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tag:blogger.com,1999:blog-73152367077287595212015-08-02T06:38:25.865-06:00Dispatches From Turtle IslandObservations That Transcend Law and PoliticsAndrew Oh-Willekehttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-10108729742990935992015-08-01T18:56:00.000-06:002015-08-01T18:56:08.682-06:00Balls Of LightIn the passage below, I use the ten hundred most common words in English to explain some important ideas about quantum electrodynamics with help from the Up-Goer Five Text Editor.

A ball of light goes every way from start to finish, not just one way, if you do not look at it.

But, if you look at it, the ball of light will only go one way from start to finish. This is called the falling down of the light wave.

To learn where the ball of light will finish, you need to line up lots of short lines with points on one end, end to end, to see where they end up, in every way that it can go. This is hard, because the short lines with points on one end move around all of the time around the end of the short line that does not have a point on the end.

If the ball of light is hot, it moves around that end fast. If the ball of light is cold, it moves around that end slowly. When balls of light are not the same in this way, it is called the color of the ball of light.

How fast does the ball of light go? As fast anyone can go.

Does time inside the ball of light change? No. Only time outside the ball of light changes.

Balls of light are important. Our eyes read balls of light. Computers use balls of light. Phones use balls of light. All stuff, almost, in our world is put together with balls of light. Even animals.

Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-92146694338554627452015-07-29T16:05:00.000-06:002015-07-29T16:05:28.424-06:00Neutrino Masses And SpeedsA feature article at the Physics Forums has a nice review of the history of efforts to determine neutrino mass and speed, and the latest developments on that front.

Neutrino Mass

In a nutshell the state of the art measurement is that the difference between the second and third neutrino mass state is roughly 49.5 +/- 0.5 meV, and the difference between the first and second neutrino mass state is roughly 8.66 +/- 0.12 meV. The heaviest neutrino type cannot have a mass of less than 56 meV with 95% confidence, but since the hierarchy of the neutrino masses ("normal" or "inverted") and the absolute neutrino masses are not known, the exact neutrino masses are also not known.

A measurement comparing the time of arrival of light and neutrinos from a distant supernova in 1987 capped the maximum neutrino mass at 6 eV. Beta decay experiments, taken together with mass difference data from neutrino oscillation measurements, imply that none of the three neutrino masses can be more than 2 eV.

Planck satellite data combined with other astronomy data and included in a cosmology model imply that there are three neutrino types and that the sum of the mass of the three neutrino types cannot exceed 230 meV at 95% confidence. In a normal hierarchy, that would imply maximal neutrino masses of 57 meV, 66 meV and 115 meV. The best fit value for the sum of the three neutrino masses for this data is considerably smaller.

The minimum sum of the mass of the three neutrino types, at 95% confidence, from neutrino oscillation data is 64.4 meV. Using the best fit value for the three neutrino types, a "normal" hierarchy and a lowest neutrino mass of 1.2 meV, the sum of the three neutrino masses would be about 68 meV, which is very close to the best fit from the Planck and other astronomy data.

New experiments whose results will probably be available within the next five to ten years, and possibly sooner, will be able to tell us if the neutrino mass hierarchy is "normal" or "inverted", greatly reducing the uncertainty in the absolute neutrino mass measurement. A new supernova like the one in 1987 would also give us much more accurate information about neutrino mass than that one did because current astronomy observations are much more precise.

Neutrino Speed

[A]1 MeV neutrino from a nuclear reaction with a mass of 1 eV travels at roughly (1-10-12) times the speed of light. For a 1 GeV neutrino from an accelerator this gets even worse with (1-10-18). While light travels 1000 kilometers, the neutrino just gets behind by 1 nanometer or 1 femtometer respectively.

There is no way to see such a tiny difference, so measurements are expected to be consistent with the speed of light. Those measurement are still interesting: apart from light, the neutrinos should be the fastest things where we can measure the speed. It is a test of special relativity. In 2011 the OPERA collaboration announced that their measurements seem to indicate neutrinos that are faster than the speed of light by one part in 40,000. They later discovered that a loose cable spoiled clock synchronisation at one point, and published updated results that are in agreement with the speed of light. Due to the increased interest, multiple other experiments performed speed measurements, the most recent one (MINOS) this week. All results agree with the speed of light, and a deviation has to be smaller than 1 part in 500,000.
A previous OPERA report that neutrinos traveled slightly faster than the speed of light was ultimately determined to be due to a loose cable connection in their detector.

As noted above, since it is difficult to be sufficiently precise, Earth bound neutrino speed measurements are largely useless for purposes of determining neutrino mass.

But, these measurements do provide a good way to directly measure the constant "c" (the speed of light in a vacuum). And, they also provide excellent proof of Einstein's law of special relativity, because neutrinos whose momenta differ by a factor of thousand differ in speed by only a little less than one part per trillion, meaning that their speeds are indistinguishable to the most precise measurements of speed known to mankind.

Breaking News

A comment to the article notes that the T2K experiment's data is a best fit to a "normal" mass hierarchy and maximal CP violation, and references a conference presentation to that effect.

The experiment has seen 3 electron anti-neutrino events when 3.73 would be expected so far for a "normal" mass hierarchy and maximal CP violation (- pi/2), and more events would be expected in any other scenario. Specifically, in the normal hierarchy with no CP violation 4.32 events would be expected, and in a normal hierarchy with +pi/2 CP violation, 4.85 events would be expected. In an inverted hierarchy with maximal CP violation, 4.18 events would be expected, compared to 4.85 with no CP violation and 5.45 with +pi/2 CP violation.

Given that three of the possibilities round to 4 expected events, and that the other three round to 5 expected events, and that there is some random variation, an actual event count of 3 isn't terribly informative, but does tend to disfavor the scenarios that expect higher numbers of events so far. There is even a 20% change that all of the three measured events are actually only background noise, for which 0, 1 or 2 events would be much more likely, but 3 events wouldn't be that unusual. Even with more exactly analysis the odds that the results are just background noise can't be reduced below about 13%.

The Missing Pieces

The parameters of the simplest neutrino mixing model has three mixing angles, a CP violation phase, and the two mass eigenvalue differences described above, as well as a determination of whether the mass hierarchy is "normal" or "inverted" and the absolute masses of the neutrino types.

There are decent measurements of all three mixing angles and the two mass differences, but the "normal" v. "inverted" mass hierarchy, the absolute masses of the neutrion types, the CP violation phase, and the "quadrant" of one of the mixing angles (i.e. is it a few degrees over or under 45 degrees) remain unresolved.

Also unresolved is the question of whether the mass of neutrinos is "Dirac" like all of the other Standard Model fermions, or "Majorana" which would be the case if a neutrino was its own antiparticle. This best experimental data to resolve this is neutrinoless beta decay experiments which are not yet quite precise enough to resolve the issue. If neutrinos have Majorana mass (at least in part), then they can violate "lepton number" conservation in neutrinoless double beta decay events, and additional parameters not mentioned above are necessary to describe them.

Another unanswered question, which is important to cosmology, is the ratio of neutrinos to anti-neutrinos, and the ratio of neutrino generations, the universe. Since the number of neutrinos in the universe vastly outnumber the number of charged leptons in the universe, this ratio is critical to determining the aggregate lepton number of the universe (a quantity conserved in all interactions in the Standard Model except in vanishing rare high energy sphaleron interactions that are theoretically possible but have never been observed and still conserve the quantity B-L; they convert baryons to antileptons and antibaryons to leptons), which has important implications for cosmology and fundamental physics. But, while it is hard to measure a neutrino at all, it is harder still to determine if what one is measuring is a neutrino or an antineutrino, although the task is not in principle impossible, and there are hints that antineutrinos greatly outnumber neutrinos in the universe. In contrast, there are quite accurate estimates of the baryon number of the universe. It is not known if dark matter, if it exists, has either baryon number or lepton number or some equivalent conserved quantity (such as R-parity if dark matter consists of supersymmetric particles).

Predictions

I predict that neutrinos will be found to have a "normal" mass hierarchy, with a lightest neutrino mass state of roughly 1 meV or less, that the quadrant of the mixing angle whose quadrant is undetermined will be a bit under 45 degrees rather than a bit over 45 degrees, that neutrinos will be found not to have Majorana mass, and that neutrino mixing will involve significant CP violation although probably not quite maximal CP violation.

While the answers may not be definitive by then, I strongly suspect that we will have strongly suggestive data on all of these questions by the year 2020.

Neutrinos and Sterile Neutrinos As Dark Matter

There has been some speculation that the universe also has "sterile neutrinos" which unlike normal neutrinos, do not interact via the weak force because they are "right handed" in the ordinary matter state, and "left handed" in the antimatter state, but which still might oscillate with ordinary neutrinos. I predict that no such particles exist, although it don't entirely rule out a "dark matter" particle of some mass that behaves like a sterile neutrino of some mass, but does not oscillate with the three ordinary neutrinos.

Ordinary neutrinos are not a fit to explain "dark matter" phenomena because they are too light, in the aggregate, to provide sufficient mass, and have too high an average speed due to their low mass, to give rise to the kind of dark matter phenomena driven structure observed in the universe. But, a single kind of keV mass scale particle with the properties of a sterile neutrino (except neutrino oscillation) would fit the experimental dark matter data fairly well.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-18418988335576257152015-07-28T11:39:00.001-06:002015-07-28T13:32:43.132-06:00Antiprotons Interact With Each Other Just Like Protons, As ExpectedBackground

In the Standard Model, the strong force of QCD and the electromagnetic force of QED should cause antiprotons (i.e. spin-1/2 baryons composed of two anti-up quarks and one anti-down quark) to interact with other antiprotons precisely the way that protons interact with other protons.

This includes the nuclear binding force that holds protons and neutrons together in atomic nuclei which is a "spillover effect" of the QCD strong force interactions between quarks by gluons within a proton or between antiquarks within an anti-proton, and is mediated by primary by pions.

Any gravitational interactions between an antiproton and another antiproton should likewise be identical to interactions between protons and other protons, although gravitational interactions should be too negligibly strong to matter at short distances and small masses involved in this experiment.

There is difference between the way that the weak force affects particles and antiparticles due to CP violation in the CKM matrix. But, since protons are stable and do not experience weak force decay, that difference should not cause any difference between the way that antiprotons interact with other antiprotons, and the way that protons interact with protons.

Thus, the symmetry between protons and their antipartricles and the stability of the proton, which should also apply to the antiproton so long as it doesn't interact with ordinary matter (a non-trivial task in a matter dominated universe), makes what otherwise might be very difficult calculations to determine how protons interact with other protons compared to how antiprotons interact with other antiprotons, facially obvious.

Previous experiments have directly measured the mass of the antiproton (which is exactly the same as a proton to within experimental limits), the charge of an antiproton (which is -1, exactly the opposite of a proton and the same in magnitude as an electron) and the mass some other simple anti-atoms (such as antihelium-4), but had not measured the strength of the strong nuclear force between two anti-protons. "Antinuclei produced to date include antiprotons, antideuterons, antitritons, antihelium-3, and the recently discovered antihypertriton and antihelium-4[.]" (The quotation is from the link below.) All measured anti-nuclei masses correspond to the masses of their ordinary matter counterparts to within experimental limits.

The fact that this antinuclei had been produced that were seemingly identical in all respects, except charge which was opposite, to their ordinary matter counterparts, strongly suggested that antiproton interactions with each other were identical to proton interactions with each other. But, that was only indirection evidence of this fact.

The New Experiment

However, while the theoretical expectation was clear and was also supported by indirect evidence, until now, nobody had actually been able to directly measure the interactions between two anti-protons.

The Star Collaboration in Brookhaven, New York, however, has now direct determined from an analysis of 500 million collisions of two gold atoms that "the strong interaction is indistinguishable within errors between proton-proton pairs and antiproton-antiproton pairs." Statistical errors in this experiment grew dramatically when the momentum of the interaction was less than about 0.02 GeV/c in a set of measurements looking at momenta from 0.1 GeV/c to about 0.15 GeV/c due to the small number of events at those energy scales in this set of collisions.

Two constants are used to parameterize nuclear force strength between atoms, the singlet s-wave scattering length, f0, and effective range, d0, of the interaction.

With respect to these parameters, direct measurement established that: "Within errors, the f0 and d0 for the antiproton-antiproton interaction are consistent with their antiparticle counterparts – the ones for the proton-proton interaction."

The error bar in the measurement of f0 is about 0.5 fm (1 fm=10-15 meters), and the anti-proton measurement is within about 0.5 fm of the proton measurement. The error bar in the measurement of d0 is about 1.5 fm, and the anti-proton measurement is again within about 0.5 fm of the proton measurement. The measured radii for protons and antiprotons were within 0.05 fm of each other and were also consistent within the margin of error. More precisely:

[T]he singlet s-wave scattering length and effective range for the antiproton-antiproton interaction to be f0 = 7.41±0.19(stat)±0.36(sys) fm and d0= 2.14±0.27(stat)±1.34(sys) fm, respectively. The extracted radii for protons (Rpp) and that for antiprotons (Rp¯p¯), are 2.75 ± 0.01(stat) ± 0.04(sys) fm and 2.80 ± 0.02(stat) ± 0.03(sys) fm, respectively

Admittedly, these measurements aren't extremely precise. The proton and antiproton radius measurements are accurately to +/- 2%, the f0 measurement is accurate to two significant digits, and the d0 measurement is accurate only to about +/- 75%. But, it is obviously better than having no direct measurement. Calculations of proton properties from first principles using QCD itself rarely get more precise than 1% or so, due mostly to uncertainties in the up and down quark masses and the strong force coupling constant.

The methodology used involving momentum correlations dates to the 1950s, but previous studies have not had instrumentation and collision numbers sufficient to make this measurement.

 Analysis

These results are not at all surprising.

Indeed it would have been profoundly shocking if they were otherwise, it is reassuring that a result predicted more than 45 years ago has now finally been confirmed with a direct measurement of antiproton-antiproton interactions. No serious beyond the Standard Model theories of physics proposed any thing different, although this experiment places new constraints on any theory that would argue otherwise.

This is yet more experimental evidence for the existence of CPT symmetry and the absence of any meaningful CP violation in the strong force, which makes previous experimental conclusions more robust because it employs a new methodology to test it and is conducted with a different apparatus by a different set of investigators than those who did prior state of the art collider experiments at LEP, Tevatron and the LHC.

The fact that predictions made by the Standard Model in the 1970s are routinely being confirmed for the first time in 2015 says volumes for its accuracy as a true description of how nature acts within the limits of our ability to observe it.

Off Topic

In other physics news, the first new data since it was reactivated this year at 13 TeV energies has been released. The LHC was turned back on in May and is a bit behind schedule. This result is based on about two months of data at the new higher energies.

The newly released report shows that the number of top quark pairs produced at 13 TeV energies, a very well understood process with an unmistakable decay signature is easily measured with a small amount of data, confirms the Standard Model expectation of about 875 top quark pairs per billion collisions at 13 TeV energies. Top quark pairs have a combined mass of about 346 GeV.

Top quark pairs were produced only about 6 times per billion collisions at the 2 TeV energies that were available at Tevatron which proceeded the LHC. But, higher energies non-linearly increases the number of very high energy events which are observed. The 13 TeV run ought to be able to discern meaningful numbers of events producing particles with combined masses of 2 TeV or more (e.g. pairs of 1 TeV mass particles, which would be about six times as heavy as a top quark).

As physicist Tommaso Dorigo explains, this well understood process is basically a calibration test to confirm that the higher energy phase of the LHC experiment is working as expected before conducting measurements where there is any real uncertainty regarding what will be seen.

In a few months, in the coming fall and winter, we should start to see more interesting experimental data out of the LHC which was previously operating at 7 TeV and 8 TeV energies.

