Tuesday, August 20, 2019

Remembering A Real Scientific Hero

Four years ago [as of August 18, 2019], Syrian archaeologist Khaled Al-Asaad was murdered by Daesh after refusing to give away the location of hidden artefacts in Palmyra. He gave his life for the heritage he had dedicated his life to, in defiance of brutality, extremism, and authoritarianism.
From here.

Reflections On Greece Part II: A 3D Divine Family Portrait

My photo of a pair of  statutes of Persephone, Hades and Cerberus 
from the archaeological museum in Heraklion, Greece. 
It is distinctive for having both Greek and Roman elements.
Hades a.k.a. Aidoneus a.k.a. Pluto, was notable for being one of the few Chthonic (i.e. underworld based) gods in the Greek pantheon. He was Zeus's brother and Persephone's uncle.

Persephone (a.k.a. "Kore", i.e. the maiden) was worshipped in a distinctive way in Crete which is notable:
In the Near eastern myth of the early agricultural societies, every year the fertility goddess bore the "god of the new year", who then became her lover, and died immediately in order to be reborn and face the same destiny. Some findings from Catal Huyuk since the Neolithic age, indicate the worship of the Great Goddess accompanied by a boyish consort, who symbolizes the annual decay and return of vegetation. Similar cults of resurrected gods appear in the Near East and Egypt in the cults of Attis, Adonis and Osiris
In Minoan Crete, the "divine child" was related to the female vegetation divinity Ariadne who died every year. The Minoan religion had its own characteristics. The most peculiar feature of the Minoan belief in the divine, is the appearance of the goddess from above in the dance. Dance floors have been discovered in addition to "vaulted tombs", and it seems that the dance was ecstatic. Homer memorializes the dance floor which Daedalus built for Ariadne in the remote past. On the gold ring from Isopata, four women in festal attire are performing a dance between blossoming flowers. Above a figure apparently floating in the air seems to be the goddess herself, appearing amid the whirling dance. An image plate from the first palace of Phaistos, seems to be very close to the mythical image of the Anodos (ascent) of Persephone. Two girls dance between blossoming flowers, on each side of a similar but armless and legless figure which seems to grow out of the ground. The goddess is bordered by snake lines which give her a vegetable like appearance She has a large stylized flower turned over her head. The resemblance with the flower-picking Persephone and her companions is compelling. The depiction of the goddess is similar to later images of "Anodos of Pherephata". On the Dresden vase, Persephone is growing out of the ground, and she is surrounded by the animal-tailed agricultural gods Silenoi
Kerenyi suggests that the name Ariadne (derived from ἁγνή, hagne, "pure"), was an euphemistical name given by the Greeks to the nameless "Mistress of the labyrinth" who appears in a Mycenean Greek inscription from Knossos in Crete. The Greeks used to give friendly names to the deities of the underworld. Cthonic Zeus was called Eubuleus, "the good counselor", and the ferryman of the river of the underworld Charon, "glad". Despoina and "Hagne" were probably euphemistic surnames of Persephone, therefore he theorizes that the cult of Persephone was the continuation of the worship of a Minoan Great goddess. The labyrinth was both a winding dance-ground and, in the Greek view, a prison with the dreaded Minotaur at its centre. It is possible that some religious practices, especially the mysteries, were transferred from a Cretan priesthood to Eleusis, where Demeter brought the poppy from Crete. Besides these similarities, Burkert explains that up to now it is not known to what extent one can and must differentiate between Minoan and Mycenean religion. In the Anthesteria Dionysos is the "divine child".
Try as I might, I did not see any visual depictions of someone else related to this husband, wife and dog family, Minthe anywhere on my trip, although at least some of their children (most famously Dionysus) were depctied. Even a store keeper in a particularly promising mythology and mythology replica store wasn't familiar with Minthe, about whom Wikipedia explains:
In Greek mythology, Minthe (also Menthe, Mintha or Mentha; Greek: Μίνθη or Μένθη) was a naiad associated with the river Cocytus
The -nth- element in menthe is characteristic of a class of words borrowed from a Pre-Greek language: compare acanthuslabyrinthCorinth, etc. 
Minthe was dazzled by Hades and made an attempt to seduce him, but Queen Persephone intervened and metamorphosed Minthe, in the words of Strabo's account, "into the garden mint, which some call hedyosmon (lit. 'sweet-smelling')".[1]

"Mint (Mintha), men say, was once a maid beneath the earth, a Nymphe of Kokytos (Cocytus), and she lay in the bed of Aidoneus [Hades]; but when he raped the maid Persephone from the Aitnaian hill [Mount Etna in Sicily], then she complained loudly with overweening words and raved foolishly for jealousy, and Demeter in anger trampled upon her with her feet and destroyed her. For she had said that she was nobler of form and more excellent in beauty than dark-eyed Persephone and she boasted that Aidoneus would return to her and banish the other from his halls : such infatuation leapt upon her tongue. And from the earth spray the weak herb that bears her name."[2] 
In ancient Greece, mint was used in funerary rites, together with rosemary and myrtle, and not simply to offset the smell of decay; mint was an element in the fermented barley drink called the kykeon that was an essential preparatory entheogen for participants in the Eleusinian mysteries, which offered hope in the afterlife for initiates. 

