Wednesday, May 23, 2018

Accurately Depicting The Internal Structure Of The Proton


Most common textbook and popular press illustrations of the internal structure of the proton get it wrong in light of the available evidence.  Sabine Hossenfelder at Backreaction, sets us straight. The middle illustration is preferred.

Replicating The 1894 Direct Measurement Of The Speed Of Light

The first decent direct measurement of the speed of light was made in 1894. 

A new paper provides step by step instructions on how to replicate that experiment with resources that would be available to most university physics programs as a widely accessible educational and public relations project for something that might otherwise seem much for difficult to pull off than it actually is in reality.

More Dark Matter And Modified Gravity Limitations

* Direct dark matter detection experiments are starting to impose meaningful limitations on dark matter particles sub-GeV masses for particle that interact via the weak force but not the other two Standard Model forces. 

Constraints are meaningful down to about 10 MeV. This is heavier than an up quark, a down quark, an electron, or any kind neutrino. But, for example, these results pretty convincingly disfavor weakly interacting dark matter particles with masses comparable to a muon (105.658 MeV), a strange quark (92-104 MeV) (which in any case is never observed outside of a hadron), or the lightest hadron (which is the neutral pion (134.977 MeV)), for which cross-sections of interaction more than 0.01 pb (10^-38 cm^2) are ruled out.

This progress was made possible by looking for interactions between electrons and dark matter, rather than atomic nuclei and dark matter.

In a related development the Standard Model prediction for the weak charge of the proton (which is relevant to the cross-section of interaction between particles that interact via the weak force and protons such as hypothetical WIMPs), and the experimentally measured value, confirm each other and are much lower than one would naively expect. This confirmation also functions as yet another of many meaningful global constraint on beyond the Standard Model physics near the electroweak scale. The measurement "can constrain new weakly coupled particles with masses up to a few TeV, or even 50 TeV particles if they are strongly coupled to matter (g*~4π)." But, the strongest constraints on deviations from the Standard Model prediction for the weak charge of the proton actually come mostly from earlier experiments rather than the most recent one.


These new direct dark matter detection doesn't impact "warm dark matter" scenarios with typical dark mark particle masses in the keV range or completely sterile dark matter candidates with no non-gravitational interactions. But, it is yet another nail in the coffin of the WIMP paradigm preferred in supersymmetry based dark matter scenarios.

* New direct dark matter search results from the Xenon1T experiment will be announced on Monday, May 28, 2018. In all likelihood, the results will exclude additional dark matter parameter space, because the rumor mill would be buzzing by now if the results would involve an actual claimed direction detection of dark matter.

* A credible argument has been made to slightly relax on of the empirical constraints on primordial black hole dark matter, by opening up more free parameters in the models considered, but only modestly.

* New empirical constraints have been placed on self-interacting sterile neutrinos.

* A new way to empirically test dark matter proposals by looking at the character of "stellar streams" around galaxies has been proposed. The theoretically predicted properties of stellar streams under various dark matter hypotheses have been determined, so now astronomers can can compare what is observed to these predictions, something that will be possible to observed with "next generation telescopes", so this is something today's graduate students and currently practicing astrophysicists will see in the medium term future. In general, heavier dark matter particles imply more clumping, more collisions, more gaps in the stream, and a concentration of stars closer to the center of the streams than lighter dark matter particles.

So far as I know, comparable predictions have not been made for theories like MOND in this system which is well within its domain of applicability but very much complicated by external field effects in these systems (which when present, tend to cause the system to behave closer to a Newtonian gravity model with no dark matter).

* A recent review article compiles limitations on the parameter space of simplified dark matter models from a variety of different kinds of evidence including both astronomy evidence and particle collider based limitations, and also conveniently and clearly explains the leading simplified dark matter models. If you click through to read the body text of any of the links in this post, you should do so for this study as it has a number of informative parameter space exclusion charts for a wide array of simplified dark matter models - almost all of which have large shaded excluded regions - that aren't suitable for including in this post as each one requires considerable explanation.

* Massive gravity is also pretty much dead due to new experimental constraints, after being revived due to a loophole that overcame earlier problems identified with it.

Massive gravity is interesting because it makes careful analysis of graviton self-interactions absolutely necessary in a way that is often glossed over in massless graviton theories, which is useful because while gravitons lack mass, they do not lack mass-energy. But, the predictions of massive gravity theories are wrong even in the limit as graviton mass approaches zero. 

* The gravitational wave event GW170817 constraints relativistic generalizations of MOND, for example, ruling out the first and most elegant of those (TeVeS), but does not rue out all relativistic generalizations of MOND.

Post-Script: QCD formulated in GR Terms

While not exactly on the point, one interesting recent paper that doesn't naturally fit in any neat box expresses the quantum chromodynamics a.k.a. QCD a.k.a. the Standard Model description of the strong force in an equation form closely analogous to the equations of general relativity. Usually, quantum gravity researchers go in the opposite direction and try to find formulas analogous to those of the other Standard Model forces for general relativity.

Tuesday, May 22, 2018

Anomalous Resonances As Hadron Molecules

A new pre-print quickly summarizes the hypothesis that most scalar mesons and axial vector mesons and a variety of other anomalous resonances not easily explained with two or three valence quarks are all basically "molecules" of pairs of mesons and/or baryons. For example:
There are many states that can be described from hadron-hadron interaction. Some well-known examples are the scalar mesons obtained from pseudoscalar-pseudoscalar interaction in S-wave and coupled channels: the a0(980) from KK¯ and πη in isospin 1, the f0(980) from KK¯ and ππ in isospin 0, and the f0(500) (σ meson) from ππ scattering in isospin 0. In the strange sector, from vector-pseudoscalar interaction one can describe the f1(1285) as a K∗K¯ + c.c. molecule. In the charm-strange sector there is the D∗ s0 (2317), which can be described as a DK bound state. Similarly, one of the most famous examples in charm sector is the X(3872) which can be explained as a DD¯ ∗ + c.c. molecule. These are just a few cases from meson-meson interaction. On the other hand, in meson-baryon interaction the best example would be the Λ(1405), which is widely accepted [1] as a quasi-bound state between the KN¯ and πΣ thresholds, generated mostly from the KN¯ scattering.
It doesn't acknowledge that this is not a consensus interpretation or what supports this interpretation relative to the alternatives, however. 

