Thursday, September 20, 2018

Ancient DNA Shows That First Anatolian Farmers Were Natives

These result were basically expected. 

While in most places in Europe, farming was brought by migrants who were genetically similar to Anatolian farmers, in Anatolia, which was at the epicenter of the Fertile Crescent Neolithic revolution, farming developed in situ with the local population since somebody had to invent it in the first place before there could be migrant populations bringing it somewhere else.

The study also detects Mesolithic migration from Anatolia to Europe.
Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000 year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity between the hunter-gatherer and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago that extends to central Europe during the post-last-glacial maximum period. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.
Michal Feldman, "Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia" bioRxiv (September 20, 2018). doi: https://doi.org/10.1101/422295

Wednesday, September 19, 2018

Proton Radius Problem Solved?

In the category of a big deal, if true, a new theoretical approach set forth in a four page paper for converting electron scattering data to a proton charge radius value calculates a proton charge radius in ordinary hydrogen (i.e. with an electron) that is the same as the value for muonic hydrogen (a proton-muon system). 

This would solve one of the major unsolved problems of physics (I have previously put this problem in the top twelve experimental data points needed in physics), called the "proton radius problem" or "muonic hydrogen problem" in which the radius of a proton in a proton-muon system appeared to be 4% smaller than measurements of the radius of a proton in ordinary hydrogen, contrary to the Standard Model. See previous substantive posts on the topic at this blog can be found on November 5, 2013, April 1, 2013, January 25, 2013, September 6, 2011, and August 2, 2011.

The measurements of muonic hydrogen traditions imply a proton charge radius of 0.84087(39) fm. The CODATA value obtained from electronic hydrogen transitions and some information from electron scattering data was 0.8751(61) fm. Their new analysis is that the proton charge radius based upon electron scattering data is 0.844(7) fm, which is consistent with the muonic hydrogen measurement. Any discrepancy is a problem, because the internal structure of a proton shouldn't be impacted materially by the kind of charged lepton that is "orbiting" it.

It has long been clear that the problem was probably in the old CODATA number, which used comparative old data, because measurements using muonic hydrogen transitions are inherently much more precise than measurements using electron hydrogen transitions (the muonic hydrogen measurement has error bars about 16 times smaller than the CODATA value).

But why?

There was really no fault to be found in the determination of the statistical or systemic errors in the electron scattering measurements.

In the view of these authors, the proton radius problem is simply a case of inferior analysis of the available experimental electron scattering data to their analysis, and of a failure to include theoretical errors involved in fitting the data to their proton charge radius conclusion in their margin of error.

Essentially, these authors found a way to more meaningfully incorporate electron scattering data in a larger swath of the momentum transfer energy scale into their calculation of the proton charge radius from the data. This brings in more data and the data that it brings in is further from the extremes of what can be measured experimentally where systemic measurement errors tend to be greatest. Their fitting method makes the result less error prone because it is less sensitive to flukes in the smaller data sets used previously which were largely confined to very low energy data points.

Put another way, in the view of these authors, previous estimates of the proton charge radius based upon electron scattering data approximately correctly state the combined statistical and systemic errors in their experimental observations of about 0.7%, but omit a theoretical uncertainty arising from the method used to fit their data into a proton charge radius, which was on the order of 1.9% (a number that, it turns out, is itself hard to calculate or evaluate properly). Alternately, there may have been an underestimate of the systemic experimental error since their fitting function overweighted the extreme low points of the distribution where systemic errors are greater, in addition to failing take into account at all theoretical uncertainty associated with an imperfect function for fitting the data to their conclusion.

The abstract and the paper are as follows:
We extract the proton charge radius from the elastic form factor data using a theoretical framework combining chiral effective field theory and dispersion analysis. Complex analyticity in the momentum transfer correlates the behavior of the spacelike form factor in different Q2 regions and permits the use of data up to Q2 ∼ 0.5 GeV2 in constraining the radius. The predictive theory describes the data with the same accuracy as current descriptive models (global fits). We obtain a radius of 0.844(7) fm, consistent with the high-precision muonic hydrogen results.

