruce, fir, birch, pine and oak trees. Beginning about 4,200 years ago, the researchers found, a dramatic transformation occurred. According to their findings . . . more than 7,770 square miles (20,000 square km) of the Hunshandake area rapidly dried up and turned into desert. The scientists suggest that a river permanently diverted water from the region, around the same time that a major climactic shift worldwide created severe droughts on all the continents in the Northern Hemisphere. As study co-author Louis Scuderi, a paleoclimatologist at the University of New Mexico in Albuquerque, told LiveScience: “We think this drying happened in northern China as well, but was augmented by massive amounts of water getting diverted away from the area.”
The event would have been similar to the sudden diversion and drying up of the Saravasti River in Northern India that brought about the collapse of the Harappan civilization.  Those events in India were accompanied by leprosy, TB and intracommunity violence.

The infectious disease in the case of this Chinese mass immolation must have been much more virulent than either leprosy or TB to cause so many deaths so quickly.  This occurred before the earliest attested small pox infestation in China.  But, this could simply be due to the lack of historical records, as it was recorded in China as far back as 1122 BCE, close in time to the dawn of the Chinese historical record, and small pox is both highly contagious and has a very high mortality rate. Plague proper also shares those features but there aren't known examples of it that are so ancient.  Still, this site has some similarities to "plague pits" in Europe. Anthrax has high enough mortality, is ancient, and can be associated with pigs, but seems to be only rarely associated with large historical outbreaks that would spread across several villages.

This site does not resemble a mass grave of 80 young women from 2000 BCE found in Shaanxi province in China, discovered in 2012, that was probably the site of a human sacrifice ritual.

Related Cultures

This disaster coincides in time with the late Neolithic transition in the Yellow River valley from the Yangshao culture (5000 BCE to 3000 BCE) and the Longshan culture (3000 BCE to 2000 BCE) and the roughly contemporaneous Liangzhu culture (3400 BCE to 2250 BCE). It seems likely that a plague like the one in Inner Mongolia could have been intimately related to the parallel events that produced this transition between archaeological cultures on the Yellow River in addition to the collapse of their own culture.

The descriptions of the Hongshan site in the news report seem more like that of the Yangshao culture or Longshan culture than the more sophisticated Liangzhu culture. Both of those cultures experienced rather dramatic collapses. The collapse of the Liangzhu culture was particularly sudden and mysterious (but too late and too far away to be connected to the site where the bodies were found). The collapse of the Longshan culture is described as follows in Wikipedia:
[T]he Neolithic population in China reached its peak during the Longshan culture. Towards the end of the 3rd millennium BC, the population decreased sharply in most of the region and many of the larger centres were abandoned, possibly due to environmental change linked to the end of the Holocene Climatic Optimum. This was matched by the disappearance of high-quality black pottery found in ritual burials. In contrast, there was a rapid growth of population and social complexity in the basin of the Yi and Luo rivers of central Henan, culminating in the Erlitou culture. The material culture in this area shows a continuous development, through a Xinzhai phase centred on the Song Mountains immediately to the south. In the Taosi area, however, there is no such continuity between Longshan and Erlitou material culture, suggesting a collapse in that area and later expansion from the Erlitou core area.
The Erlitou culture was the earliest Bronze Age culture of China.

Both the Yangshao culture and the Longshan culture had primarily millet, pig and dogs as sources of sustenance, cultivated silkworms, and had minor use of rice, with few cattle, sheep or goats.

Wednesday, August 12, 2015

A Teaser and Recap Of Recent Developments Post UPDATED

Summer vacation is ending and people who aren't me are enjoying it.  I'm working like mad, but want to make a few quick teasers about working in progress, even though I don't have time for proper analysis of any of them.

I call particular attention to a key post at Gene Expression that sheds light on Paleo-Asians from a 2014 paper and a collection of recent posts on the pre-history of the Balkans that have the potential to reshape the narratives of key moments in prehistory.

Paleo-Asians 2.5

Gene Expression has several important recent posts related to the Paleo-Asian story, and Eurogenes has one as well.

Razib discusses the non-relatedness of people with a pygmy phenotype and other issues that come up in the PBS series "First Peoples" now available in part for streaming.  This has great relevance to the issues related to Paleo-Asians.

His post on South Asian population structure  and here with an expansion to East Asians, and to Southeast Asians and the South Chinese adds only a little that is mostly background.  His posts about the pre-European colonial cultural formation of South Asia, however, is golden.  Discussion of cultural and genetic Japanese ethnogenesis with few major new insights but a nice recap here.

Razib's Paleo-Asian paper post is here.

But, the really seminal paper that he discusses and I need to discuss more, looks at the pattern of Negrito and Austro-Asiatic dispersal in Southeast Asia (the mostly stops at the Wallace line) and argues for an Ancestral Southeast Asian component, perhaps a paraphyllic group to the Phillipino Negrito that really isn't Austro-Melanesian.  This is a big deal in interpreting Denisovan ancestry and in making sense of the early layers of Asian migration.  Before this, there really wasn't much solid data on Paleo-Asian ancestry in Asia on the west side of the Wallace line, and wasn't the level of detail on the various split branches of first wave Asian migration.

Denisovan ancestry is a smoking gun to show that the Australian-Papuan wave of migration into Southeast Asia, which has it, while it is absent from populations attributable to later waves, was the first modern human wave there.  But, just when the key later waves were will take more work to parse.  The termination of Negrito ancestry in Indonesia (which is a small part there and mostly proportionate to Austro-Asiatic ancestry which terminates more or less in the same place) points to a pre-LGM wave of that population's arrival in island Southeast Asia.  It is hard to know in Andaman Onge ancestry, which is close to a pure type for Ancestral South Indian, is connected to Negrito or to Australian-Papuan ancestry, although it is clearly distinct from Austro-Asiatic which is found in the Nicobarese.  There are also interesting questions about the pathway of mtDNA N - was it a Northern route, or a Southern one, and when?

Eugogenes adds to the discussion with a post on a cranial analysis study from a large Holocene skull data set, and also notes a paper on South Asian/Central Asian genetics.  A good counterpoint to the cranial study which ignores genetic evidence and archaeology to reach conclusions that its data are inherently ill equipped to provide (because they are mostly Holocene, which is too late in the game to answer the questions it sees to answer), is a recent review paper evaluating the evidence on different possible theories of modern human expansion beyond Africa that looks at a larger body of evidence and keep an open mind on a variety of scenarios that aren't inconsistent with that data.  This question is ripe for reconsideration now, because archaeological evidence makes clear that modern humans had left Africa by 100,000 years ago, yet the defining Y-DNA, mtDNA and to the extent possible, autosomal estimates of the age of the non-African population's most recent common ancestor is more like 60,000-80,000 years ago or less.  This makes consideration of less parsimonious and complex models necessary to fit the data.

I also want to explore at more depth the legendary history of pygmy-like people in many cultures which I noted in my Paleo-Asians II blog post.  My attitude towards legendary history is that while it shouldn't be taken as true at face value that it shouldn't be ignored either because it often contains seeds of truth.  I'll repost quotes here from the source, before I lose them, so it is easier to think about the ideas without clicking back and forth (useless comments omitted):
Urisahatu says:
July 27, 2015 at 3:37 am 
The Polynesians – especially the Hawaiians have Myths and Legends about the Menehune (also referred to as Manahune) who are short dark skinned people (Negrito – Negrito like people).

Even the ‘aboriginal’ Taiwanese (especially the Saisyiat and the Paiwan tribes) have myths and legends about short dark skinned people (Negrito) living side by side untill recent history. The aboriginal Saisyiat called them ‘Ta’ay’ and they hold ceremonies to commemorate the Ta’ay (short black people) in a festival called ‘Pasta’ay’.