In other hadron physics news, the BFKL theorem, named after the authors of the paper that proposed it in the 1970s to explain how the strong force interactions of high energy particles change at high energies in a subtle but important way, has now largely been proven and refined.
One striking feature of particles which are strongly interacting (like the proton) is that if two of them are approaching each other, the chance of them actually colliding increases as the energy of the particles increases. This behaviour was well-known experimentally, and was modelled in a precursor to the Standard Model called “Regge theory”. Amongst other things, the BFKL approach offered, for the first time, a chance of understanding this behaviour from first principles using the Standard Model. . . .
The scattering probability for electrons and protons is generally expressed in terms of mathematical objects called structure functions, and the BFKL predictions said that one particular structure function should rise very rapidly as the fraction of the proton’s momentum involved in the collision got smaller. 
We measured that structure function, and it did rise. But there were problems to sort out before declaring BFKL vindicated. The structure function did not rise as quickly as might have been expected by BFKL. It was also possible to explain the rise using different calculations – not featuring their sums. Most importantly, none of these calculations, by BFKL or others, was very precise, and nor were the data. We were in a grey area. 
Over the years, many more data have come in, and better calculations have been made, by a generation of theorists and experimentalist wrestling with some formidable challenges. The qualitative impact of the BFKL sums is not now expected to be as dramatic as the initial calculations indicated, but it is still there, and still important.
A global analysis published on the arXiv this year by physicists from Amsterdam, Edinburgh, Genoa, Oxford and Rome pulls lots of this work together and makes the qualitative statements about the BFKL sums quantitative. Including these sums (in their newer and more precise form) gives a significantly better description of the data than is the case if they are omitted. 
What this means is that we have pushed our understanding of the strong force into a new, previously unobserved region, and verified a qualitatively new emergent behaviour. 
The formidable mathematics behind these calculations connects a deceptively simple underlying theory with a ubiquitous and counter-intuitive observational fact: scattering probabilities rise at high energies. This has implications for our understanding of many things, from the collisions at the Large Hadron Collider at CERN to the propagation and detection of high energy particles in cataclysmic cosmological events. It may even be important in understanding possible new strongly-interacting theories that may still to be discovered beyond the Standard Model.

How Big Was The Founding Population Of The Americas?


A current best estimate, based upon genetic data, places the size of the founding population of the Americas in the range of 229 to 300 with a best fit of about 284 people.

The source scientific journal article for the material in the link is as follows:
In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. 
In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. 
Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.
Nelson J.R. Fagundes, et al., "How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data", 41(1) Genetics and Molecular Biology (2018).

This number is the "effective population size" of the Founding population of the Americas which is generally significantly smaller than the actual adult census size of the same population, and requires additional adjustment for non-reproductive age adults. Depending upon the circumstances, effective population size could be somewhat more than half to less than 1% of the total census size of the population.

The review of the literature in the paper recounts many previous estimates of the same quantity, after which the authors argue that their approach is better than their predecessor's approaches, despite a quite small data set that was analyzed.
The first quantitative approach to infer the effective population size of the founder Native American population was developed by Hey (2005), who did a meta-analysis of nine sequence loci, used a likelihood-based inference and assumed a isolation with migration (IM) population model to suggest an extreme population bottleneck with an effective population size of ~70 individuals. Since this pioneer work, other groups tried to replicate this result using multilocus autosomal data, with partial success. Kitchen et al. (2008) re-analyzed Hey’s dataset, adding mtDNA genomic data under different priors for migration rates and suggested an effective population size ranging from 1,000 to 5,400 individuals. Ray et al. (2010), using a dataset of 401 STRs, estimated an effective founder population size between 42 and 140 individuals (with a median of 87 individuals). Between these two extremes, Fagundes et al. (2007), based on the re-sequencing of 50 short loci, estimated an effective founder size of ~450 individuals (with a 95% credible interval (CI) ranging from 71 to 1,280 individuals). Recent autosomal data generated from admixed Latino populations also provided very different figures. Gutenkunst et al. (2009), based on a very large dataset of more than 13,000 SNPs, suggested a value of 800 effective individuals, with a confidence interval between 140 and 1,600 individuals; while Wall et al. (2011), using resequencing data, estimated a bottleneck effective population size not larger than 150 individuals. Gravel et al. (2013) proposed intermediate values of about 514 effective individuals, ranging between 316 and 2,264 individuals.

Wednesday, May 16, 2018

What Is Negative Heritability?

As Wikipedia explains:
Heritability is a statistic used in the fields of breeding and genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population. In other words, the concept of heritability can alternately be expressed in the form of the following question: "What is the proportion of the variation in a given trait within a population that is not explained by the environment or random chance?"
Naively, negative heritability shouldn't exist if the assumptions of the probability model used to estimate heritability are true. But, sometimes experimental data appears to imply that something has negative heritability.

Actually, the concept of a negative probability isn't entirely foreign to mathematics and science. In quantum mechanics, you can have negative probabilities in linear contributions to the probability of an observable so long as all observables have non-negative probabilities. Something similar could be at work in the area of gene expression.

