Sunday, May 21, 2017

Do Yamnaya Autosomal Genetics Derive From Caucasian Mail Order Brides?

Davidski at Eurogenes proposes a model for the formation of the Yamnaya genotype that makes a couple of key assumptions set forth below (emphasis in the original): 
- It's likely that low population densities in Eastern Europe during the Eneolithic ensured the rapid spread and rise of admixture from the Caucasus across much of the Pontic-Caspian steppe, which then plateaued at around 50% during the Yamnaya period, when population densities on the steppe may have become high enough so that continued gene flow from the Caucasus no longer had much of an impact. 
- The process that led to the Yamnaya genotype eventually led to its extinction by the Late Bronze Age, due to the large scale spread of Middle Neolithic European farmer ancestry across the entire Pontic-Caspian steppe, probably from its western half, resulting in the formation of the Steppe_MLBA genotype, exemplified by the Sintashta and Srubnaya people. 
- Ancient DNA suggests that Bronze Age steppe groups were highly patrilocal, and if so, it's likely that most of the mixture on the steppe at this time was facilitated via female exogamy (i.e. foreign brides), which would explain the lack of typically Caucasian Y-haplogroups, such as J2, in Bronze Age steppe and derived ancient groups sampled to date, such as the Corded Ware people and eastern Bell Beakers.
He also notes that Steppe people were highly mobile and that the circumstances encouraged admixture of Steppe peoples. There are some key unstated points are key as well (my statements, not a quotation):
* Steppe men are overwhelmingly Y-DNA R1, while this is rare among Caucasian men of any time period. Actually, Yamnaya culture men are predominantly Y-DNA R1b in the case of the Yamnaya, although the ancient DNA of Steppe men further to the North and in the Corded Ware Culture (which also had a more northern orientation) overwhelmingly reveals Y-DNA R1a.  (In both cases, of high derived version of each haplogroup, not the most basal versions.)
* Yamnaya autosomal genetics can be decently approximated by blending ancient DNA from Eastern Hunter-Gatherers (60%) and Caucasian Hunter-Gatherers (40%). This is what makes it necessary to hypothesize an influx of foreign Caucasian brides. See, e.g., here (migration from the Steppe paper) and here (earlier Eurogenes post analyzing ancient DNA samples). Genetic evidence of Caucasian admixture in ancient DNA is absent on the steppe until the Eneolithic (i.e. the Copper Age).
* Early Neolithic Caucasian farmers appear to have been largely derived from Caucasian Hunter-Gatherers, in situ, rather than largely replacing existing hunter-gatherers in places where they expanded as first wave Neolithic people in Europe derived from Anatolian Neolithic people did.  (See also here).
* There is strong physical evidence of patrilocality and large numbers of wives who migrate to their husband's homes from considerable distances from the remains of central European Bell Beaker men who have significant steppe ancestry. Other physical anthropology studies of Bronze Age European women have reached similar conclusions.
There is also anthropological corroboration for this hypothesis (again, my observations and not a quotation):
* Much of the metallurgy technology package that will subsequently be spread across Europe by people with significant steppe ancestry was probably first developed in the Caucasus mountains area. 
* The source of the steppe farming and herding package is less obvious, with David Anthony making a fairly solid case from archaeology in The Horse, The Wheel and Language for a basically Balkan origin of farming and herding technologies on the steppe. In general, there is considerable confusion among historical linguists and pre-historians over why Proto-Indo-European seems to have so many horticulture specific  and maritime shared root words for a society often conceptualized as made up of herders. Hunter-gatherers tend to transition much more easily to a pastoralist lifestyle (i.e. herding) than to horticulture that requires a much greater lifestyle and worldview change. But, the Early European Farmer autosomal DNA does not show up in Steppe populations until the Middle Bronze Age, so it is hard to seem Balkan farmers playing an important demic role in the formation of the steppe genotype. 
* The Caucasus mountains is also one possible source of a religious theme of a fire cult (also here) that is visible in the Zoroastrian religion which was established by Indo-Iranians (although also possibly in BMAC temples in the Harappan trade network and there is some linguistic evidence to support the idea that they shared a language with the Harappans from substrate words in Indo-Iranian and Indo-Aryan languages), although the center of gravity of this cult seems further east and later in time to be a good fit. A possibly residual fire cult can also be found in the cult of Hephaestus in the Aegean (with parallels in both Indo-European and non-Indo-European deities elsewhere in the region), although Hephaestus may have pre-Mycenean Greek roots as this blacksmith god is closely associated with the island of Lemnos which was one of the last non-Indo-European language hold outs in the region which was spoken until the 6th century BCE. The God's deformity is characteristic of Bronze Age rather than Iron Age smiths, who were often poisoned by arsenic associated with tin needed to make Bronze. 
The link between Caucasian brides and the people of the Pontic-Caspian steppe which is pretty much the only credible source of the main expansion (at least) of the Indo-European languages, however, is complicated. 