Implications Of New Particle Discoveries

Any new fundamental particle seen at the LHC would involve beyond the Standard Model physics, although a variety of new heavy hadrons could be produced without any BSM physics.

The Standard Model has no fundamental particles heavier than the top quark, and there are good reasons in light of prior experiments to expect that no "fourth generation" Standard Model-like fermions exist.

For example, if there were a heavy b' quark (excluded up to masses of 675 GeV as of 2013, compared to a top quark mass of about 173 GeV and a b quark mass of about 4.2 GeV), production of b' quark pairs would be expected to decay almost instantaneously to top quark pairs and produce an excess number of top quark pairs in the 13 TeV energy scale experiments that would also be notable for their energy scale in their own right. A fourth generation top quark is currently excluded up to masses of 782 GeV as of 2014, but that limit too will quickly be extended by the 13 TeV run. A t' or b' quark would presumably have a shorter mean lifetime (and hence greater width) than all currently known quarks, but that limitation runs up against the mean lifetime of the W boson which governs quark flavor transitions which is only slightly shorter than that of the top quark. It would be paradoxical for a t' or b' quark to have a shorter mean lifetime than the W boson, which argues for the proposition that they do not exist.

Fourth generation charged leptons are excluded up to 100.8 GeV as of 2001 (compared to 1.776 GeV for the tau charged lepton). A variety of measures exclude fourth generation "fertile" leptons as well, directly up to about 39.5 GeV as of 2001 (when the other three neutrino mass eigenvalues are all under 1 eV and are probably each under 0.1 eV) and indirectly through cosmology and oscillation measurements, which tend strongly to show the existence of only three neutrino varieties.

A heavy charged gauge boson W' is excluded up to masses of 2.9 TeV and a heavy neutral gauge boson Z' is excluded up to masses of 2.59 TeV. Heavy neutral Higgs bosons are excluded up to a little less than 1 TeV and heavy charged Higgs bosons are excluded over a fairly similar mass range.

Failure to observe new fundamental particles drives up the masses at which extra beyond the Standard Model Higgs bosons and superpartners of Standard Model particle must have if they exist, narrowing the parameter space of beyond the Standard Model theories like supersymmetry (SUSY) to increasingly unnatural scales.

Implications Of Coupling Constant Measurements

The 13 TeV scale interactions will also provide a solid test of the accuracy of the "beta functions" of the Standard Model which explain how particle masses and the three gauge coupling constant strengths change as a function of the energy scales involved. As I noted a year and a half ago, these beta functions provide one of the most experimentally accessible ways to compare the Standard Model to supersymmetry.

Observations of the running of the fine structure constant of electromagnetism and of the weak force coupling constant at the LHC in this run should start to allow researchers to discriminate between Standard Model and SUSY predictions for the running of those constants at high energies. The differences between the predictions of the Standard Model and SUSY for the running of the fine structure constant are subtle, but the extreme precision with which they can be measured makes it plausible that the two hypothesizes can be distinguished. The weak force coupling constant is harder to measure precisely, but the differences between the Standard Model expectation and the SUSY expectation for the running of this constant at high energies is much greater (indeed, the direction in which this constant runs is different between the two theories).

Of course, any SUSY model can escape these concerns by pushing the energy scale at which SUSY phenomena appear higher by adjusting its parameters. But, the indirect measurement of this scale made using the running of the gauge coupling constants can probe higher energies than the direct measurements based upon the detection or non-detection of the myriad of new particles predicted by SUSY.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-80128597381880294292015-07-23T16:09:00.002-06:002015-07-23T16:09:35.251-06:00Paleo-Asians Part I Overview, Definitions, Archaic Hominins and the JomonOverview

A number of recent academic papers have investigated Paleo-Asian ancestry in Asian and New World populations.[1][2][3][4][5]

Much of the most recent research confirms the existing paradigm, or quantifies it in a manner generally in agreement with old results although with some quantitative differences.

The big headlines are that there is evidence suggestive of Paleo-Asian ancestry in indigenous South American populations of the Amazon (that does not look like modern East Asian ancestry), but not in places in between it and the Andaman Islands that are the best match to this ancestry component today.[4] Naively, this Andaman Islands-like component appears to have arisen more than 4,000 years ago (perhaps much earlier), which is before any Asian population had the boating technology to reach South America without leaving signs of their passage along the way in settlements left over centuries. [4]

There is also a trace amount of Denisovan ancestry, embedded proportionately in Paleo-Asian ancestry that looks like the founding population common to Papuans and Aboriginal Australians throughout Southeast Asia, East Asia and the Americas in populations that lack the elevated Andaman Island-like ancestry. [1]

There is also some evidence of population structure in the founding population of the Americas that would break that population into two (or even three) parts, excluding subsequent migration. [5] A new study doubts previous conclusions supported by linguistics, archaeology and genetics that there was a separate Na Dene wave of migration sometime around the early Bronze Age.[5]

There are questions over what proportion of Japanese ancestry is traceable to the Jomon with a new estimate coming in lower than previous ones (although possibly due to methodological flaws).[2]

Yet another study demonstrates that there were at least two major into Eurasia waves of migration, an earlier one to Asia via India, and a later one with a more northern orientation.[3] But, it notes that evidence of recent admixture in Asia obscures the older layers of population and migration history that can be discerned from genetic data in Asia.[3]

All of this new data goes into the cauldron as we try to piece together a comprehensive narrative of the modern human settlement of the region and the interactions of these wave of migration with the hominins archaic or otherwise who came before them, that can explain all of the evidence in a persuasive manner.

That task if left for a latter post. This post looks at the data on Jomon ancestry, and lays some of the related groundwork, without plunging into a full analysis of the big questions set forth above.

Definitions

By Paleo-Asians, I mean to include modern humans from their earliest arrival in Asia in the Upper Paleolithic era (or, at least, post-Toba explosion ca. 75,000 years ago), the founding population of North America and South America, the founding populations of Papua New Guinea and Australia, the Jomon people of Japan, the Andaman Islanders, the populations commonly classified as Paleo-Siberian, and any other modern humans who arrived roughly speaking, prior to the Mesolithic era that immediately preceded the Neolithic Revolution (i.e. populations that arrived more than ca. 10,000 or so years ago), many of whom no longer exist as distinct populations, as well as modern humans who have substantial ancestry from these early arriving populations.

In contrast, I intend to exclude modern human populations that expanded during, after, or immediately prior to the Neolithic revolution in the area where they were located (outside Papua New Guinea or the Americas). For example, populations that arrived in Siberia only after the Neolithic revolution, like the Tocharians and the Indo-Iranians and the Russians, are not Paleo-Asians Neither are the Han Chinese, the rice farming cultures of South China and Southeast Asia, the Austronesians after their ethnogenesis (in each case),

I also intend to exclude archaic hominins, although genetic traces of admixture between Paleo-Asians and archaic hominins are critical to working of the prehistoric story of the Paleo-Asians.

The term Asia, as used in this post does not include West Asia or Southwest Asia, and is also sometimes used in the sense of East Eurasian, or in the sense of East Eurasian and Native American.

Archaic Hominins and Modern Humans Outside Africa

Homo Erectus

It is widely acknowledged that the first hominin in Asia, first appearing around 1,800,000 years ago, was Homo Erectus, for which type fossils are found on the island of Java in Indonesia (Java Man), and in the vicinity of Peking, China. (Peking Man). There is no indication in the archaeological record that Homo Erectus ever made it to Japan, the Philippines, the island of New Guinea, Australia, Oceania, or the Americas. The most recent Homo Erectus remains that are reliably dated and classified is 250,000 years old. Another specimen from China, Dali Man is dated to 209,000 years ago +/- 23,000 years, but the classification of the specimen as Homo Erectus is not as definitive.

There is virtually no direct archaeological evidence of hominins within the range of Asian Homo Erectus in the time from from about 200,000 years ago to the time of the Toba eruption.

Homo Erectus was not limited to Asia. For example, it was also found in the Caucasus Mountains that form one of the boundaries of Europe. Homo Erectus in Asia (i.e. east of India) do not show any change in their associated tools in the archaeological record. Non-Asian Homo Erectus, in contrast, show a single major advance in their tool kit in the archaeological record.

No ancient DNA has been obtained from this species.

Denisovans and Homo heidelbergensis

Ancient DNA from a hominin species, known as Denisovans, has been recovered from a 41,000 year a fragment of a finger bone and two teeth in a cave in Denisova, Siberia. But, these were found without other sufficient accompanying bones to make an archaeological classification of the species relative to archaic hominins who are known only through their skeletal remains and characteristic tool kits.

As noted below, there is also a species, whose existence is disputed, called Homo heidelbergensis found in Europe after the earliest Homo Erectus sites, but before Neanderthals appeared, and are usually presumed to have evolved from Homo Erectus. Before ancient DNA was available, Homo heidelbergensis was commonly believed to be intermediate species between the two archaic hominin species, but the picture is now more complicated. Homo heidelbergensis disappear from the fossil record around the time that Neanderthals appear and no examples of Homo heidelbergensis remains have been found in the area where Asian Homo Erectus is found.

Wikipedia notes that (references renumbered to correspond to the order in this blog post):

Analysis of the mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from the mtDNAs of Neanderthals and modern humans.[6] Subsequent study of the nuclear genome from this specimen suggests that this group shares a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some present-day modern humans, with about 3% to 5% of the DNA of Melanesians and Aboriginal Australians deriving from Denisovans.[7] DNA discovered in Spain suggests that Denisovans at some point resided in Western Europe, where Neanderthals were thought to be the only inhabitants. A comparison with the genome of a Neanderthal from the same cave revealed significant local interbreeding, with local Neanderthal DNA representing 17% of the Denisovan genome, while evidence was also detected of interbreeding with an as yet unidentified ancient human lineage.[8] . . . In 2013, mitochondrial DNA from a 400,000-year-old hominin femur bone from Spain, which had been seen as either Neanderthal or Homo heidelbergensis, was found to be closer to Denisovan mtDNA than to Neanderthal mtDNA.[9]
Comparison of this ancient DNA to whole genomes of modern humans reveals that there is significant Denisovan admixture in modern humans from the Flores side of the Wallace line and beyond, including Aboriginal Australians (3-5%), indigenous Papuans (3-5%), and Oceanian populations that had admixed with any of the foregoing. In all of these populations, Denisovan admixture is closely correlated with Papuan ancestry, but not with Australian Aboriginal ancestry (which is basically absent).[1] It is also found at elevated levels in Philippino Negrito populations. The fact that modern humans with Densiovan admixture are found so far from Siberia is a mystery.

The Denisovan sample itself shows a 17% introgression of autosomal DNA from a Neanderthal population for which ancient DNA from the same case, several thousand years later in a different archaeological stratum was recovered.

Homo Florenesis

Remains of a small hominin colloqially named after J.R.R. Tolkein's Hobbits whom they resemble in size and build, were present on the island of Flores at the same time that modern humans were present there. They have been hypothesized as a possible candidate for Denisovan admixture because they were an archaic homin specifies known to be in the right place at the right time to account for most observed Denisovan admixture in modern humans. No ancient DNA has been obtained from this species.

Neanderthal

Neanderthals are found in the Middle East, West Asia, Europe (although not in environments as frigid as the most extreme environments where hunter-gatherer modern humans lived), in Northern Asia as far east as the Denivosan cave in Siberia and the Altai Mountains, and in South Asia as far as Pakistan or perhaps slightly further east, but not close to the eastern boundary of India. They went extinct a little less than 30,000 years ago. There are multiple good ancient DNA samples from Neanderthals.

All existing modern humans with ancestry from outside of Africa have Neanderthal ancestry, as do Africans who have back-migrated Eurasian ancestry in proportion to that ancestry (e.g. many North Africans and many East Africans). Neanderthal ancestry in living modern humans tends to be slightly higher in Asians than in Europeans and averages 1-3% of their ancestry. Individuals who have Denisovan ancestry also have typical amounts of non-African Neanderthal admixture.

As noted above, the available Denisovans DNA samples from Siberia also have substantial Neanderthal admixture.

Modern Humans

The oldest modern human remains (other than the controversial Dali Man claim from China) are Omo 1 and Omo 2 from Ethiopia which are dated to 190,000 years ago and were discovered in 1967. The oldest modern human remains outside of Africa are Qafzeh 6, IX and VI which are dated to 90,000 to 100,000 years old, and Skhul V and IX dated to 80,000 to 120,000 years ago, each of which is in Israel. Archaeological relics support an earlier out of Africa and into Arabia date as early as about 130,000 years ago.

No modern human remains or archaelogical relics associated with modern humans have been found in Asia to the east of India in prior to the massive eruption of the Toba volcano ca. 66,000-77,000 years ago. But, within a few thousand years after the Toba eruption, modern human remains are found in Southeast Asia and Australia. There is archaeological evidence of modern humans in Southern India both before and after the Toba eruption that tends to show that a single archaeological culture spanned that event.

The Jomon

 One Paleo-Asian population is the Jomon people whose closest surviving descendants are the Ainu people of modern Japan.

A paper analyzed at Bernard's blog examines the Paleo-Asian substrate in linguistically Japonic or Ainu populations using genetic data from "classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)."[2]

Japan was first inhabited by hominins about 30,000 years ago, and about 16,000 years ago, an archaeological culture known as the Jomon arose either due either to new migration or to in situ cultural development of Japan's existing inhabitants. The timing is after the Last Glacial Maximum (LGM), ca. 20,000 years before present, at which Japan was at its most easily accessible in modern human times due to low sea levels, at around the time that the wild fluctuation in climate the followed the LGM started to stabilize somewhat.[10]

The Jomon were fishermen who also hunted and gathered food. The sedentary lifestyle associate with fishing based subsistence allowed the Jomon to become the first culture to develop pottery. In contrast, pottery did not appear in the Levant until sometime in the vicinity of 6200 BCE to 5500 BCE, even though the herding and farming and towns (Jericho) arose in the Levant as part of the pre-pottery Neolithic period starting around 8500 BCE to 8000 BCE and even though sedentary fishermen who also hunted and gathered and engaged in proto-farming of wild type crops were present in the Levant as early as 23,000 years ago.[11] There is even suggestive evidence that implies that all pottery in Eurasia is derived from the Jomon invention of that craft.[12] According to [13]:

The upper Paleolithic populations, i.e. Jomon, reached Japan 30,000 years ago from somewhere in Asia when the present Japanese Islands were connected to the continent. The separation of Japanese archipelago from the continent led to a long period (∼13,000 – 2,300 years B.P) of isolation and independent evolution of Jomon. The patterns of intraregional craniofacial diversity in Japan suggest little effect on the genetic structure of the Jomon from long-term gene flow stemming from an outside source during the isolation. The isolation was ended by large-scale influxes of immigrants, known as Yayoi, carrying rice farming technology and metal tools via the Korean Peninsula. The immigration began around 2,300 years B.P. and continued for the subsequent 1,000 years. Based on linguistic studies, it is suggested that the immigrants were likely from Northern China, but not a branch of proto-Korean.
Thus, around 1300 BCE, a rice farming, horse riding, warrior dominated people called the Yayoi from mainland East Asia, arrives in Japan oversea from what is now South Korea, and become a superstrate population which integrates substantial proportions of Jomon people into their society, but incorporates almost no Jomon linguistic elements into what will become the Jomon language.

The timeline in Okinawa is potentially consistent in broad brush strokes with the rest of Japan (the oldest human remains are 32,000 years old), but the archaeological record is thinner (there is no archaeological record indicating a human presence of any kind from 18,000 to 6,000 years ago), rice farming arrives only many centuries after the Yayoi do, and earliest historical mention of Okinawa in surviving written documents is from 607 CE.