So, it isn't unthinkable that negative heritability does exist. A new pre-print considers this issue:
We consider the problem of interpreting negative maximum likelihood estimates of heritability that sometimes arise from popular statistical models of additive genetic variation. These may result from random noise acting on estimates of genuinely positive heritability, but we argue that they may also arise from misspecification of the standard additive mechanism that is supposed to justify the statistical procedure. Researchers should be open to the possibility that negative heritability estimates could reflect a real physical feature of the biological process from which the data were sampled.
David Steinsaltz, Andy Dahl, Kenneth W. Wachter "On negative heritability and negative estimates of heritability" bioRxiv (May 14, 2018).

Monday, May 14, 2018

Chicken City?

The Old European culture blog examines some interesting conjectures based upon Harappan seals.

One is that symbols for certain kinds of cities or areas within cities may have been shared between Harappans and the Egyptians according to a 2010 academic conference paper:


The crescent moon symbol is hypothesized to represent the "outer city" or places outside the walls of the city.

Another is that the Harappan city of Mohenjo Daro may have been known as the City of Cockerels (or perhaps Chicken City), based upon its recently domesticated chickens (even though it was founded 500 years before the earliest attested evidence of chicken domestication in the region). The symbol of two Roosters seems to be associated with the symbol following a symbol that seems to be associated with a large city. See, for example, the following seal found in Mohenjo Daro:



It also appears that the word for "Cock" or "Cockerel" in Sanskrit and probably also in the Dravidian languages and in many other Indo-European languages of West Eurasia may have a common origin in the Harappan substrate language. (I find that the theory that this word was borrowed from Dravidian which is often associated with the South Asian Neolithic Revolution ca. 2500 BCE unconvincing.)

Monday, May 7, 2018

Did Hittites and Other PIE Anatolian Language Speakers Lack Steppe Ancestry?

Iosif Lazaridis, in the pre-print "The evolutionary history of human populations in Europe" (May 4, 2018) casts doubt on the Steppe hypothesis as applied to the Anatolian language family within the Indo-European languages. While I understand the basis for his speculation, I think that this possibility is improbable and that late Bronze Age samples from Hittite individuals will show steppe ancestry.

The most prominent of the languages in this family was the Hittite language of the Bronze Age Hittite people who conquered essentially all of Anatolia and some of the Northern Levant and Northern Mesopotamia in the Bronze Age before collapsing in the Bronze Age collapse.

Contemporaneous historical accounts from Akkadian traders suggest that this conquest started shortly before 1740 BCE. Advocates for an early arrival of Anatolian language speakers (on linguistic grounds) argue that these languages should have been pervasive in Anatolia for more than a thousand years before this expansion, despite evidence that the territory conquered by the Hittites mostly spoke a non-Indo-European Hattic language.

But, the archaeology does not support this conclusion and there are not early historical accounts to support this claim either. Physical anthropology of remains from the region also point to a late arrival of physically distinct people in Anatolian linguistic communities.

The only other pre-Hittite empire Anatolian language which is attested is Luwian, a sister language to Hittite possibly spoken by the Trojans. The other Anatolian languages are only attested after the collapse of the Hittite empire and could have a relationship to it similar to that of Latin to the Romance languages.

They key passage states:
Steppe migrants Steppe populations during the Eneolithic to Bronze Age were a mix of at least two elements[28], the EHG who lived in eastern Europe ~8kya and a southern population element related to present-day Armenians[28], and ancient Caucasus hunter-gatherers[22], and farmers from Iran[24]. Steppe migrants made a massive impact in Central and Northern Europe post5kya[28,43]. Some of them expanded eastward, founding the Afanasievo culture[43] and also eventually reached India[24]. 
These expansions are probable vectors for the spread of Late Proto-Indo-European[44] languages from eastern Europe into both mainland Europe and parts of Asia, but the lack of steppe ancestry in the few known samples from Bronze Age Anatolia[45] raises the possibility that the steppe was not the ultimate origin of Proto-Indo-European (PIE), the common ancestral language of Anatolian speakers, Tocharians, and Late Proto-Indo Europeans. In the next few years this lingering mystery will be solved: either Anatolian speakers will be shown to possess steppe-related ancestry absent in earlier Anatolians (largely proving the steppe PIE hypothesis), or they will not (largely falsifying it, and pointing to a Near Eastern PIE homeland).
Note 45 is a reference to Lazaridis I, et al.: "Genetic origins of the Minoans and Mycenaeans." 584 Nature 214 (2017), which contains three Bronze Age Anatolian samples from Southwest Turkey. The one male and two female Bronze Age Anatolian samples relied upon are as follows (from the Supplemental Materials):
I2495I2495A4-11240K2558-2295
caIBCE

(3925±35 BP,
Poz-81111)
Anatolia_BAHarmanӧren-
Gӧndürle
Hӧyük,
Isparta
Turkey37.9230.71M1.981637146HJ1a
I2499I2499UC11240K2836-2472
caIBCE

(4040±35 BP,
Poz-82213)
Anatolia_BAHarmanӧren-
Gӧndürle
Hӧyük,
Isparta
Turkey37.9230.71F0.285243348K1a2
I2683I2683G3-951240K2500-1800
BCE
Anatolia_BAHarmanӧren-
Gӧndürle
Hӧyük,
Isparta
Turkey37.9230.71F3.695749308T2b

The man has Y-DNA J1a, mtDNA H and no steppe ancestry and is from 2558-2295 BCE. One woman is from 2836-2472 BCE, has mtDNA K1a2 and has no steppe ancestry. The other woman is from 2500-1800 BCE, has mtDNA T2b and has no steppe ancestry.

We don't have heaps of information about the archaeological context, but two of the three samples clearly pre-date the Hittite expansion that is attested historically and archaeologically in Anatolia and the third, a woman, could pre-date or post-date that expansion which in every other case was male dominated.

This data is a blow to the theory that the Anatolian languages broke away especially early form the Indo-European languages and were present in Anatolia long before 2000 BCE. 