The discussion in the body text explains (citations omitted) that:
The proton charge radius is a fundamental quantity of nuclear physics and attests to the hadron’s finite spatial extent and composite internal structure. It is defined as the derivative of the proton electric form factor (FF) at zero momentum transfer, 
(rpE)2 ≡ −6dGpE/dQ2 (Q2 = 0), 
and describes the leading finite-size effect in the interaction with long-wavelength electric fields. The electric and magnetic FFs at Q2 > 0 are measured in elastic electron-proton scattering experiments. The radius is also extracted from nuclear corrections to atomic energy levels measured in precision spectroscopy experiments. . . . 
Determining the charge radius from electron scattering data amounts to inferring the derivative of the FF at Q2 = 0 from the data at finite Q2 . From an empirical point of view, the problem presents itself as one of “extrapolation” of the measured FF to Q2 → 0. Two approaches have been taken in most studies so far. Descriptive fits (e.g. higher-order polynomial fits) provide excellent descriptions of the data over a wide range of Q2, but the functions are generally not well-behaved outside the fitted region. Predictive models (e.g. fits with low-order polynomials or other smoothly varying functions) permit stable extrapolation but are constrained by either the selected functional form or tightly bounded parameters. In both approaches the question arises over what Q2 range the extrapolation should optimally be performed, and what uncertainties are associated with this choice. . . .
In our analyticity-based framework the main impact on the proton radius comes from FF data at moderate Q2 (∼0.1–0.5 GeV2 ) rather than at the lowest available Q2. . . . 
The proton radius was extracted previously from dispersive FF fits in which the two-pion spectral functions were constructed using empirical πN amplitudes. Our approach is different in that the two-pion spectral functions are computed in DIχEFT and contain low energy constants, which can vary (consistently with the nucleon radii) and adjust the strength of the spectral functions in the ρ meson peak and above. This increases the flexibility of the FF description and represents a major advantage of our approach. We note that the empirical dispersive fits have consistently obtained radii ∼0.84 fm, in agreement with our result.
Other Recent Physics News

The Weak Radius Of The Proton

Another new study calculates the analogous "weak" radius of the proton (i.e. its effective size for purpose of weak force interactions as opposed to electromagnetic ones). 
The weak charge of the proton determines its coupling to the Z0 boson. The distribution of weak charge is found to be dramatically different from the distribution of electric charge. The proton's weak radius RW1.580±0.033 fm is over 80% larger than its charge radius Rch0.84 fm because of a very large pion cloud contribution. This large weak radius can be measured with parity violating electron scattering and may provide insight into the structure of the proton, various radiative corrections, and possible strange quark contributions.
C. J. Horowitz, "Weak radius of the proton" (September 17, 2018).

BSM Lepton and Lepton Family Number Violations Constrained

Further afield, the Standard Model physics constraints of possible violations of lepton number and lepton family number have been considerably tightened as reported in a short LHCb paper.

Theorists would really like for their to be low energy sources of baryon number violation and lepton number violation as this could explain the baryon asymmetry of the universe in cosmology, but the hard reality is that both of these numbers of been perfectly conserved in every experiment to date and those experiments are among the most precise experiments ever conducted. There is simply no experimental data on any of the multiple fronts (including searches for proton decay, neutrinoless double beta decay, the lepton number violating decays searched for in three different kinds of decays reported on in the LHCb paper linked above, and flavor changing neutral current searches), to believe that baryon number or lepton number are not conserved, and the only theoretical hint that there might be violations of these numbers involve temperatures only found in the very early moments of the Big Bang that could not plausibly ever be reproduced in an experiment or a "natural experiment" in Nature at any observable point of the history of the universe.

Cross-Sections Of Interaction Of High Energy Neutrinos

Measurements of the cross-section of high energy neutrinos and nucleons have been improved using IceCube data from highly energetic cosmic ray neutrinos.

Invisible Higgs Boson Decays

And, constraints on invisible decays of the Higgs boson (which would imply BSM physics) have tightened in light of new data that continues to confirm the Standard Model, although the constraints aren't yet particularly tight (a limit on branching fractions not in excess of 37%).

Who Were The Late Archaic Hominins Of China?

Were the late archaic hominins of China "Southern Denisovans?"

This author answer the question in the negative, instead arguing for great regional diversification and evolution of distinct H. erectus populations in Asia, arguing that Homo floresiensis is a basal dwarf branch of H. erectus, and that the influences of Denisovans on Late Archaic hominins in China are limited to admixture with various late H. erectus descended populations rather than complete replacement.