The Yayoi spread as far South as the Ruyukyu island in the South. Japan has four major islands, Hokkaido, Honshu, Shikoku and Kyushu, but initially the Yayoi control only Kyushu, Shikoku and Southern Honshu until around 1000 CE. Northern Honshu and Hokkaido are home to a population related linguistically and genetically to the modern Ainu indigenous people of Japan who are descendants of the Northern-most of the Jomon people.

Previous Y-DNA and mtDNA data on Japanese population genetics can be summed up as follows (from [13]):

Genetic studies on Y-chromosome and mitochondrial haplogroups disclosed more details about origins of modern Japanese. In Japanese, about 51.8% of paternal lineages belong to haplogroup O6, and mostly the subgroups O3 and O2b, both of which were frequently observed in mainland populations of East Asia, such as Han Chinese and Korean. Another Y haplogroup, D2, making up 35% of the Japanese male lineages, could only be found in Japan. The haplogroups D1, D3, and D*, the closest relatives of D2, are scattered around very specific regions of Asia, such as the Andaman Islands, Indonesia, Southwest China, and Tibet. In addition, C1 is the other haplogroup unique to Japan. It was therefore speculated that haplogroups D2 and O may represent Jomon and Yayoi migrants, respectively.

However, no mitochondrial haplotypes, except M7a, that shows significant difference in distribution between modern Japanese and mainlanders. Interestingly, a recent study of genome-wide SNPs showed that 7,003 Japanese individuals could be assigned to two differentiated clusters, Hondo and Ryukyu, further supporting the notion that modern Japanese may be descendent of the admixture of two different components.
Previous autosomal DNA studies of the Ainu and Ryukyu confirm that they are a tightly clustered group relative to other populations for which autosomal DNA is available.[14] This supports the inference that both populations have predominantly Jomon and Yayoi ancestry, albeit perhaps in slightly different proportions with minor additional elements in one or both of these populations.

This most recent study analyzes whole genomes from Ainu, Ryukyuans and Mainland Japanese populations, using Han Chinese and Korean populations as outgroups.[2] It finds that:

(1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago [1,450 years], and 43 to 44 generations ago for the Ryukyuans [1,100 years], depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes.
The first result is to be expected, both because of mainland East Asian admixture in the people of Northern Honshu in the last 1,000 years, and because of a likely North to South cline in the non-East Asian genetics of the Japanese people that probably reflects more Northeast Asian (i.e. basically Siberian) admixture in the north.

Bernard appropriately notes that the date of admixture estimates in the study can be considered as lower bounds knowing that the rolloff program assumes a single genetic mixing event and the most recent estimates in the case of several events. The rolloff dates are consistent with the end points of a roughly one thousand year period of admixture from the first arrival of the Yayoi in Central Japan and Okinawa respectively.

Bernard also notes that some of the genes with known phenotypic effect distinguishing the Ainu and Central Japanese are genes associated with facial structure of European (and PAX3 COL7A1) and the morphology of the teeth and hair of East Asians (EDAR), which is unsurprising given the different physical appearance of approximately pureblooded Ainu people and Central Japanese people, with the Ainu looking much more similar to Europeans despite not having strong genetic ties to them.

The fact that Ryukyuans appear to have more Jomon ancestry (28%) than Central Japanese people (18%) is interesting, because Ryukyuan is actually closer to the Yayoi proto-language than the principal Japanese language. Realistically, in both cases, the Jomon language(s) was overcome by the Yayoi language, but Ryukyuan received less subsequent linguistic influence from China, Siberia and global trade. These estimates are conservative. A 2012 study that similarly used the whole genomes of modern populations to estimate the pre-Yayoi population's contribution to the autosomal DNA of the Japanese people using a different statistical approach concluded that "the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin."[13] Both studies agree that the Jomon contribution is higher in the Ryukyuans than in the Central Japanese people, and concludes the the relative proportions are about the same, but finds that the absolute proportions are about twice as high, and are more in line with the roughly 38% that we would expect for Central Japanese individual from the combined Y-DNA and mtDNA data, all other things being equal. (It is perfectly possible for the autosomal ancestry percentage attributable to an ancestral population to differ greatly from the average of the percentage of Y-DNA from that population and the percentage of mtDNA from that population; but the assumptions necessary to cause the autosomal ancestry percentage to be close to the average of the Y-DNA percentage and mtDNA percentage aren't particularly stringent and are a reasonable expected value unless one knows something special about the nature of the admixture event between the different admixed populations.)

As I noted in a January 24, 2015 post discussing Japanese and Korean linguistic features reported in the WALS database, Wikipedia, and certain other sources, ejective glottal consonants are found in Korean and they are also found in the North Ryikyuan languages (such as the language of Okinawa) which, "in general, preserve features found in Old Japanese that are absent in modern Japanese. The fact that the North, rather than the South Ryukyuan languages have these consonants also suggests (in accord with other lines of evidence regarding the prehistory and ancient history of these islands) that glottal consonants in the North Ryukyuan likely derive from the language spoken by the Yayoi migrants to Japan, rather than an areal influence from the island of Formosa (Taiwan) or Southern China, of some kind.

The percentage is lower than might have been expected from the fact that about 43% of Japanese Y-DNA and about a third of Japanese mtDNA is attributable to Jomon sources. More fundamentally, it is disappointing that the study used an Ainu proxy, when ancient Jomon automsomal DNA is apparently available.[15]

References

[1] Pengfei Qin and Mark Stoneking, "Denisovan Ancestry in East Eurasian and Native American Populations" (April 3, 2015) (pre-print).
[2] Jinam, et al., "Unique characteristics of the Ainu population in Northern Japan", Journal of Human Genetics (July 16, 2015).
[3] Tassi, et al., "Early modern human dispersal from Africa: genomic evidence for multiple waves of migration" (July 20, 2015) (pre-print).
[4] Skoglund et. al., "Genetic evidence for two founding populations of the Americas" Nature (July 21, 2015).
[5] Raghavan, et al., "Genomic evidence for the Pleistocene and recent population history of Native Americans" Science (July 21, 2015).
[6] Krause, et al., "The complete mitochondrial DNA genome of an unknown hominin from southern Siberia" Nature 464 (7290): 894-897 (April 8, 2010).
[7] "About 3% to 5% of the DNA of people from Melanesia (islands in the southwest Pacific Ocean), Australia and New Guinea as well as aboriginal people from the Philippines comes from the Denisovans." Oldest human DNA found in Spain -- CNN reporter Elizabeth Landau's interview of Svante Paabo, a co-author of [6], accessdate= (December 10, 2013).
[8] Pennisi, Elizabeth, "More Genomes from Denisova Cave Show Mixing of Early Human Groups", Science 340 (6134): 799 (2013).
[9] Callaway, Ewan, "Hominin DNA baffles experts". Nature (journal) 504: 16–17 (5 December 2013).
[10] Samuel Bowles and Jung-Kyoo Choi, "Coevolution of farming and private property during the early Holocene", PNAS (July 16, 2012).
[11] Snir, et al., "The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming" PLOS ONE (July 22, 2015).
[12] Jordan, Zvelebil, "Ceramics Before Farming: The Dispersal of Pottery Among Prehistoric Eurasia Hunter-Gatherers" Left Coast Press (2009).
[13] Yungang He et al., Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data, Scientific Reports (April 5, 2012).
[14] Japanese Archipelago Human Population Genetic Consortium, "The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations" 57 Journal of Human Genetics 787-795 (December 2012).
[15] Hideaki Hanzawa-Kiriyama, "Nuclear Genome Analysis of Ancient Japanese Archipelago Humans" (January 15, 2015) (symposium paper).
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-75750054478517775002015-07-22T23:30:00.001-06:002015-07-22T23:30:28.086-06:00Evidence of Proto-Farming 23,000 Years Ago On Sea Of GalileePlant remains recovered from a sedentary fishing hunter-gather camp on the Sea of Galilee from 23,000 years ago shows that proto-farming of wild type crops was conducted at the site and that the cereals were processed to produce flour.

The source is: Ainit Snir, Dani Nadel, Iris Groman-Yaroslavski, Yoel Melamed, Marcelo Sternberg, Ofer Bar-Yosef, Ehud Weiss. The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming. PLOS ONE, 2015; 10 (7): e0131422 DOI: 10.1371/journal.pone.0131422

Since these were wild types of the plants that would be later domesticated, this sedentary farming of these plants would not have sustained the farmers without the supplementation from the fishing that made sedentary living at the camp possible, and other hunting and gathering activities as well (140 different plant types were gathered).
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-15500093955185250632015-07-20T16:25:00.002-06:002015-07-20T16:37:02.880-06:00An Anniversary And An ObituaryToday is the 46th anniversary of mankind first setting foot on the Moon.

* * * *

Yoichiro Nambu, winner of the 2008 Nobel Prize in Physics, has died at age 94. He was one of perhaps a dozen or so physicists who can rightly be called a "founding father" of the Standard Model of particle physics.

He taught at the University of Chicago from 1954 to 1991 and was awarded U.S. citizenship in 1970. Prior to joining the faculty at the University of Chicago, he sent two years at the Institute for Advanced Studies in Princeton, and three years before that (prior to receiving his doctoral degree) as an associate professor at Osaka City University in Japan.

Nambu was awarded the Nobel prize "for the discovery of the mechanism of spontaneous broken symmetry in subatomic physics." He shared the prize with two Japanese scientists, Makoto Kobayashi and Toshihide Masukawa.
His 1961 co-authorship of the Nambu–Jona-Lasinio model, an effective theory of nucleons and mesons that is now considered a low energy effective theory of quantum chromodynamics (a theory that did not exist at the time) is still used as a practical tool for making computations in QCD, and is one of a handful of leading means by which QCD is approximated in ways that are numerically tractable. This theory was one of the first to correctly determine that most of the mass of a proton or neutron arises from the self-interacting field of the proton with itself, rather than from the fermions itself. A 2006 QCD paper described this model as "one of the most successful efficient models in the QCD of light hadrons in the non-perturbation region." This model is frequently applied in the context of "Lattice QCD" which is a numerical approach to modeling QCD in the low energy non-perturbative ("infrared") regime. The main feature of QCD not included in the early versions of the model was "confinement" (i.e. the reality that quarks always appear confined in hadrons). A later version of the model called the Polyakov-Nambu-Jona-Lasinio model addressed this shortcoming.

As QCD developed he was the one to propose the concept of "color charge" which is one of the central concepts of QCD.

The massless bosons that arise in field theories with spontaneous symmetry breaking are sometimes referred to as Nambu–Goldstone bosons, although more often these days, this has been abbreviated to "Goldstone bosons". These bosons were discovered by Nambu, and then generalized to quantum field theory by Jeffrey Goldstone.

Italian QCD physicist Marco Frasca remarks that: "It is a severe loss for physics but his legacy will survive him forever." He also provides this historical footnote on Nambu and his colleague Jona-Lasinio:

Giovanni Jona-Lasinio is one of the greatest Italian physicists and it is well-known for his contributions to quantum field theory and statistical physics. . . . His model, postulated together with Yoichiro Nambu, represents the right behaviour of quantum chromodynamics at very low energies and put the basis for the future understanding of broken symmetries in particle physics. Indeed, Jona-Lasinio took the Nobel medal Giovanni Jona-Lasinio Nobel Lecture on behalf of Nambu and presented also the lecture. Nambu could not go to Stockholm and so, the award passed by the hands of Jona-Lasinio.
Only a few of these "founding fathers" of the Standard Model are still living now, but many of today's leading physicists worked under them as they established their own careers in the field. We are only a single generation removed from the beginning of the truly modern, post-Standard Model, era of fundamental physics.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-49240602709661056342015-07-20T13:20:00.002-06:002015-07-20T17:32:30.587-06:00Progress In Understanding Kalash Genetics And Its Linguistic Implications
Eurogenes reports progress in understanding Kalash genetics (from his own analysis of public datasets including newly available ancient genomes).

A couple of years ago Moorjani et al. concluded that present-day Georgians of the Transcaucasus were the best available proxy for the ancient West Eurasian population that mixed into the South Asian gene pool. This was a solid statistical fit. . . . But it was also a big fat coincidence . . . .

Thus, the Indo-Iranian and hence Indo-European speaking Kalash no longer looks very similar to the Kartvelian speaking Georgian. In fact, [the Kartvelian speaking Georgian] appears to be most closely related to the supposedly Indo-European speaking Afanasievo and Yamnaya nomads of the Early Bronze Age Eurasian steppe. The rest of his ancestry is probably best described as South Central Asian, which is an unknown quantity to me at this stage, but probably in large part of indigenous South Asian origin (see here).

I'm only able to show this thanks to the ancient samples that are on the tree, for which, as far as I know, there aren't any useful substitutes among present-day populations. Obviously, Moorjani et al. didn't have this luxury, so they ended up with a model that was statistically sound, but didn't make much sense otherwise, especially in terms of linguistics.

My . . . model is easily reproducible with most of the other South Asian samples from the Human Origins, and it gels nicely with uniparental marker data too. For instance . . . not only do Pathans cluster among these ancients from the Eurasian steppe, but most of them also carry the same Y-chromosome haplogroup: R1a-Z93, which is derived from R1a-M417, and in all likelihood first expanded in a big way with the Proto-Indo-Iranians of the Trans-Ural steppe.
In another his own posts, linked above in the block quote, the key conclusion is that:

One of the toughest nuts to crack in population genetics has proved to be the story of the people of the Hindu Kush. However, using Treemix and ancient genomes from the recent Allentoft et al. and Haak et al. papers, I'm seeing most of the Kalash and Pathan individuals from the HGDP modeled as ~65% Late Neolithic/Early Bronze Age (LN/EBA) European and ~35% Central Asian. . . . [T]he Kalash and Pathans come out ~65% LNE/EBA European (which includes substantial Caucasus or Caucasus-related ancestry), ~12% ASI, and ~23% something as yet undefined. If I had to guess, I'd say the mystery ~23% was Neolithic admixture from what is now Iran. But ancient DNA has thrown plenty of curve balls at us already, so that's a low confidence prediction, even though it does make good sense.
Kalash Y-DNA is about 45% West Eurasian, and the percentage of Kalash mtDNA that is potentially West Eurasian in character (a somewhat less definitive geographic attribution than for the available Y-DNA data) is about 43%. The absence of a strong gender imbalance in uniparental markers is notable. Also, LN/EBA Europeans, themselves, aren't necessarily purely European and have a significant indigenous steppe component. So those percentages aren't necessarily inconsistent and given the small effective size of the Kalash population, genetic drift and founder effects are also to be expected.

It has long been recognized that the Kalash may look like a high level branch of the population genetic history of non-African modern humans, when in fact, they are merely an admixed population that has been isolated and inbred for a sufficiently long time to look like something unique. (The alternative view that the Kalash were isolate for 11,800 years that was expressed in Qasim Ayub, et al. (2015) is a completely implausible interpretation of the genetic data that they examined in what was otherwise a useful paper.) But, this analysis is starting to finally establish precisely what is happened to form this genetically distinctive people of the Hindu Kush with more than guess work.

This puts the oldest possible point of Kalash ethnogenesis at about 4500 years ago, a few centuries before the earliest archaeological evidence (Cemetery H), of Indo-European appearance in South Asia, but after the replacement of the Afanasievo culture with a genetically distinct successor culture in the Central Asian steppe around 2500 BCE to 2000 BCE. The Yamna culture is contemporaneous with it and more or less contiguous to the west of the Afanasievo culture.

The collapse of these cultures in favor of Y-DNA genetically distinct cultures that are otherwise quite similar to their north (who are the proto-Indo-Iranians) as the northern cultures penetrate South Asia appears to be another remarkable untold story of prehistory. The timing, however, strongly suggests that the 4.2 kiloyear climate event was almost surely an important cause of this sudden upset.