Taiwan is said to be the homeland of ‘Austronesians’ who are the ancestors of Polynesians. Some Negrito’s (or perhaps mixed Negrito’s and aboriginal Taiwanese) have sailed the Kuroshio current and reached the Aleutian Islands from where they spread to the west-coast of mainland North America.

Urisahatu says:
July 29, 2015 at 5:00 am
Perhaps you’re right about paddling; but we don’t know who (and how) migrated to Mainland North America (MNA) first.

The Saisiyat (Taiwanese aborigines) say the Ta’ai (short dark skinned people / Negrito) were living in the same land – territory.

If the Ta’ai (unmixed DNA) migrated to MNA first between 25.000 – 10.000 years ago; than yes they would have paddled their canoes (if they had such skills).
If the Ta’ai (Either unmixed or admixed DNA) migrated to MNA later after 10.000 (between 6.000 – 4000 years ago = the Austronesian expension into the Pacific) years ago; there’s a chance they sailed along with Austronesians (Taiwanese aborigines) who would have superior canoes and canoe skills.

The Ainu aborigines on the islands of Hokkaido (Northern Japan) also have Myths / Legends (traditions) of an ancient race of short (little) people.
They call them ‘Koropokkuru’ also spelled as: Kor-pok-un-kur, Koro-pok-guru and Koro Pokunguru. 
They are also sometimes referred to as Tsuchigumo.

Taking into account that the DNA research on the origins and migration to mainland America also states that some Amerindians are linked to Mamanwa (Philippines Negrito); you can see an upward migration from south to north; in other words; atleast from the Philippines to Taiwan towards Japan (Hokkaido island).

This would in my opinion make the Kuroshio current migration-route more plausible atleast for the Negrito DNA link.

The Polynesians (Hawaiians – Tahitians) have myths and legends about short dark skinned people they call Menehune (also Manahune).

The aboriginal Taiwanese (especially the Saisiyat also spelled Saisiat and Paiwan tribes) have myths and legends about short dark skinned people they call Ta’ay also spelled Ta’ai. 
The Saisiyat tribe have ceremonies commemorating the short dark skinned people (Ta’ai) in a festival they call Pasta’ai.

The aboriginal Taiwanese are referred to as Austronesians and are beliefed to be the ancestors of the Polynesians. 
The Ta’ai (unmixed or mixed with Austronesians) could have sailed along the Kuroshio current made a landfall on the Aleutian islands before sailing to the west coast of mainland North America.

Urisahatu says:
July 28, 2015 at 3:44 am

In this article posted on July 22, 2015 – at; it states that Aleutian islanders, Surui (Brazil) and Athabascans are closer to Australo-Melanesians compared to other Native Americans.

The Athabascan natives live directly east of the Aleutian islands / region. Their neighbouring natives (nations) Cree, Ojibwa / Chippewa, Algonquian (Anishinaabe) have myths and legends of little (short) people.

Little (short) people – Nation Myths – Legends
Menegishi – Cree
Memegwesi – Anishinaabe
Pa’iins – Anishinaabe

Menehune – Hawai’i
Manahune – Tahiti
Ta’ai – Taiwan (Saisiyat / Saisiat tribe)

Were those Little (Short) People actually Negrito (Negrito like people)?
Maybe it’s too far fetched; yet one could see the resemblance in names these nations (natives / tribes) give these mythical / legendary little people.

TWS says:
July 28, 2015 at 2:52 pm
The natives around here call them “stick Indians”. They can’t talk just in whistles but can mimic speech to lure unsuspecting children. They can’t hunt properly preferring to scavange along the tide line, pick berries, or will take food offered if you whistle they assume you are offering. They are small of stature and called stick indians because they can’t make proper stone tools. 
Urisahatu says:
July 29, 2015 at 6:22 am
I have found this ‘unconfirmed’ story on the so called “Stick Indians” at Wikipedia.

Native American beliefs in “Little People”

Stories and religious beliefs about “Little People” are common to many if not most Native American tribes in the West. Some tribes (such as the Umatilla of Oregon) referred to them as the “Stick Indians,” while the Nez Perce called them Itśte-ya-ha.

In 1804, the Lewis and Clark Expedition stayed for a time with a band of Wičhíyena Sioux on the Vermillion River in modern-day South Dakota. On August 25, Meriwether Lewis, William Clark, and 10 other men traveled about 9 miles (14 km) north of the river’s junction with the Missouri River to see the “mountain of the Little People”. Lewis wrote in his journal that the Little People were “deavals” (devils) with very large heads, about 18 inches (46 cm) high, and very alert to any intrusions into their territory.

The Sioux said that the devils carried sharp arrows which could strike at a very long distance, and that they killed anyone who approached their mound. The Little People so terrified the local population, Lewis reported, that the Maha (Omaha), Ottoes (Otoe), and Sioux would not go near the place.

The Lakota people who came to live near the “Spirit Mound” after the Wičhíyena Sioux have a story no more than 250 years old which describes how a band of 350 warriors came near the mound late at night and were nearly wiped out by the ferocious Little People (the survivors were crippled for life).

If this story is found to be true; it implies that the “Stick Indians” were very well capable of making proper tools.

The story in question reminds me of the Sentinel islanders in the Andaman islands.

Sentinel island is situated directly west of Great Andaman island and north west of Little Andaman island (Little Andaman is where the Onge Negrito live).

The Sentinelese islanders have always fended off outsiders by shooting arrows (and throwing spears).

There even was a case in 2006; where Sentinelese islanders killed two fishermen.

TWS says:
July 29, 2015 at 10:01 am
That’s a thousand miles to the east. Around here they are not quite so fierce more like leprechauns than ‘devils’. They mostly throw rocks if they are angry and then from behind. The people I have talked to who have encountered them (yes it still happens) report being struck with something like a small pebble or such usually in the ankle region or back of the lower leg. 
TWS says:
July 29, 2015 at 10:05 am
I suspect it is stories about an earlier population that were mostly coastal gatherers that lived in small bands. 
Urisahatu says:
July 30, 2015 at 3:31 am
You are right about the Little People (LP) the Wičhíyena Sioux are referring to is 1000 miles to the east.
That doesn’t mean the LP (Stick Indians) on the westcoast aren’t related to the LP inland to the east.

If the natives can migrate 1000 miles inland; why can’t a Negrito-like people do the same?

Than there’s the difference between the westcoast LP and the inland LP.
Just like modern humans there are some who are peaceful and there are some who are warlike.
The westcoast (western) LP can be considered peaceful and the inland (eastern) LP can be considred warlike.

Another example is from the Andaman islands. There are 4 Negrito tribes living on the Andaman islands:
1. Great Andamanese
2. Onge
3. Jarawa
4. Sentinelese

The first three Negrito tribes are peaceful and live side by side with the newcomers which are the Indians (mainland south asians). The latter fourth Negrito tribe ‘Sentinelese’ is warlike.

Jim says:
July 30, 2015 at 5:40 am
I’m not sure that describing the Sentinelese as “warlike” is very accurate. I don’t believe that they raid any of the other people in the Andaman Islands and I don’t think much is known about whether there is a lot of internal conflict on the island.

They kill outsiders who venture too close but this is a very wise precaution on their part considering how vulnerable they probably are to contact with outsiders and all their diseases. 
TWS says:
July 30, 2015 at 10:45 am
Very true. If there was a Melanesian/ Australoid population there is no reason at all to assume they were all alike anymore than all the tribes were alike when Columbus sailed the ocean blue.

