Friday, September 28, 2018

What Should A Deeper Theory Of The Fine Structure Constant Look Like?

Sean Carroll has a nice little musing at his blog that explains (along the same lines I raised concerns at Physics Forums in a post when I saw the latest high profile effort to derive a mathematical formula that produces the Fine Structure Constant a.k.a. alpha a.k.a. the physical constants that governs the strength of electromagnetism) the intuitions of people who are familiar with the Standard Model and electroweak theory about what a formula that can determine the value of the Fine Structure Constant from a deeper theory out to look like in general terms.

Obviously, we don't have the deeper theory yet, so we can't be sure. But, his insights explain why, given the many deep interrelationships between the physical constants of the electroweak theory, the Fine Structure Constant doesn't look like it is a constant that should be capable of being deduced from pure mathematics because it is fundamental in a deeper theory from which these mathematical formulas arise.

A good analogy is the width of a particle that decays (either fundamental or composite) which is roughly speaking the inverse of its mean lifetime. It turns out that in the Standard Model, the width of a particle can always be derived by conceptually determining every possible decay chain for the particle in question, giving those decay chains weights based upon some constants of the Standard Model (like coupling constants and the masses of particles in the decay chains). The width of a particle that can decay in the Standard Model is basically the sum of the width of each of the possible decay chains of the particle.

So, even though every fundamental particle and every composite particle that can decay in the Standard Model (which is basically every particle except the composite proton and the fundamental particle electron in the Standard Model), none of those physical constants are fundamental and none of them would be expected to have a derivation that could be derived directly from a formula involving only pure mathematics.

The general consensus is that the proposed formula is the flawed numerology of a once world class mathematical genius who is now past his prime and making embarrassing mistakes without realizing it. But, on the other hand, as even a formerly great professional mathematician, even these flawed proposals can look pretty spectacular and deep compared to the usual fare in physics numerology circles.

Bread Predates Domesticated Grains

Bread predates the domestication of grains by at least 4000 years in the Near East (it also predates beer, although not by much). Flour made from wild type grains, in turn, is probably significantly older than bread. 

Long Patterns That Fail To Hold

Part of the lore of rigorous mathematics is that there are many relationships and patterns in mathematics that hold true numerically to many, many terms, but eventually fail.

The mathematician in me knows this but has never really seen it. The physicist in me assumes that anything that holds numerically to very high N will almost always hold forever even if you can rigorously prove that this is true.

John Carlos Baez at his Azimuth blog, however, has some doozies of the kinds of patterns that mathematicians lose sleep over and physicists wrongfully assume are universally true in his most recent post.

For example, describes a mathematical rule that holds for all numbers up to roughly1.397 \times 10^{316}, which is a very, very big number, even for physicists and economists. Ultimately, the rule is violated infinitely many times, oscillating between very large intervals where the rule works and very large intervals where the rule is always wrong.

Paternal Age Largely Explains Mutation Rates Across Species Boundaries

Paternal age at time of reproduction accurately predicts mutation rates in a range of species from owls monkeys to humans and beyond.

The theory is simple. Mutations accumulate at a certain rate per year, starting at the age of sexual maturity, and the longer a father lives after sexual maturity but before a father has children, the more time there is for mutations to accumulate in germ line cells. Thus, a species that reproduces on average two years after sexual maturity is going to have fewer mutations than one that reproduces at age ten years after sexual maturity, which in turn will have fewer mutations than one that reproduces at thirty years after sexual maturity.

The study in question uses the mutation rate in owl monkeys to accurately predict the mutation rate in chimpanzees and humans for a given paternal age with only this very simple model.

Thursday, September 27, 2018

Another Problem With String Theory

Sabine Hossenfelder explains a potential phenomenological test of string theory involving information loss from black holes at their horizons via Hawking radiation: "if the string theory calculations were correct then the information should leak out of the black hole."

She notes that a superfluid analog of a black hole tested in an laboratory does not show the properties predicted to exist in string theory for black holes, although admittedly, the margins of error in the experimental black hole analog are large.

The superfluid analog is notable because it is described by the same equations as GR mathematically, even though the quantities in the respective equations refer to different things.