Monday, August 19, 2019

Dark Humor II

From here.

As usual, not only funny, but true in its essential scientific essence.

Reflections On Greece Part I: Palimpsest Layers In The History Of Greece

So, I am back from a couple of weeks in Greece, in Athens, the Cyclades, and Crete. Naturally, this got me thinking about a lot of issues of deep history. I'll start with a historical backgrounder.

The Eastern Mediterranean (image from here).

Any assessment of genetic or archaeological or linguistic evidence from Greece and historiography require one to consider the many confounding palimpsest layers in its past that must be considered and stripped away before considering older materials.

Greece had Neanderthals and the earliest modern humans in Europe (as expected almost definitionally as it is the most Southeastern part of Europe).

A One Paragraph Overview Of Holocene Era Greek History

Wikipedia sums up its history this way:
Generally, the history of Greece is divided into the following periods:
Greece was near the birthplace of the Fertile Crescent Neolithic and had very early Neolithic communities. 

Bronze Age Greece

Greeks metal age civilizations including the Minoan civilization were among the earliest, if not the earliest, in Europe, and were pre-Indo-European. A parallel, somewhat less advanced metal age culture arose on the Greek mainland.

Greece has one of the best documented transitions from the non-Indo-European to Indo-European cultures in prehistory with even some written attestation in the form of the Linear A to Linear B and Eteocretan transitions in addition to rich oral legendary history documented not too long after fact, and contemporaneous Akkadian and Egyptian records.

Iron Age And Early Medieval Greece

In the Iron Age, Greece had periods of Persian invasion and rule. Briefly, in the early Iron Age, before the Romans became ascendant, they had an ancient maritime colonial civilization that stretched from the Mediterranean coast in Spain to the Black Sea. Culturally and linguistically, "Ancient" and "Classical" Greece in the early Iron Age were in direct cultural continuity with the Mycenaean Greek society that fell during Bronze Age collapse.

The Roman Empire at its greatest extent, 117 CE, the time of Trajan's death (with its vassals in pink) via Wikipedia.

Fun fact: Emperor Hadrian, who is famous for his wall in Britain at something close to the Roman Empire's peak, also built an archway in new half of the city in Athens that survives today and is now at the center of the city. I checked it out in person the day before yesterday.

They spent four and a half centuries ruled by the Romans.

But, they are one of the best examples of a people who were conquered militarily but ended up culturally integrating and subsuming their conquerors to a great extent. When the Western Roman Empire collapsed, the Greek speaking Eastern Roman Empire survived and morphed into the Byzantine Empire centered in Constantinople, which prevailed in Greece for another eleven centuries (although this was not uniform across all parts of Greece).

Ottoman and Venetian Greece In The Late Middle Ages And Early Modern Period

The division of the Byzantine Empire after the Fourth Crusade (1204-1261 CE) via Wikipedia. The purple territory is the Byzantine Empire proper and the rust colored states are Greek successor states of the Byzantine Empire. The green areas are parts of the Republic of Venice shown with the year that they joined the Republic of Venice. The Brown Sultanate is an immediate predecessor of the Ottoman Empire which would come into being a generation later. 

The Byzantine Empire greatly reduced since the 7th century, in the face of an expanding Islamic Empire, lasted for eight centuries, but it was all downhill after 1261 CE, and finally imploded in 1453 CE, after being defeated by the Ottoman Empire (1299-1922 CE).

The Republic of Venice in the 15th and 16th centuries via Wikipedia.

The Ottoman Empire at its greatest extent in Europe, under Sultan Mehmed IV via Wikipedia.

But, some of Greece resisted the Islamic expansion by becoming an integral part of the Republic of Venice for many centuries with Heraklion, the current regional capital of Crete, becoming a Venice of the East (the understanding that the term "Oriental" originally referred to what is now often referred to as the "Near East" sunk in).

Eventually the Ottoman Empire did conquer Greece, but this left a remarkably thin lasting impression. Even the "Turkish delights" made famous by C.S. Lewis are called "Greek delights" everywhere in Greece which is allergic to Turkey with whom it has a tortured history of conflict that is ongoing. A brief period of Greek absolute monarchy under Austro-Hungarian King Otto's brother-in-law (from 1832 to 1843 when he established a constitutional monarchy in which he remained king) left more of a lasting mark on the country than about four centuries of Ottoman Empire rule.