European Pre-History

The Aurignacian culture of the Cro-Magnons, the first modern humans in Europe was to a great extent a false start, in Razib's view.  I think he overstates that case relative to post-LGM (Last Glacial Maximum ca. 20 kya) modern humans, although there have clearly been multiple large contributions to European population genetics since then - in the Mesolithic (the biggest waves being after the LGM and before the Neolithic, in the Neolthic, in the Copper Age/Early Bronze Age).  Also here.  A There is ancient DNA from a Cro-Magnon whose ancestors admixed with Neanderthals just 200 years before he died providing excellent date calibration of this event.

English origins discussed here and here.  There were no huge surprises.  English is very homogeneous, although recent prehistory can be reconstructed to some extent and some historical debates about population replacement when the Anglo-Saxons and others arrived can be put on firmer foundations.

Analysis of Indo-European origins and a tentative realization that "whites" as we know them didn't exist until recently (i.e. 5kya).  There is more discussion of the European phenotype and parallel "white-like" phenotypes that aren't genetically that similar like the Kalash (also this Kalash post), and the modern East Asian phenotype, with the conjecture that they could be adaptions to a common disease threat as a possible explanation (I suggest TB in the comments).  Eurogenes recaps the case against the Anatolian hypothesis, provides some conference abstracts on Indo-European origins (see also here), an important paper on Armenia origins, a post on Tarim Basin genetics, some unimpressive papers on Northeast European origins also here.*  Aside from the recent origins of "white", there are no real paradigm shifting developments here for me.

* (This second paper, by a group of Chinese authors, gets some deserved criticism by the Eurogenes blog proprietor for an inaccurate statement that the Finns and Russians get their ancestral East Eurasian ancestry from the Mongolians, even though neither reality, nor the body text of the paper in any way support this conclusion.  It isn't uncommon for these kinds of papers to dig right into the statistical analysis of the DNA dataset in a purely mathematical way without very deep analysis of the known historical context, anthropological descriptions of the groups sampled, or implications of the patterns that they saw in light of a serious examination of the prior literature or prevailing theories in the field about what we should expect. At first glance, it had looked like a simple English as a second language issue, but, upon reading the body text, it became clear that this particular study's discussion of the historical context was particularly shallow, inept and scattershot and that it was barely connected at all to the statistical discussion. This might be O.K. for an occasional amateur work in progress blog post interspersed with deeper posts, but it is really unimpressive for a published academic journal article. My kids could do better with a couple of hours in front of Wikipedia, and I would have given an undergraduate writing this paper a C- for this part of the assignment if I were a professor. Unfortunately, Chinese papers in this field in my experience seem to be particularly prone to being quant heavy and context and analysis poor. People who publish in the area of human archaeogenetics and population genetics really need to acknowledge that this is an interdisciplinary field that they need to master is all respects and need to have more self-respect when it comes to publishing their work. This discipline is ultimately about using numbers to understand people alive today and human history, not playing with databases for the sheer mathematical exercise of doing so.)

The first Anatolian ancient autosomal DNA from ca. 4700 BCE (pre-Early Bronze Age, post-Neolithic) and some less ancient Anatolian mtDNA. A comment to a post at Eurogenes provides more of a teaser to a major forthcoming Anatolian ancient DNA release:
Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic. I. Lazaridis, D. Fernandes, N. Rohland, S. Mallick, K. Stewardson, S. Alpaslan, N. Patterson, R. Pinhasi*, D. Reich*.

So the rumours that they all look like EEF (like the Barcin sample) seem to be correct, but I guess it's restricted to early Neolithic samples (or up to Middle Neolithic).
The reference to "EEF" is to the population described in a previous paper for which Reich was an author as "Early European Farmer" and was Sardinian-like automsomal genetic component found, for example, in first wave Neolithic LBK farmers, particularly those closest to Anatolia. While this is plausible and not really surprising, if true, it would resolve an important historical question. EEF is basically itself a blend of a European Hunter-Gatherer component, and a "Basal European Farmer" component that is more Near Eastern Fertile Crescent-like.

It would have been plausible to think that the Anatolian Neolithic individuals would have been Basal European, since Anatolia is one of the places where the Neolithic crop package actually came into being in the first place, and that the European hunter-gatherer component was something assimilated into the migrating population of first wave farmers on the frontier once they left their Urheimat, perhaps by assimilating local hunter-gatherer wives, perhaps to cement peace deals with local tribes, much as early fur traders at Bent's Fort in Southern Colorado did before Colorado became a state in the early 1800s. But, if early Neolithic farmers in Anatolia are genetically more or less indistinguishable from first wave Neolithic farmers everywhere else in Europe who are quite similar to modern Sardinians (whose island isolation meant almost nobody lived there when they arrived and spared them the post-Neolithic demic impacts of later waves of migration to Europe), then the implication is that the ethnogenesis of the EEF population that integrated European hunter-gatherers and Fertile Crescent Basal European farmer populations (probably multiple such populations that exchanged brides from all over the Fertile Crescent given the mix of mtDNA haplogroups in the mix) happened in situ at the places where the first farmers of the Fertile Crescent Neolithic first domesticated their crops, and then had much less subsequent admixture with the European hunter-gatherers that they encountered in their migration than it would have been necessary to infer otherwise, given the similarity of a good chunk of their ancestry to the hunter-gatherers around them (who would have been more different in appearance and genotype as the Native Americans were from the first Europeans they encountered in the Americas despite having some overlapping ancestry).

It also suggests that this round of ancient DNA isn't going to shed much light on which localities contributed what to the final EEF melting pot that brought farming and herding to Europe for the first time. I am inclined to speculate that there were previously distinct population genetic populations in Mesopotamia, the adjacent West Asian highlands, South Central Anatolia, the Levant, and the Southeastern Balkans that all contributed to this final mix, based upon what we know about the places of origin of crops that were included in the original Fertile Crescent Neolithic package that was assembled by the time that the LBK culture and Cardial Pottery cultures migrated to Europe, and based upon the uniparental and autosomal components that are present in the final EEF mix. But, it looks like we're going to need ancient DNA going back before the first farmers of Anatolia to Mesolithic peoples and proto-farmers in the Fertile Crescent and the Balkans to unravel that question.

It also sounds as if the EEF first farmers of Anatolia didn't have the distinctive West Asian/Caucasian/Ancestral Northern European component that is found later in Anatolians particular in the East of Asia Minor. This in turn, tends to imply that this component arrived after the LBK and Cardial Pottery EEF peoples migrated away, which would most likely suggest that it was brought by the Hattic and Hurrian peoples of Anatolia from the Caucasus, present day Armenia, and highlands of West Asia, probably around the time of the Eneolithic era (i.e. Copper Age), that preceded the Early Bronze Age rise to prominence of the linguistically Indo-European Hittites. The Hattic and Hurrian and other Anatolian cultures that were present before the Indo-European speakers of Anatolian languages arrived probably spoke a language in the same language family of the Northwest Caucasian languages such as Circassian (something we can discern from attested examples of their languages in mostly liturgical sources from the Hittite and Akkadian Empires).   FWIW, I suspect that Minoan is probably also part of the same language family as Hattic and Hurrian (i.e. Northwest Caucasian), based upon proximity and the way that the Minoan language sounds based on Egyptian phonetic transcriptions of some Minoan spells/prayers, and based upon what the Hattic language sounds like.