Thursday, September 20, 2018

Ancient DNA Shows That First Anatolian Farmers Were Natives

These result were basically expected. 

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

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

Wednesday, September 19, 2018

Proton Radius Problem Solved?

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

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

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

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

But why?

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

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

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

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

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

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

The Weak Radius Of The Proton

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

BSM Lepton and Lepton Family Number Violations Constrained

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

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

Cross-Sections Of Interaction Of High Energy Neutrinos

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

Invisible Higgs Boson Decays

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

Who Were The Late Archaic Hominins Of China?

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

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

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

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

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

Early Sorghum Domestication In Eastern Sudan In The Four Millennium BCE

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

Were Humans Present In Madagascar In The Early Holocene?

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

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

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

Tuesday, September 18, 2018

Lambda CDM Predicts That There Are Lots Of Ultra-Diffuse Galaxies With Little Dark Matter

A new ΛCDM prediction is unlikely to be well supported by observational evidence.

The toy model theory MOND has predicted since 1983 that ultra-diffuse galaxies have high inferred dark matter proportions except when the external field effect applies.

A new paper proposes that there should be lots of ultra-diffuse galaxies with little dark matter relative to luminous matter without regard to external field effects.
Surveying dark matter deficient galaxies (those with dark matter mass to stellar mass ratio Mdm/Mstar<1) in the Illustris simulation of structure formation in the flat-ΛCDM cosmogony, we find $M_rm star approximately 2 times 10^8, M_sun galaxies that have properties similar to those ascribed by (vanDokkumetal 2018a) to the ultra-diffuse galaxy NGC1052-DF2. The Illustris simulation also contains more luminous dark matter deficient galaxies. Illustris galaxy subhalo 476171 is a particularly interesting outlier, a massive and very compact galaxy with M_rm star approximately 9 times 10^10 M_sun and Mdm/Mstar ≈ 0.1 and a half-stellar-mass radius of ≈ 2 kpc. If the Illustris simulation and the ΛCDM model are accurate, there are a significant number of dark matter deficient galaxies, including massive luminous compact ones. It will be interesting to observationally discover these galaxies, and to also more clearly understand how they formed, as they are likely to provide new insight into and constraints on models of structure formation and the nature of dark matter.

The link regarding the galaxy in question in the abstract of the article quoted above is to a prior post at this blog on the controversy, with several updates and updating comments, related to that galaxy.

So far, the data tends to favor MOND as the overwhelming majority of ultra-diffuse galaxies show a high inferred dark matter to stellar mass ratio. The exceptions are galaxies to which an external field effect applies as predicted by MOND.

ΛCDM, even to the extent that it predicts that there will be dark matter deficient galaxies, is very vague about where those galaxies will be located, something for which MOND provides a prediction.

More Successful MOND Predictions

MOND has done a good job of predicting, a priori, the dynamics of the dwarf galaxies of Andromeda, which is something that lambda CDM doesn't even have a way to predict.

MOND also, a priori, predicted that what naively looked like a satellite galaxy of Andromeda was actually a background galaxy. MOND also has an a priori rule that allows it to determine when a result is likely to be quirky and hard to estimate because the system won't be in equilibrium because the external field effect varies over time due to a highly eccentric orbit around a host galaxy (bringing the galaxy in and out of the external field effect regime leading to tidal disruption).

The Navarro-Frennk-White Model Still Doesn't Fit The Data

In other observational news, another study finds that the analytically predicted NFW distribution of cold dark matter is not the observational reality, which instead, is a better fit to the largely theoretically unjustified pseudo-isothermal halo mass structure in a dark matter particle theory. There is really no good explanation for why the analytically determined NFW profile, that should arise as a simple matter of mathematics with collisionless cold dark matter, usually isn't observed, or for why a pseudo-isothermal halo mass structure is inferred instead.