Did Caucasian brides and their children come to speak their husband's steppe language?  Or, could Indo-European be a Caucasian origin language passed from mother to child on the steppe?

The Caucasian mountains are currently home to several families of non-Indo-European languages that appear in a variety of respects (e.g. elaborate grammar and uncommon phonemes) to relict languages from a very long time ago (probably back at least to the early Neolithic in the region) that have not been heavily influenced by language contact or first language learners in highly isolated mountain valleys. The evidence from ancient mtDNA tends to confirm population genetic continuity in the Caucasus, although the ancient Y-DNA evidence seems to show more change over time.

So, the former hypothesis, that brides and their children came to speak their husband's language, seems more likely and has some corroboration in the pattern observed in similar situations that are historically attested.

One possibility is that Southern steppe people were not originally Indo-Europeans and had a strongly Caucasian influenced language (possibly related to Minoan and Basque), but that northern steppe people were Indo-Europeans. The fact that early Iberian Bell Beaker culture people seem to largely lack steppe ancestry, even though non-Iberian Bell Beaker people have it to a great degree, however, complicates the story.

New ancient DNA to come from ancient Minoans (non-Indo-European pre-Greeks of Crete), Mycenaeans (the first Greek speaking people of the Aegean), Maykop culture people (a technological source culture at the foothills of the Caucasus mountains near the Black Sea coast), and Harappans (pre-Indo-Europeans of the Indus River Valley civilization) will help shed some light on the different possible hypotheses in the near future.

How To Rule Out The Extra Dimensions Of String Theory

A blog post by Sabine Hossenfelder at Backreaction reviews a new paper that discusses how the existence of more than four dimensions, even is accessible only to gravitons, as required by string theory (which needs ten or eleven dimensions), could be ruled out with the LIGO gravitational wave detector and two comparable independent gravitational wave detectors.

Current experiments place bounds on the size of any extra dimensions as follows:
The mass of these excitations is inversely proportional to the radius (in natural units). This means if the radius is small, one needs a lot of energy to create an excitation, and this explains why he haven’t yet noticed the additional dimensions. . . .
From the current lack of observation, one can then derive bounds on the size of the extra-dimension. These bounds depend on the number of extra-dimensions and on their intrinsic curvature. For the simplest case – the flat extra-dimensions used in the paper – the bounds range from a few micrometers (for two extra-dimensions) to a few inverse MeV for six extra dimensions (natural units again).
Basically, gravitational waves, even the ordinary ones we can detect with LIGO (as opposed to the excited ones that involve exited gravitons that have excitations in extra dimensions) behave differently in a world with extra dimensions (even compactified dimensions that only gravitons can enter), than they do in general relativity.

If extra dimensions exist, there are excited states of all particles, gravitons have additional polarizations, and they exhibit a kind of oscillation known as a "breathing mode" that does not exist in general relativity. 

Absolutely ruling out the possibility is a technically difficult feat, but placing profoundly more strict limits on their number and size is considerably more straight forward. Only a narrow sub-type of extra dimensions is particular hard to detect with this methodology. So, it would be fairly easy to limit any possible string theory to the kind with that narrow subtype of extra dimensions.

Saturday, May 20, 2017

Sometimes Simple Things Are Complicated

In quantum physics, some interactions that seem simple, like two photons that interact in a manner that ultimately produces two photons, are actually wickedly complex. This is because you have to consider every conceivable way consistent with the laws of quantum mechanics that you can get from the starting state to the end state.

In this simple scenario, called light by light scattering, that means considering the possibility that the two photons have paths that include all sorts of mesons (two quark particles) that are created and destroyed in intermediate steps in the interactions, either as "real" particles or "virtual" ones (called "off shell").

A recent paper tackling some of the deep complexities of this seemingly simple interaction by analyzing fifteen of the most important intermediate meson paths is here.

Wednesday, May 17, 2017

Quick Physics Hits

Another experiment favors lepton universality and casts doubt on data tending to show lepton universality violations.

The XENON-100 direct dark matter detection experiment again sees no dark matter and extends the exclusion range in WIMP parameter space.

The First Mass Extinction Was Probably Caused By Volcanos

There have been five mass extinctions since the divergent evolution of early animals 600 -450 million years ago. The cause of the third and fourth was volcanic activity, while an asteroid impact led to the fifth. But triggers of the first and second mass extinctions had, until now, been unknown. 
The first mass extinction occurred at the end of the Ordovician. This age is between the divergence of the Ordovician and land invasion of vascular land plant and animals. Animals in the Ordovician-Silurian comprised marine animals like corals, trilobites, sea scorpion, orthoceras, brachiopods, graptolite, crinoid and jawless fish. Approximately 80% of species disappeared at the end of the Ordovician.
From here.