But, this ancient DNA, if as expected, makes it less likely that the probably common language family of the LBK and Cardial Pottery first farmers of Europe belonged to the Northwest Caucasian languages (and it has already been established elsewhere that they were very likely not Indo-European linguistically either). Given their contacts with the Mesopotamian and Levatine peoples, it could easily have been, for example, related to Sumerian, to early Semitic languages, or could have been something else entirely indigenous perhaps to the parts of Anatolia in the Fertile Crescent and as different from the Sumerian and Semitic languages as those languages are from each other. If none of the various cultures whose fusion of farming package components was clearly socio-economically superior to the other, there is no good reason that the Anatolians whose farmers are the ones who ultimately brought farming to Europe, would have felt the need to adopt the languages of their trade partners and rivals in the Fertile Crescent who probably didn't rule them.

As the reasoning above illustrates, pinning down this data point sometime soon and probably later this year, even if it may seem ho-hum on the surface, will turn out to be a pretty key lynch pin in understanding the overall, quite complex picture of early Neolithic and metal age prehistory and historical linguistics of Europe and the Near East with any kind of real confidence.

Maju has a post on an old monolith found underwater in Sicily.  Abstract here.  The 9350 BP Meoslithic date is remarkable for such an epic structure.  There is also a major megalithic architectural work in Anatolia near the place where wheat was domesticated but built before that happened, and while Stone Henge in England was built after the Neolithic revolution arrived there, it was in regular use and improved upon during the near total reversion to hunting and gathering in England that happened when the first wave of farming there collapsed before a new wave of farming, roughly coinciding with the Bell Beaker people's arrival in England, restored farming and herding as the predominant means of subsistence again in England.  So, certainly, hunters and gatherers are capable of erecting grand stone structures, but it is also the case that pre-Neolithic structures of these kinds were rare (and it could be that proto-farming of non-domesticated crops which was present in some places by then, or sedentary food production from fishing, or both, was necessary to make these monuments economically possible). There is also a new study on modern Y-DNA from Sicily.

The real seminal developments, however, involve a much clearer picture of what was going on in the Balkans during key phases of pre-history which have the potential to be paradigm shifting.  The Balkans have largely been a blind spot in my knowledge of pre-history but may have played a role in bringing Bell Beaker culture to Western Europe, in providing a seed of Aegean and Anatolian Indo-Europeans, and may have also received Corded Ware impacts as it was on a borderline between the key regional areas of the Bronze Age.  Some ancient Greek DNA results can help here as well.  Corded Ware had a major impact in the Balkans.  Corded Ware genetics are explored here.  There are also reports that the Dolmenic megalithic culture was big in Montengro in the late Bell Beaker era (2400 BCE).  Old European Culture has more details, and develops a fragile but credible line of evidence culturally connecting Irish prehistory to the Balkans.  Both points are further explored here.  There is a post tracing Racka sheep to Serbia.  Understand the Balkan's prehistory and you are much further along in putting together a coherent narrative for Europe as a whole.

One other point that has been knocking around in my head is the Robin Hood myth. Canonically, it is an Iron Age English or later story. But the prominence of bowmen who are outsiders from and don't accept the legitimacy of the new ruler, is highly suggestive of Bell Beaker to Celtic transition in England. Could Robin Hood be a retread of an older myth from this era?  Similar points can be made about the King Arthur myth. Was this story set in the time of pagan to Christian transition in Iron Age England a reappropriation of earlier material originally developed in connection with a prior transition such as the Bell Beaker to Celtic transition in England? Or was it purely a product of the Middle Ages as it purports to be a face value? Less ambitiously, could these myths reflect lingering Bell Beaker cultural influences from pre-Celtic times that the pagan Celtic peoples and the Romans may have not felt any great compulsion to purge from the local culture in favor of their own particular Indo-European cultural traditions (particularly when the Bell Beaker cultural influences were not necessary cast in a fully positive or respectable light - Merlin, identified with the pre-Christian old cultural regime of Celtic pagan England, is often portrayed as a somewhat sinister figure and Robin Hood for all his noble deeds was an out of power outlaw exiled to the forest).

The New World

Razib has a nice riff on Albion's Seed and its premise of long term region cultural continuity.

Gambler's House continues to try to understand Chaco culture and its larger context.

There was also a news report today on a possible archaeological trace of some of the refugees from the failed colony of Roanoke (a subject of one of my earliest posts at Wash Park Prophet), in a sound about 50 miles to the west of the island.

African Genetics

I'm not sure if I mentioned a new Y-DNA E paper with good analysis at Ethio Helix.  There is a new Western Pygmy genetics paper. There is more data on Ugandan mtDNA, Sudanese mtDNA, and Ethiopian uniparental data.


Monday, August 10, 2015

Measuring The Strong Force Coupling Constant

The strong force coupling constant is a dimensionless constant that tells you how strongly gluons and quarks couple with each other which runs with the energy scale of the interaction in quantum chromodynamics (QCD), according to its beta function, whose Standard Model terms are known exactly in the high energy "ultraviolet" regime.

If you plot the strong force coupling constant's strength against energy scale, near its peak it looks like a bell curve (with a linear strength scale and logarithmic energy scale), with a peak close to 1 (maybe even as much as 1.25) at roughly q2=0.5 GeV2, that declines in a very long tail towards higher energies, and in a much shorter tail towards lower energies. It isn't entirely resolved whether the strong force coupling constant takes a value that is 0 (a value sometimes called "trivial") or some fixed value greater than zero in the limit at an energy scale of q2=0 (called an "infrared fixed point"). The value that the strong force coupling constant takes at the Z boson mass of 91.1876(21) GeV on the ultraviolet side of the peak is roughly the same as the value it takes at a hair over q2=0.01 GeV2 on the infrared side of the peak.

The most accurate world average measurement of this quantity (as of 2014) at an energy scale equal to the Z boson mass is 0.1185 +/- 0.0006.  By comparison, twenty years ago, back in 1994, the most accurate world average measurement was 0.123 +/- 0.006.  So, since then, the best fit value has fallen by about 3.8% and the precision of the measurement has improved by a factor of ten (the values are consistent with each other to within the margin of error).  We've improved, but only a little.  At this rate, we'll have a measurement as accurate as the current electromagnetic coupling constant measurement in another ten million years, and will reach the accuracy with which we have measured the Newton's constant of gravitation in about 250 years.

This is about 20 times less precise than the most accurate combined measurement of the W boson mass.  It about 50 times less precise than the most accurate combined measurement of the Newton's constant in general relativity.  It is about 1,200,000 times less precise than the the most accurate combined measurement coupling constant for electromagnetism, and it is about 100,000 times less precise than the most accurate combined measurement of the coupling constant for the weak force.

The only constants in the Standard Model known less precisely than the strong force coupling constant are some of the quark masses, some of the tiniest CKM matrix entries, and some of the neutrino physics constants.

The latest ATLAS measurement of this quantity as 7 TeV is 0.1173 +/- 0.0046, with a theoretical error of about four times as much as the experimental error.  This is consistent with previous measurements at the one sigma (i.e. one standard deviation) level.

This ATLAS experiment in question was primarily measuring something else and wasn't designed to produce a world class strong force coupling constant measurement, so the 4% margin of error doesn't reflect badly on ATLAS and confirms once again that Standard Model constants measured in many different ways have the same values within error bars, confirming that it is robust and that the quantity defined in theory corresponds to a meaningful quantity in the real world.

The great inaccuracy with which the strong force coupling constant is known does, however, does represent a fundamental barrier to accurate QCD calculations.  For example, the proton mass can be calculated from QCD first principles to a precision of only about 1%, about half of which is attributable to uncertainty in the strong force coupling constant, even though the proton mass has been directly measured to a precision of eight significant digits.

And, while this would seem like it is the fault of imprecise experiments, it really isn't. We have measured observable properties of all manner of hadrons (particle made of quarks that are bound together by the strong force such as protons, neutrons and pions), which are much more precise. But, there is so much theoretical uncertainty in how to correctly calculate those measured observables that it isn't possible to reverse engineer them into very precise measurements of quark masses and the strong force coupling constant.