Most of Greece gradually became part of the Ottoman Empire in the 15th century. The Eastern Roman, the direct continuation to the ancient Roman Empire who ruled most of the Greek-speaking world for over 1100 years, had been fatally weakened since the sacking of Constantinople by the Latin Crusaders in 1204. 
The Ottoman advance into Greece was preceded by a victory over the Serbs to its north. First, the Ottomans won at 1371 on the Maritsa River – where the Serb forces were led by the King Vukašin of Serbia, the father of Prince Marko and the co-ruler of the last emperor from the Serbian Nemanjic dynasty. This was followed by a draw in the 1389 Battle of Kosovo
With no further threat by the Serbs and the subsequent Byzantine civil wars, the Ottomans captured Constantinople in 1453 and advanced southwards into Greece, capturing Athens in 1458. The Greeks held out in the Peloponnese until 1460, and the Venetians and Genoese clung to some of the islands, but by 1500 most of the plains and islands of Greece were in Ottoman hands. The mountains of Greece were largely untouched, and were a refuge for Greeks to flee foreign rule and engage in guerrilla warfare. 
Cyprus fell in 1571, and the Venetians retained Crete until 1670. The Ionian Islands were only briefly ruled by the Ottomans (Kefalonia from 1479 to 1481 and from 1485 to 1500), and remained primarily under the rule of Venice. 

Territorial evolution of Kingdom of Greece until 1947 CE via Wikipedia
The territories in yellow, acquired in 1920, were ceded back to Turkey in 1923. 

Eventually, staring with the proclamation of the Greek Revolution in October of 1821, the Greeks finally secure independence after a long hiatus (I'm not sure that Greece was ever a unified kingdom before this time, as opposed to a civilization of interacting balkanized city-states and small principalities, even in its Golden Age). This was a period of tremendous growth, urbanization and modernization, a bit like that of countries emerging from Eastern Europe and the Communist regimes in the 20th century. As explained here:
The urban population tripled from 8% in 1853 to 24% in 1907. Athens grew from a village of 6000 people in 1834, when it became the capital, to 63,000 in 1879, 111,000 in 1896, and 167,000 in 1907.

In Athens and other cities, men arriving from rural areas set up workshops and stores, creating a middle class. They joined with bankers, professional men, university students, and military officers, to demand reform and modernization of the political and economic system. Athens became the center of the merchant marine, which quadrupled from 250,000 tons in 1875 to more than 1,000,000 tons in 1915. As the cities modernized, businessmen adopted the latest styles of Western European architecture.
This was actually the second rebirth of Athens, which was also entirely abandoned in favor of a more defensible neighboring island in the 400s BCE, following a Persian invasion. Athens is now home to about 4 million people, a third of the twelve million people in modern Greece, more than half of whom live in its three largest cities (only about 12% of the population lives permanently on its islands today, and most of those people live in urban settings as well).

With more than a century of territorial adjustments, Greece eventually reached something like its current boundaries. For example, as a result of the Balkan Wars of 1912–1913, most of Epirus, southern Macedonia, Crete and the northern Aegean islands were incorporated into the Kingdom of Greece. Greece was divided internally between the major sides in World War I with the prevailing allies ousting the King and becoming ascendant. Today's boundaries of Greece are the same as they were in 1919, except for the Dodecanese islands off the shore of Turkey ceded by Italy to Greece in 1947.

The 19th and 20th century brought major territorial realignments and mass migrations of people "ethnic cleansing" style with non-Greeks leaving independent Greece and Greeks with a handful of exceptions leaving Anatolia and the Black Sea region (something reminiscent of the mass migrations of Jews leading up to World War II and for those who survived the Holocaust, in its aftermath, to Israel and the United States, and also of the realignment of populations in South Asia following the partition of India and Pakistan).

Per Wikipedia, in the next key time period:
At the end of the war, the Great Powers agreed that the Ottoman city of Smyrna (Izmir) and its hinterland, both of which had large Greek populations, be handed over to Greece. 
Greek troops occupied Smyrna in 1919, and in 1920 the Treaty of Sèvres was signed by the Ottoman government; the treaty stipulated that in five years time a plebiscite would be held in Smyrna on whether the region would join Greece. However, Turkish nationalists, led by Mustafa Kemal Atatürk, overthrew the Ottoman government and organised a military campaign against the Greek troops, resulting in the Greco-Turkish War (1919-1922). A major Greek offensive ground to a halt in 1921, and by 1922 Greek troops were in retreat. The Turkish forces recaptured Smyrna on 9 September 1922, and setting the city ablaze and killing many Greeks and Armenians. 
The war was concluded by the Treaty of Lausanne (1923), according to which there was to be a population exchange between Greece and Turkey on the basis of religion. Over one million Orthodox Christians left Turkey in exchange for 400,000 Muslims from Greece. The events of 1919–1922 are regarded in Greece as a particularly calamitous period of history. Between 1914 and 1923, an estimated 750,000 to 900,000 Greeks died at the hands of the Ottoman Turks, in what many scholars have termed a genocide.
World War II was not kind to Greece either, where it was a major area of active conflict, and a period of Nazi occupation left definite marks. Once restored to allied control, civil war between nationalist and communist forces broke out (1944-1949) before World War II was even over, in the first conflict of the Cold War. Subsequent U.S. led post-war Marshall Plan reconstruction efforts that flooded Athens or other major Greece cities with "International style" "brutalist" architecture that remains predominant in much of the mainland. 