But, it is not at all in conflict with my longstanding hypothesis that the Anatolian languages arrived in Anatolia with steppe people at a time similar to their arrival in Europe, the Aegean, South Asia and West Asia (i.e. Iran) and that the divergence of the Anatolian languages from other PIE language families is due to stronger and more divergent substrate influences rather than from great antiquity.

If my hypothesis is right, these data are a perfect fit and steppe ancestry should start to become widespread especially in specifically Anatolian language speaking men, and more generally, in late Bronze Age Anatolia. It will take future ancient DNA finds from those periods to determine if this is correct.

I also disagree with his conclusion that an absence of steppe ancestry would imply a Near Eastern PIE homeland. Instead, it would imply that the Anatolian languages arrived in Anatolia largely via elite transmission which could also help explain why it is more divergent than Indo-European languages that arrived with large communities of native speakers via mass migration.

UPDATE May 14, 2018: Davidski does some analysis of the Bronze Age Anatolian genomes discussed above, and agrees with me that these are likely Hattian and not Hittite individuals, albeit for slightly different reasons. He also notes, in data completely consistent with my late Anatolian expansion hypothesis that: "I am actually seeing a minor, but persistent, signal of steppe ancestry in one of the two Old-Hittite Period (~1750–1500 BCE) samples: Anatolia_MLBA MA2203." Also, not inconsistent with the historical record or a late Anatolian expansion hypothesis is his observation that: "None of the other Anatolia_MLBA individuals, three of whom are from the Assyrian Colony Period (~2000–1750 BCE), show such obvious steppe ancestry."

Saturday, May 5, 2018

Cutting Stone For Bronze Age Palaces


A stone discarded near a Bronze Age palace, midway through the process of being cut 
provided important clues about how the finished cut stones were made.

What kind of tools were used to precisely cut tough conglomerate stone for elaborate structures Bronze Age Hittite, Mycenaean and Minoan palaces?

Experimental archaeology combined with close observation of the cuts made and debris abandoned partially cut suggest that long straight edged metal blades, either in a pendulum saw configuration or a two man, two handled saw similar to one used by loggers was used, as explained in a Science News article. Abrasive sand, from the Greek island of Naxos, and water were also probably placed in the cuts to lubricate the blades and increase their cutting power.

A pendulum blade would offer more power to cut through hard rock and help explain the near circular curvature of many of the larger cuts. But, the logger's saw configuration would have made it easier to cut stone at multiple precise angles and has an archaeological precedent in double-handled loggers’ saws excavated from sites from the Late Bronze Age Minoan society on Crete that could have been adapted to cut stone.


Experimentation revealed that the Bronze blade used must have resembled 
the modern recreation on the bottom right of this image.

The Science News article was:

* Bruce Bower, "Making the cut: Swinging blade slices into Bronze Age mystery." Science News (April 28, 2018).

The Science News article cites the following journal articles:

* N. Blackwell, "Experimental stone-cutting with the Mycenaean pendulum saw." 92 Antiquity 217 (February 2018) doi:10.15184/aqy.2017.226.

* N. Blackwell, "Making the Lion Gate relief at Mycenae: tools marks and foreign influence." 118 American Journal of Archaeology 451 (July 2014). doi:10.3764/aja.118.3.0451. 

* J. Wright, "The formation of the Mycenaean palace. In Ancient Greece: From the Mycenaean Palaces to the Age of Homer", eds. S. Deger-Jalkotzy and I. Lemos, 3 Edinburgh Leventis Studies 7-52, Edinburgh University Press (2006).

Tuesday, May 1, 2018

Earth-Like Exoplanet Identified


The TRAPPIST-1 red dwarf star compared to the Sun (via Wikipedia)

One of the most Earth-like exoplanets yet discovered has been identified, but it is a bit of a hike to visit at 39.6 light years from Earth.
The TRAPPIST-1 system provides an exquisite laboratory for understanding exoplanetary atmospheres and interiors. Their mutual gravitational interactions leads to transit timing variations, from which Grimm et al. (2018) recently measured the planetary masses with precisions ranging from 5% to 12%. Using these masses and the <5% radius measurements on each planet, we apply the method described in Suissa et al. (2018) to infer the minimum and maximum CRF (core radius fraction) of each planet. Further, we modify the maximum limit to account for the fact that a light volatile envelope is excluded for planets b through f. Only planet e is found to have a significant probability of having a non-zero minimum CRF, with a 0.7% false-alarm probability it has no core. Our method further allows us to measure the CRF of planet e to be greater than (49 +/- 7)% but less than (72 +/- 2)%, which is compatible with that of the Earth. TRAPPIST-1e therefore possess a large iron core similar to the Earth, in addition to being Earth-sized and located in the temperature zone.
Gabrielle Suissa, David Kipping, "TRAPPIST-1e Has a Large Iron Core" (April 26, 2018).

Planet e has a surface gravity of 0.93 times that of Earth, a radius 0.91 times that of Earth, a mean surface temperature of −16.69 ± 6.30 °F, and a six day orbital period. The red dwarf star TRAPIST-1 that it orbits is much less potent than our Sun and would be somewhat more dim than our Sun. It could have water. We don't know if it has an atmosphere.

It is tidally locked, however, which means a light side always faces the star and a dark side is always pointed away from it. This would make it warmer on the light side, but colder on the dark side, potentially making the light side a quite comfortable temperature for humans (perhaps ca. 50 °F).

Monday, April 30, 2018

Descendants Of Inca Royalty Walk Among Us

Studies of modern populations have revealed common Y-DNA origins (and diverse mtDNA origins) among the descendants of Inca royal families.

This is reminiscent of the Genghis Khan genes found in places once ruled by the Mongol Empire (whose fall was reasonably close in time to that of the Inca Empire on historical genetics time scales) and of the genetic traces of the Aaronic priesthood in the Jewish diaspora (which is about four or five times as remote in history).