I don't find this argument terribly compelling, but it isn't inconsistent with the spotty available evidence either. The article is also worthwhile as a particularly broad and comprehensive review of the relevant evidence over a broader geographic scope than is usually considered in a single paper.
Our traditional scheme during the twentieth century was that Homo erectus had thrived on the vast terrain of eastern Asia since the Early Pleistocene, followed by the appearance of a more advanced but still primitive form of Homo in China during the mid-Middle Pleistocene. Recent discoveries or (re-)recognitions of other archaic hominins, such as Homo floresiensis from an Indonesian island, Neanderthals and the “Denisovans” from southern Siberia, as well as an extremely robust mandible from Taiwan, now open up a different view. By incorporating these latest discoveries, this paper intends to offer a phylogenetic model of diverse archaic Asian hominins distributed from southern Siberia to Southeast Asia and India. On the basis of this new model, I discuss how paleoanthropological data inform the taxonomic identity of the Denisovans and the admixture event with modern humans.
Yousuke Kaifu, "Archaic Hominin Populations in Asia before the Arrival of Modern Humans: Their Phylogeny and Implications for the “Southern Denisovans”," 58 (S17) Current Anthropology S418 (December 2017). https://doi.org/10.1086/694318 (open access).

There is more discussion of this paper before the fold (the author thinks Javanese erectus may have been the Southern Denisovans, although I am skeptical).

But, it is also worth noting that this is post 150 of the year at this blog and is post 1501 since the blog's inception.


Early Sorghum Domestication In Eastern Sudan In The Four Millennium BCE

The overlap of traces of wild type and domesticated sorghum in the same pottery samples suggest that this site was close to the place of domestication of this crop. 
Since the 1970s, the quest for finding the origins of domesticated sorghum in Africa has remained elusive despite the fact that sorghum (Sorghum bicolor (L.) Moench. sensu stricto) is one of the world’s most important cereals. Recognized as originating from wild populations in Africa (Sorghum arundinaceum (Desv.) Stapf), however, the date and cultural context of its domestication has been controversial, with many scholars inferring an early Holocene origin in parallel with better-known cereal domestications. This paper presents firm evidence that the process of domesticating sorghum was present in the far eastern Sahel in the southern Atbai at an archaeological site associated with the Butana Group. Ceramic sherds recovered from excavations undertaken by the Southern Methodist University Butana Project during the 1980s from the largest Butana Group site, KG23, near Kassala, eastern Sudan, were analyzed, and examination of the plant impressions in the pottery revealed diagnostic chaff in which both domesticated and wild sorghum types were identified, thus providing archaeobotanical evidence for the beginnings of cultivation and emergence of domesticated characteristics within sorghum during the fourth millennium BC in eastern Sudan.
Frank Winchell, Chris J. Stevens, Charlene Murphy, Louis Champion, and DorianQ. Fuller, "Evidence for Sorghum Domestication in Fourth Millennium BC Eastern Sudan: Spikelet Morphology from Ceramic Impressions of the Butana Group," 58(5) Current Anthropology 673 (October 2017). https://doi.org/10.1086/693898

Were Humans Present In Madagascar In The Early Holocene?

Austronesian together with East Africans arrived in Madagascar around 500 C.E. and dramatically changed the island's ecology, among other things, causing megafauna extinction. There is solid evidence of much more marginal human occupation that had only modest ecological impact about 2500 years before then (i.e. about 2000 BCE).

A new study argues that a couple of isolated elephant bird bones showing signs of cuts that look like they were butchered from ca. 8500 BCE, constitute evidence of a much earlier, if potentially even more marginal, early human occupation. 

But, in the absence of corroboration in the form of stone tools or human remains or other more definitive evidence of a human presence, this find merely provides a plausible reason to look for more evidence rather than truly establishing a human presence. In my view, it is too easy for a rare outlier non-human caused event to look like a butchered bone for this thin evidence pushing back the earliest potential human occupation of the island by 6500 years, for this evidence alone to establish what it is trying to prove.
Previous research suggests that people first arrived on Madagascar by ~2500 years before present (years B.P.). This hypothesis is consistent with butchery marks on extinct lemur bones from ~2400 years B.P. and perhaps with archaeological evidence of human presence from ~4000 years B.P. We report >10,500-year-old human-modified bones for the extinct elephant birds Aepyornis and Mullerornis, which show perimortem chop marks, cut marks, and depression fractures consistent with immobilization and dismemberment. Our evidence for anthropogenic perimortem modification of directly dated bones represents the earliest indication of humans in Madagascar, predating all other archaeological and genetic evidence by >6000 years and changing our understanding of the history of human colonization of Madagascar. This revision of Madagascar’s prehistory suggests prolonged human-faunal coexistence with limited biodiversity loss.
J. Hansford et al. Early Holocene human presence in Madagascar evidenced by exploitation of avian megafauna. Science Advances. (September 12, 2018). doi:10.1126/sciadv.aat6925.