Wednesday, July 29, 2015

Neutrino Masses And Speeds

A 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).


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.

Tuesday, July 28, 2015

Antiprotons Interact With Each Other Just Like Protons, As Expected


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.


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.

Thursday, July 23, 2015

Paleo-Asians Part I Overview, Definitions, Archaic Hominins and the Jomon


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.


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.


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]


[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).

Wednesday, July 22, 2015

Evidence of Proto-Farming 23,000 Years Ago On Sea Of Galilee

Plant 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).

Monday, July 20, 2015

An Anniversary And An Obituary

Today 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.

Progress 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.

Saturday, July 18, 2015

About Pluto And Other Dwarf Planets And Satellite Planets

In 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.


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.


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.

Monday, July 13, 2015

Temporarily Out of Action

I am in trial this week and out of action for the duration.  Carry on.


Monday, July 6, 2015

A Native American Linguistic Megafamily

A 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.

CP 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.

Friday, July 3, 2015

Admixture 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.