The boundaries on the possible youth of Kalash ethnogenesis aren't quite as specific, but the fact that their Dardic language is very basal within the Indo-Aryan languages (or alternately, its status as a fourth basal branch of Indo-Iranian) suggests that the earliest possible date is an appropriate place to expect to find Kalash ethnogenesis. Asko Parpola suggests in a 1999 scholarly anthology that the Dardic languages broke off from proto-Rig Vedic Sanskrit around 1700 BCE based upon Rig Vedic linguistic features found in Dardic languages and absent in other Indo-Aryan languages.

While Eurogenes understates the point a bit, I will underline it:

The long standing hypothesis that the Y-DNA R1b dominated Afanasievo and Yamnaya peoples were linguistically Indo-European is increasingly ill supported. The Afanasievo and Yamnaya peoples had closer ties to their Caucasian neighbors than their definitely linguistically Indo-European neighbors to the North of them.

This also tends to support my hypothesis that heavily Y-DNA R1b people of Western Europe were probably part of the same Vasconic language family as the modern Basque until around the time of Bronze Age collapse, when there was a mass language shift to Germanic, Celtic and Italic language, respectively, in Western Europe, with only a fairly modest population genetic impact.

And, it also supports the argument that the Vasconic languages are distant relatives (at a time depth of about 4000-5000 years ago) of languages spoken in the highlands of the Caucasus Mountains, Iran and/or Anatolia, perhaps with a strong Atlantic Megalithic linguistic substrate, whose closest surviving relatives are one or more of the modern languages of the Caucasus mountains.

I remain agnostic regarding which of those languages are the closest relative and it could be that the proto-Vasconic languages were a sister language family to all of them.

Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-67181972726891727942015-07-18T09:00:00.000-06:002015-07-20T13:35:09.787-06:00About Pluto And Other Dwarf Planets And Satellite PlanetsIn honor of the New Horizon's flyby of Pluto and Charon, I am discussing the subject of the bodies found in our solar system and Pluto in particular.

If high resolution photos of Pluto look like this, we're really in trouble.

Highlights

 In addition to providing the most close up pictures ever of Pluto and Charon, the New Horizon space probe which took nine and a half years to arrive, has allowed us to discern the topography of Pluto and Charon. For example, the tallest mountain on Pluto is about 11,000 feet, several thousand fee less than the tallest mountain in Colorado. It also appears that Pluto's atmosphere is leaking nitrogen gas, some of which is ending up in Charon's gravitational hold.

Previous Posts At Wash Park Prophet.

I made a number of posts at sister blog Wash Park Prophet, before this blog was established, that are related to the dwarf planet and Pluton called Pluto. I link to them here.

One post reviewed the new IAU definitions that demoted Pluto from its status among the classical planets and examined the various bodies that come close to meeting the definition of a dwarf planet, which is formally defined as smaller the Mercury which has a diameter of 4879.4 +/- 1 km and is the smallest of the "classical planets" which have an unchanging rank order of distance from the sun and are observable with the naked eye or very weak magnification from Earth. Another post shortly thereafter located the exact text of the new resolution and engaged in some meta commentary on the discovery. A post in 2007 reported on a stupid New Mexico law that attempted to defy the IAU definition of Pluto.

Another post in 2007 listed the largest objects in the solar system by diameter (from the Sun to Orcus) including Moons, and reported that Eris was larger than Pluto, something that is true when measured by mass, but which new measurements have shown is not true measured by diameter. A post in June of 2008 distinguished between Plutoids and the four other large objects in the solar system in the main asteroid belt that are not Plutoids.

A post in 2008, almost exactly seven years ago, reported on the formal naming of Makemake (formerly known as Easter Bunny).

The Terrestrial and Giant Planets

Within the eight "classical planets", four are "terrestrial" (Mercury, Venus, Earth, Mars), all of which are within the main asteroid belt of the solar system, and four are "giants" (Jupiter, Saturn, Uranus and Neptune) which happen to be outside the main asteroid belt of the solar system, are much larger, and have a proportionally much greater fluid makeup relative to solid makeup than the terrestrial planets. Mercury, Venus, Earth, Mars, Jupiter and Saturn have been known since ancient times and can be seen with the naked eye on Earth (although it was not clear until the 1500s that Earth was a planet like the others that rotated around the Sun, and that Earth's moon was not a planet).

Uranus was first observed in 128 BC, and was observed but not accurately classified numerous times by independent astronomers from 1690-1783, when it was correctly described as a planet. Neptune was discovered in 1846.

Dwarf Planets

Dwarf planets defined

To be a planet at all, a body must be approximately round due to gravitational effects which imposes a floor diameter of approximately 650 km to 800 km (with close cases resolved by inspection of whether it is round or not), in addition to not being a moon, or a star (the least massive of which is a brown dwarf with a minimum diameter of about 600,000 km). Thus, dwarf planets have diameters (by definition) from about 650 km to 4879 km, and in practice from 650 km to perhaps 2600 km (assuming that there might be a few Plutons in distant solar orbit a bit bigger than Pluto that are not yet discovered).

An inner dwarf planet and three near misses

One of them, Ceres, and three near asteroids that aren't quite round enough to qualify as planets are in the main asteroid belt and were discovered in the 19th century.

* Ceres 963x891 km
* Vestas 578x560x458 km,
* Pallas 570x525x500 km, and
* Hygiea 500x400x350 km

Ceres makes up about a third of the matter in the main asteroid belt between Mars and Jupiter. These four bodies combined make up about half of the matter in the main asteroid belt. About a third of all asteroids by number are part of one of 20 to 30 clusters of asteriods known as asteroid families.

Ceres was discovered in 1801 and was initially considered a planet. Pallas was the second asteroid discovered and was discovered in 1802 and was considered a planet until the discovery of more asteroids caused Ceres and Pallas to be downgraded to asteroids in 1845. Ceres was upgraded to dwarf planet status again in 2006.

Plutons

The remaining dwarf planet candidates (except Eris, 2007 OR10 and Sedna which are further out from the Sun) are Kuniper Belt Objects with orbits around the sun of 200 years or more (aka Plutons), the largest of which is Pluto, which was first discovered in 1930 before any of the rest. A classical Kuniper Belt object that aren't quite large enough to be classified as dwarf planets are sometimes called a cubewano (after the type specimen 1992QB1) or, depending upon its orbit, a plutino.

In addition to Ceres, the four other officially recognized dwarf planets, also known as Plutons, are (in order of largest dimension of size):

*Pluto 2370 +/- 10 km diameter (as of July 2015).
*Eris (aka Xena) 2326 +/- 12 km diameter (Eris is more massive than Pluto)
*Haumea (aka 2003 EL61 aka Santa) 1920 x 1540 x 990 km.
*Makemake (aka 2005 FY9 aka Easter Bunny) 1434 x 1422 +/- 14 km.

Eris is the most distant from the sun of these, about 60% further out than Pluto.

Another dozen strong dwarf planet candidates in order of size include:

* Sedna 1830-2320 km
* 2007 OR10 1280 +/- 210 km (the largest unnamed object in the solar system)
* Quaoar 1110 +/- 5 km
* Orcus 917 +/- 25 km
* Salacia 854 +/- 45 km
* 2002 MS4 934 +/- 47 km (the second largest unnamed object in the solar system)
* 2002 AW197 626-850 km (best fit 734 km)
* 2003 AZ84 661-789 (best fit 727 km)
* Varda 630-786 km (best fit 705 km)
* Varuna 574-812 km (best fit 658 km)
* Ixion 430-910 km (best fit 650 km)
* Chaos 470-740 km (best fit 600 km)

Beyond these there are probably about a dozen additional solar system bodies without names that are serious dwarf planet candidates.

Eris is the most distant dwarf planet or dwarf planet candidate from the Sun other than Sedna. All of these except Orcus and Sedna are between Pluto and Eris in the Kuniper Belt, in their average distance from the Sun. Orcus is only about 1% closer to the Sun than Pluto. Almost all of the potential dwarf planets are no further from the Sun than Eris.

Sedna is the largest body not yet officially recognized as a dwarf planet, and is also about seven and a half times as far from the Sun as Eris.

Other than Sedna, there are only four known objects significantly further out than Eris in the solar system, and only one is further out than Sedna. The sizes and shapes of these four objects aren't known with great certainty. Current estimates putting them on the borderline of qualification as dwarf planets.

Pluto was discovered in 1930 and its moon, Charon, was discovered in 1978.

A host of new dwarf planets have been discovered in the solar system in the last fifteen years. Varuna was discovered in 2000, Ixion was discovered in 2001, Quaoar was discovered in 2002 (its moon, Weywot was discovered in 2007) as were 2002 MS4 and 2002 AW197, Sedna and 2003 AZ84 were discovered in 2003, Salacia, Orcus and Haumea were discovered in 2004, and Eris and Makemake were discovered in 2005. 2007 OR10, unsurprisingly, was discovered in 2007.

Many of the 21st century discoveries were made by Mike Brown whose blog is in the sidebar. Another leading astronomer in this field is Gonzalo Tancredi.

The discovery of these new Plutons or near Plutons in 2000-2005 is what prompted the reclassification of Pluto from classical planet status to a dwarf planet and Pluton. It is estimated that there may be as many as a couple dozen Plutons in the solar system, some as large as or even a bit larger than Pluto, most of which have not yet been discovered.

Satellite Planets

Charon 1207 +/- 3 km diameter as of July 2015 is part of the same system of Pluto. Since Pluto is larger than Charon, Charon is currently officially classified by the IAU as a moon of Pluto under the existing definition, which disqualifies it from planet status. There are also four other moons in the Pluto-Charon system: Styx, Nix, Kerberos, and Hydra.

The IAU has proposed to classify Pluto and Charon as a double planet (with both Pluto and Charon having dwarf planet status) because the center of their rotation around each other is not within either planet. This would make it the only double planet system in the solar system. But, one analogy that discourages IAU members from adopting the double planet definition, is that the same definition would conclude that Jupiter is not a satellite of the Sun, but is instead as "double" object with it, since their center of gravity is no within either body due to Jupiter's great distance from the Sun.

Charon is not the only big planet-like moon in the solar system, sometimes called satellite planets:

Nineteen moons are known to be massive enough to have relaxed into a rounded shape under their own gravity, and seven of them are more massive than either Eris or Pluto. They are not physically distinct from the dwarf planets, but are not dwarf planets because they do not directly orbit the Sun.

The seven that are more massive than Eris are the Moon, the four Galilean moons of Jupiter (Io, Europa, Ganymede, and Callisto), one moon of Saturn (Titan), and one moon of Neptune (Triton).

The others are six moons of Saturn (Mimas, Enceladus, Tethys, Dione, Rhea, and Iapetus), five moons of Uranus (Miranda, Ariel, Umbriel, Titania, and Oberon), and one moon of Pluto (Charon).

The term planemo ("planetary-mass object") covers both dwarf planets and such moons, as well as planets. Alan Stern calls them "satellite planets".
Thus, while the number of first rank planets has been reduced to eight, the number of named and significant dwarf planets and near dwarf planets in the solar system has dramatically expanded in recent years. There are 24 known bodies dwarf planets and satellite planets in the solar system that are officially recognized, and perhaps twice as many that have not yet received official recognition with at least six of them that are almost certain to be ultimately classified as dwarf planets.

Solar System Real Estate

While the solar system is a big place, there is surprisingly little solid ground on the surface of planets, dwarf planets or other known solar system objects, as illustrated nicely in the xkcd illustration above which I blogged about a little more than a year ago.

The vast majority of the mass of the solar system is in the Sun and its four giant planets, but none of those are suitable for standing on or building upon. If one were to remove Venus, which is too hostile an environment to stand upon or build upon for any reasonable length of time, the Earth makes up a very large portion of the total amount of real estate in the solar system indeed.

There are lots of little islands of land in the solar system, but they are all much smaller than Earth in terms of surface area. Pluto, for example, which is the largest of the dwarf planets, has roughly the same amount of surface area as Australia, and Ceres is roughly five times smaller in surface area.

All of these little islands, moreover, are much less inviting for human habitation, a point I made in one of the very first blog posts at Wash Park Prophet. Much of that real estate is also very deep in space compared to the Moon and Mars, which are the most plausible places for human colonization outside Earth, making these places difficult and time consuming to travel to, hard to conduct trade with, and ill supplied with light from the Sun for solar power compared to closer in locations.

Mass In The Solar System

 The Sun accounts for 99.85% of the mass in the solar system. The eight non-dwarf planets account for about 0.135% of the mass in the solar system (more than two-thirds of which is in the planet Jupiter). Perhaps 0.01% of the mass in the solar system is in comets.

The moons of planets, dwarf planets, asteroids, other meteroids and space dust (some of which are discussed in this post at length), combined, account for something on the order of 0.005% or less of the mass in the solar system (i.e. about two parts per million) combined, of which moons, dwarf planets, and the three large asteroids in the main asteroid belt of the solar system account for a very significant share of this remainder.

Individual comets have a modest mass. The mass of Earth's moon, for example, is about 200,000,000 times the mass of Halley's Comet, for example. But, there are probably a lot of them out there.

A gravitational model of the solar system that ignores everything but the Sun is quite accurate. One that incorporates the four gas giants and their moons as four point sources, is considerably more accurate, despite modeling only five objects in addition to the target whose dynamics are to be inferred.

A model that includes one hundred point sources based upon the best available data (for example, the Sun, all of the planets, all of the dwarf planets, all of the known moons of planets, each major asteroid family, and a couple dozen of the biggest comets or clusters of comets) would have exquisite precision (particularly if non-Newtonian gravitational physics were approximated), although finding enough computing power for chaotic dynamics to not overwhelm the calculation could be difficult.

Dark Matter In The Solar System

If dark matter exists in the solar system, it should exist in such a homogeneous distribution at such a low density that it is undetectable through solar system gravitational dynamic. The total amount of dark matter in the solar system (if it exists) has a mass comparable to a single medium sized asteroid, but it is spread evenly throughout the spherical space centered at the Sun and including the entire solar system out to Pluto and beyond. Dark matter adds up at the galactic level but has only insignificant relevance to solar system gravitational dynamics.

How Did The Solar System Get This Way?

A new (and short) preprint offers a nice skeletal outline of the forces that shaped the dynamic history of the solar system over the last 4.5 billion years. The analysis can be summed up as the natural implications of chaotic gravitational dynamics on what was originally a fairly homogeneous disk of matter around the Sun.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-48801681606364526742015-07-13T20:12:00.000-06:002015-07-13T20:52:29.776-06:00Temporarily Out of ActionI am in trial this week and out of action for the duration. Carry on.

:(
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-60695865065718997472015-07-06T22:26:00.000-06:002015-07-06T22:26:03.986-06:00A Native American Linguistic MegafamilyA 2006 paper finds that the three North American language in a band from the Atlantic to the Pacific, immediately below the lands where Inuit and Na-Dene languages are spoken (i.e. Algic, Kutenai and Salish) are part of the same language family. These language families combined were spoken in the lion's share of what is now the most densely populated part of Canada, near the U.S. border.

This finding would add to an increasing tendency of linguistics studying North American languages to fit languages previously described as language isolates or small language families into larger language families, a trend that has been particularly notable in cases involving languages spoken in what is now California.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-77152282287260914252015-07-06T16:59:00.000-06:002015-07-06T17:47:31.733-06:00CP Violation Has Been Seen In The Decays Of Heavy Charged Mesons* The earliest evidence of CP violation was in light, neutral mesons. But, in 2012, the LHCb experiment provided experimental evidence of CP violation in the decays of charged B mesons, where the effects are less obvious without precision experimental measurements.

This confirms the Standard Model, while ruling out theories predicated on the limited circumstances in which CP violation had actually been observed, despite its presents in every W boson interaction as a result of the CP violating phase of the CKM matrix.