The Bell Beaker People Were Genetically Diverse

Bell Beaker blogger's commentary on an analysis of many of the oldest Bell Beaker ancient DNA samples from various locations illustrates nicely that the Bell Beaker folk were very genetically diverse. This commentary also does a fairly decent job of contextualizing the samples in time and space, something that professionals in the ancient DNA field and amateurs alike, often fail to do entirely.

Evidence Continues To Support Multiple Rice Domestications

The number of times that rice was domesticated in Eurasia has been a long standing question, but once again, this time in an article published in Nature based upon genetic analysis, the answer is more than once.
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.
From the Introduction:
For over 2,000 years, two major types of O. sativaO. sativa Xian group (here referred to as Xian/Indica (XI) and also known as Hsien or Indica) and O. sativa Geng Group (here referred to as Geng/Japonica (GJ) and also known as Keng or Japonica)
have historically been recognized. Varied degrees of post-reproductive barriers exist between XI and GJ rice accessions; this differentiation between XI and GJ rice types and the presence of different varietal groups are well-documented at isozyme and DNA levels. Two other distinct groups have also been recognized using molecular markers; one of these encompasses the Aus, Boro and Rayada ecotypes from Bangladesh and India (which we term the circum-Aus group (cA)) and the other comprises the famous Basmati and Sadri aromatic varieties (which we term the circum-Basmati group (cB)).
From the Discussion:
3K-RG population structure analyses based on SNPs and SVs were consistent with the five major groups that were previously known, additional subpopulations in the XI and GJ groups were identified and were suggestive of nine subpopulations that are correlated with geographic origin. Large numbers of SNPs, genes and gene families, and SVs were found to be unique to or predominant in single subpopulations. Varying patterns of diversity reduction across different rice subpopulations were observed in and around about 1,000 well-characterized genes. A closer look at patterns of haplotype sharing at domestication genes suggests that not all ‘domestication’ alleles came to XI from GJ. Taken together, our results—combined with archaeological evidence of XI cultivation for >9,000 years in both India and China.
I would include a figure or two from the paper, but none of them were all that compelling in explaining the paper's finding, and honestly the discussion was not particularly articulate either. I would have liked one superimposed on a map comparing the results geographically, or on images of the various types of rice or rice plants discussed. There was also no effort made to link the various domestication events to historical times or places despite the fact that the paper contains the data necessary to do so with a modicum of interdisciplinary effort.

Carl Friedrich Gauss

Today's Google doodle is of Johann Carl Friedrich Gauß a.k.a. Carl Friedrich Gauss on the 241st anniversary of his birth, who is best known for his contributions to mathematics and physics. 

He lived from 1777 to 1855, yet he is still a "household name". His name is the source of the term "Gaussian" to refer to a "normal" distribution in statistics; he was the first to prove the fundamental theorem of algebra; his gravitational constant, k, which is the positive square root of Newton's constant G, was still in use as an official physical constant until 2012 at very nearly the value he determined for it; and his calculations were used to rediscover dwarf planet Ceres. 
The year 1796 [when he was 19 years old] was most productive for both Gauss and number theory. He discovered a construction of the heptadecagon on 30 March. He further advanced modular arithmetic, greatly simplifying manipulations in number theory. On 8 April he became the first to prove the quadratic reciprocity law. This remarkably general law allows mathematicians to determine the solvability of any quadratic equation in modular arithmetic. The prime number theorem, conjectured on 31 May, gives a good understanding of how the prime numbers are distributed among the integers. 
Gauss also discovered that every positive integer is representable as a sum of at most three triangular numbers on 10 July and then jotted down in his diary the note: "ΕΥΡΗΚΑ! num = Δ + Δ' + Δ". On 1 October he published a result on the number of solutions of polynomials with coefficients in finite fields, which 150 years later led to the Weil conjectures.
He was a monarchist and a faithful Lutheran who never lived to see Germany as a unified country. He spent most of his life as an royal astronomer.

His first wife and love of his life life died in connection with the birth of their third child who died as an infant. Shortly thereafter, he married his late wife's best friend and they had three more children over the next twenty years after which she died, but he spent his entire life after the death of his first wife and his infant child in mourning.

He was one of the great mathematical geniuses of all time, but deliberately concealed from the world the methods by which he reached his final crystalized conclusions and declined to publish a large share of his findings and discoveries which he felt were inferior to his greatest accomplishments. He had few students, but was a mentor to Bernhard Riemann, whose non-Euclidian geometry was pivotal to the formulation of General Relativity, and a correspondent of Bessel (after whom "Bessel functions" are named) for whom he secured an honorary degree.

Sunday, April 29, 2018

Mass Child Sacrifice In Peru

Less than a century before Columbus arrived in the Americas, a community near modern Trujuilo, Peru sacrificed 140 children aged five to fourteen (a majority were between eight and twelve years old) who had their hearts ripped out and were buried facing the West, 200 lamas with their hearts ripped out and buried facing the East, a man, and two women, who had "blunt force trauma to the head" and were not buried.

Child sacrifices weren't uncommon in Meso-American culture, but their significance remains unclear and no other site has so many children sacrificed at once. Explanations that might help shed light on other child sacrifices, like terminally ill children, make no sense in this context.

National Geographic notes that:
While incidents of human sacrifice among the Aztec, Maya, and Inca have been recorded in colonial-era Spanish chronicles and documented in modern scientific excavations, the discovery of a large-scale child sacrifice event in the little-known pre-Columbian Chimú civilization is unprecedented in the Americas—if not in the entire world. . . . The sacrifice site, formally known as Huanchaquito-Las Llamas, is located on a low bluff just a thousand feet from the sea. . . . Less than half a mile to the east of the site is the UNESCO World Heritage site of Chan Chan, the ancient Chimú administrative center, and beyond its walls, the modern provincial capital of Trujillo. 
At its peak, the Chimú Empire controlled a 600-mile-long territory along the Pacific coast and interior valleys from the modern Peru-Ecuador border to Lima. . . . Only the Inca commanded a larger empire than the Chimú in pre-Columbian South America, and superior Inca forces put an end to the Chimú Empire around A.D. 1475. . . . rope and textiles found in the burials are radiocarbon dated to between 1400 and 1450. . . . 
"When people hear about what happened and the scale of it, the first thing they always ask is why." 
The layer of mud found during excavations may provide a clue, say the researchers, who suggest it was the result of severe rain and flooding on the generally arid coastline, and probably associated with a climate event related to El-Niño.