The article below also contends with the problem of reconciling the similar behavior of spiral galaxies with and without bulges also remains a problem for CDM theories (as does the higher than expected frequency of galaxies without bulges in its galactic matter assembly model). 
Mass models of 100 nearby spiral and irregular galaxies, covering morphological types from Sa to Irr, are computed using Hα rotation curves and Rc-band surface brightness profiles. The kinematics was obtained using a scanning Fabry-Perot interferometer. One of the aims is to compare our results with those from Korsaga et al. (2018), which used mid-infrared (MIR) WISE W1 (3.4 μm) photometric data. For the analysis, the same tools were used for both bands. 
Pseudo-Isothermal (ISO) core and Navarro-Frenk-White (NFW) cuspy models have been used. We test Best Fit Models (BFM), Maximum Disc Models (MDM) and models for which M/L is fixed using the B - V colors. Similarly to what was found in the MIR 3.4 μm band, most of the observed rotation curves are better described by a central core density profile (ISO) than a cuspy one (NFW) when using the optical Rc-band. In both bands, the dispersion in the (M/L) values is smaller for the fixed M/L fits. As for the W1 photometry, the derived DM halos' parameters depend on the morphological types. We find similar relations than those in the literature, only when we compare our results for the bulge-poor sub-sample because most of previous results were mainly based on late-type spirals. Because the dispersion in the model parameters is smaller and because stellar masses are better defined in that band, MIR photometry should be preferred, when possible, to the optical bands. It is shown that for high-z galaxies, sensible results can still be obtained without full profile decomposition.

Yet another article also alludes to these issues in the model formation context:
In this paper we develop a new semianalytical approach to quantifying the density profile of outer dark matter halos, motivated by the remarkable universality those profiles, for a wide range of dynamical parameters of the inner halos. We show that our minimalist model is robust under significant variations of its input parameters around the currently known values and we identify the turnaround radius as the most important scale of the problem. Based on that observation, we argue that the turnaround radius accurately represents the transition to the external density profile, and we provide a universal test based on geometrical characteristics of the outer profile as a proposal for measuring the turnaround radius of structures.

The introduction to this paper does a good job, often omitted in other papers, of laying out the true complexities and uncertainties involved in inferring dark matter halo mass distributions from observable luminous matter, so I will quote it at length (bold emphasis, underlining, and bullet point before questions added editorially for reading ease in blog format):
One of many widely discussed problems in cosmology is the problem of the definition of a structure. In general, due to hardships posed by the non-linearity of Einstein’s equations, the lack of a globally accurate description of the so-called ”dark matter”, but most importantly by the complexity of many-body problems in general relativity, defining a structure has been non-trivial. Many notions regarding a structure are ill-defined. Even when the structure is in equilibrium, there is no concrete way of determining the boundaries of a structure (see [9] and [10] for a detailed discussion). Consequently, measuring the total mass of a cosmological structure is also a poorly defined problem. In this context, other measurable quantities such as the density profile and the average radial velocity profile become important.

More specifically, the mass of a structure is a difficult quantity to define experimentally. In principle, it is easy to imagine that the mass of a structure corresponds to the mass of the maximum number of objects we can include in the structure that form a gravitationally bound system. As simple as this definition may seem, the lack of accurate information on the velocities and relative positions of the constituents of the structure demonstrates the difficulty of implementing the definition directly. Even theoretical calculations pose difficulties, due to the innate complexity structures exhibit as many body systems. The result of those difficulties is that the prevailing physical scales used to describe structures are not always suitable for all kinds of phenomena. The necessity of accurate description of structure formation has therefore led to various proposals of scales which depend on the velocity or density profiles, which can substitute ambiguous concepts used up to present day.

The first exact estimate for the density profile of a structure came from the pioneering work of Gunn & Gott (1972), who utilized the spherical top hat model in order to approach in a simple way a highly non-linear problem. Since then and in the following few decades the field has known significant advancements. Earlier work in these steps was primarily focused on the density profiles of the innermost regions of structures as in [11]. Progress in calculating the density profile of the outskirts of structures has been made only fairly recently. Furthermore, in the absence of observations for outer regions of halos, most effort was put in interpreting results for the innermost regions. However, these regions nowadays can be effectively probed by virtue of several methods (see [12]),  thus necessitating the theoretical interpretation of existing observations.

