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 ( 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:


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)