Elevated sea temperatures characteristic of El Niño would have disrupted marine fisheries in the area, while coastal flooding could have overwhelmed the Chimú's extensive infrastructure of agricultural canals. 
The Chimú succumbed to the Inca only decades after the sacrifices at Las Llamas.
The story has echoes of the Biblical story of King Herod's "slaughter of the innocents", which purportedly look place about 1400 years earlier, albeit with the New World event occuring on a larger scale and in a very different context.

Thursday, April 26, 2018

Progress In Determining The Standard Model Neutrino Parameters

In the Standard Model, there are seven experimentally determined constants pertaining to neutrinos - the three neutrino masses and the four parameters of the PMNS matrix that governs neutrino oscillations. Progress has been made recently in determining some of those parameters:
We present an up-to-date global analysis of data coming from neutrino oscillation and non-oscillation experiments, as available in April 2018, within the standard framework including three massive and mixed neutrinos. We discuss in detail the status of the three-neutrino (3nu) mass-mixing parameters, both known and unknown. Concerning the latter, we find that: 
normal ordering (NO) is favored over inverted ordering (IO) at 3sigma level; 
the Dirac CP phase is constrained within ~15% (~9%) uncertainty in NO (IO) around nearly-maximal CP-violating values; 
the octant of the largest mixing angle and the absolute neutrino masses remain undetermined. 
We briefly comment on other unknowns related to theoretical and experimental uncertainties (within 3nu) or possible new states and interactions (beyond 3nu).
F. Capozzi, E. Lisi, A. Marrone, A. Palazzo "Current unknowns in the three neutrino framework" (April 25, 2018).

In addition, the differences between the masses of the three neutrino masses are all known to reasonable accuracy, and that combined with the lower bound that none of the neutrino masses can be less than zero, and the upper bounds provided by cosmic background radiation experiments, actually places moderately strong limitations on each of the possible absolute neutrino masses, although all are known only to order of magnitude precision.

Saturday, April 21, 2018

The High Steppe

Drugs are not new to the human experience.
[T]he Yamnaya people, who swept out of Central Asia about 5000 years ago and left their genes in most living Europeans and South Asians, appear to have carried cannabis to Europe and the Middle East. In 2016, a team from the German Archaeological Institute and the Free University, both in Berlin, found residues and botanical remains of the plant, which originates in East and Central Asia, at Yamnaya sites across Eurasia. It's difficult to know whether the Yamnaya used cannabis simply to make hemp for rope or also smoked or ingested it. But some ancient people did inhale: Digs in the Caucasus have uncovered braziers containing seeds and charred remains of cannabis dating to about 3000 B.C.E.
From here.

Wednesday, April 18, 2018

Progress Made On 68 Year Old Math Problem

How many colours are needed to colour the plane so that no two points at distance exactly 1 from each other are the same colour? 
This quantity, termed the chromatic number of the plane or CNP, was first discussed (though not in print) by Nelson in 1950 (see [Soi]). Since that year it has been known that at least four and at most seven colours are needed. 
The lower bound was also noted by Nelson (see [Soi]) and arises because there exist 4-chromatic finite graphs that can be drawn in the plane with each edge being a straight line of unit length, the smallest of which is the 7-vertex Moser spindle [MM] (see Figure 7, left panel). 
The upper bound arises because, as first observed by Isbell also in 1950 (see [Soi]), congruent regular hexagons tiling the plane can be assigned seven colours in a pattern that separates all same-coloured pairs of tiles by more than their diameter. 
The question of the chromatic number of the plane is termed the Hadwiger-Nelson problem, because of the contributions of Nelson just mentioned and because the 7-colouring of the hexagonal tiling was first discussed (though in another context) by Hadwiger in 1945 [Had]. The rich history of this problem and related ones is wonderfully documented in [Soi]. Since 1950, no improvement has been made to either bound. 
From here.

The author, a professional scientist and amateur mathematician, proves in the linked pre-print that the lower bound is 5 and not 4.

So, the correct answer is now 5, 6 or 7, although we still don't know which of those three integers is the correct answer.

Saturday, April 14, 2018

Neanderthals And Modern Humans Experienced Hybrid Incompatability

Also know as Haldane's law, heterozygotes for sex determination genes are strongly disfavored as children of cross-species hybrids. And, the evidence is strong that this hybrid incompatibility prevented Neanderthal-human hybrids from being born. This is strong evidence that Neanderthals and modern humans were biologically separate species.

As the author explains in an open access summary:
After years of sequencing the genomes of female Neandertals, researchers have finally got their first good look at the Y chromosome of a male Neandertal—and found that it is unlike that of any other Y in modern humans living today. Even though Neandertals and modern humans interbred several times in the past 100,000 years, the DNA on the Y chromosome from a male Neandertal who lived at El Sidrón, Spain, 49,000 years ago has not been passed onto modern humans, researchers report today in The American Journal of Human Genetics. The finding fits with earlier studies that have found that although living Asians and Europeans have inherited 1% to 3% of their DNA from their ancestors’ interbreeding with Neandertals, they are missing chunks of Neandertal DNA on their Y chromosomes. This has suggested that female modern humans and male Neandertals were not fully compatible and that male Neandertals may have had problems with sperm production. The new study finds a clue to why: The El Sidrón Neandertal had mutations in three immune genes, including one that produces antigens that can elicit an immune response in pregnant women, causing them to reject and miscarry male fetuses with those genes. So even though male Neandertals and female modern humans probably hooked up more than once over the ages, they may have been unable to produce many healthy male babies (such as the reconstruction of this Neandertal boy from fossils from Gibraltar)—and, thus, hastened the extinction of Neandertals.
There are also no Neanderthal mtDNA sequences in modern humans. This is probably because the children of hybrid couples were probably raised in the tribe of the mother. Hybrid children with modern human mothers were raised in modern human tribes and left descendants who are alive today. Hybrid children with Neanderthal mothers were raised in Neanderthal tribes that ultimately went extinct. 