Numerical simulations, such as the ones presented by Diemer & Kravtsov (2014), proved that the outskirts of simulated halos exhibit strong deviation from the commonly used density profiles of inner regions (NFW, Einasto), which manifests itself through a steep drop in the power law locally describing the density profile over a narrow interval of radii. Additionally, their simulations revealed that the radial density profile tends to evolve almost self-similarly in time. Although it has been confirmed that there are several universal scalings related to external profiles, their physical significance and role are yet to be specified, since such studies along with semianalytical treatments cannot reveal whether this apparent universality is a well-established consequence of some physical aspect of the system. Characterization of halos has not been an easy task to tackle, there is no rule of thumb for picking out the best criteria for detecting density peaks, and inevitably results, especially concerning halo counting purposes, differ from author to author, depending on their particular choice of definition scale. For a discussion and comparison between several halo simulation algorithms see [13].

Another issue is that the most important and actual physical changes in the behavior of the matter density profile of structure happen at lengths which are not described well by the standard scales used for the analysis of structure formation. Analysis of the spherical top hat model gives a concrete result for the radius of virialization of an idealized structure and predicts no other significant length scale for its density profile. More detailed cosmological simulations however contradict this result, proving that structures are far more complex, both inside and outside the virial radius. Important characteristics of the structures, such as peaks and second order critical points of the density profile, tend to appear around the virial radius, but also at greater distances, see [5] and [14]. Recent results [16] have shown that a reasonably robust choice of scale that distinguishes between regions where accretion is happening is the splashback radius, and that this transition manifests itself as a steep drop in the logarithmic derivative of the density profile.

In the light of these considerations, several related questions arise: 
* Does the category of spherical collapse models suffice for the description of radial density profiles of structures at large radii, where effects of nonsphericities are minimal? 
* If that is true, could it possibly succumb to analytical methods and produce a prediction for the density profile of structures outside their virial radius that agrees with simulations? 
* What physical mechanisms dictate the special characteristics of the external matter profiles? 
* Is there any chance outer halo profiles are universal for all types of structures? 
* Finally, at a more practical level, is there an easy and intuitive way for an experimenter to determine useful physical lengths of a structure, assuming that he is able to measure the outer radial density profile of a structure?

In this paper we calculate analytically the post virialization equilibrium density profile of a spherically evolving structure, which is assumed static. This analytical treatment is aimed at being reasonably accurate a considerable distance away from the center of collapse. We intend to draw conclusions from this treatment about the universality of the external matter profiles and determine explicitly on which parameters of the collapse they depend on. Also, we show that the scale that signifies the transition to the outer halo is no other but the well known turnaround radius of the overdensity. Finally, we propose a fitting function in the range of distances we are interested in, along with the best fit parameters of our approximate approach.
Another Dark Matter Candidate Ruled Out

Strange dibaryons have never been a very strong contender as a dark matter candidate, even though a tiny number of these particles may exist. This paper puts a nail in that coffin.
The hypothetical SU(3) flavor-singlet dibaryon state S with strangeness −2 has been discussed as a dark-matter candidate capable of explaining the curious 5-to-1 ratio of the mass density of dark matter to that of baryons. We study the early-universe production of dibaryons and find that irrespective of the hadron abundances produced by the QCD quark/hadron transition, rapid particle reactions thermalized the S abundance, and it tracked equilibrium until it "froze out" at a tiny value. For the plausible range of dibaryon masses (1860 - 1890 MeV) and generous assumptions about its interaction cross sections, S's account for at most 10^−11 of the baryon number, and thus cannot be the dark matter. Although it is not the dark matter, if the S exists it might be an interesting relic.
Edward W. Kolb, Michael S. Turner, "Dibaryons cannot be the dark matter" (September 17, 2018).