Results from 2012 are old news, but it seemed new to me when I discovered this result this spring (although I now known that I've mentioned this in at least one previous post), and I feel compelled to call attention to this discovery, because I've called attention to its non-discovery to date in earlier posts (some of which were accurate at the time or made the appropriate qualifications, but some of which may have been sloppy or inaccurate).

* In other useful background basic physics, Tommaso Dorigo, explains parton distributions functions.

This sheds interesting insight on the nature of the proton (which is more complex than a naive three quarks linked by gluons model would lead you to believe), and also illustrates have particle physicists of circumvented an inability to do some key QCD calculations from first principles by fitting curves (parton distribution functions) to a very rich data set.

The reality is that it is not currently possible to predict the outcome of LHC class proton-proton collisions doing calculations from first principles using only the fundamental constants of the Standard Model, although in principle, it should be possible to do so with enough computing power and the right techniques. Where the data run out, at about 3 TeV, the uncertainty in calculating cross-sections of interactions (i.e. likelihoods of particular decays) rises quickly to above 10%, which greatly impairs the ability of scientists at the LHC to distinguish background phenomena from signals of new physics.

Dorigo's concluding remarks on this point bear mentioning:

What this means is that we will have a hard time discovering new particles at that high-energy end, given our insufficient knowledge of the proton PDF: if we see an excess in the data we might be tempted to call it a new resonance, but we will always have to reckon with the fact that we cannot be sure of the real behaviour of the PDF at the very high end.

Something similar happened to CDF in 1996, when an excess at high energy of the cross section of inclusive jet production got many excited, as it could be the first signal of small constituents within quarks. Later it was discovered how the PDF model used was insufficiently precise, and the data returned in agreement with the new predictions.

But let's not be discouraged - what everybody hopes in fact is that we'll hit some pretty unmistakable new physics signal in Run 2, one which no PDF uncertainty could explain away. I remain sceptical, but I would be among the first to celebrate...
Of course, an inability to detect subtle new physics at high energies also implies in inability to rule out subtle new physics at high energies.

Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-82276537740478110832015-07-03T16:04:00.002-06:002015-07-03T16:06:00.370-06:00Admixture Analysis Of Global and Ancient Genomes
What Is Admixture Analysis?

 A computer program called Admixture uses a mathematical algorithm whose application to genome data includes a little art as well as a lot of science, to fit data from large numbers of genomes as well as possible into a model. This model assumes that each person's genome is mix of different proportions of a preset number of hypothetical ancestral populations determined in a manner that maximizes the quality of the fit using linear algebra. It is also possible to tweak the program, for example, by designating some real individual as the exemplar of an ancestry component, rather than having the computer derive its clusters entirely without outside input.

I don't know precisely which choices were used to generate the latest and greatest result from Eurogenes analyzing a sample of more than 2059 modern and ancient genomes that maximally capture all varieties of modern human genetic variation in an Admixture run at K=10 (i.e. requiring the program to fit the individuals in the sample into percentage contributions from ten ancestral populations generated by the computer). This sample includes almost every available complete ancient genome (which number in the hundreds) and some global databases of genomes that are widely used in the professional literature (such as the thousand genomes database) to represent the rest of the world.

An Example Of Admixture Analysis

For example, the first ten samples in his analysis are African-Americans from Denver (because AA for African-American comes first in the alphabetical listing). For each individual a percentage of ancestry from each of ten groups that have been labeled for convenience after the fact to give a sense of where that component is most often found. These categories are (with abbreviations spelled out):

1. Middle Eastern
2. San Bushman
3. American Indian
4. Northern Siberian
5. East Asian
6. Hindu Kush
7. Sub-Saharan African
8. European Hunter-Gatherer
9. Oceanian.
10. East Siberian.

For example, individual number 15 from the African-Americans from Denver sample included in his Admixture run is determined to be:

88.6% Sub-Saharan African
8.5% European Hunter-Gatherer
1.6% Middle Eastern
0.5% San Bushman
0.4% American Indian
0.4% Hindu Kush

The proportion of the other four ancestral components is negligible.

In terms an average person would understand, this individual is 89% black, 10.5% white, and 0.4% American Indian, these proportions reflect the American reality that African-Americans typically have higher proportions of African ancestry, and lower proportions of non-African ancestry, than is typical of people with some African ancestry in Latin America and the Caribbean.

This individual's African ancestry overwhelmingly from populations more like typical Niger-Congo language speaking West Africans and much less like "Paleo-African" populations like the Khoi-San bushmen of the Kalahari desert and the Pygmies of the Congo jungle. This reflects the typical sources of individuals in the American slave trade.

The mix of "European hunter-gatherer" ancestry, "Middle Eastern" ancestry, and "Hindu Kush" ancestry in the "white" component of his ancestry is roughly in line with what you would expect in someone of Scottish origins (which is typical of Southern whites in the U.S., many of whom were Scotch-Irish).

Small but measurable amounts of Native American ancestry are common in African Americans.

All of this is exactly what one would expect from other data in a typical African-American from Denver. One of the African-Americans from Denver in the sample, however, who is an exception, is almost half-white and not quite half-black, and is probably light skinned relative to a typical African-American in Denver.

Similar break downs are available for all 2059 people, modern and ancient alike, in the database, although it takes a certain amount of familiarity with how the individuals are identified to know which are modern, which are ancient, and what modern ethnic groups or his archaeological cultures are represented by the label given to an individual in the spreadsheet.

Insights: Genetic Variation Is Highly Structured And Far From Maximal

 The fact that a reasonably accurate description of someone's ancestry, relative to seven billion or so living people and untold numbers of deceased individuals who preceded us, can be summed up with a fair degree of specificity with percentages of ten ancestral components, is itself remarkable.

The reality of human genetic variation observed in the real world is dramatically narrower than the default assumption that each SNP is random relative to the entire human population, in which each individual would be their own "special snowflake". Each individual is unique, but the differences within ethnic communities often colloquially described in terms of race, linguistic affiliation and ancestral religious identification, are often quite subtle.

Indeed, vast areas of the human genome are totally ignored by people interesting in genealogy, forensic applications, or ancient DNA research, because all modern humans are identical in that part of the genome. Indeed, a significant component of the part of the genome that has reached fixation in modern humans has also reached fixation in archaic hominins (like Neanderthals and Denisovans for which we have ancient DNA to compare to), for primates, for mammals, and for vertebrates. Indeed, all multi-celled animals, no matter how primitive, share more than 40% of their DNA at locations that are so functionally important that they have reached fixation. The more that parts of a person's genome are ancestry informative and variable within modern humans, the more likely it is that those parts of a person's genome are not important to evolutionary fitness.

Every Ethnicity Has At Least One Distinctive Genetic Profiles

Still, a person's genomes are ancestry informative and can often pin down a person's likely self-identified ethnicity, race, ancestral religious affiliation and familial place of origin with great specificity, in Europe, for example, pinning down the likely place of origin of someone with ancestors all from the same region, to a location within a hundred miles or so.

For example, when I compared the mix of "white" ancestral components of the African-American individual from Denver described above, it was possibly to obviously rule out a white ancestor from the Near East, Southern Europe or Iceland (because the Middle Eastern component was proportionately too small compared to the other ancestral components), or from Russians (who generally have a significant Northern Siberian component).

Similarly, a recent African immigrant from Somolia would have about ten times or more as much of the San Bushman ancestry component as someone descended from slaves from the American Southeast, as is typically the case with African-Americans, even though the former would not be unheard of in Denver's African-American population.

There are some cases where a population that culturally is just one ethnicity, such as "African-Americans" in the United States, can actually have several distinct genetic profiles (e.g. Ethiopian-Americans and other Africa-Americans in Denver might be classified socially as both being African-American, but would have different genetic profiles).

This reflects that fact that the history of human migration and diversification through mutations, isolation into separate reproductive populations, adaptation to new environments, and admixture, has been highly structured and has involved a finite number of populations, that these populations had enough time to homogenize while isolated from other populations, and that there have been a modest and finite number of significant admixture events in modern human history.

Few People Are Pure Types

Another descriptive observation of the data set is that at the K=10 level, few individuals are "pure types" with 99%+ ancestry from a single ancestry category.

There is no one in the sample with more than 83.1% Middle Eastern ancestry. There is no one with more than 86.6% Hindu Kush ancestry (a component that would be more accurately described as Kalish).

There are 2 of 2059 individuals with more than 99% European hunter-gatherer ancestry from many thousands of years ago (both of whom are ancient DNA samples with sequences released within the last couple of years).

There are 8 of 2059 individuals with more than 99% San Bushman ancestry. There are 35 of 2059 individuals with more than 99% American Indian ancestry. There are 6 of 2059 individuals with more than 99% North Siberian ancestry. There are 19 of 2059 individuals with more than 99% East Asian ancestry. There are 79 of 2059 individuals with more than 99% Sub-Saharan ancestry. There are 14 of 2059 individuals with more than 99% Oceanian component (a component that would be more accurately described as Papuan). There are 2 of 2059 individuals who are more than 99% East Siberian.

Thus, in a sample of 2059 modern and ancient individuals, only 163 are "pure type" individuals (less than 8% of the sample), while the rest have at least two measurable ancestral components in their genomes. Two of the ten ancestral populations have no "pure type" representative (Middle Eastern and Hindu Kush), and a third has no modern "pure type" representatives.

Also, it is worth recognizing that representation in the sample is not proportionate to modern population size, and indeed, is deliberately chosen to over represent genetically distinct populations. This is a maximally diverse sample, rather than a representative sample of human genetic diversity.

The populations that are pure types for the San Bushman, for Northern Siberians, and East Siberian (three of the seven ancestral types with modern representatives) are tiny relict populations that subsist in large part on hunting and gathering.

Pure type Papuans are present only on an island between Australia and China that has little contact with the outside world and uses traditional indigeneous non-mechanized agriculture. Only a very small percentage of Native Americans a "pure blooded" and those who are generally live in economically marginal reservations or remote jungles or mountain villages. The "pure type" individuals in all of these populations combined in the entire world alive today make up considerably less than 1% of the world's entire population.

Only the Sub-Saharan component and East Asian components have pure type individuals who are present in modern populations that are not tiny and marginalized.

No One Has Measurable Amounts Of All Components:

 While few individuals are "pure types" almost no one has measurable contributions to their genome (defined as more than one part per 100,000) from all ten of the globally determined ancestral components.

I was able to identify only six individuals who had measurable amounts of nine of the ten ancestral components in the sample: Turkish4BA57, SaudiA7, HGDP00148 (Makrani, a South Asian Muslim ethnicity), Jordan646, usb25 (an Uzbek) and Yemenese1529. Given that all of these individuals are from predominantly Muslim areas, it is plausible to infer that global, religiously mandated pilgrimages to Mecca have led to trace admixture in many Muslim populations from all over the Muslim world, and indirectly from almost everywhere around the globe.

Everyone in the sample of 2059 individuals (modern and ancient), except the 163 pure types and 6 nine type individuals, had two to eight ancestral components, and the lion's share have fewer than eight.

With a cutoff that excludes negligible contribution from an ancestral component (say, e.g., less than 0.1%), there would be no individuals with nine ancestral components, and the average number of ancestral components per person would be much smaller.

In any given region or ethnicity, individuals typically have slightly varying percentages of just a few components.

For example, of the seven Finnish people in the sample, all have generally similar percentages of four of the ten ancestral components (Middle Eastern 9.1%-14.8%, Northern Siberian (4.6%-9.7%), Hindu Kush (4.8%-13.0%), European Hunter-Gatherer (66.6%-76.2%). Six of the seven had small amounts of Eastern Siberian 0.7%-2.5% ancestry, and four also having trace amounts of American Indian ancestry (0.2%-1.2%) including the one with non East Siberian ancestry. None of the Finnish individuals had any San Bushman, East Asian, Sub-Saharan African, or Oceanian ancestry.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-86617770084477342182015-07-03T12:55:00.002-06:002015-07-03T12:59:58.070-06:00A GUT Model That Makes Some Progress On SM ConstantsGrant Unified Theories are notorious for trying to find a unified structure that encompasses the Standard Model particles, while not providing any meaningful insight into the origins of the fundamental mass and mixing parameters of the Standard Model.

An exception is the pre-print Feruglio, Patel and Vicinoa, "A realistic patter of fermion masses from a five-dimensional SO(10) model" (July 2, 2015). It's abstract states that:

We provide a unified description of fermion masses and mixing angles in the framework of a supersymmetric grand unified SO(10) model with anarchic Yukawa couplings of order unity. The space-time is five dimensional and the extra flat spatial dimension is compactified on the orbifold S1/(Z2 x Z'2), leading to Pati-Salam gauge symmetry on the boundary where Yukawa interactions are localised. The gauge symmetry breaking is completed by means of a rather economic scalar sector, avoiding the doublet-triplet splitting problem. The matter fields live in the bulk and their massless modes get exponential profiles, which naturally explain the mass hierarchy of the different fermion generations. Quarks and leptons properties are naturally reproduced by a mechanism, first proposed by Kitano and Li, that lifts the SO(10) degeneracy of bulk masses in terms of a single parameter.

The model provides a realistic pattern of fermion masses and mixing angles for large values of tan β. It favours normally ordered neutrino mass spectrum with the lightest neutrino mass below 0.01 eV and no preference for leptonic CP violating phases. The right handed neutrino mass spectrum is very hierarchical and does not allow for thermal leptogenesis. We analyse several variants of the basic framework and find that the results concerning the fermion spectrum are remarkably stable
As the authors explain further:

Below the GUT scale the theory looks like the MSSM and we expect standard SUSY gauge coupling unification. In order to suppress the higher order corrections in Eq. (2.8), we take c ≡ ΛπR ≈ O(100) so that the cut-off of the theory, Λ can be lifted up to the Planck scale . . . . The higher order corrections are at the percent level and remain smaller than experimental uncertainty in the fermion mass data we adopt. The theory provides a predictive framework for fermion masses and mixing angles[.]
This model does not reproduce the Standard Model constants exactly (it assumes that a group of constants relevant to determining the observable values are random numbers on the order of 1), is not terribly original, and has some rough spots that mark it as an incomplete work. But, it at least takes a serious stab at developing a model that reproduces the hierarchy of Standard Model mass and mixing constants up to an order of magnitude level, and even risks displaying calculations made with it. This makes it quite notable relative to the ordinary flurry of toy models that make no concrete predictions at all about the Standard Model constants.

They renormalize the observable parameters up to the GUT scale using the results for this in the Minimal Supersymmetric Standard Model (MSSM) from prior literature and derive their predicted values at the GUT scale.

By choosing a "normal" neutrino hierarchy, setting tan β = 50, and testing random values of the nine free parameters of the theory within the range 0.5-1.5 (i.e. of order 1), they manage to get results that are within two sigma of the observed values of the parameters about 0.05% of the time, i.e. one time in 2000 (compared to less than one in 100,000 trials in an inverted hierarchy, and a poor fit indeed with a smaller value of tan β).

In the MSSM, tan β is the ratio of the vacuum expectation values of the two Higgs doublets, so there is one Higgs field at the electroweak scale of about 246 GeV, and another Higgs field at a scale of about 12.3 TeV, which is very roughly speaking the scale where supersymmetric effects would be more visible.

The model predicts, which fitted to known experimental values, a lightest neutrino mass of about 3.9 meV, a neutrinoless double beta decay Majorana mass of 4.96 meV, and a spectrum of right handed neutrino masses of 190 GeV, 802 TeV, and 1.42*1011 TeV.

I personally seriously doubt that there are right handed neutrinos at all, suspect that neutrinos do not have any Majorana mass, and expect that the lightest neutrino mass is on the order of 1 meV or less. In other words, I think all of these predictions are wrong. But, they are at least not yet contradicted by direct experimental evidence.