This isn't for want of trying. Theoretical physicists like the author of the 4gravitons blog devote the lion's share of their professional efforts every day to "come up with mathematical tricks to make particle physics calculations easier."  Physicist have been working steadily on this problem for half a century and have made only modest progress, although steady advances in computers computational power over that time period have helped a great deal.  But, given that computation power has increasing according to Moore's law by a factor of about 2.6 billion over that time period since QCD was invented, progress has still been painstakingly slow.  The math really is just that hard.

The Strong Coupling Constant and BSM Theories

You might think that people crafting beyond the Standard Model physics theories would be swarming to produce theories that would predict slightly higher or slightly lower strong force coupling constants because this is an area where there is considerable room to make contradictory predictions within the existing margin of error.  But, in fact, there is almost no activity on this front and beyond the Standard Model physics proposals tend to leave the strong force coupling constant and the QCD equations of the strong force, more or less unchanged apart from the number of strongly interacting particles.  There isn't even a great deal of work being done that makes differing predictions regarding the quark masses.

Supersymmetry theories, generically, predict that the running of the strong force coupling constant will take place at a different rate (i.e. that it will have a different "beta function") than in the Standard Model, which may be possible to compare to the Standard Model prediction at LHC Run II.  Basically, the strong force coupling constant gets weaker with higher energies in the Minimal Supersymmetric Model (MSSM) at about half the rate that it does in the Standard Model (the weak force coupling constant gets weaker at higher energies in the Standard Model but stronger at higher energies in the MSSM, and the electromagnetic force coupling constant which gets stronger at higher energies in both theories gets 30% stronger at given higher energies in the MSSM than in the Standard Model).

The actual value of the strong force coupling constant, however, is actually harder to measure at high energies than at low energies, because using the Standard Model beta function for the strong force coupling constant, a comparatively wide range of low energy values at lower energies when run according to the strong force coupling constant beta function of the Standard Model, all converge at points which are extremely close to each other at much high energies.  So high energy measurements of the strong force coupling constant must be much more precise at higher energies than at lower energies to make a measurement of the same precision.  As a result, LHC Run II probably won't do much to improve the accuracy with which the strong force coupling constant is measured.

Many beyond the Standard Model physics proposals either don't answer these questions at all, leaving them as experimentally measured physical constants, just as the Standard Model does, or assumes relationships between these valuable that are right at an order of magnitude level but impossible to calculate more precisely at this time.  Phenomenologists try to look for patterns in the currently measured values of these constants, but even there, the results have thus far been underwhelming.

The three coupling constants in superysmmetric theories have one less degree of freedom than in the Standard Model (i.e. two instead of three).  This is because, in principle, in supersymmetric theories, the strong force coupling constant can be calculated exactly from an ultraviolet fixed point where the strength of the strong, weak and electromagnetic force coupling constants are the same at the "GUT" scale of about 1016 GeV, using the supersymmetric strong force coupling constant beta function. The coupling constant strength and the fixed point energy scale could be calculated using supersymmetric beta functions for the weak force coupling constant and electromagnetic force coupling constant whose values are known much more precisely than the strong force coupling constant.  This fixed point, calculated from much more precise experimental inputs, could in turn be used to back out a strong force coupling constant at a measurable energy which should be much more precise than the experimentally measured version.  The result should be almost 10,000 times as precise as the current experimentally measured values, since the beta functions, in both the Standard Model and supersymmetry, in principle, ought to be possible to determine exactly without experimental inputs from the theory.

I have not seen a paper making the calculation this way, although it should be straightforward to do once the supersymmetric beta functions are established.  This calculation wouldn't be useful from a predictive perspective, because there are so many different variations on the supersymmetry theme out there.  But, it would make it possible to use the measured strong force coupling constant value at low energy scales to discriminate experimentally between the possibilities, thus narrowing "theory space" and the parameter space of theories.  Perhaps existing supersymmetric parameter fitting software does this in a way that isn't transparent to a casual observer like me.

My own conjecture (meaning that I am someone who thinks that this might be true, not that I am the first or only person to have come up with it) is that the three Standard Model force coupling constants do actually converge at a GUT scale, but that this happens only once quantum gravity effects on the ultraviolet running of these constants are considered, which the Standard Model beta functions do not.

Newton's constant is generally a running coupling constant in quantum gravity theories, something which greatly impacts the physics of the very early universe, and a number of beta functions, such as this one, have been proposed.

Thursday, August 6, 2015

New and Improved Archaic Hominin Body Size Data

A new study refines the most recent industry standards for archaic hominin body size from a 1992 paper based upon more remains and better analysis methods. The study is Mark Grabowski, Kevin G. Hatala, William L. Jungers, Brian G. Richmond, "Body mass estimates of hominin fossils and the evolution of human body size.", 85 Journal of Human Evolution 75 (2015). Some pertinent parts of the abstract state that:
Our results show that many early hominins were generally smaller-bodied than previously thought, an outcome likely due to larger estimates in previous studies resulting from the use of large-bodied modern human reference samples. Current evidence indicates that modern human-like large size first appeared by at least 3–3.5 Ma in some Australopithecus afarensis individuals. Our results challenge an evolutionary model arguing that body size increased from Australopithecus to early Homo. Instead, we show that there is no reliable evidence that the body size of non-erectus early Homo differed from that of australopiths, and confirm that Homo erectus evolved larger average body size than earlier hominins.
It turns out that all examples of the genus Homo were much smaller than modern humans until Homo Erectus came along and increased considerably in size.

Homo Erectus is also notable for having much more sexual dimorphism than modern humans, which is strongly suggestive of a gorilla-like harem social structure, with an alpha male having multiple female mates while being stalked by mate-less males seeking to displace him.  This only abated sometime after Homo Erectus. While strong sexual dimorphism has been claimed to be significantly more pronounced in Neanderthals than in modern humans, the linked 1997 article in the New York Times reports a study that disputes that claim:
Dimorphism in primates is especially pronounced in gorillas and orangutans; the males are almost twice the size of females. Male chimpanzees are about 35 percent larger than females, which may also have been the size difference among Lucy and her kind, the early human ancestors known as australopithecines.

The celebrated Lucy, a fossil female from 3.2 million years ago, was a diminutive adult, 3 feet 7 inches tall and no more than 60 pounds. Another skeleton found in related African fossil beds, presumably that of a male, measured 5 feet 3 inches and 110 pounds. By contrast, modern humans are not only bigger, but their body-size dimorphism has declined. On the whole, men today are only about 15 to 20 percent heavier and 5 to 12 percent taller than women. . . .

LUCY (3.2 million years ago)

Lucy was a member of the Australopithecus afarensis branch of the human family tree, which flourished frm 4 million to 3 million years ago. Males were about 35 percent larger than females in her day, about the same as the dimorphism in chimpanzees today.

HEIDELBERG (300,000 years ago)

Homo heidelbergensis, a species ancestral to the Neanderthals, had males about 15 percent larger than females, on average, new findings in Spain show. This deviation is comparable to the male-female size differences of today.


Men are still 15 percent larger than women. However, scientists still don't know when dimorphism began to diminish from its early high level, which could indicate the timing of important shifts in early sexual and family behavior, as size became less of an advantage.
A 2012 study concurs in the conclusion that there is weak evidence for strong sexual dimorphism in Neanderthals.

Another completely different methodology based upon digit ratios, which are a phenotypic marker of in utero testosterone exposure, favors polygnny in early apes, Ardipithecus, Neanderthals, and early modern humans, but not in Australopithecus ("Lucy").