Neutron star behavior also disfavors the existence of these kinds of dibaryons in Nature.
We study the effect of a dibaryon, S, in the mass range 1860 MeV < m_S < 2054 MeV, which is heavy enough not to disturb the stability of nuclei and light enough to possibly be cosmologically metastable. Such a deeply bound state can act as a baryon sink in regions of high baryon density and temperature. We find that the ambient conditions encountered inside a newly born neutron star are likely to sustain a sufficient population of hyperons to ensure that a population of S dibaryons can equilibrate in less than a few seconds. This would be catastrophic for the stability of neutron stars and the observation of neutrino emission from the proto-neutron star of Supernova 1987A over ~ O(10)s. A deeply bound dibaryon is therefore incompatible with the observed supernova explosion, unless the cross section for S production is severely suppressed.
Samuel D. McDermott, Sanjay Reddy, Srimoyee Sen, "A Deeply Bound Dibaryon is Incompatible with Neutron Stars and Supernovae" (September 18, 2018).

A Review Of Lepton Universality In B Meson Decays

A new review of apparent lepton universality violations in b quark decays, which is absent in all other lepton decays, quantifies the evidence in favor of this phenomena and notes some possible explanations. The following excerpt is from the conclusion of the paper.
In recent years, several observations of tree- and loop-level b-hadron decays hint at a possible violation of LU [Lepton Universality]. This article has discussed the relevant measurements as well as their potential implications. 
LU plays a peculiar role in the SM [Standard Model] of particle physics, as the same interactions and couplings characterise all three fermion generations. As a consequence, a violation of LU would be an unambiguous sign of the existence of physics beyond the SM. This property has been tested throughout the years by using a variety of different probes: the production and the decay of electroweak gauge bosons, the decay of quarkonia, the leptonic and semileptonic decays of mesons with light quarks (including the c quark), however, no significant signs of deviations from the SM predictions have been observed. 
A possible violation of LU is hinted at in two different classes of semileptonic b-quark decays. The measurements are obtained from experiments at the B-factories (BaBar, Belle and soon Belle-II) as well as at the LHC (LHCb). For these processes the SM predictions can be computed using an effective Hamiltonian approach that separates short and long-distance contributions, and require non-perturbative inputs (e.g. form factors) obtained through diverse theoretical methods. Tensions at the level of 4–5 σ are observed in b→ clν [charm quark, negative charged lepton, corresponding anti-neutrino] decays, which are mediated at tree level through a W± boson in the SM, when the branching ratios of decays with l = τ and l = e, µ are compared. Deviations at the level of 3–4 σ are also present in b→ sll [strange quark, lepton and anti-lepton] decays, which are mediated through a loop in the SM, when comparing the branching ratios for l = e and l = µ.
From Simone Bifani, et al., "Review of Lepton Universality tests in B decays" (September 17, 2018).

One factor that makes this anomaly particularly tricky to explain is that absences of deviations of lepton universality in all other contexts makes it particularly difficult to explain the phenomena that is only observed in b quark decays with some sort of general theory, such as a charge lepton CKM matrix that is almost, but not exactly, the matrix that would produce lepton universality.

Monday, September 17, 2018

Where Does Bamboo Grow?

One reason that we might see fewer stone tools in the archaeological record is that bamboo industries, which don't preserve as well, developed instead. Where does bamboo grow?

Via Marnie.

Friday, September 14, 2018

Pope Stephen VI Was A Very Messed Up Individual

Secular monarchies and republican governments are not the only systems that sometimes put madmen in charge. 

The Roman Catholic Church's non-hereditary monarchy, in which a College of Cardinals serving a role analogous to a self-perpetuating board of directors of an ordinary non-profit has also produced some dubious leaders, with the late 9th century CE being a particularly troubled time for the papacy. Consider for example, Pope Stephen VI.