There are a host of good reasons to believe that the universe is not described by the MSSM or something quite similar to it, particularly after the first run of the LHC's data is out, but the MSSM does provide a more mathematically tractable way to deal some general concepts related to grand unified theories generally that may be pertinent to one that actually does explain the Standard Model. So, while these results must be taken with the heap of salt, it is nice to see something working on a model they can do some calculations with in order to get some intuition about which corner of MSSM parameter space is the best fit to the real world, from which the nature of a GUT that actually does describe the universe might be more easily conceived.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-54576922138968930552015-07-02T20:56:00.004-06:002015-07-02T21:03:33.599-06:00The Old European Culture blogThe Old European Culture blog, which commenced a little more than a year and a half ago, explores historical linguistics, archaeology, the legends of European people from prehistory, and and their connection to archaeogenetics. It is a true treasure with in depth analysis, well reasoned conjectures, quality illustrations, and more.

The most recent post, for example, puts a deadly skirmish that killed about 1200 BCE near a river in the middle of nowhere to the southeast of Denmark, in the largely historical context of Bronze Age cultures that brings to life the industries and commerce that drove those societies.

Another recent post makes some striking observations about the origins of the word for embassy in Greek and words with a related meaning and very similar form in South Serbian. (This also got me thinking about pre-Greek substrates).

Yet another digs deep into Irish origin legends (after you look at that it is also an appropriate to look at the Wikipedia article on a possible non-Indo-European Goidelic substrate in the Celtic Irish language).

Go read it.

Elsewhere around the blogosphere there is a nice account of the sequencing of a complete woolly mammoth genome.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-13451100127197846562015-06-30T17:58:00.000-06:002015-07-02T21:50:02.268-06:00Ancient DNA from the Carpathian Basin (5700 BCE to 3900 BCE)A new study reviews ancient DNA results from six successive archaeological cultures from the terminal culture of pre-Neolithic hunter-gatherers to the middle Neolithic era in Western Hungary. I was slightly influenced by it when writing my recent R1b post, but it deserves separate mention.

Bernard's blog provides the source data on mtDNA haplogroups, Y-DNA, the geographic context of the cultures, and PCA analysis based upon haplogroup frequencies.

While the results aren't paradigm busting, a few observations about the data are in order:

The Ancient DNA Sample

* There are a remarkable 336 ancient DNA samples in the study from which at least mtDNA results are obtained. The data I've seen from the study do not discuss autosomal DNA, although it must be present for at least the samples from which Y-DNA haplogroups were obtained.

The Cultures

 * There are six Neolithic cultures studied. The earliest is Starcezo, which precedes the Vinca culture in essentially the same territory. The Vinca culture, LBK culture, Sopot culture and Lengyel culture are neighbors geographically and essentially contemporaneous with each other. The Vinca is the most Southeastern of the four contemporaneous cultures. The Lasinja culture post-dates the Vinca, LBK and Lengyel culture and is contemporaneous with the late Sopot culture. The Sopot culture is in a small area basically to the due north of the Vinca culture.

* Starcezo may be a first wave Neolithic culture, with the Vinca culture as the culture that follows after the first major farming bubble bust in the Neolithic era with a resurgence of hunter-gatherer DNA. Alternately, the resurgence of hunter-gatherer DNA in Vinca samples may be due to the "economic stresses caused by decreasing soil fertility" after two millennia of intensive farming that this culture itself experienced in its declining years. But, the Neolithic cultures further north and west don't experience the same resurgence of hunter-gatherer population genetics.

* Historically, there has been debate in anthropology between those who see Vinca as a local evolution of Starcezo, and those who see it as a result of migration from Anatolia. The genetic data seems to favor the former scenario, but suggests that the LBK, Sopot and Lengyel cultures may involve more new migration from Anatolia or elsewhere.

* The Vinca culture is notable as one of the earliest in which proto-writing and commercial seals, similar to those found in the Harappan civilization, appear in Europe and pre-dates the use of the Indus Script of the Harappan civilization by more than 700 years (seals were also used in the Copper and Bronze Age civilization of Anatolia, Sumeria, Assyria and Egypt). Per Wikipedia on Vinca culture:

The Vinča culture occupied a region of Southeastern Europe (i.e. the Balkans) corresponding mainly to modern-day Serbia, and Kosovo, but also parts of Romania, Bulgaria, Bosnia, Montenegro, Macedonia, and Greece. This region had already been settled by farming societies of the First Temperate Neolithic, but during the Vinča period sustained population growth led to an unprecedented level of settlement size and density along with the population of areas that were bypassed by earlier settlers. Vinča settlements were considerably larger than any other contemporary European culture, in some instances surpassing the cities of the Aegean and early Near Eastern Bronze Age;a millennium later. One of the largest sites was Vinča-Belo Brdo, it covered 29 hectare and had up to 2,500 people.
mtDNA

* All 19 of the hunter-gatherer samples have one of five different mtDNA U haplogroups (counting 2 mtDNA U not further specified due to degradation of the sample as a separate category).

* All of the Neolithic samples have substantial mtDNA diversity (at least six or more mtDNA top level haplogroups represented). At least some Neolithic sample has examples of mtDNA not found in the hunter-gather sample including H, HV, V, J, K, N1a, T1, T2, U3, U8, W and X. This tends to suggest that at least the maternal origins of the first wave Neolithic peoples of Europe were part of the culture that fused populations that before the Neolithic revolution were distinct into a melting pot whole. As I note below, there was far less Y-DNA diversity, a fact that casts some doubt on the anthropological conception of the archaeological cultures of "Old Europe" as matrilineal.

* A quite significant share of the Vinca samples are also mtDNA U (about 22.5%), but it is quite rare in the other Neolithic samples. This is a resurgence in mtDNA U frequencies from the previous Starcezo culture.

* There is a significant mtDNA mix difference between Starcezo and Vinca on one hand, and the other Neolithic cultures, including a significantly higher frequency of mtDNA H in the other cultures, and a significantly lower frequency of mtDNA U in the other cultures. The Starcezo culture has only 6.9% mtDNA H and the subsequent Vinca culture has even less, but the levels of mtDNA H are much higher in the other Neolithic cultures in the sample (LBK, Sopot, Lengyel and Lasinja), which have percentages of mtDNA H from 16.67% to 28.54%, still lower than modern levels, but much higher than Starcezo and Vinca.

Y-DNA

* There is no hunter-gatherer ancient Y-DNA in the sample. Elsewhere in Europe, ancient hunter-gatherer Y-DNA has almost universally been haplogroup I1.

* The Neolithic samples (pre-Bronze Age) include Y-DNA G2a, F*, I2, E-M78, J2 and surprisingly C. There is also one sample of Y-DNA I1 from the LBK culture (possibly representing a hunter-gatherer male integrated into farmer society at some point). There are Y-DNA samples from all six of the Neolithic cultures studied.

It bears noting that this is not a "Near Eastern" mix, a description often ascribed to the genetics of first farmers in Europe. Y-DNA G2a, F* and J2 are what we would expect from a source in Anatolia or the Caucasus Mountains or the highlands of Iran, not the Levant or Arabia or even the lowlands of Mesopotamia (although J2 would surely be found in Mesopotamia in significant proportions). Y-DNA I2 suggests Paleolithic variation in European hunter-gatherer populations that happened to crop up in the Balkans (and later re-emerged as a post-Nordic Neolithic revolution Scandinavian Y-DNA clade). Y-DNA E-M78 is the only Y-DNA clade in the first farmer population of Europe that evokes Near Eastern origins and this makes up only about 6.67% of the Neolithic ancient Y-DNA population sample in this study and could have been picked up by the populations where it is found en route from their place of origin to the places that they settled in Europe in the Neolithic era.

The first European farmers probably emerged from the highlands that form the Southern boundaries of Europe and West Asia, rather than from what we would conventionally think of as the "Near East" proper.

* The Starcezo and Vinca culture combined have 4 examples of Y-DNA G2a, 3 of F*, and one of I2a1. The absence of Y-DNA E-M78 is notable, because this is present at quite high levels in the part of Europe where the Vinca culture was present. Instead, the two E-M78 samples in the study come from further north, where E-M78 is found only in moderate frequencies today.

* But, one shouldn't read too much into a sample size of just eight men, when other evidence suggests that there is more to the story. If the N=8 sample were random and independent (which it isn't) a proportion of Y-DNA E-M78 in the Neolithic era as E-M78 of about 33% (the peak modern European percentage found in Albania) is just barely ruled out at the 95% confidence level, and moderately lower modern proportions of E-M78 in the Starcezo and Vinca regions are not excluded in a statistically significant way. A Neolithic proportion of E-M78 of 17% for example, would be perfectly consistent with a failure to find any samples of it in a sample size of N=8 which is random and independent (which these samples are not).

The Starcezo and Vinca cultures are in just the right place at just the right time to be the source of the high levels of Y-DNA E-M78 in the region in modern Europe (and for that matter as the place where the E-M78 introgressed into other early Neolithic culture's gene pools). The explosion in the regions population relative to the Starcezo culture upon the appearance of the Vinca culture's much more successful agricultural society, also creates a moment in time where founder effects might cause a moderate underlying level of E-M78 (and in particular, E-V13), to be dramatically amplified relative to the Starcezo background in a way that would leave a permanent imprint on the region's population genetics.

Everything we know about Bronze Age migration into the region disfavors that migration period as a major source of E-M78 in this region. So, one is left between a choice of a Neolithic source and an Iron Age or later source for this part of the Y-DNA gene pool in the Balkans. In the latter scenario, perhaps E-V13 arrived in the Balkans during the time period when it was part of the Ottoman empire, since some accounts assert that there was significant population replacement and mass resettlement of Ottoman populations into its borderland. But, given the antiquity of E-M78 in Europe (e.g. in a 7000 year old Spanish individual), the Neolithic possibility still seems more likely, despite the lack of Hungarian ancient DNA to support this hypothesis in this small sample. The Neolithic theory also has support from the time depth of the E-V13 subclade of E-M78 which is the predominant Y-DNA E clade in the Balkans of about 8,100 years ago, right around the time of the Neolithic revolution and the Vinca population explosion there.

UPDATE (July 2, 2015): Wikipedia recalls a literary reference that could be relevant to the question of Y-DNA E in the Balkans:

In Aeschylus's play, The Suppliants, the Danaids fleeing from Egypt seek asylum from King Pelasgus of Argos, which he says is on the Strymon including Perrhaebia in the north, the Thessalian Dodona and the slopes of the Pindus mountains on the west and the shores of the sea on the east; that is, a territory including but somewhat larger than classical Pelasgiotis. The southern boundary is not mentioned; however, Apis is said to have come to Argos from Naupactus "across" (peras), implying that Argos includes all of east Greece from the north of Thessaly to the Peloponnesian Argos, where the Danaids are probably to be conceived as having landed. He claims to rule the Pelasgians and to be the "child of Palaichthon (or 'ancient earth') whom the earth brought forth".

The Danaids call the country the "Apian hills" and claim that it understands the karbana audan (accusative case, and in the Dorian dialect), which many translate as "barbarian speech" but Karba (where the Karbanoi live) is in fact a non-Greek word. They claim to descend from ancestors in ancient Argos even though they are of a "dark race" (melanthes ... genos). Pelasgus admits that the land was once called Apia but compares them to the women of Libya and Egypt and wants to know how they can be from Argos on which they cite descent from Io.

In a lost play by Aeschylus, Danaan Women, he defines the original homeland of the Pelasgians as the region around Mycenae.
The original legend is also set out more fully here, where it is notable that Pliny the Elder;s "Natural History" is another source for the legend, and it is conjectured that:

Even a cautious reading of the subtext as a vehicle for legendary history suggests that a Pelasgian kingship in archaic Argos was overcome, not without violence, by seafarers out of Egypt (compare the Sea Peoples), whose leaders then intermarried with the local dynasty. The descendants of Danaus' "blameless" daughter Hypermnestra, through Danaë, led to Perseus, founder of Mycenae, thus suggesting that Argos had a claim to be the "mother city" of Mycenae.
Naively, this story suggests that rather than being European hunter-gatherers who were assimilated into the first wave of Neolithic farmers in the Balkans, that the Pelasgians may have been the first wave Neolithic farmers in the Balkans (who probably arrived ca. 7000 BCE-6000 BCE), and that a Y-DNA E-M78 people called the Danaids arrived in a post-Neolithic folk migration from Egypt or Libya after the Pelasgians were established, but before the arrival of the Indo-European Greeks (who probably started to appear around 2000 BCE). The fact that this migration was not lost to the tradition when Aeschylus was writing in classical Iron Age Greece, and that Egypt may have been a meaningful polity at the time, suggests that the Danaids may have arrived in the Eneolithic era (i.e. Copper Age) ca. 4000 BCE - 2000 BCE in this part of Europe.

The comparison to the Sea Peoples (who are associated with Bronze Age collapse ca. 1200 BCE and some of whom were ethnically Indo-European Greek), however, poses the intriguing possibility that there may have been a similar phenomena in the wake of the similar empire felling climate event around 2000 BCE, placing the Danaids in a very specific time and place indeed, and having them arrive on the scene very shortly indeed before the arrival of the Mycenians whose language become Ancient Greek, just as in the narrative.

Obviously, legendary history alone shouldn't be taken at face value, but Aeschylus gives us a general time frame and a very specific geographical pointer regarding where to look for archaeological evidence that the Danaid migration ever happened. One could point to a pyramid like structure in Argos whose age and interpretation is disputed as a sign of an Egyptian connection to Argos though the Danaids. END UPDATE.

* Y-DNA R1b does not appear until the Bronze Age, where there are 2 Y-DNA R1b samples and there is one Y-DNA I1 sample. The study does not appear to include Bronze Age ancient mtDNA samples. Naively, I would have expected Y-DNA R1a rather than R1b in the Bronze Age this far to the east in Europe. Could it be that R1b made its way to Western Europe via the Balkans and then across the Southern part of Europe to Iberia, perhaps originating in the Yamnaya people?

As Maju has noted at this blog and in comments on one of my recent posts, it isn't sufficient to look merely at crude top level Y-DNA clades to resolve these questions, because what may look the same at gross level, may imply an impossible phylogeny when more detailed Y-DNA clade descriptions are considered. We are looking for a trail of parent to daughter clades from East to West until you get to the root of Western European Y-DNA R1b clades.

As noted above, small samples can be misleading, but the total absence of any Y-DNA R in any of the 30 pre-Bronze Age samples from the region, while it may not rule out the possibility that there was some Y-DNA R in the region during the Neolithic, does seriously disfavor the possibility that Y-DNA R was present at anything approaching its modern frequency in the region during the Neolithic era. Modern populations in this region have from 20%-60% Y-DNA R1, with significant amounts of both R1a and R1b in almost all of these populations.

If the N=30 sample were random and independent (which it isn't) a proportion of R1 in the Neolithic era or more than about 10% is disfavored at the 95% confidence level, and the expected proportion of R1 would be not more than about 5% given the data in the sample that we do have and ignoring our Baysean priors from our wider knowledge of ancient DNA. The nature of sample size statistics is that even the slight improvement from N=8 to N=30 dramatically improves statistical power, even though this improvement shows diminishing returns as N increase (to the point where, for example, the difference in statistical power between a sample size of 800 and 3000 is quite modest).