Neither the monarchy nor democratic nature of the constitutional monarchy was uninterrupted:
Following the National Schism during World War I and the subsequent Asia Minor Disaster, the monarchy was deposed in March 1924 and replaced by the Second Hellenic Republic. Between 1924 and 1935 there were in Greece twenty-three changes of government, a dictatorship, and thirteen coups d'etat. In October 1935, General Georgios Kondylis, a former Venizelist, overthrew the government and arranged for a plebiscite to end the republic. On 3 November 1935, the official tally showed that 98% of the votes supported the restoration of the monarchy. The balloting was not secret, and participation was compulsory. As Time described it at the time, "As a voter, one could drop into the ballot box a blue vote for George II and please General George Kondylis, or one could cast a red ballot for the Republic and get roughed up." George II returned to the Greek throne on 25 November 1935. 
On 4 August 1936, the King endorsed the establishment of a dictatorship led by veteran army officer Ioannis Metaxas, signing decrees that dissolved the parliament, banned political parties, abolished the constitution, and purported to create the "Third Hellenic Civilization." An Index of banned books during that period included the works of Plato.
George II followed the Greek government in exile after the German invasion of Greece in 1941 and returned to the throne in 1946, after a referendum that resulted in the restoration of constitutional monarchy.
Greece got yet another military coup and military dictatorship (which abolished the constitutional monarchy once and for all) in 1967 and lasted until 1974 when it fell to another coup that also precipitated a coup in Cyprus that led to the Turkish invasion of Cyprus whose consequences remain a point of tension that has not been fully resolved.
In 1967, the Greek military seized power in a coup d'état, overthrowing the centre right government of Panagiotis Kanellopoulos. It established the Greek military junta of 1967-1974 which became known as the Régime of the Colonels. The junta government's accession to power lead to an isolation to Greece from European affairs and froze Greece's entry to the European Union. In 1973, the régime abolished the Greek monarchy and in 1974, dictator Papadopoulos denied help to the United States. After a second coup that year, Colonel Ioannides was appointed as the new head-of-state. 
Ioannides was responsible for the 1974 coup against President Makarios of Cyprus. The coup became the pretext for the first wave of the Turkish invasion of Cyprus in 1974 (see Greco-Turkish relations). The Cyprus events and the outcry following a bloody suppression of Athens Polytechnic uprising in Athens led to the implosion of the military régime.
But, democracy was ended and the end of the monarchy was confirmed, later in 1974, and Greece joined the E.U.
After the end of the military régime, democracy was restored. 
The fall of the junta was followed by the metapolitefsi. Metapolitefsi was initiated when Konstantinos Karamanlis returned from self-exile in Paris at the invitation of the junta, to become interim prime minister on July 23, 1974 and later gained re-election for two further terms at the head of the conservative New Democracy Party. In August 1974, Greek forces withdrew from the integrated military structure of NATO in protest at the Turkish occupation of northern Cyprus. 
In 1974, a referendum voted 69%–31% to confirm the deposition of King Constantine II. A democratic republican constitution came into force. Another previously exiled politician, Andreas Papandreou also returned and founded the socialist PASOK Party (Panhellenic Socialist Movement), which won the 1981 election and dominated Greek politics for almost two decades. 
After the restoration of democracy, Greece's stability and economic prosperity improved significantly. Greece rejoined NATO in 1980, joined the European Union (EU) in 1981 and adopted the euro as its currency in 2001.
This didn't bring happily ever after, however. 

In 2009, a sovereign debt crisis flowing from a U.S. led global financial crisis hit Greece and the country was thrust into a state of extreme economic distress until about 2015. Everywhere in Greece there are abandoned half built homes and commercial buildings, the construction of which was derailed in that crisis, which have not completed and are covered with graffiti, some serving as homeless camps, as of August of 2019. Successive elections brought tidal waves of political change and also gave far right parties considerable power, although the far right parties and more democratic socialist leaning parties were swept out earlier this year in an election that brought a center-right party into power, and as I my visit, affairs had returned to relative normalcy. 

Friday, August 2, 2019

Away Note

I will be in a place of great historical interest for the next couple of weeks in celebration of my 25th wedding anniversary, and may not be posting very much either here or in the blog's sister blog, in that time period.

Theories Whose Truth Isn't Proveable

In mathematics there are a class of theories which you can prove can't be "disproven" and you can also prove can't be "proven" such as the Continuum Hypothesis (the theory that there is a class of infinities that is bigger than countable infinities and smaller than non-countable infinities). 4gravitons discusses this in greater detail.

Monday, July 29, 2019

Iran Is Genetically Distinctive

Iran is fairly distinctive population generically from Southwest Asia and five of the eight ethnicities studied form one big supercluster, although the Arab ethnicity breaks out distinguishably from the other four ethnicities in the supercluster that overlap to a great extent, mostly on Principal Component 2 of the data. PC 1 and PC 3 are pretty much an overlapping jumble for the five core Iranian populations.