Pope Stephen VI was the Pope from May 22, 896 CE to August 897.
Stephen is chiefly remembered in connection with his conduct towards the remains of Pope Formosus, his penultimate predecessor. The rotting corpse of Formosus was exhumed and put on trial, before an unwilling synod of the Roman clergy, in the so-called Cadaver Synod (or Synodus Horrenda) in January 897. Pressure from the Spoleto contingent and Stephen's fury with his predecessor probably precipitated this extraordinary event. 
With the corpse propped up on a throne, a deacon was appointed to answer for the deceased pontiff. During the trial, Formosus's corpse was condemned for performing the functions of a bishop when he had been deposed and for receiving the pontificate while he was the bishop of Porto, among other revived charges that had been levelled against him in the strife during the pontificate of John VIII. The corpse was found guilty, stripped of its sacred vestments, deprived of three fingers of its right hand (the blessing fingers), clad in the garb of a layman, and quickly buried; it was then re-exhumed and thrown in the Tiber. All ordinations performed by Formosus were annulled. 
The trial excited a tumult. Though the instigators of the deed may actually have been Formosus' enemies of the House of Spoleto (notably Guy IV of Spoleto), who had recovered their authority in Rome at the beginning of 897 by renouncing their broader claims in central Italy, the scandal ended in Stephen's imprisonment and his death by strangling that summer.
N.B. Pope Boniface VI, who served as Pope between Stephen VI and Formosus for just fifteen days.
His election came about as a result of riots soon after the death of Pope Formosus. Prior to his reign, he had twice incurred a sentence of deprivation of orders as a subdeacon and as a priest. After a pontificate of fifteen days, he is said by some to have died of the gout, by others to have been forcibly ejected to make way for Stephen VI, the candidate of the Spoletan party. 
At a synod in Rome held by John IX in 898, his election was pronounced null and void.
Given some of the antic of Kim Jong-Un, the current supreme leader of North Korea, however,  we should not kid ourselves into thinking that society and human decency has advanced all that far in the meantime. For example:
O Sang-hon (Chosŏn'gŭl: 오상헌; RR: O Sangheon; MR: O Sanghŏn) was a deputy security minister in the Ministry of People's Security in the government of North Korea who was reportedly killed in a political purge in 2014. According to the South Korean newspaper The Chosun Ilbo, O was executed by flamethrower for his role in supporting Kim Jong-un's uncle Jang Song-taek.

Thursday, September 13, 2018

Non-European Admixture in Modern South African Whites

Razib Khan notes that in his small sample (N=12) the typical modern South African white person has about 6.5% non-European ancestry. This is consistent with other data which also suggests that the non-European contribution was predominantly female (i.e. European men had children with non-European women).
Traditional genealogical estimates suggested in the range of 5-7.5% non-European ancestry in Afrikaners, and one study of 185 individuals showed 18% non-European mtDNA.

As the chart he generated from the raw data above shows, most white South Africans have multiple kinds of non-European admixture, and many have several kinds of non-European admixture. He makes comparisons (based upon historical accounts) with South Asians (represented by Telegu), Southeast Asian (represented by Malay), relict Paleo-African hunter-gatherer represented by Khoisan ("San") and Hadza, and West African/Bantu ancestry (represented by "EsanNigeria"). Consistent with the historical accounts, he uses Dutch ancestry as the proxy for European ancestry of white South Africans.

He concludes (very plausibly) based upon this data that:
[T]he non-European ancestry of Afrikaners is uncannily similar to the non-European ancestry of the Cape Coloureds. That to me leads us to the conclusion that in the early European settler community a fair number of mixed-race women married in. Those mixed-race women who married mixed-race men helped found the Cape Coloureds.
The genetic data suggest a time of admixture that is probably well before the mid-1800s, as greater time depth is necessary to develop multiple kinds of admixture at small percentages each. This fits with the observation that the Dutch were the primary colonial power in South Africa from 1652 to 1806, and that admixture tends to be most common in the earlier days of outside settlement when there has been less mass migration of women from a colonist's homeland than there has been mass migration of colonist men.

These results largely confirm historical accounts and effectively provide a test of the soundness of the methodologies used, which often in other contexts where historical accounts are unavailable or unreliable.

The also confirms that South African whites, also known as Afrikaners, really do indeed have continuous descent from African born Afrikaner ancestors have European immigrant ancestors who arrived in Southern Africa as far back (or farther back) to their non-European home than almost all North American whites, most Latin Americans with European ancestry, and all whites in Australian and New Zealand with European ancestry.

Indeed, Afrikaners were present in South Africa, for example, before the Miami Indian tribe (which migrated to Southeast Ohio from what is now Wisconsin) arrived in Ohio's Miami River Valley area. (The Miami Indians were then forcibly relocated to Oklahoma in the early 1800s).

