Saturday, March 31, 2018

Ancient DNA From Pakistan And The Vicinity

The big South Asian ancient DNA paper is finally out (in pre-print form) after many months of waiting and publication delays (purportedly for political reasons). UPDATE: This is not actually the long awaited Indian DNA paper, although it answers many of the same questions by using different ancient DNA data. END UPDATE.

The big news that we've been awaiting is the twelve ancient DNA samples from a cemetery in Pakistan. The gender, mtDNA, Y-DNA and Y-DNA classification of those samples follows. 

There are also hundreds other ancient DNA samples over a wide range of time from the vicinity included. I will update my analysis and the findings as time permits. The abstract, some key figures and lots of discussion in the comments is available at Eurogenes. Razib does a nice job of dissecting the pre-print.

M R30b1 L1a South Asian Private
M .. L1a South Asian Private
M W3a1b R1b1a1a2a1a1c2b2b1a2 R-M269/U106/Z381/S499
M W3a1b R2a South Asian Private
M U2e1'2'3 C1b1a1a1 SW Asia, Central Asia and South Asia
M M4 L1a South Asian Private
M M5a Q1b2 SW Asia
M U7a .. Female
F T2g1 .. Female
F U2c1 .. Female
F U3b1a1 .. Female
M T2g1 L1a South Asian Private

It strongly appears that Y-DNA L1a, R2a and Q1b2 al derive from Iranian farmers.

UPDATE April 4, 2018: I left this comment at Razib's blog:

“Also, the polytomy at the base of the eastern Eurasian human family tree, where all the major lineages diverge rapidly from each other, makes me wonder about gene flow vs. admixture. It seems possible that the polytomy may mask a phylogenetic tree topology which had gradually bifurcating nodes, if periodically a single daughter population replaced all its sister lineages in a local geographic zone. Much of history in human meta-populations may be characterized by isolation-by-distance and gene flow, erased by the extinction of most lineages and expansion of a favored lineage.”

This is a really interesting observation, and both possibilities, naively, seem pretty plausible.

It is almost unthinkable that there was complete genetic continuity and stasis in South Asia from prior to 65,000 BP to 6000 BP. All of the examples we have point to very sustained stasis as very rare, even though turnover may have happened less frequently among hunter-gatherers than among Holocene people at the continental level. The late modern history of hunter-gatherer tribes of Native Americans, for example, suggests that moderately long distance folk wanderings and exterminations of whole tribes were relatively common even on time scales of 1000 years or so.

There were probably at least two significant waves of migration and expansion after the one that gave rise to the Papuans in mainland Asia that greatly interrupted HG genetics there.

Y-DNA D people were probably a mid Upper Paleolithic Northern route arrival in Asia (although pre-LGM given Y-DNA D in the Andamanese) and were possibly male dominated (given that the Onge autosomally are close to AASI), that migrated to South Asia from Tibet to the South ultimately reaching Burma and the Andamans (since phylogeny-wise the Y-DNA D of India and the Andamans is closer to Siberian and Tibetan Y-DNA D than to Japanese Y-DNA D which splits at a very basal point from other Y-DNA D). Other Y-DNA D people take the Northern route to become the founding Jomon people of Japan. Most Y-DNA D people of Northern Asia in between are wiped out in the LGM.

Y-DNA C is remarkably rare and quite low if phylogenetic diversity in South Asia. This could simply mean that the coastal route theory for Y-DNA C is wrong, and that instead it took a clockwise northern route to reach East Asia, mainland SE Asia and Island SE Asia, and the lack of phylogenetic diversity of Y-DNA C in South Asia tends to support that reading of the data. But, another possibility, given the proportionately high level of C-M130* in South Asia relative to other Y-DNA C haplotypes is that Y-DNA C differentiated from Y-DNA CF in India, with lots of Y-DNA C people migrating east, but a few remaining, and that Y-DNA F people (including sister Y-DNA clade Y-DNA H people) subsequently wiped out most of the original Y-DNA C right population of South Asia, and that a lot of Y-DNA C people in India today are associated with a Y-DNA C1b1 back migration later in the Upper Paleolithic. The fact that autosomal ASI ancestry in India is pretty much proportional to Y-DNA C proportions in India, even though the proportions are low, also points to the antiquity of Y-DNA C in India, followed by later events.

In particular, the Y-DNA C people in India were probably marginalized by the expansions of Y-DNA F*, F1, F3 and H in India in the pre-Neolithic period, with other clades of F and daughter clades derived from F expanding into both West Eurasia and East Eurasia where the expanding clades became dominant. It is hard to know what gave the Y-DNA F/H people a decisive advantage over the Y-DNA C people in India and elsewhere, although forced to supply my best guess, I might suspect dog domestication or perhaps mastering how to turn wild grains into flour (flour predates the Neolithic revolution by at least ten or twenty thousand years).

It is also worth noting that ancient DNA suggests that in parallel with these developments in India, that Y-DNA C was once much more common than it is today in Europe, which definitely reflects Neolithic and Steppe driven replacement of remaining European HGs with Y-DNA C, but which may also reflect Mesolithic era replacement.

Similarly, in East Asia and SE Asia, Y-DNA O which is also a remote descendant of Y-DNA F, also sweeps those regions even before the Neolithic revolution.