In the top two PCA charts, light purple is Turkmen, light blue is Persian Gulf Islanders, orange is Baluch. In all four PCA charts, dark blue is Arab, red is Lur, green is Azeri, yellow is Persian, and dark purple is Kurd. The close up is of the PCA chart labeled "C" comparing PC 1 to PC 2 for the five core Iranian ethnicities only.
Considering the application of human genome variation databases in precision medicine, population-specific genome projects are continuously being developed. However, the Middle Eastern population is underrepresented in current databases. Accordingly, we established Iranome database (www.iranome.ir/com) by performing whole exome sequencing on 800 individuals from eight major Iranian ethnic groups representing the second largest population of Middle East. We identified 1,575,702 variants of which 308,311 were novel (19.6%). Also, by presenting higher frequency for 37,384 novel or known rare variants, Iranome database can improve the power of molecular diagnosis. Moreover, attainable clinical information makes this database a good resource for classifying pathogenicity of rare variants. Principal components analysis indicated that, apart from Baluchs, Turkmen and Persian Gulf Islanders, who form their own clusters, rest of the population were genetically linked, forming a super-population. Furthermore, only 0.6% of novel variants showed counterparts in "Greater Middle East Variome Project", emphasizing the value of Iranome at national level by releasing a comprehensive catalogue of Iranian genomic variations and also filling another gap in the catalogue of human genome variations at international level. We introduce Iranome as a resource which may also be applicable in other countries located in neighboring regions historically called Greater Iran (Persia).
Fattahi Z et al., Iranome: A catalogue of genomic variations in the Iranian populationHum Mutat. (July 25, 2019). doi: 10.1002/humu.23880. [Epub ahead of print]

Supplemental information including population descriptions and PCA plots is here (MS Word).

Standard Model Point Particles In Classical General Relativity

One of the main reasons that we know we don't know everything about fundamental physics is that classical general relativity and the Standard Model of Particle Physics are mathematically inconsistent. The point particle problem isn't the only mathematical inconsistency between general relativity and the quantum mechanics of the Standard Model, but it is one of the most obvious ones.

The Schwarzschild Radius Of Fundamental Particles

In classical general relativity, any true point particle with a non-zero mass gives rise to a singularity, because it involves division a finite mass by zero radius and volume.

The Schwarzschild radius of a mass is distance from the center a black hole to the event horizon of a black hole, in the case of a mass of that amount in general relativity.

The Schwarzschild radius of an election's mass is about 1.353 * 10-57 meters v. the Planck length of 1.616 * 10-35 meters.

Schwarzschild radius is proportional to mass, so a top quark pole mass mass black hole would have a Schwarzschild radius of 4.58 * 10-55 meters (which is significant because the top quark is the heaviest fundamental particle in the Standard Model).

A black hole with a Plank length radius would have a mass of 3.85763 * 10−8 kg, which is 1.772 Planck masses. Note that a mass of 1 kg = 1.780 * 10−27 GeV/c2. So a Plank radius black hole would be roughly 1017 times more massive than the pole mass of a top quark.

The Heisenberg Uncertainty Principle

The Heisenberg uncertainty principle says that uncertainty in position times uncertainty in momentum measured at the same time is always greater to or equal than the reduced Planck's constant divided by 2.

The Heisenberg uncertainty principle also states that uncertainty in amount of energy times uncertainty in time measured at the same time is always greater to or equal than reduced Planck's constant divided by 2.

The reduced Planck's constant is 6.582 * 10-16 eV * second/radian. Mass and energy are basically equivalent with an E=mc2 conversion factor for these purposes.


So, while you need some finite radius for a point particle in the Standard Model, for example, a la string theory, or some finite distance length in space-time to avoid the point particle problem that the pure point particle Standard Model causes in classical general relativity, that scale can be much less than the Planck scale. In particular, the necessary scale is deeply within a domain where mass and position cannot be well defined to sufficient precision in a single measurement.

Friday, July 26, 2019

Iron Age Indo-European Ancient DNA Found East Of Tarim Basin

Ancient Iron Age DNA found in Tianshan, a part of what is now Inner Mongolia well to the east of the Tarim Basin, has been determined to have a strongly Indo-European profile. This is pretty much the most eastern example of pre-modern Indo-European communities.

The authors then used the f3 statistic to show that the old Shirenzigou individuals are best modeled as derived from a genetic mix between a Yamnaya population as a western source and a North Asian or Korean population as an eastern source. The f3 statistic also confirms the lack of Neolithic farm ancestry among the old Shirenzigou individuals, like those of the Yamnaya culture, but unlike the old individuals of the Srubnaya, Andronovo or Sintashta cultures.

The authors then used the qpAdm software to estimate the Yamnaya ascendance proportions. The result gives a value which varies from 20 to 80% according to the individuals of Shirenzigou. The best modeling gives a genetic mix of three sources: Yamnaya, Oultchesor Hezhen and Han Chinese. While the majority of Shirenzigou individuals have more Oultches or Hezhen ancestry, two individuals (M820 and M15-2) have more Han ancestry.