Also, knowing what I know now about the fact that Slavic peoples made their way into the Balkans from the North and had a significant demic component (unlike many other migration period "barbarians"), it isn't implausible that at least some of the Y-DNA R1a in the Balkan region today arrived as late as the Iron Age from Slavic migration (which would have predominantly Y-DNA R1a relative to Y-DNA R1b), and that the ratio of R1b to R1a in the Balkan region was higher in the Bronze Age than it is today. And, the R1b blending proportions with R1a in the Balkans, unlike in many other parts of Europe, is not a good fit to historical boundaries between the Bell Beaker cultural area and the Corded Ware cultural area that succinctly describes the relative proportion of these Y-DNA types in most of Europe. So there is a window in time in the Bronze Age during which R1b could plausibly have been dominant in a population that migrated through Western Hungary on to Western Europe.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-82741961947158333742015-06-29T19:06:00.000-06:002015-06-29T22:39:59.250-06:00Y-DNA E Better UnderstoodA new study of the phylogeny of Y-DNA E (via Bernard's blog) shows more regionally defined structure of different subclades of the Y-DNA haplogroup than had previously been discerned, particularly in Eastern and Southern Africa.

It also provides a wealth of data on the time depth of various Y-DNA E subclades, although given the wide disparities that exist in establishing mutation rate dates, this is more useful in terms of establishing relative ages than absolute one.

The study puts the split of Y-DNA D and Y-DNA E at 69,000 to 69,800 years ago.

Y-DNA E-M81, which is the predominant Berber clade (also found in moderate frequencies in Iberia, in Turkey and in Bedouins, and at low frequencies in Italy), breaks off from the clade that includes my own Y-DNA E-V13 (which is found in high frequencies in the Balkans and moderate frequencies in much of the rest of Europe and Turkey and among the Druze) between 24,100 and 25,000 years ago, around the time of the Last Glacial Maximum.

E-M81 probably arrives in Europe via the Strait of Gibraltar, in the Mesolithic or early Neolithic era, with an additional significant influx to Moorish Spain in the last 1,300 years.

E-V13 probably arrives in Europe via the Levant and disperses from there to the rest of Europe at roughly the same time or perhaps a bit later, around the Mesolithic or Neolithic era (mutation rate dating puts the origin of this clade at about 8,100 years ago). Ancient DNA from clade E-M78 (which is a parent of E-V13) is found in Iberia ca. 7,000 years ago and Y-DNA clades that are part of the E-M78 clade are present in Iberia in similar frequencies to E-M81. The spread of E-V13 to the Balkans and its expansion there must have happened sometime in pre-history, because no known historical migrations prior to first wave Neolithic migrations could account for its strong presence in the Balkans.

While a number of individuals have argued for an Eurasian origin for Y-DNA E, based on the fact that its sister clade Y-DNA D is predominantly found in Asia, an examination of the phylogeny of Y-DNA E together with the geographic distribution of its currently known branches argues strongly for an African origin for Y-DNA E, rather than a Eurasian one, as do other factors such as the presence of individuals with Y-DNA DE not further distinguished between D or E in both Tibet and Africa.

Many relatively basal branches of Y-DNA E are found almost entirely in Africa and the African diaspora (e.g. African-Americans and Afro-Caribbean populations), while only a couple of relatively young branches of Y-DNA E are found (mostly at moderate frequencies) in parts of Europe and the Near East adjacent to Africa. See, e.g., page 4 of the supplementary materials for the new study. Those branches of Y-DNA E found outside Africa, moreover, are related to each other only via branches of Y-DNA E found only in Africa.

As Wikipedia notes:

E1a and E-M75 are found almost exclusively in Africa. By looking at the major subclade frequencies, five broad regions of Africa can be defined: East, Central, North, Southern and West. The division can be distinguished by the prevalence of E-V38 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-V38 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions except the northernmost and easternmost portions of the continent. E-M243 (especially its subclades M78 and M81) is found at high frequencies in North East Africa and North Africa and is the only subclade that is found in Europe and Asia at significant frequencies. E-M243 is common among Afro-Asiatic speakers in the Near East and North Africa as well as among some Nilo-Saharan and Niger–Congo speakers in North East Africa and Sudan. E-M243 is far less common in West, Central, and Southern Africa[.]
It is also unlikely that Y-DNA had origins in Northwest, West, Central or Southern Africa. E-V38, which is most common in these regions, according to the new study, mostly expanded and diversified in the last 15,300 years, making it the youngest major branch of Y-DNA E. Y-DNA E diversity also tends to decline from East to West across North Africa. Instead, East Africa is the likely place of origin of Y-DNA E.

Ethio Helix has some solid analysis of the new data, although his page is hard to read in some browsers. In particularly, he notes that the study localizes the older part of one of the main branches of Y-DNA E in Northern Ethiopia and Sudan.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-61667642217761473332015-06-24T15:27:00.000-06:002015-06-24T15:27:09.447-06:00Parasites and the Rise and Fall of EmpiresJohn Hawks notes the possibility that widespread parasite infestation in a particular region could make it vulnerable to conquest by another group of humans without that infestation.

The quoted passage cites no documented historical examples of this happening, but it is worth putting into the mix of possible causes of the rise and fall of ancient (and not so ancient) empires.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-42092053144644761152015-06-23T12:00:00.003-06:002015-06-23T12:00:57.003-06:00More Ancient DNA!Via Eurogenes (emphasis added):

The Y-chromosome belongs to macrohaplogroup F and the mtDNA to macrohaplogroup N. For details see the supp info PDF here. The full paper is freely available <a href="http://www.nature.com/articles/nature14558.epdf?referrer_access_token=eBNwzv2b44jxLSRkDN7gN9RgN0jAjWel9jnR3ZoTv0MjYp5MQz8mXGCmEqqZEWLuPVa54FDKgGTfdqyW2mt9g4eGfhFHdwEbJSmri7eCRb1eQpzSNPlysVZVMFZRwxMnCNSTEkAZU9Vi2vz7qY7q4Wkjjr7ePp5TrM4r22ZaA4RSQOuwj9ty8dwAU7m_BKq5FeEvjDTN-INTld6if5NjwF_dm3wYyKA5zkN_7ohqms4nWKnELkDUWS07-OKcCj_6Ggh8tI4A2QcaREBFbU8VIQ%3D%3D&tracking_referrer=www.nature.com" style="background-color: white; color: #4d469c; font-family: arial; font-size: 13px; line-height: 18.2000007629395px; text-decoration: none;">here.

Qiaomei Fu et al., An early modern human from Romania with a recent Neanderthal ancestor, Nature(2015) doi:10.1038/nature14558

Abstract: Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000–42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.
The ability of science to present this evidence is absolutely stunning. The lack of a West Eurasian v. East Eurasian genetic leaning more than 10,000 years into the Upper Paleolithic, despite lacking any private East Eurasian Y-DNA or mtDNA haplogroups, is surprising. This also brings to mind the fact that none of the Y-DNA samples of European hunter-gatherers has Y-DNA D or E.

Also via Eurogenes, is the paper below, which analyzes a limited reconstruction of a Neolithic individual from what is today Barcin, Turkey:

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102
A PCA analysis places the sample near Sardinians, but shifted in the direction of Near Easterners. Another analysis shows Sardinians, Italian Tuscans, Basque, Turkish Jews, and Western Ukrainians all fairly close. An ancestral component analysis concludes that:

The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.

Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border.
Bottom line: Neolithic Western Anatolians look a lot like other first wave Neolithic farmers, confirming the leading paradigm of demic migration in the first wave of the European Neolithic.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-63119179784457877082015-06-22T16:49:00.000-06:002015-06-22T16:49:24.362-06:00Lubos Plays Dumb On Non-Locality In Quantum EntanglementLubos makes a big fuss at this blog arguing that the correlation of quantum properties of particles that were previously entangled at a common point does not constitute non-locality and that people who believe otherwise are "anti-quantum zealots" (and more particularly in response to this post which starts on the right course but then starts to get weird at about the third paragraph past the second video clip).

Lubos does so by defining "local" phenomena as acting on particles that are in the same light-cone from their common origin (i.e. that a decision that is at space-like separated point from a measurement can't influence the measurement), and stubbornly refusing to acknowledge that this is a far broader definition than most people who talk about non-locality in quantum mechanics mean. For example, he succinctly sums up his definition of "local" when he states:

When I say that the entanglement always and exclusively exists when the two subsystems have a common origin, it's important to realize "where this claim comes from" and "why we know it's right". It's right because:
1. it follows from the locality of the quantum field theory etc. at the beginning: a sudden creation of correlated bits at spacelike-separated points could be used to send information instantaneously, and that would violate locality (which can be mathematically proven to be impossible)
2. this fact is also compatible with all the experiments that have ever been done.
While surely this is a true statement, the mere fact of having a common origin is normally only considered proof of locality, in the usual sense of the word, if the ultimate outcome of the measurement, and not merely their correlation, (a concept that I call "fate") is determined at the time that the particles have a common origin.

Normal people discussing non-locality, mean that measuring one formerly entangled particle allows you to know with certainty, something about the properties of the other particle whenever it happens to be measured, even if the particles are some distance apart from each other at the time of measurement and that the outcome of whichever measurement took place first (for example, in proper time relative to the point of entanglement) was not predetermined at the time of entanglement.

But, it isn't obvious that "fate" is what is going on in the quantum mechanics of entangled particles. If the outcome of the measurement is truly still indeterminate at the point in space and time of common origin (which is what we usually assume in quantum mechanics for good reason), then the correlation does not fit any conventional definition of non-locality in the case of entangled particles.

The definition of causality that Lubos uses is more conventional: "The relativistic locality ends up being equivalent to the relativistic causality: the cause must precede its effects, t is less than t′, in all inertial systems." The would preclude what I call the Feynman explanation of information going backward in time from the point of measurement, and then forward in time from the point of entanglement (even though this isn't necessarily inconsistent with Lorentz invariance, because photons and other massless particles travel at the speed of light and don't experience the passage of time "subjectively"; everything in the path of a photon or other massless particle in a light-cone happens simultaneously in the reference frame of the massless particle, so causality isn't a meaningful concept from its perspective).

The probability that any measurement made in isolation will take a particular value, however, is perfectly random.

One possibility is that the values that the entangled particles will take when they are ultimately measured is "fated" at the time of entanglement, even though it won't be learned until much later. This seems inconsistent with the general notion in quantum mechanics (established in many other contexts) that quantum mechanical measurements are indeterminate until measured and that an unmeasured set of probabilities for a quantum system before measurement differs from a measured quantum system. (Sometimes this is called the question of "reality"). The notion of "hidden variables" is similar although not necessarily identical.

The notion that Bertlmann's socks are anti-correlated (i.e. different in color) whenever they are measured because he always picks two opposite colored socks at the start of the day at some point, fits with the idea that the outcome you will get is predetermined at the time of entanglement even though, so that even though you have no way of knowing which sock you will measure in advance (making the probability of picking one or the other perfectly random), the answer was predetermined when that sock started on its path to being measured, as we the answer to the color of the other sock when it started on its path to being measured. The outcome of the measurement existed at the time that the entangled particles separated, even though it was not known until later.

Another possibility is that the values that the entangled particles will take when they are ultimately measured is determined at the time of the first measurement and "communicated" instantaneously when the other particle is measured (implying a superluminal exchange of information). This what is commonly called "non-locality" by people discussing the subject.

A third possibility is that the values that the entangled particles will taken when they are ultimately measured is determined at the time of the first measurement and "communicated" by a message that goes backward in time to the point of entanglement and then forward in time to the other particle when it is ultimately measured. This is what is commonly called a "causality" violation by people discussing the subject (because causality implies that information travels only forward in time).

It is called a "paradox" because if hidden variables and non-locality and acausality are all not true, then how this happens doesn't fit in our classical physics trained brains.

In a key passage he states:

All this confusion began with the flawed 1935 paper by Einstein, Podolsky, and Rosen. Einstein and the two postdocs were thinking in the classical way and they found it unbelievable that the correlations could exist for all the components j⃗ ⋅n⃗ simultaneously.

They thought that if the two electrons are guaranteed to have anticorrelated values of jz, they objectively have to exist either in the state |↑↓⟩ or the state |↓↑⟩ before the measurement. But because both |↑⟩ and |↓⟩ predict 50% probability for jx=+1/2 and 50% probability for jx=−1/2 and this "split" applies to each electron, EPR and their followers found it "necessary" for the probabilities of j1x,j2x to be either "positive,positive" or "positive,negative" or "negative, positive", or "negative,negative" to be 25%, 25%, 25%, 25%, respectively.

However, that's simply not what quantum mechanics predicts. Everyone who understands quantum mechanics agrees that the perfect anticorrelation will exist if we measure j1x and j2x, too. The wrong assumption in the EPR derivation is classical physics. They assume that the two spins already have some independent well-defined states before they are measured. But they don't. Before they are measured, the two spins are entangled – which is nothing else than the most accurate and most general quantum elaboration on the adjective correlated.

The correlations between the results of measurements is a correlation. The previous sentence is a tautology. There are still some people who try to pretend that the correlation is something else than a correlation even though they use the word "correlation" themselves. We say that the measurements of the two electrons are correlated because the probability distribution p(j1x,j2x) for all four possible arrangements of the values of j1x and j2x does not factorize:

∄p1(j1x),p2(j2x):p(j1x,j2x)=p1(j1x)p2(j2x)

The full probability distribution for the two objects (electrons' spins) simply cannot be written as a simple product of two distributions for one object (for the objects separately).

Assuming the initial singlet state, quantum mechanics predicts these correlations for all the spin measurements you can think of. There is nothing "paradoxical" about it. There isn't any classical theory (or a "classical model") that makes the predictions. This fact isn't a problem with quantum mechanics or a mystery about quantum mechanics; instead, this fact is a proof that all classical theories are ruled out as theories of Nature. They are wrong. People who keep on defending them may be easily proven to be complete idiots. That's obviously the only right interpretation of the result.

What is the reason of these correlations? According to the right theory – quantum mechanics (e.g. quantum field theory where this EPR experiment may be easily embedded), the reason of the correlation(s) is not an action at a distance. At the beginning, I reminded you of the proofs that there is no action at a distance in quantum field theory!

Instead, the reason of all these correlations – the reason of the entanglement – is the two subsystems' being in the contact in the past.
Lubos is basically arguing that the equations of quantum mechanics tell us how reality behaves and that we shouldn't need to try to impose any further interpretation upon it, and that trying to ask the question of the mechanism by which quantum entanglement produces anti-correlations is essentially a category error. But, he also argues stringently that non-locality and acausality are not involved, which makes it feel like he is arguing for the "fate" version of the options, even though that overstates somewhat what he is really saying.

Indeed, he hedges in this paragraph:

The same comment applies to the anticorrelation of the spins in the singlet state. They're anticorrelated because they were prepared together. In the ER-EPR correspondence, this anticorrelation (or any entanglement) may be interpreted as a non-traversable wormhole. But such wormholes have to be created locally i.e. have a common origin, too. You create the two "throats" of the Einstein-Rosen bridge and then you may increase the distance between them. But there's no way to "suddenly" create a bridge between two spacelike-separated points!
In other words, he's basically acknowledged both a "fate-like" interpretation with the correlations arising in the past at the time of entanglement, and a "non-local" non-traversible wormhole interpretation so long as the wormhole has to be created locally, are interpretations consistent with observation.

Nobody is actually seriously arguing that entanglement can arise without a common point of contact, a straw man that he argues against that is indeed contrary to scientific fact.

The argument that one is talking about a category error could arise one of a couple of ways. First, if there is not even in principle any way to distinguish different interpretations of what is going on in entanglement, then it would seem that one is asking a nonsensical question.

Second, if we have a true paradox where any proposed interpretation leads to a logical contradiction, then we again we seem to have asked a nonsensical question, although in that case the question of which of our assumptions is wrong comes to the fore, and the problem is that canonically two of our three assumptions may be wrong and yet reach the right answer, but again, it isn't obvious that there is any way to do experiments that consistently tell us that one assumption and not another, is incorrect.

The Bohmian formulation of quantum mechanics tries to use a "fate-like" interpretation.