This inferred pattern of matrilocality for hybrid children, despite the fact that Neanderthals were predominantly patrilocal, also favors the possibility that hybrid children were largely a result of rape or brief encounters, rather than than marriage-like couple relationships. There is not a single example archaeologically of a hominin tribe containing both full blooded Neanderthal and full blooded modern human members.

Wednesday, April 11, 2018

Modern Humans At Monte Verde Ca. 18,500 Years Ago?

Two and a half years ago, a paper that I had missed announced strong evidence of a human presence in Monte Verde (in South America) about 18,500 years ago. This is about 4,000 years older than the next oldest reliably dated evidence (from the same site).

Less significantly, evidence of wild potato use in Utah (which was converted into flour) from 10,900 years ago.

Tuesday, April 10, 2018

Koreans v. Japanese v. Chinese Genetic Ancestry

A new paper purports to be able to distinguish almost perfectly between Koreans, the Japanese, and Chinese individuals based upon autosomal genetics. This is something that consumer genetic services such as 23andMe struggle with right now.

For example, 23andMe claims that my son has more Japanese ancestry than Korean ancestry, when, in fact, he probably has no recent Japanese ancestry and has entirely North Korean ancestry on his mother's side (something upon which we have very solid genealogical support from living memory back to his great-great grandparents because his last great-grandparent died just a few years ago at the age of 98).

In the case of 23andMe, this is probably because ancestry in Japanese people from Yayoi people (including mounted warriors) who invaded Japan from Korea ca. 1000 BCE is being classified as Japanese in origin, rather than Korean, despite the fact that these genetic component originated in Korea, because there are more Japanese individuals in their samples than there are Koreans. 

The paper also controversially suggests that these three populations have a common origin at about 1200 BCE (in the Shang Dynasty of China). 

Indeed, we are pretty much certain that this is not true in the case of the Japanese who have substantial Jomon ancestry that has a much greater time depth. 

The common origin hypothesis is also contrary to the hypothesis that the non-Jomon genetic component of the Koreans and Japanese has a significant "Altaic" component (also hypothesized linguistically) derived from Manchuria and Mongolia and the vicinity, in addition to substantial Chinese admixture in both Korean and Japanese populations, which is well documented historically at least in the case of the Japanese.

So, this 1200 BCE common origin date may be due to some methodological artifact (i.e. flaw) that might, perhaps, simply be measuring a common origin for the Chinese admixture component in all three populations that is significant in all of them, since this is around the time that the Chinese component of these nations would have diverged historically.

Both the linguistic and genetic origins of the Yayoi prior to their migration from Korea to Japan are disputed. Wikipedia (from the link above) notes that:
Origin 
There are several hypotheses about the origin of the Yayoi people. 
The most popular one is that they were the people who brought wet rice cultivation to Japan from the Korean peninsula and Jiangnan near the Yangtze River Delta in China.[1] This is supported by archeological researches and bones found in today southeastern China.[2] 
Another is that they are from Primorskaya Oblast or northern part of the Korean peninsula. It is because the human bones of the Doihigahama ruins resemble the ancient human bones of the northern part of the Korean peninsula, and pottery is similar to the "Engraved band sentence pottery", widely used during the Yayoi period, was discovered in the Sini-Gai culture in the southwestern coastal province of Primorskaya Oblast.[3] 
The theory that Yayoi people have multiple origins is suggested and influential.[4][5] 
It is estimated that Yayoi people mainly belonged to [Ed. Y-DNAHaplogroup O-M176 and Haplogroup O-M122 which are typical for East- and Southeast-Asians.[6] 
Language 
The Yayoi may have spoken an Austroasiatic language or Tai-Kadai language, based on the reconstructed Japonic terms *(z/h)ina-Ci 'rice (plant)', *koma-Ci '(hulled) rice', and *pwo 'ear of grain' which Vovin assumes to be agricultural terms of Yayoi origin. Vovin suggests that Japonic was in contact with Austronesian, before the migration from Southern China to Japan, pointing to an ultimate origin of Japonic in southern China.[7][8] Although Vovin (2014)[8]does not consider Japonic to be genetically related to Tai-Kadai, he suggests that Japonic was later in contact with Tai-Kadai, pointing to an ultimate origin of Japonic in southern China with possible genetic relation to Austroasiatic
There is typological evidence that Proto-Japonic may have been a monosyllabic, SVO syntax and isolating language; which are features that the Austroasiatic languages also famously exhibit.[8] 
A 2015 analysis using the Automated Similarity Judgment Program resulted in the Japonic languages being grouped with the Austroasiatic languages. The same analysis also showed a connection to Ainu languages, but this is possibly because of heavy influence from Japonic to Ainu.[9]
Many linguistic scholars, however, think that Japonic and Korean are distant members of the Altaic language family which also includes the Turkish, Mongolian and Manchurian (a.k.a. Tungistic) languages.

Japanese has borrowed heavily in the historic era from the Chinese language, without changing its underlying grammar and structure, and has virtually no linguistic connection to the Ainu language which was related to the language of the Jomon people who were invaded by the Yayoi. 