The Ordovician spans 41.2 million years from the end of the Cambrian Period 485.4 million years ago (Mya) to the start of the Silurian Period 443.8 Mya (per Wikipedia). The cause of the Devonian extinction event ca. 365 million years ago, which killed many tropical marine species is still not known.

Elevated mercury levels at the transition point measured in two locations suggest a volcanic trigger for the extinction, although it isn't clear why these volcanic eruptions took place at this time. The paper is:

David S. Jones, Anna M. Martini, David A. Fike, Kunio Kaiho. "A volcanic trigger for the Late Ordovician mass extinction? Mercury data from south China and Laurentia." Geology (May 2017) G38940.1

Movius Line Discredited By Acheulian Artifacts Found In Asia

[T]he Movius Line (Movius, 1948) over which no Acheulian artefacts were argued to occur in East Asia is no longer an appropriate concept for the Early Paleolithic of East and Southeast Asia and should be disregarded[.]
From here.

In 1948, it appeared from the archaeological record that Homo Erectus in Asia was completely technologically static. Advances in the design and construction of stone tools, called Acheulian technology, were found elsewhere, but not in Asia to the east of the "Movius Line".

But, new well dated Asian finds of Acheulian artifacts tell a different story. As the body text of the new paper explains:
Acheulian technology is characterized by bifacially and unifacially shaped tool types, such as handaxes, cleavers, picks and other large cutting tools (LCTs) (Isaac, 1969; Bar-Yosef and Goren-Inbar, 1993; Goren-Inbar et al., 2000; Semaw et al., 2009; Lepre et al., 2011; Beyene et al., 2013 ; Diez-Martín et al., 2015). Its appearance represents a technological advance over the preceding Oldowan technology, and is associated with innovative hominin cognitive and adaptive abilities (Goren-Inbar, 2011 ; Stout, 2011). Current thinking is that Acheulian technology originated in East Africa (possibly West Turkana, Kenya) at least 1.76 million years ago (Ma) (Lepre et al., 2011), that it became distributed somewhat widely across Africa (e.g., Vaal River Valley and Gona) at ∼1.6 Ma (Gibbon et al., 2009 ; Semaw et al., 2009), and then spread to the Levant at ∼1.4 Ma (Bar-Yosef and Goren-Inbar, 1993), South Asia at 1.5–1.1 Ma (Pappu et al., 2011), and Europe at 1.0–0.9 Ma (Scott and Gibert, 2009 ; Vallverdú et al., 2014) (Fig. 1). The 0.8–0.9 Ma Acheulian stone stools from South and central China (Hou et al., 2000 ; de Lumley and Li, 2008) (Fig. 1) suggest that Acheulian technology arose in China at least during the terminal Early Pleistocene. However, there are only a few sites with in situ Acheulian artefacts from North China with ages ranging from the late Mid-Pleistocene to the Late Pleistocene ( Wang et al., 2014 ; Yang et al., 2014) (Fig. 1). Thus, it remains enigmatic as to how early Acheulian technology can be traced back in North China, compared with its Early Pleistocene occurrence in South and central China. 
Sanmenxia Basin (also Sanmen area), which lies on the southeastern Loess Plateau, is a rich source of stone artefacts and is an important area for understanding the early human occupation of North China (Jia et al., 1961; Huang, 1964; Jia, 1985 ; Li, 1990). The first Early Pleistocene Paleolithic site in China, that is the Xihoudu site dated at 1.4–1.27 Ma (Zhu et al., 2003 ; Kong et al., 2013), was found in northwestern Sanmenxia Basin (Fig. 1) in 1961–1962 (Jia, 1985). In 1963, 128 stone artefacts were found from 6 localities in eastern Sanmenxia Basin (Huang, 1964). Among the 128 artefacts, 94 were from the Shuigou and Huixinggou sites (Huang, 1964). At that time the chronology of the Chinese loess-paleosol sequence was not yet established; a tentative Mid-Pleistocene age was suggested for the lithic assemblage based on lithostratigraphic arguments (Huang, 1964). Furthermore, when these artefacts were discovered, consensus was that Acheulian handaxes and cleavers were lacking in East Asia during the period when they flourished in Africa and western Eurasia (Movius, 1948). Therefore, the handaxe and cleavers from the Shuigou and Huixinggou sites (Fig. 2) were not recognized and reported as Acheulian artefacts; instead, they were considered to represent different kinds of choppers that are indicative of a chopper-chopping tool industry (Huang, 1964; Huang, 1987; Huang, 1993 ; Lin, 1992).
This matters because it gives us a detailed assessment in time and space of the range of Homo Erectus and of the spread of a new kind of lithic tool technology by this archaic hominin species. It also suggests that Asian Homo Erectus was more plastic mentally than early estimates supported by the now disprove Movius Line theory suggested. The paper is: 

Xingwen Li, et al. "Early Pleistocene occurrence of Acheulian technology in North China" 156 Quaternary Science Reviews 12-22 (2017).