The strong difference in Yamanaya ancestry (between 20 and 80%) among Shirenzigou individuals suggests that genetic mixing occurred shortly before the formation of the archaeological site during the Iron Age. But other explanations are possible, such as the fact that the region was a crossroads of exchange for millennia, or that the western source was already very heterogeneous. 
In conclusion, this study shows that Yamnaya culture or Afanasievo culture has spread south-east to the slopes of the Tianshan Mountains probably as early as the second millennium BC. JC. and thus favors the steppe hypothesis in the formation of the people of Xinjiang.
More discussion from Razib Khan who notes this money quote:
Our study supports the “Steppe hypothesis” over the “Bactrian Oasis hypothesis” for the peopling of the Xinjiang region. The high amount of Yamnaya or Afanasievo-related ancestry in the Iron Age Xinjiang individuals indirectly supports the introduction of Indo-European languages into the region that survived in the form of Tocharian until the late first millennium CE.  
Razib then explains in his own words that:
Historical records indicate that some of the cities of the Tarim, particular those of the southern fringe of the basin, were Iranian speaking. Additionally, Iranian cultures are associated with haplogroup R1a, and the Sintashta-Andronovo cultures all had European farmer ancestry. In contrast, R1b is rare outside of Europe (though it is found in Kalash and Yaghnobi), but is found among Uyghurs and among these samples. Tocharians are the most likely descendants of these people, who arrived in the region almost 5,000 years ago. 
This explains how the Tocharian languages were so distinct, and, their deep separation from other Indo-Europeans. The Tocharians were isolated and diverged very early. Later they were joined by Iranian groups. Eventually both these were absorbed by Turkic populations, first the Uyghurs, and later the Salar Turks (the modern Uyghurs revived an ancient ethnonym).
Eurogenes also has good commentary.  Davidski explains that:
During the Early Bronze Age, around 2,900 BCE, a population associated with the Yamnaya archeological culture migrated from the Pontic-Caspian steppe in Eastern Europe deep into Asia, as far as the Minusinsk Basin in South Siberia. 
This rapid, long-range expansion was likely to have been the first significant migration of a Yamnaya-related group far to the east of the Ural Mountains, and it resulted in the formation of the Afanasievo archeological culture (see here). 
The appearance of Tocharian languages in the Tarim Basin, in what is now western China, is often associated with the Afanasievo culture, mainly because of the confirmed presence of European-related populations in the Tarim Basin during the Bronze Age, as well as the likely highly divergent position of the Tocharian node in the Indo-European language phylogeny. 
But the Afanasievo people were separated by considerable distance in space and time from the Tocharians, and can't yet be reliably linked to them with archeological or genetic data. So even though the inference that the former are linguistically ancestral to the latter is quite plausible, it's far from certain. 
However, thanks to a new paper at Current Biology by Ning et al., at least we now know that a population with significant Yamnaya/Afanasievo-related ancestry was living in the eastern Tianshan Mountains just a few hundred years before Tocharian languages were attested nearby.
The citation to the paper is:

DOI: https://doi.org/10.1016/j.cub.2019.06.044

UPDATE July 29, 2019: Eurogenes discusses the alternative theory that these individuals are ancestors of the Huns with no clear relationship to Tocharians and points out evidence that supports this analysis.

Thursday, July 25, 2019

How Has History Shaped Modern French Genetics?

Two large samples were used to analyze modern French population genetics in a recent preprint. The core results are as follows (references omitted, style altered to reflect American style conventions in some instances, and omissions of details made as indicated, images from the paper):

Pie charts indicating the proportion of individuals from the different “départements” assigned to each cluster. Results are reported for the partition in 6 clusters obtained by running FineSTRUCTURE. Geographic coordinates of three rivers of France are drawn in black: Loire, Garonne and Adour from north to south.