Tuesday, August 4, 2015

Paleo-Asians Part II Some Observations And Preliminary Conclusions

This post continues the discussion at Part I on this blog of new reports on Paleo-Asian ancestry in some recent published papers.  References, if any, will be included in an update to this post.

Executive Summary

The bottom line is that the evidence is consistent with the possibility that a very small number of individuals in the founding population of the Americas had some Paleo-Asian admixture that did not penetrate into the larger founding population during the period in Beringia, either due to population structure in the founding population, or due to a late arrival to Beringia shortly before the commencement of migration from there to the Americas, or both.  The percentages are tiny enough that a few other sources of this genetic ancestry that did penetrate beyond the band that founded the Amazonian population where these genes are found today could have been lost to genetic drift in the meantime.  The longer that these individuals were part of an unstructured Beringian population with a reasonably high and stable effective population, the less statistically plausible this scenario becomes.

I see the most likely explanation involving the integration of one or two individuals (maybe three or four tops) from the same Asian community with some Paleo-Asian ancestry, into a single tribe within the Beriginian population that had been germinating there for thousands of years during the glacial period, who arrive not long before migration to the Americas begins and are integrated into a tribe that happens to be one of the first to migrate along the Pacific Coast, with a vanguard status and cohesive tribe structure that isolates them genetically from populations that follow them at a slower pace.

This isn't the only way to explain the data, but it is adequate to do so without making any terribly implausible assumptions.  Few other narratives that explain the data can rival this hypothesis in plausibility.

Key Observations

Some key observations:

* The Paleo-Asian ancestry is limited to about 2% of the ancestry of some small Amazonian populations near the source of the Amazon.  Even the populations in question have 98% of their ancestry from Native American founding populations.

* The Amazonian populations in question are currently quite small.  The Suuri people, for example, number about 1,200 all told in ten villages, although in fairness, this is in part due to the death of about 90% of their population in the years immediately following first contact in 1969.  The death rate on first contact also rules out pretty much any conceivable contact with Europeans in the post-Columbian era, as they would have had the same diseases and the population would probably harbor more immunity to those diseases in 1969.

The populations with this 2% Paleo-Asian admixture may have made up less than 0.1% of the Pre-Columbian population of the Americas, and definitely make up less than 1% of the Pre-Columbian population of the Americas.  So, we are talking about Paleo-Asian genes that collectively account for 0.02% to 0.002% of the Native American gene pool (i.e. 1 part per 5,000 to 1 part per 50,000) that has disappeared in every population except the descendants of one band out of the founding population of South America.  Many genetic studies of American indigenous population genetics support a founding population of the Americas with an effective population of fewer than 5,000 people.

If Paleo-Asian admixture was that rare in the founding population, even an occasional introgression of a population with this admixture into one that lacked it would be diluted to almost nothing within a few generations and the Paleo-Asian component would be very susceptible to genetic drift out of the population over the next many thousands of years.

No Y-DNA or mtDNA not derived from founding Native American population clades is found in either, which is unsurprising for a low frequency contribution to the gene pool of the Native America founding population, due to genetic drift, but which would be more surprising if found following a much more recent admixture event in which the introgressing population with Paleo-Asian ancestry had some important cultural or genetic fitness enhancing impact on these Amazonian tribes.

This phenomena could all be attributable to a single mixed ancestry individual in the founding population who arrived late to Beringia (perhaps a fisherman in a canoe of the coast of mainland Asia cast adrift by a storm that disorients him causing him to think that the way home is east rather than southwest until he meets these new people) and was at the vanguard of migratory advance as the founding population.  It makes sense that any population that made it all of the way to the Amazon was in the vanguard of migratory advance.

If the Paleo-Asian ancestry level in this proto-Amazonian band of people had not reached fixation until after leaving Beringia, the likelihood that this person's Paleo-Asian genes did not spread to other populations would be even greater.  And, any low frequency genetic component in a population is prone to leaving the gene pool through random genetic drift, particularly prior to the full on expansions into the Americas (because low frequency genetic components are preserved much better in expanding populations than in stable ones).

* We know that the Beringians integrated some individuals whose mtDNA haplogroups (e.g. X2) had a different source population than the rest of the mtDNA haplogroups found in the Americas (A, B, C and D), which may have been there for all or most of the eight thousand or so years of their isolation, and that the proportions of the mtDNA haplogroups varied greatly from one population to the next for populations for which we have Pre-Columbian ancient DNA data, for example, in the American Southwest.  We also know that there were several other low frequency uniparental haplogroups in addition to the dominant ones in the Native American founding population.  So it is not unprecedented for a stray bit of ancestry unrelated to the bulk of the Native American founding population's population genetic makeup to introgress into the founding population, or for there to be structure in population genetics despite many thousands of years during which populations could have equalized their gene pools through admixture.  There are also a number of "gaps" between Asian genetics and Native American genetics that probably reflect ancestry lost during the Beringian period.

* There seems to be some significant structure in the frequency with which mtDNA X2 and a few less common mtDNA clades are seen in Native American populations (mostly in parts of North America), compared to others in South America that have a smaller subset of North American genetic diversity.  This suggests that the hypothesis that the founding population of the Americas in Beringia had reached complete fixation and homogenization while "germinating" in Beringia is probably false.  The more genetically varied the Beringian tribes were before migrating to the Americas, the more plausible it is that Paleo-Asian ancestry found in one such tribe would not spread widely to other tribes.

If mtDNA X2 had enough structure to exclude it from South America, it isn't so surprising that Paleo-Asian ancestry could have been isolated by population structure enough to keep it out of North America.

* The upper boundary of the time period of migratory advance from Beringia to South America is on the order of 1,000 years, but the possibility that some migrating populations made the trip more quickly, particularly if they had a thin preservable material culture, is not precluded.  The shorter the trip, the more likely it would be to see the anomaly that we see in the Amazon.  Also, it is entirely possible that there were waves of migration then that are impossible to discern as separate from what we know now 14 millenia removed.

A scenario in which a few bands take the Pacific route (not knowing that anyone was following them), followed a few years or decades later by a few more bands, until it becomes a wholesale mass migration once climate based push factors are added to the pull of a virgin frontier, could have left early migrating peoples in the vanguard of the migration quite isolated as a genetic population starting the moment the left Berginia.

One doesn't have to be in all that much of a rush to make the 5,600 mile or so trip by foot in a mere seven generations (210 years), which is an average migration of less than 3 miles a month (about 500 feet a day) for a group of nomadic hunter-gatherers who could have subsisted on a similar coastal shallow water flora and fauna diet for much of the trip.  But, if everyone else who follows them is making the trip even slightly more slowly (e.g. 1.5 to 2 miles per month), the vanguard population becomes isolated genetically from the rest of the founding population within a few years of leaving in the very first generation.  An intentional "go South along the coast" strategy may have been a successful one since it consistently led people who followed it to virgin territory in a warmer climate for most of the trip while staying close to food and water resources, until the principle had become almost sacred in the group.

* On the other hand, any other time in the last 12,000 years, you would need a very small group of travelers with at least partial Paleo-Asian ancestry (effective population size 1-3ish) to make a 7,000+ mile trip all of the way from the Amazon to Asia (on the order of 200 miles a month for 35 straight years), across a well populated couple of continents, in a few decades, to have children at the end of the trip in late middle age (by modern standards), and to decide not to stop anywhere else before reaching their destination.  We can be quite certain that the trip was made made across the South Pacific Ocean (something the Austronesians managed only in the last couple of thousand years with their greatest consquests in the last thousand years).  This is highly implausible.