Richard Feynmann, when he was explaining quantum mechanics to the public, tended to favor explaining the "acausal" approach in which information could travel both forward and backward in time. I tend to favor this description because:

1. It emphasizes that quantum mechanics does not itself have an arrow of time and treats space-like and time-like separations essentially identically. You can rotate the space-time coordinates of a Feynmann diagram and still have quantum mechanically equivalent statements.

The lack of a fundamental arrow of time in quantum mechanics, and Feynman's notion of antiparticles as particles traveling backward in time, also has potentially great utility in explaining the matter-antimatter asymmetry in the universe. My conjecture on this point is that anti-matter goes backward in time from the Big Bang (or much less commonly, from points after the Big Bang when it is created/annihilated depending upon your point of view), and ordinary matter matter goes forward in time. Photons, which are timeless, go in both directions at once. Thus, there is an absence of anti-matter in our universe, because most of the anti-matter created around the time of the Big Bang is in a parallel universe before the Big Bang in which time runs in the opposite direction. Feynman's characterization of anti-matter solves this cosmological mystery elegantly, with matter-antimatter pairs that are on opposite sides of the event horizon of the Big Bang, without the need for violations of baryon number or lepton number sufficient to explain the matter-antimatter asymmetry that we observe which is otherwise far too great to explain within the context of Standard Model sphalerons.

2. It emphasizes the pre-measurement indeterminacy of quantum mechanical objects (illlustrated, for example, by double slit experiments) which is of such importance for a variety of purposes in quantum mechanics, that it makes sense to believe may be rightly considered to be a general rule.

Now, if one of the particles is measured long in time before the other, you have some of the same issues as predetermination at the time of entanglement. But, perhaps the timelessness of the photon or massless communication of information in the information carrier's frame of reference eliminates these concerns.

3. It maintains the principle of locality in the stronger sense that I have defined, rather than merely in the weaker sense (existence in the same light cone from a point of common origin) that Lubos prefers to use.

Also, the mere fact that something doesn't contradict the laws of science, doesn't mean that a scientific reality that is wildly contrary to intuition isn't remarkable and worth a lot of discussion about its meaning, since that goes to the meaning of the universe itself and our assumptions about it.

Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-82241274196094819432015-06-22T14:28:00.000-06:002015-06-22T14:58:03.968-06:00Improving Our Understanding of R1b in Western EuropeMaju analyzes some new data on predominantly Western European clades of Y-DNA R1b and fits that into a working hypothesis based on the larger picture of R1b distributions in West Eurasia.

In a nutshell, it appears that R1b-S116 expands into three different daughter clades in three directions from somewhere in the vicinity of central France, one to Normandy and the British Isles, one to Central Europe and the Alps, and one to the Southeast (especially Iberia).

R1b-S116, in turn, could have origins in Iberia via Southern Italy, or in Central Europe, or both in parellel routes to central France. These way stations could in turn come from R1b-M269 in the Balkans or Highlands West Asia (e.g. including Iran). The answer to this question (when and where this happened) is one of the hottest questions in European archaeogenetics, because it is in furtherance of the goal of determining the archaeological culture(s) which were involved in this massive genetic transmission of the dominant Y-DNA clade today in Western Europe to its current location. To answer this question is to unveil the face of the patrilineal ancestors of most Western European men.

Maju figures that from where ever the launching point might be that the most basal R1b would have its ultimate origins in West Asia. This seems plausible enough, with R2 centered in South Asia and Western Iran, particularly in the Indus River Valley which is mostly Pakistan today, and R1 found in Iran and much of Europe and Central Asia, as well as appearing in South Asia in close correlation with hypothetical Indo-Aryan invaders (particularly R1a).

But, the fact that R1a and R1b were both present and bifurcated on the Russian steppe in the Mesolithic era, along with ancient DNA that seems to point to the Altai is the deeper place of origin for the entire Y-DNA R clade, suggests that West Asia may have received R2 from the steppe, during the Paleolithic era, rather than the other way around, with R1a and R1b arriving later in the Copper Age or early Bronze Age by different routes. It is hard to distinguish between the scenarios given the available data.

Analysis

Recent ancient Y-DNA studies put examples of Y-DNA R1b and R1a on the European Steppe by the early Bronze Age or even a few centuries earlier.

In particular, European hunter-gatherer populations in Russian have ancestral Y-DNA R1 to the herders and farmers who subsequently live there, suggesting that the spread of R1 to the Russian steppe was

Corded Ware people, as expected, are predominantly R1a and have origins to the North of the Yamnaya people. The story of R1a in Europe, to quote Eurogenes, can be summed up as follows:

- Mesolithic Hunter-Gatherer from Karelia: R1a (xM198)

- Late Neolithic Corded Ware pastoralist from Germany: R1a (M198, M417, xZ282)

- Late Bronze Age Urnfielder from Germany: R1a (M198, M417, Z282, Z280).
The Corded Ware people and their successors were almost surely Indo-Europeans.

The story of R1b is complicated, however, and the question of how R1b got to Western Europe remains more cryptic.

For example, Tarim Basin mummies are R1a, but the Yamnaya people, the hunter-gatherers from the area where the Yamnaya culture emerged (the Samara Valley), and the Afansievo people are R1b. This means that the Yamnaya and Afansievo people are unlikely direct ancestors for the Tarim Basin mummies, despite the fact that the Afansievo people arrived nearby before the Tarim Basin culture arose. It suggests a more Northerly route of arrival for the Tarim Basin people, or a later one, as the Indo-Iranians are predominantly R1a.

All ancient Bell Beaker Y-DNA to date are R1b, but the sample to date isn't very representative and is limited largely to Germany, while missing core areas where the Bell Beaker culture was found,

The modern distribution of R1b in Europe, however, is a decent fit to the range of the Bell Beaker culture (with declining frequencies in places where it was more marginal).

Importantly, as well, the Basque are very high in R1b, suggesting strongly that R1b was brought to Western Europe by people who were not Indo-European linguistically and that Indo-European languages only arrived in Western Europe with the Celts or realistically, with their predecessor Urnfield people whose language was probably the source of both the Italic and Celtic languages. In other words, Indo-European languages arrived in Western Europe only around the time of Bronze Age collapse. (A similar argument for an origin of Germanic languages in Northwestern Europe around the time of Bronze Age collapse is also consistent with the evidence.)

Taken to its logical conclusion, if the Yamnaya people are the forebears of the Bell Beaker and other Western European Y-DNA R1b peoples, and while the Corded Ware people are the forebears of the European R1a people, the Yamnaya people may not have been Indo-Europeans after all. Instead, they could very well have been linguistically Vasconic (i.e. linguistically in the same family as the Basque language).

As Dienekes notes, the data tend to show that "the later steppe cultures of the Sintashta and Andronovo (putative Indo-Iranians according to some), were not a continuation of the Yamnaya-Afanasievo people," as had been widely assumed before the ancient DNA data was available. Dienekes also notes genetic continuity between modern Armenians and those of the early Bronze Age.

As Maju notes, it isn't clear if R1b took a continental route, Mediterranean route, or both, to Western Europe from an origin in Southeast Europe and/or West Asia.

Maju demurs on the timing of R1b's arrival, but suggests that Atlantic Megalithic as well as Bell Beaker were likely involved, rather than a later arrival with Bell Beaker people alone.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-42923890931232295092015-06-22T12:40:00.003-06:002015-06-22T15:00:06.105-06:00New Experiment Tends To Confirm Electron-Muon UniversalityIn the Standard Model, electrons and muons are assumed to have all of the same properties except mass. This is called lepton universality.

Some recent experimental results from the LHC involving B meson decays have shown seemingly statistically significant deviations of electron-muon universality, with decays from the same source particle producing statistically significant differences in the number of decay products with electrons, from the number of decay products with muons, when they are predicted to be the same subject to adjustments based upon the relative masses of the particles (at roughly a 2.6 standard deviation level before considering look elsewhere effects).

Those results, while not very interesting in isolation, seemed notable because of two other anomalies of similar significance, one involving lepton flavor violation a somewhat similar phenomena, that could have origins in a single theory.

But, a new experimental results, looking at the decays of positively charged pions to electrons and muons respectively, confirms Standard Model prediction of muon-electron universality to within 0.1%.

The electron to muon decay product ratio from charged pions predicted in the Standard Model is (1.2352 ± 0.0002) × 10−4. The experimentally measured value is (1.2344 ± 0.0023(stat) ± 0.0019(syst)) × 10−4, which is 0.0008 × 10−4 less than the Standard Model prediction. The combined uncertainty of the comparison of the measurement to the prediction (theoretical, statistical and systemic) is about 0.0030 × 10−4. Thus, the difference between the measured result and the predicted one is within a quarter of a standard deviation of the theoretical prediction (suggesting that the true systemic error in the experiment is probably much smaller than reported and is actually nearly zero).

This result makes it appear more likely that the apparent deviations from lepton universality seen at the LHC are actually just statistical flukes or the product of systemic error, rather than actual evidence of beyond the Standard Model physics.

The new result also makes a common source for three modest anomalies seem less likely.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-62345934306243060432015-06-22T12:24:00.001-06:002015-06-22T12:24:29.956-06:00NEMO-3 Set Bounds On Neutrinoless Double Beta DecayThe Standard Model predicts that neutrinoless double beta decay does not occur, because it involves lepton number violation, but many beyond the Standard Model theories, including those in which neutrinos have Majorana mass, predict that neutrinoless double beta decay occurs but it merely very rare, which the frequency being a function of the Majorana mass of the neutrino.

The NEMO-3 experiment using a sample of the isotype Molybdenum-100 sees no instances of neutrinoless double beta decay and sets a minimum half-life on the process of 1.1*1024 years at a 90% confidence interval.

This does not exceed the limits set at GERDA of 2.1*1025 years, in the summer of 2014, which is about 20 times longer, and the most strict limits to date. The next phase of the GERDA experiment will increase its sensitivity by a factor of ten.

The universe is roughly 1.4*109 years old, so the current limit from GERDA means that no more than one in 1.5*1016 of hadrons that could experience neutrinoless double beta decay since the formation of the universe have actually done so.

But, each neutrinoless double decay experiment's null results makes the null result more robust (i.e. not subject to the peculiar methodology issues in any particular experiment) and incrementally increases the combined limit since multiple experiments which all fail to detect neutrinoless double beta decay can all be combined to show the total time that observations have been conducted without seeing the phenomena.

Neutrinoless double beta decay also constrains the maximum Majorana mass of the neutrino. The limit of less than 0.62 eV set by the NEMO-3 experiment, which is not as strict as those set by cosmology measurements or other neutrinoless beta decay experiments like GERDA, but still forecloses a great deal of parameter space for beyond the Standard Model theories that permit limited lepton number violation.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-64242449418468387152015-06-18T15:10:00.004-06:002015-06-18T15:14:58.339-06:00Ancient DNA From Kennewick Man Confirms Native American Founder Population MembershipA new study by Rasmussen, et al., entitled "The ancestry and affiliations of Kennewick Man", in the journal Nature was published online today (open access). Much of the information in the study was available in advance of publication, six months ago.

It finds that ancient DNA from Kennewick Man confirms his membership in the founding population of Native Americans (as opposed to Arctic or Na-Dene populations of Native Americans), despite physical anthropology measurements suggesting an East Eurasian or Polynesian ancestry. The abstract is as follows:

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon-dated to 8,340–9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy.

Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans.

In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ~1× coverage and compared it to worldwide genomic data including the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide.

Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man.

We revisit the cranial analyses and find that, as opposed to genomic-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.
In short, Kennewick Man's ancient DNA largely confirms the dominant paradigm of the initial human settlement of the Americas, as have other ancient DNA samples from the Americas.

This said, many Native American populations have diverged genetically over time from Kennewick man who is closest to the non-Na-Dene modern Native American populations in the general vicinity of the Pacific Northwest. Native American ancestry components that are only a part of Kennewick man's DNA are dominant components of many modern Native American populations, suggesting scenarios such as a serial founder effect.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com:blogger.com,1999:blog-7315236707728759521.post-15485544407037912942015-06-15T16:55:00.003-06:002015-06-17T15:49:12.101-06:00Improved Y-DNA Determination of TMRCA Favors Steppe Hypothesis It is widely known that estimates of The Most Recent Common Ancestor (TMCRA) of a group of Y-DNA lineages by conventional means grossly overestimates dates that make sense based upon historical and archaeological evidence.

Often the factor that has been used to mitigate the discrepancy has been the implied mutation rate of Y-DNA, but room for manipulation of that calibrating factor has declined as direct measurements of mutation rates have accumulated with a declining margin of error.

But, a preprint by David Hamilton at biorXiv has found another culprit that fits data points from the emerging pool of ancient Y-DNA. The subtle issue is that conventional estimates of TMCRA include only clades that we see, and doesn't make allowance for the fact that many other clades developed in parallel and died off before being observed. Considering this factor generically lowers the TMCRA observed:

Our method for ``Time to most recent common ancestor'' TMRCA of genetic trees for the first time deals with natural selection by apriori mathematics and not as a random factor. Bioprocesses such as ``kin selection'' generate a few overrepresented ``singular lineages'' while almost all other lineages terminate. This non-uniform branching gives greatly exaggerated TMRCA with current methods. Thus we introduce an inhomogenous stochastic process which will detect singular lineages by asymmetries, whose ``reduction'' then gives true TMRCA. Reduction implies younger TMRCA, with smaller errors. This gives a new phylogenetic method for computing mutation rates, with results similar to ``pedigree'' (meiosis) data. Despite these low rates, reduction implies younger TMRCA, with smaller errors.

We establish accuracy by a comparison across a wide range of time, indeed this is only y-clock giving consistent results for 500-15,000 ybp. In particular we show that the dominant European y-haplotypes R1a1a & R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. This contradicts current clocks dating R1b1a2 to either the Neolithic Near East or Paleo-Europe. However our dates match R1a1a & R1b1a2 found in Yamnaya cemetaries of c3300BC . . . together proving R1a1a & R1b1a2 originates in the Russian Steppes.
This methodological advance undermines one of the last genetic evidence arguments for a Neolithic/Anatolian hypothesis of Indo-European linguistic origins in favor of a Copper Age/Bronze Age Steppe hypothesis.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://firstname.lastname@example.com:blogger.com,1999:blog-7315236707728759521.post-78350515293581365682015-06-14T18:55:00.001-06:002015-06-14T18:55:35.545-06:00Pre-History In A NutshellRazib has a lengthy synopsis of the recent history of archeogenetics (most of which has happened in my adult lifetime) at Gene Expression to put into context two major new ancient DNA studies in the Journal Nature published this month.

The big headline from these studies is that they provide new ancient DNA confirmation for the increasingly well supported hypothesis that there was an episode of dramatic population genetic change between the first farmer populations of the Neolithic era and modern Europeans, driven by mass migration from the Eurasian steppe, around the time of the early Bronze Age in Europe and almost surely coinciding with a major expansion of the Indo-European languages.

One important emphasis of Razib's account is that the phenotype of the modern European's appearance which we think of when we say that someone is racially "white", like the modern European gene pool more generally, did not really stabilize in Europe until the Bronze Age. Northern Europeans prior to Indo-European migration into Europe, for example, may have been blue eyed but dark skinned, while the invaders from the steppe may have had lighter skin and dark eyes. The light skinned phenotype we associate with Europeans today didn't reach fixation until the Bronze Age. People who look like typical Northern Europeans today didn't exist when the Egyptians were building their pyramids.

Critics of some of the recent analysis of these studies suggest that important details of the narrative may be inaccurate, because Y-DNA haplogroup subtypes and evidence of ancient Northern European ancestry in some putative parent populations to European populations that were transformed demographically at this time don't track properly to the simplest of narratives advanced to explain the new ancient DNA result.
Copywrite Andrew Oh-Willeke (2012)
andrewhttp://email@example.com