Bell Beaker People Probably Brought Cystic Fibrosis To Europe

Bell Beaker blogger has a nice post examining the evidence supporting the case that Cystic Fibrosis to Europe.
I'll give you the ultra Cliff's Notes version: 
- Cystic Fibrosis is mostly limited to Caucasians and it clearly peaks in Northwestern Europeans 
- The mutation spread around the time Beakerfolk were marauding through Western Europe 
- Cystic Fibrosis sucks to death if you have two copies 
- But for others, it must have some useful purpose - exposure to heavy metals is a strong possibility 
- The ancestral carriers were from the neighborhood of the Black and Caspian Seas
Note that in the Cliff's Note version above the reference to "Caucasians" is to white people and not the people specifically from the Caucasus mountains region.

Sunday, September 9, 2018

Vitamin D Strikes Again To Explain EDAR

Two of the biggest known evolutionary adaptations found in modern humans (as measured by inferred selection on a derived trait from basal Africans) are lactase persistence (found in Northern Europeans and arising around 5000 years ago in Europe) and EDAR (found in all pre-Columbian Native Americans, about 40% of Asians, and almost no Europeans, with an inferred place of origin possibly near Northern China and probably during the last Ice Age about 20,000 years ago, which reached fixation in Beringia).

One leading hypothesis regarding lactase persistence which allows adults to drink cows milk, is that it addressed Vitamin D deficiencies, especially in pregnant and nursing mothers, thereby greatly reducing infant morality. Vitamin D is useful for many purposes, but one of those is as an immune system enhancer.

A similar hypothesis may explain the EDAR mutation in Asians and New World populations according to new research, in what amounts to two different paths of convergent evolution that accomplished similar adaptive results.
We were trying to understand selection for a mutation in the gene called EDAR – it encodes the ectodysplasin A receptor that plays a role in how tightly cells adhere to each other during the development of hair, teeth, sweat glands and breasts. All of these anatomical structures form via a very similar developmental process that happens while you’re still in your mother’s womb. Slight changes to the developmental mechanism results in the final differences between hair and teeth and sweat and mammary glands. But there is a fundamental similarity that, among other things, includes the activity of EDAR. 
This shared development is especially obvious when things go wrong. For example, 1 in 10,000 newborns have a disorder called ectodermal dysplasia, which causes disruption to the development of their hair, teeth, skin, sweat glands and breasts. 
The V370A mutation that we focused on, the one that experienced strong selection, doesn’t disrupt development of these structures; rather, it augments them. People with V370A have thicker and straighter hair shafts, and their incisors have extra buttressing on the tongue side – a feature biologists call “shoveling.”
. . . 
It’s not easy to live that far north. Sure, it’s cold. But more importantly, at high latitudes, the sun is lower in the sky so sunlight must travel through more atmosphere to reach Earth’s surface. This journey through the atmosphere mostly filters out the Sun’s ultraviolet radiation. Most life forms need sun exposure to be healthy, in large part because UV exposure induces the body to make vitamin D
Lighter skin tones let in more UV and have been selected for multiple times in human history. But once you get to the Arctic, skin depigmentation alone won’t suffice. In order to live with so little UV, people have culturally innovated, eating diets rich in vitamin D, such as oily fish. But nursing infants don’t eat these foods. Babies get their nutrients through their mother’s milk. 
This is where our EDAR gene comes back into the picture. The V370A mutation in mice increases the branching density of the mammary ducts, and very likely does the same exact thing in human breasts. Scientists know that vitamin D deficient conditions induce more ductal branching during the breast development that happens with pregnancy. All of the evidence suggests that the increased ductal branching associated with V370A helped transfer nutrients from mother to infant through breast milk in a population that was extremely vitamin D deficient. 
So the selection wasn’t for thicker hair or shovel-shaped incisors – instead, it was much more likely to have been on mammary ducts. The thicker hair and tooth variation just went along for the ride because they are created by the same basic developmental pathway. Selection on genetic variation in EDAR is probably related to health consequences for nursing infants rather than its effects on hair, teeth or sweat glands.
The process by which the researchers came to this conclusion involved a mix of methodologies and really deserves a read of the whole piece that is linked.