This lack of linguistic borrowing from the Jomon is the case even though Jomon genetic input into the modern Japanese gene pool was very substantial for a hunter-gatherer population, perhaps because hunter-gatherers who fish, like those in Japan, the Pacific Northwest and the Baltic-Finnish region, seem to have more staying power than terrestrial hunter-gatherers, vis-a-vis farmers and herders.

Rethinking The Survival Of The Flattest

In evolution, there is a tradeoff between genomes that are maximally fit but particularly vulnerable to deleterious mutations, and those that are more capable of ignoring deleterious mutations that are less maximally fit, a type of genome known as a "flat" genome. Hence, the notion "survival of the flattest". 

But, it turns out that the trade off is not a perfect one, so minimizing the load in a genome of deleterious mutations still confers improved fitness, according to a recent pre-print:
Populations exposed to a high mutation rate harbor abundant deleterious genetic variation, leading to depressed mean fitness. This reduction in mean fitness presents an opportunity for selection to restore adaptation through the evolution of mutational robustness. In extreme cases, selection for mutational robustness can lead to "flat" genotypes (with low fitness but high robustness) out-competing "fit" genotypes with high fitness but low robustness-a phenomenon known as "survival of the flattest". 
While this effect was previously explored using the digital evolution system Avida, a complete analysis of the local fitness landscapes of "fit" and "flat" genotypes has been lacking, leading to uncertainty about the genetic basis of the survival of the flattest effect.  
Here, we repeated the survival of the flattest study and analyzed the mutational neighborhoods of fit and flat genotypes. We found that flat genotypes, compared to the fit genotypes, had a reduced likelihood of deleterious mutations as well as an increased likelihood of neutral and, surprisingly, of lethal mutations. This trend holds for mutants one to four substitutions away from the wild-type sequence. We also found that flat genotypes have, on average, no epistasis between mutations, while fit genotypes have, on average, positive epistasis. 
Our results demonstrate that the genetic causes of mutational robustness on complex fitness landscapes are multifaceted. While the traditional idea of the survival of the flattest effect emphasized the evolution of increased neutrality, others have argued for increased mutational sensitivity in response to strong mutational loads. Our results show that both increased neutrality and increased lethality can lead to the evolution of mutational robustness. Furthermore, strong negative epistasis is not required for mutational sensitivity to lead to mutational robustness. Overall, these results suggest that mutational robustness is achieved by minimizing heritable deleterious variation.

A Notable Paper Potentially Falsifying String Theory

There are vast numbers of mathematically possible concrete theories called vacua within the class of theories that make up string theory. This makes finding the needle in the haystack that could match reality difficult. This has been one of the main obstacles to developing a string theory phenomenology that can be tested with experiments.

But, it turns out that all, or almost all, of the vacua are topologically inconsistent with observed reality which has a "de Sitter" topology:
De Sitter space and anti-de Sitter space are named after Willem de Sitter (1872–1934), professor of astronomy at Leiden University and director of the Leiden Observatory. Willem de Sitter and Albert Einstein worked in the 1920s in Leiden closely together on the spacetime structure of our universe. 
In the language of general relativity, de Sitter space is the maximally symmetric vacuum solution of Einstein's field equations with a positive cosmological constant (corresponding to a positive vacuum energy density and negative pressure). When n = 4 (3 space dimensions plus time), it is a cosmological model for the physical universe; see de Sitter universe
De Sitter space was also discovered, independently, and about the same time, by Tullio Levi-Civita.
The class of topologically inconsistent vacua are called the "Swampland" and if all or most String theory vacua are in the Swampland then the task of finding a String theory vacuum consistent with our reality, or ruling out String theory entirely becomes much easier.

Woit notes an important new pre-print on "Swampland" string theory vacua (paragraph breaks  and emphasis in bold added), which suggests that all of the Sting theory vacua are in the Swampland.
I haven’t paid much attention to the Swampland business since then, but noticed last night a new preprint with the title What if string theory has no de Sitter vacua?. The authors summarize their argument:
From this analysis we conclude that string theory has not made much progress on the problem of the cosmological constant during the last 15 years. There is a general agreement that the presence of dark energy should be an important clue to new physics. So far, string theory has not been up to the challenge. Or to be more precise, string theorists have not been up to the challenge. 
The well-motivated introduction of the anthropic principle and the multiverse, was a big relief. The mathematical standards were lowered, and unconstrained model building could set in exploring a wild and free landscape of infinite possibilities. But beyond this suggestive connection between a possible multiverse and the rich mathematical structures of string theory not much solid results have been achieved. 
We reviewed some fraction of the mounting evidence that most, if not all of this landscape, is a swampland and we refer to [14,16,149] for similar lines of thought. We believe it makes more sense to listen to what string theory is trying to tell us, then to try to get out of the theory what one would like to have. In recent years, especially with the program of the Swampland [14, 150–152], there is luckily a growing community that embraces this idea. Perhaps this program really already made its first prediction: no measurable tensor modes in the CMB. 
From what we have seen so far, we believe that the most sensible attitude is to accept there are no dS vacua at all because string theory conspires against dS vacua. 
The suggestion here is basically that effective field theories on a deSitter background are in the Swampland, so can’t be derived from string theory. Since we seem to live in a deSitter space, the obvious conclusion to draw from this is that string theory is falsified: it can’t be the fundamental theory we are looking for. The authors discuss various unconvincing ways to try and avoid this conclusion.
Physicists have been working on String Theory for basically my entire life. It has turned out to be a dead end and a distraction for the most part, although it has revealed some important mathematical insights including some relevant to quantum gravity. It is time to look for alternatives.

For what it is worth, it is also possible that gravity and the cosmological constant observed are not actually topological effects as in General Relativity, but are instead has a mechanism that involves the behavior of gravitons in a spacetime that is itself, fundamentally flat rather than being deSitter or anti-deSitter, even though that graviton behavior is similar to and in most circumstances almost exactly equivalent to, a topologically curved spacetime.