* We don't know how much of the Paleo-Asian ancestry is functional, and how much is merely ancestry informative.  If it was functional, we would expect genetic drift to remove low frequency components until someone bearing the genes arrived in the Amazon where their functionality (which was obscured in Beringia) emerged and elevated what may have been an even lower percentage of this band's gene pool because these genes were fitness enhancing in this environment.

In other words, if the Paleo-Asian ancestry was functional in the Amazon, but not in Beringia, it could have had a fixation level in the migrating band that was well below the 2% level seen now (which might represent near fixation levels of all functional Paleo-Asian genes, with almost all other Paleo-Asian genes that arrive in the Amazon lost in the meantime).

* One of the studies estimates that the date range of admixture with this component is 4,000 to 40,000 years old.  To the extent that this is not an underestimate, that date is too old to be due to any known human contacts between the Americas and Asia after the founding period ca. 13,000 years ago.  It is not inconsistent with admixture occurring during a Beriginian sojourn prior to the founding population entering the Americas or simultaneously with the founding population's migration into North and South America.  Given the infrequency with which this component is seen and the estimated size of the Native American founding population, this ancestry component could be entirely attributable to a single individual in the founding population who was not himself or herself a full blooded Paleo-Asian.

It is hard to imagine a significant separate wave of migration of members of relict population containing Paleo-Asian ancestry not found now in any human population, in the time period from 13,000 to 4,000 years ago, that would not have left traces in any intermediate populations, that would have left no archaeological mark, and that would have left such a thin trace in the modern populations of uncontacted persons in the Amazon.

* The Surui people, and most Amazonian Native Americans who speak languages in the same language family, have origins legends that accentuate the necessity of marrying and having children with close relatives which is consistent with modern practice (e.g. a marriage between a maternal uncle and a niece is exemplified as an ideal, and the marriage between "cross-cousins" who have two independent cousin relationships to each other is considered second best).  Some other tribes in that linguistic family have legendary histories support mother-son child bearing in the tradition of "Jaguar Woman", as a one time necessity.  Other Surui legends, such as the origin of the moon, allude to later instances of incest involving people who are even more closely related.

If this population were in the vanguard of the race to populate the Americas, admixture on the journey from Beringia and the Amazon, it is reasonable to think that they may have been strongly endogamous simply because all of the other human (in this context there is no need to qualify that with "modern human") populations were far behind them in their migration.

This long tradition of tolerance for marriages between closely related people also suggests that these populations have never had very large effective populations relative to their geographic range.

The hybrid fitness advantages of a single individual with partial Paleo-Asian ancestry might give his (or her) descendants an edge in an otherwise highly inbred population until those genes reached fixation in the Amazonian population where these genes are found today.

* The distinctiveness of the populations including the Amazonians who have this Paleo-Asian ancestry, as a genetic cluster distinct from other South American populations (as shown in previous studies comparing language groups and genetic clusters) argues for the fact that they have probably been endogamous for a long time; so does the relatively forbidding environment in which they live (jungles have historically been strong barriers to population movement in modern humans).

The inference that there was genetic diversity in the founding population of the Americas that reflects the phenotypic diversity of Paleo-Americans has been fairly definitively rebutted, once again.

* The Paleo-Asian ancestry observed does not appear to involve any of the populations that are likely descendants of a "lost civilization" of the Amazon that built structures in the Amazon when that was possible in another climate era.

* The likely route of migration for all of the Amazonian peoples affected is along the northern coast of South America, up a river basin, and a short distance over a "continental divide" between river basins in South America into the river basin of a tributary of the Amazon River, not over the mountains on the Pacific Coast of Peru (this is illustrated by earlier population genetic studies of current Native Americans).

* While this 2% Paleo-Asian component has similarity to that found in Australian Aborigines, indigenous Papuans, Negrito Philippinos, and Oceanian populations derived from Papuans, all of whom have elevated Denisovan ancestry, this population does not have elevated Denisovan ancestry, is not more Papuan than Australian Aborigine in origin, and also shows affinity to Andaman Island populations.  In short, this is a trace of a generic Paleo-Asian modern human population that did not experience Denisovan admixture in an measurable amount.

The fact that the Paleo-Asian component does not correspond to any known living population, and certainly not to any living population that could have admixed with the Amazonians in the last 4,000 years tends to corroborate the inference that this ancestry component had its origins in the founding population of the Americas, rather than in Bronze Age or more recent contacts between the Amazon and known somewhat similar populations in Asia.

For example, the available genetic information rules out contact with Polynesians, Papuans and Australian Aborigines, and Negrito Philippinos.  It is not an exact match for Andaman Islanders, who have been non-contacted people from ca. 20,000 years ago until probably the last 1,000 years.

There is also no indication that the Paleo-Asian component reflects any archaic hominin admixture.

* The populations with Paleo-Asian ancestry are not populations that had been singled out as having distinct phenotypes relative to other early Native Americans that might reflect a separate wave of migration in addition to that of the founding population.  Where DNA tests have been done of individuals with distinct phenotypes that has corresponded with pure founding population ancestry.

* The comments at a West Hunter post on the subject (also here) note legendary histories of Polynesians and Native Americans and mainland Asians that seem to reference a darker colored, physically small population of people, many of which assign the population similar names that could have a common origin that could be legendary descriptions of a relict Paleo-Asian population, Such legends seem to imply that such relict populations may have persisted into the Holocene or later in many places in East Eurasia.

* The existence of Paleo-Asians in mainland Asia who could have, in theory, contributed to the founding population of the Americans but no longer exist as distinct populations is highly plausible.

We know to a certainty that the recent population history of East Eurasia has seen the expansion of some populations, like the Han Chinese, at the expense of other populations (such as pre-food producing populations of regions that came under the rule of food producing populations), in a pattern that has been repeated again and again worldwide.

It is reasonable to hypothesize that Jomon-like populations (rich in distinctively Japanese clades of Y-DNA D) existed somewhere outside Japan before they arrived in Japan, ca. 30,000 to 15,000 years ago, a time frame appropriate for some member of that population to join the Beringian founding population.  The genetic affinity of the Onge of the Andaman Islands (who all have Y-DNA D) to the Ancestral South Indian (ASI) component of South Asian populations (which have low frequencies of Y-DNA D), strongly suggests that there was a Paleo-Asian population in mainland South Asia which was genetically similar to the Onge, and no longer exists in unadmixed form.  This is also suggested by the existence of people with related Y-DNA D in a path more or less straight to Tibet (which has significant amounts of Y-DNA D) from the Andaman Islands and then in a dispersed mix in Siberia to the North of Tibet (where Y-DNA D is found at low levels).  It is worth noting that in Japan and Tibet, it seems likely that Y-DNA D male populations had overwhelmingly mtDNA M female counterparts.  Thus, this population would be distinct from the putative Northern route mtDNA N bearing population that purportedly gave rise to the Australian Aborigines and original modern human Papuans in [17].  The generic Paleo-Asian ancestry seen in the Amazonian tribes in these studies may draw from a population with origins in both the Y-DNA D/mtDNA M wave (Andamanese-like), and from the mtDNA N wave of Asian migration (Melanesian-like) of Paleolithic era migration by modern humans to Asia.

It is likely that many pre-Last Glacial Maximum populations of northern Asia went extinct or were rendered moribund with surviving members assimilated piecemeal into other populations by this climate event.

The existence of several relict Negrito populations in Southeast Asia, are presumably the descendants of Paleo-Asian populations and unlike the Negrito people of the Philippine Islands, Melanesia and Australia, they lack significant Denisovan ancestry (although recent studies show that some mainland Asian populations do have slight, but measurable levels of Denisovan ancestry).