An important division separates Northern from Southern France. It may coincide with the von Wartburg line, which divides France into “Langue d’Oïl” part (influenced by Germanic speaking) and “Langue d’Oc” part (closer to Roman speaking). This border has changed through centuries and our North-South limit is close to the limit as it was estimated in the IXth century. This border also follows the Loire River, which has long been a political and cultural border between kingdoms/counties in the North and in the South. Regions with strong cultural particularities tend to separate. This is for example the case for Aquitaine in the South-West which duchy has long represented a civilization on its own. The Brittany region is also detected as a separate entity in both datasets. This could be explained both by its position at the end of the continent where it forms a peninsula and, by its history since Brittany has been an independent political entity (Kingdom and, later, duchy of Bretagne), with stable borders, for a long time.
The extreme South-West regions show the highest differentiation to neighbor clusters. . . . This cluster is likely due to a higher proportion of possibly Basque individuals . . . . which overlap with HGDP Basque defined individuals. The FST between the south-west and the other French clusters were markedly higher than the FST between remaining French clusters. . . . [T]hese values are comparable to what we observed between the Italian and the British heritage clusters (FST=0.0035). . . . We also observe that the broad-scale genetic structure of France strikingly aligns with two major rivers of France “La Garonne” and “La Loire”. At a finer-scale, the “Adour” river partition the SW to the SO cluster. . . . 
While historical, cultural and political borders seem to have shaped the genetic structure of modern-days France, exhibiting visible clusters, the population is quite homogeneous with low FST values between-clusters . . . . We find that each cluster is genetically close to the closest neighbor European country, which is in line with a continuous gene flow at the European level. However, we observe that Brittany is substantially closer to British Isles population than North of France, in spite of both being equally geographically close. Migration of Britons in what was at the time Armorica (and is now Brittany) may explain this closeness. These migrations may have been quite constant during centuries although a two waves model is generally assumed. A first wave would have occurred in the Xth century when soldiers from British Isles were sent to Armorica whereas the second wave consisted of Britons escaping the Anglo-Saxon invasions. . . .
Studying the evolution of French population size based on genetic data, we observe a very rapid increase in the last generations. This observation is in line with what has been seen in European populations. We also observe, in most cases, a depression during a period spanning from 12 to 22 generations ago. This may correspond to a period spanning from 1300 to 1700. Indeed, this period was characterized by a deep depression in population size due to a long series of plague events. While the population size in kingdom of France was estimated to be 20 million in 1348, it dropped down to 12,415 million in 1400, followed by an uneven trajectory to recover the 20 million at the end of Louis XIVth reign (1715). However, the decrease we observe in the genetic data does seem to affect mainly the Northern part of France, and for instance is mainly observed in the NO cluster. We see no reason for this trend based on historical records except perhaps the last plague epidemics in 1666-1670 that was limited to the North of France. Alternatively, a more spread population in the South (which is in general hilly or mountainous) may explain a lower impact of these dramatic episodes. Plague is expected to have had a very strong impact on the population demography in the past as some epidemics led to substantial reduction in the population sizes.
Thus, in a nutshell, Northern France is more Germanic, Brittany is more Celtic, the far southwest corner of France looks Basque. the core of "yellow" component France in modern populations shown in the study result map above correspond to the historic Kingdom of Aquitaine. The population segment in the Southeast of France above is very similar to the Tuscan population of Italy sample in the 1000 Genomes Project study.

The demographic impact of the Black Plague on French population genetics is apparent and the highlands were less hard hit by the plague than the lowlands were.

Friday, July 19, 2019

Non-Standard Neutrino Interactions Tightly Constrained By LHC and IceCube

Since experiments have finite precision, they are rarely rule out something entirely, but they can tightly constrain it.

Strong constraints on non-standard neutrino interactions: LHC vs. IceCube

We find the constraints on various non-standard interactions~(NSI) of neutrinos from monojet+$\slashed{E}_T$ searches at the Large Hadron Collider~(LHC). Also, we show that the measurement of neutrino-nucleon cross-section from the observation of high energy astrophysical neutrino events at IceCube facilitates strong constraints on NSI as well. To this end, we pursue a comparative study of the prospects of LHC and IceCube in detecting NSI, also mentioning the role of low-energy experiments. We discuss the case of NSI with a new vector boson Z and it is found that for some range of mZ LHC puts more stringent bound, whereas IceCube supersedes elsewhere. We also pay special attention to the case of Z of mass of a few GeVs, pointing out that the IceCube constraints can surpass those from LHC and low-energy experiments. Although, for contact-type effective interactions with two neutrinos and two partons, constraints from LHC are superior.
Comments:31 pages, 8 figures
Subjects:High Energy Physics - Phenomenology (hep-ph)
Cite as:arXiv:1907.07700 [hep-ph]
 (or arXiv:1907.07700v1 [hep-ph] for this version)

Wednesday, July 17, 2019

Beliefs About Bees In The Balkans

Slavs believed that bees were the purest beings and the only ones whose soul devil can't corrupt and that beehives are the only place where devil can't hide.... In South Slavic languages, the word "uginuti" means "to die" but is only used for animals. The word "umreti" also means "to die" but is only used for people. And bees... The reason for this could be that in some parts of Serbia people believed that the soul of the deceased migrated into a bee. So bees and humans had the same soul. Slavs believed that bee only bites people who committed some kind of sin. In Lika (Croatia), at Christmas people would fill a small wooden vessel used for scooping flour from storage with grains, and would stick three beeswax candles in the grain, one for dead, one for bees and one for grain.
From the Old European Culture blog.

There are also rituals which strongly suggest that the ancient Slavs knew that bees were closely linked to the fertility of grain, although they probably did not know precisely the way that pollination caused this to occur.

"Death By Dark Matter"

Some of the dark matter parameter space can be ruled out because people aren't suddenly slammed great distances or killed by random particles of dark matter flying around on a regular basis.