Another PLOS paper along the same lines is also noted at Linear Population Model.

The Movius Line was previously discussed at this blog in 2011.

Riding Cows

Both Spain and Crete have historic "cow" cultures and, of course, cows are sacred in India.

I don't normally post videos from YouTube at this blog, but a video of a New Zealand girl riding a cow like a horse suggests that maybe we underestimate the ways the cows can be utilized.

Tuesday, May 16, 2017

Brain Size Increased Before Brain Region Specialization

The study of 58 species of songbirds also found that once a species evolved a larger brain, brain regions that control the beak and mouth, and the area for song, developed additional complex neural networks. . . . 
The findings suggest that this principle may also help explain human evolution; we may have first evolved larger brains, which then allowed for adaptations that enhanced brain regions that control specific abilities, such as language.
From here.

From a practical perspective, this makes the task of a would be trans-humanist attempting nootropic enhancements of the human genome straightforward. Select for a larger brain size and see what happens.

The paper is:

Jordan M. Moore, Timothy J. DeVoogd. "Concerted and mosaic evolution of functional modules in songbird brains." 284 Proceedings of the Royal Society B: Biological Sciences 1854 (May 10, 2007): 20170469.

Domesticated Crops Have Larger Seeds

Domesticated crops have larger seeds than the comparable wild type, even though there is good reason to doubt that early proto-farmers intended this result.

The paper is:

Thomas A. Kluyver, et al., "Unconscious selection drove seed enlargement in vegetable crops." Evolution Letters (2017).

Recent Experimental Measurements Of Standard Model Constants

W Boson Mass At The LHC (ATLAS) and Tevatron (CDF)
The result of the CDF analysis is MW = 80 387±12(stat.)±15(syst.) MeV; the result of the ATLAS analysis is MW = 80 370 ± 7(stat.) ± 11(exp.syst.) ± 14(mod.syst.) MeV. The total uncertainty is 19 MeV in both analyses.
From here.

My comments: The lighter ATLAS result is closer to a result expected from a global electroweak fit. The Tevatron based results will never get better because that experiment has concluded. The LHC based results will almost surely get better before the experiment concludes, if for no other reason, because the statistical error will get a bit smaller over time and because independent results from ATLAS and CMS can be combined reducing a little systemic error as well.

Heavy Quark Masses And The Strong Coupling Constant From HERA

New results on the measurements of the hadronic final state in neutral-current deep-inelastic scattering at HERA are presented. A combination of reduced charm and beauty cross sections is presented and the masses of the heavy quarks are determined to mc=1290(+7853)MeV and mb=4049(+138118)MeV. The measurement of the production of prompt photons accompanied by a jet provides a precise test of QCD predictions. Measurements of jet production cross sections are presented and compared for the first time to next-to-next-to-leading order predictions (NNLO). The strong coupling constant is determined from inclusive jet and dijet production cross sections using NNLO predictions to αs(mZ)=0.1157(6)exp(+3126)th.

My comments: The charm quark mass is a bit high, (also here and here) and bottom quark mass is a bit on the low side, as is the strong force coupling constant. But, all of the measurements have significant margins of error, so the differences aren't very meaningful.

CKM Matrix Elements Involving Bottom Quarks At Belle II

Semileptonic B meson decays involving low-mass charged leptons e or μ are expected to be free of non-Standard Model contributions and therefore play a critical role in determinations of |Vub|and |Vcb|. Of all the CKM matrix parameters, |Vub| is the least precisely measured and in most need of additional studies in order to better constrain the apex of the Unitarity Triangle. We focus on exclusive reconstruction of charmless semileptonic B meson decay Bπν, and present prospects and estimates for measuring |Vub| at Belle II with the full planned dataset of 50 ab1 of integrated luminosity.

My comments: These two element are hard to measure because Vtb = 0.99914 +/- 0.00005 is dominant, and Vub = 0.00355 ± 0.00015, in particular, is very small. The square of Vub which represents the probability is 1.26 per 100,000. The paper discusses prospects for improvements in accuracy in future measurements of this CKM matrix elements and does not actually contain any measurements.

UPDATE May 18, 2017: A survey of recent measurements of four CKM matrix elements is found here. END UPDATE.

Theoretically Expected Higgs Boson Diphoton Decays

Physicists have replicated, in a more general matter than a previous result, the conclusion that many of the terms that go into calculating the likelihood that a Higgs boson will experience a diphoton decay cancel out. In particular, they show "the cancellation of all terms among the Feynman diagrams which are to be integrated to give divergences higher than logarithmic." This conclusion which requires 30 dense pages of calculations implies that calculating the likelihood of this decay is much easier than would be naively expected.