Prior papers looking at the uniparental genetic makeup of Asia have proposed a multi-wave model with often more than one pre-Holocene wave of migration.  Towards that end the comments at the previous post rightly call attention to [16] and [17].

* The argument that there was no new migration to the Americas with the Na-Dene people despite some private mtDNA clades and Reich's estimate of about 10% new migration wave architecture, and consistent with linguistic and archaeological evidence for a separate wave of migration, is not convincingly rebutted by the new study making that claim.

* The argument that the Paleo-Asian ancestry could be of recent (i.e. Bronze Age or later) origins in one study is contradicted pretty decisively by the evidence in the other study.

More Questions

* To what extent is the Paleo-Asian ancestry in these populations fitness enhancing as opposed to selectively neutral?

* What other relict traces and low frequency admixture traces of Paleo-Asian populations are found in modern Asia?

* Highly inbred populations without unknown population histories that are isolated for long periods of time can distort ancestry analysis.  It is plausible that the tools used to analyze the highly inbred populations of the Amazon were tuned to global assumptions about population dynamics and not inbred and isolated assumptions ones.  It could be that what looks like Paleo-Asian ancestry is really just a case of distinctive locally evolved Amazonian genetic patterns being clearly Eurasian, but gravitating towards the Eurasian outgroup populations that are least like extant modern populations simply because the Australian, Papuan and Andamanese outgroups including this one are collectively dissimilar to other Eurasians, with Eurasian similarities at these loci haven arisen with a time depth of less than 25,000 years.  Thus, is it possible that this is a case of mis-identification due to a methodological flaw of the software used that is particularly vulnerable to confusion in a highly inbred population that has been isolated for many thousands of years?

* Is it possible to use other genetic data to model a range of substructure models for the founding population of the Americas and then to see how difficult in those models it would be for Paleo-Asian ancestry that is not lost to drift to end up in just one tribe after a prolonged period of germination in Beringia (possibly 8,000 years)?

One needs quite strong substructure relative to what one would expect from an even slightly exogamous group of tribes, each of small population, to persist over 8,000 years, although low effective population size and multiple potential bottlenecks in that 8,000 years could counteract the tendency towards homogeneity in that population.  Over 300 or so generations or so of even slight admixture between populations (one pairing every two or three generations even) there is enough time to really blend everyone's gene pools pretty completely and to push any gene that is functional in that environment to fixation.  But, a low effective population size throughout that time period and multiple bottlenecks could insert enough founder effect randomness and genetic drift to produce what is observed.  The shorter the "germination" period, the lower the average effective population size, and the more bottlenecks were experienced, the easier it would be to reproduce the observed level of population structure.

* There is pretty decisive evidence from population genetics that later Paleolithic wave of migration to Asia by modern humans came quite close to totally replacing earlier Paleolithic waves of migration to Asia by modern humans in huge swaths of territory that include almost any place that can be reached without crossing substantial bodies of water and that are not isolated in pockets of mountainous environments.  Indeed, I'd say that there is pretty good evidence that there were at least two significant waves of pre-modern migration to Asia.

What process brought about this replacement of one "race" of hunter-gatherers with another?  Could it be that admixture with archaic hominins by first contact wave hunter-gatherers while providing some fitness enhancing traits like immune system genes, also came with disadvantages of some kind compared to their unadmixed modern human peers in later waves?

Or, did the Neolithic revolution in Asia deal a final blow to Paleo-Asian communities that had survived as relict populations up until then, maybe as late as the Bronze Age, possibly giving rise to the persistent legendary histories of dark, small people given similar sounding names in many East Eurasian civilizations.

* Did populations that made first contact with archaic humans in mainland Asia have similar levels of Denisovan ancestry to that of existing Melanesian populations at first contact, only to see that ancestry wiped out as later Asian hunter-gatherers mostly replaced earlier Asian hunter-gatherers, and then Asian first and subsequent farmers replaced Asian hunter-gatherers?  Or, did Denisovan admixture simply not take place at first contact in mainland Asia the way that it did in or around the Wallace Line and Flores?  For example, perhaps the Denisovans and the Hobbits are one and the same, and admixture achieved by the Hobbits was made possible only because they were dwarf types of their mainland kin.

* What kind of hominins lived in Asia (beyond South Asia) in the time period from roughly 200,000 years ago to the Toba eruption around 75,000 years ago, during which the hominin archaeological record in this part of Asia is almost nil.  The oldest evidence of Homo floresiensis on the island of Flores is about 94,000 years old.  This predates the arrival of modern humans by tens of thousands of years, but is still 100,000 years after the oldest really definitive examples of Homo Erectus from either bones or archaeological tools kits associated with them.

Did the same climate factors that caused Neanderthals to become distinctive and eventually dominant in West Eurasia lead to the gradual (or not so gradual) near extinction of Homo Erectus in Asia at about the same time?  Jungles and mountains could have impeded Neanderthal advancement on Homo Erectus territory via a Southern route.  Perhaps other biogeographic barriers preventing Neanderthals from reaching Homo Erectus territory via a Northern route.  So, Homo Erectus could have had 125,000 years or more to gradually decline pre-Toba, protected from replacement by biogeographic barriers until Toba temporarily destroyed Southeast Asian jungles that had prevented other hominin species from moving into its territories in numbers large enough that the Homo Erectus tribes in the borderlands could not repel them.

Could it be that fitness testing challenges of life in West Eurasia which was quite unlike Africa, placed greater pressure on archaic hominins in West Eurasia to evolve in ways that produced generalized fitness enhancements rather than merely locally adaptive ones, while Homo Erectus in tropical Asia could continue to manage perfectly well with behaviors established in Africa at the time of that species' migration to Eurasia, and that Asian Homo Erectus then reached stasis in its own evolution?

Were Homo Erectus replaced by Denisovans who for some reason left a much lighter archaeological footprint?  Alternately, was Homo Erectus so incapable of responding the climate change in the wake of the Toba eruption, that this species collapsed of its own accord leaving a near vacuum in Asia until modern humans filled that void?

When did Denisovans arrive in Asia?  Certainly in time to admix with proto-Melanesians ca. 50,000 years ago, but could they have entered Asia around the same time as modern humans, although perhaps by a different route?

Were the Denisovan an offshoot of Homo Erectus or did they have only modest admixture, at most, with Homo Erectus?  If they weren't were Denisovans capable of producing hybrid offspring, while Homo Erectus, which may have remained dominant on the mainland, was not?  Could Denisovans have been some clade of hominin more closely related to West Eurasian archaic hominins than to Asian Homo Erectus that made a more tentative and less effective invasion of Asia than subsequent modern humans that left them confined to territory that Homo Erectus couldn't handle, just as land across the Wallace Line, high altitudes in Tibet, and remote cave in Siberia?  A single Denisovan skeleton that also produced ancient DNA could connect so many dots while ruling out so many other possible theories.

Was the only technological advance experienced by West Eurasian Homo Erectus but not by Asian Homo Erectus due to admixture with a more recent archaic hominin type in the West but not the East, of a species that had far less plastic intellectual hardware than we do?

We know that Neanderthals and modern humans were different enough that Haldane's rule that hybrids tend to be female (when female is XX and male is XY), held true.  But, the time depth of the separation of Homo Erectus and modern humans was several times greater.

Additional References

[16] Fregel, et al., "Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route", PLoS One (June 8, 2015).
[17] Morten Rasmussen, et al. "Dispersals into Asia An Aboriginal Australian Genome Reveals Separate Human Dispersals Into Asia", 334 Science 94 (2011). The abstract of this paper, which is based on modern autosomal population genetics and some 100 year old hair from an unadmixed Aboriginal Australian states that:
We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.