Death by Dark Matter

Macroscopic dark matter refers to a variety of dark matter candidates that would be expected to (elastically) scatter off of ordinary matter with a large geometric cross-section. A wide range of macro masses MX and cross-sections σX remain unprobed. We show that over a wide region within the unexplored parameter space, collisions of a macro with a human body would result in serious injury or death. We use the absence of such unexplained impacts with a well-monitored subset of the human population to exclude a region bounded by σX108107 cm2 and MX<50 kg. Our results open a new window on dark matter: the human body as a dark matter detector.
Comments:3 pages, 1 figure
Subjects:Cosmology and Nongalactic Astrophysics (astro-ph.CO)
Cite as:arXiv:1907.06674 [astro-ph.CO]
(or arXiv:1907.06674v1 [astro-ph.CO] for this version)
This is not really all that informative, however, as there is good reason to believe for a variety of reasons that the cross section of interaction between dark matter particles (if they exist), and ordinary matter, is less than 10^-40 per square centimeter (i.e. at least roughly as weak as the neutrino cross-section of interaction).

In other news, a dark matter annihilation explanation for certain cosmic ray signals in a particular case, as opposed to a more conventional explanation, is strongly disfavored although not quite ruled out, certain other kinds of dark matter annihilation signals are ruled out, and solar system bounds on dark matter halo effects are reconsidered.

On the origin of the gamma-ray emission from Omega Centauri: Milisecond pulsars and dark matter annihilation

We explore two possible scenarios to explain the observed gamma-ray emission associated with the atypical globular cluster Omega-Centauri: emission from millisecond pulsars (MSP) and dark matter (DM) annihilation. In the first case the total number of MSPs needed to produce the gamma-ray flux is compatible with the known (but not confirmed) MSP candidates observed in X-rays. A DM interpretation is motivated by the possibility of Omega-Centauri being the remnant core of an ancient dwarf galaxy hosting a surviving DM component. At least two annihilation channels, light quarks and muons, can plausibly produce the observed gamma-ray spectrum. We outline constraints on the parameter space of DM mass versus the product of the pair-annihilation cross section and integrated squared DM density (the so-called J-factor). We translate upper limits on the dark matter content of Omega-Centauri into lower limits on the annihilation cross section. This shows s-wave annihilation into muons to be inconsistent with CMB observations, while a small window for annihilation into light quarks is allowed. Further analysis of Omega-Centauri's internal kinematics, and/or additional information on the resident MSP population will yield much stronger constraints and shed light about the origin of this otherwise mysterious gamma-ray source.
Comments:13 pages, 5 figures
Subjects:High Energy Astrophysical Phenomena (astro-ph.HE); Cosmology and Nongalactic Astrophysics (astro-ph.CO); High Energy Physics - Phenomenology (hep-ph)
Cite as:arXiv:1907.06682 [astro-ph.HE]
(or arXiv:1907.06682v1 [astro-ph.HE] for this version)

Bounds on WIMP dark matter from galaxy clusters at low redshift

The study of the cross-correlation angular power spectrum between gravitational tracers and electromagnetic signals can be a powerful tool to constrain Dark Matter (DM) microscopic properties. In this work we correlate \Fermi\ diffuse \g-ray maps with catalogues of galaxy clusters. To emphasize the sensitivity to a DM signal, we select clusters at low-redshift 0<z<0.2 and with large-halo mass M500>1013M. The analysis is performed with four catalogues in different wavebands, including infrared, optical and X-rays. No evidence for a DM signal is identified. On the other hand, we derive competitive bounds: the thermal cross-section is excluded at 95\% C.L. for DM masses below 20 GeV and annihilation in the τ+τ channel.
Subjects:Cosmology and Nongalactic Astrophysics (astro-ph.CO)
Cite as:arXiv:1907.06905 [astro-ph.CO]
(or arXiv:1907.06905v1 [astro-ph.CO] for this version)

Effect of the Solar dark matter wake on planets

The Galaxy is conventionally thought to be surrounded by a massive dark matter (DM) halo. As the Sun goes through this halo, it excites a DM wake behind it. This local asymmetry in the DM distribution would gravitationally affect the motions of Solar System planets, potentially allowing the DM wake to be detected or ruled out. Hernandez (2019) recently calculated that the DM-induced perturbation to Saturn's position is 252 metres net of the effect on the Sun. No such anomaly is seen in Saturn's motion despite very accurate tracking of the Cassini spacecraft, which orbited Saturn for >13 years. Here, we revisit the calculation of how much Saturn would deviate from Keplerian motion if we fix its position and velocity at some particular time. The DM wake induces a nearly resonant perturbation whose amplitude grows almost linearly with time. We show that the Hernandez (2019) result applies only for an observing duration comparable to the 250 million year period of the Sun's orbit around the Galaxy. Over a 100 year period, the perturbation to Saturn's orbit amounts to <1 cm, which is quite consistent with existing observations. Even smaller perturbations are expected for the terrestrial planets.
Comments:6 pages, 2 figures, 1 table. Accepted for publication in the Monthly Notices of the Royal Astronomical Society in this form
Subjects:Earth and Planetary Astrophysics (astro-ph.EP); Astrophysics of Galaxies (astro-ph.GA); Solar and Stellar Astrophysics (astro-ph.SR)
Journal reference:MNRAS, 487, 4565 - 4570 (2019)
Cite as:arXiv:1907.07130 [astro-ph.EP]
(or arXiv:1907.07130v1 [astro-ph.EP] for this version)