EDAR is also notable from a cultural perspective because the phenotypic traits that it codes for are among the suite of traits frequently used by lay people with limited information as litmus tests for "Asian" descendent and a stereotypical "Asian" appearance. There was a previous post at this blog about EDAR in 2013.

The source paper is:
The frequency of the human-specific EDAR V370A isoform is highly elevated in North and East Asian populations. The gene is known to have several pleiotropic effects, among which are sweat gland density and ductal branching in the mammary gland. The former has led some geneticists to argue that the near-fixation of this allele was caused by selection for modulation of thermoregulatory sweating. We provide an alternative hypothesis, that selection instead acted on the allele’s effect of increasing ductal branching in the mammary gland, thereby amplifying the transfer of critical nutrients to infants via mother’s milk. This is likely to have occurred during the Last Glacial Maximum when a human population was genetically isolated in the high-latitude environment of the Beringia.  

Because of the ubiquitous adaptability of our material culture, some human populations have occupied extreme environments that intensified selection on existing genomic variation. By 32,000 years ago, people were living in Arctic Beringia, and during the Last Glacial Maximum (LGM; 28,000–18,000 y ago), they likely persisted in the Beringian refugium. Such high latitudes provide only very low levels of UV radiation, and can thereby lead to dangerously low levels of biosynthesized vitamin D. The physiological effects of vitamin D deficiency range from reduced dietary absorption of calcium to a compromised immune system and modified adipose tissue function. The ectodysplasin A receptor (EDAR) gene has a range of pleiotropic effects, including sweat gland density, incisor shoveling, and mammary gland ductal branching. The frequency of the human-specific EDAR V370A allele appears to be uniquely elevated in North and East Asian and New World populations due to a bout of positive selection likely to have occurred circa 20,000 y ago. The dental pleiotropic effects of this allele suggest an even higher occurrence among indigenous people in the Western Hemisphere before European colonization. We hypothesize that selection on EDAR V370A occurred in the Beringian refugium because it increases mammary ductal branching, and thereby may amplify the transfer of critical nutrients in vitamin D-deficient conditions to infants via mothers’ milk. This hypothesized selective context for EDAR V370A was likely intertwined with selection on the fatty acid desaturase (FADS) gene cluster because it is known to modulate lipid profiles transmitted to milk from a vitamin D-rich diet high in omega-3 fatty acids. 

Hat tip to DDeden for calling attention to this important article which I did not catch when it came out.

Tuesday, September 4, 2018

Mole Rat Mind Control

From PNAS via The Atlantic “Naked-Mole-Rat Queens Control Their Subjects by Having Them Eat Poop":
And according to a new study from Japan, naked-mole-rat queens use their hormone-rich poop to govern their subordinates. When the subordinates eat the hormone, it turns them into attentive caretakers of the queen’s own pups. It’s mind control, via poop. 
Naked mole rats had interested Kazutaka Mogi, a biologist at Azabu University, because of their unusual social structure. Like ants and bees, but unlike almost all other mammals, naked mole rats live in large colonies where the queen is the only female that reproduces. Her subordinates take care of the pups, and they never make sex hormones of their own or become sexually mature. Mogi and his team had investigated parenting in mice, and they knew that hormones play a key role in triggering parental behaviors in mammals. If the bodies of the subordinate naked mole rats aren’t making any hormones, how do they become such attentive caretakers—to pups that aren’t even their own? 
The team collected fecal pellets from pregnant queens and gave them to a handful of subordinate females, which soon became much more responsive to the cries of pups. Then they repeated the experiment to make sure the hormones were really the key component of the poop. This time, they took fecal pellets from nonpregnant queens and added estradiol—a type of estrogen—to only half of the pellets. Only the naked mole rats that ate the estradiol-supplement poop became more responsive to pup cries. 
Mogi was excited. He had never seen hormones work like this before. Hormones are powerful mediators of behavior, but their effects are normally limited to the body of the animal making them. Here the queen seems to be making hormones to alter the bodies of totally separate animals. Insect colonies have sometimes been called superorganisms for the way thousands of individuals behave as one unit; in this case, hormones seem to be acting on naked-mole-rat colonies as a single superorganism.
This is pretty amazing stuff that I would not have expected in mammals.