If Indian nationalists want to discuss their basal and formative influence on the rest of the world, they would be well advised to de-emphasize the Bronze Age and to instead focus on how, on one hand, Y-DNA F is the dominant ancestor of modern Eurasian Y-DNA clades and that it probably originated in India (or at least had its first major expansion there), and how, on the the other hand, in the Iron Age, Buddhism, which also has its origins in India, came to be a profound and arguably dominant religious influence in East Asia.

Of course, the problem is that Indian Nationalism today is Hindu rather than Buddhist, which is a religious movement that India didn’t heavily export and which outside Bali didn’t have much staying power where it was exported, and which isn’t entirely home grown, even though much of it has local roots.

Similarly, the expansion of Y-DNA F people to become the predominant people of Eurasia (especially West Eurasia) is so remote and thinly attested archaeologically that it is hard to identify with those ancient hunter-gathers.

Friday, March 30, 2018

A Galaxy Without Dark Matter?

The Hubble Space telescope has observed an ultra diffuse galaxy which does not seem to have any dark matter or modified gravity effects. The abstract of the preprint states:
Studies of galaxy surveys in the context of the cold dark matter paradigm have shown that the mass of the dark matter halo and the total stellar mass are coupled through a function that varies smoothly with mass. Their average ratio M_{halo}/M_{stars} has a minimum of about 30 for galaxies with stellar masses near that of the Milky Way (approximately 5x10^{10} solar masses) and increases both towards lower masses and towards higher masses. The scatter in this relation is not well known; it is generally thought to be less than a factor of two for massive galaxies but much larger for dwarf galaxies. 
Here we report the radial velocities of ten luminous globular-cluster-like objects in the ultra-diffuse galaxy NGC1052-DF2, which has a stellar mass of approximately 2x10^8 solar masses. We infer that its velocity dispersion is less than 10.5 kilometers per second with 90 per cent confidence, and we determine from this that its total mass within a radius of 7.6 kiloparsecs is less than 3.4x10^8 solar masses. 
This implies that the ratio M_{halo}/M_{stars} is of order unity (and consistent with zero), a factor of at least 400 lower than expected. NGC1052-DF2 demonstrates that dark matter is not always coupled with baryonic matter on galactic scales.
Pieter van Dokkum, et al., "A galaxy lacking dark matter",  arXiv (March 27, 2018). A follow up paper by the same authors is here. It's abstract is as follows:
We recently found an ultra diffuse galaxy (UDG) with a half-light radius of R_e = 2.2 kpc and little or no dark matter. The total mass of NGC1052-DF2 was measured from the radial velocities of bright compact objects that are associated with the galaxy. Here we analyze these objects using a combination of HST imaging and Keck spectroscopy. Their average size is <r_h> = 6.2+-0.5 pc and their average ellipticity is <{\epsilon}> = 0.18+-0.02. From a stacked Keck spectrum we derive an age >9 Gyr and a metallicity of [Fe/H] = -1.35+-0.12. Their properties are similar to {\omega} Centauri, the brightest and largest globular cluster in the Milky Way, and our results demonstrate that the luminosity function of metal-poor globular clusters is not universal. The fraction of the total stellar mass that is in the globular cluster system is similar to that in other UDGs, and consistent with "failed galaxy" scenarios where star formation terminated shortly after the clusters were formed. However, the galaxy is a factor of ~1000 removed from the relation between globular cluster mass and total galaxy mass that has been found for other galaxies, including other UDGs. We infer that a dark matter halo is not a prerequisite for the formation of metal-poor globular cluster-like objects in high redshift galaxies.

This is an extreme outlier of a result, which, if true, poses serious issues for modified gravity theories and for theories about how dark matter usually ends up tightly correlated with baryonic matter if it exists.

There are several possibilities:

1. It could be the product of MOND with an external field effect. The paper notes that the MOND prediction is off by about a factor of two (which beats the factor of 400 problem with the expectation from dark matter theory noted in the abstract handily), but the calculation, at first glance, didn't appear to have considered the external field effect, which should tweak the result in the right direction. If MOND with an external field effect makes an accurate prediction it is a huge vindication of that particular theory (which obviously still have to be generalized to the relativistic case) and very close cousins of it. But, if the reality is contrary to the MOND with external field effect prediction, it could suggest that, at a minimum, MOND is not the right way to modify gravity. Specifically, the paper states with respect to what MOND would predict that:
For a MOND acceleration scale of a0 = 3.7 × 10^3 km^2 s^−2 kpc^−1, the expected velocity dispersion of NGC1052–DF2 is σM ≈ (0.05 GMstarsa0) 1/4 ≈ 20 km s^−1 , a factor of two higher than the 90% upper limit on the observed dispersion.
The external field effect reduces velocity dispersion in dwarf galaxies when present by an amount that appears to be about right on an order of magnitude basis.

This would happen if the gravitational field was NGC1052 at a range of 20 MPc was greater than a0 or greater than the gravitational field due to the dwarf galaxy.

2. It could be a function of a unique geometry that causes gravitational effects from dark matter and/or modified gravity to cancel out (or at least appear to cancel out for a viewer from our direction). In Deur's work, this happens when a galaxy or other structure is spherically symmetric or nearly so. In other cases, some geometries can cause force vectors from gravitational pulls in opposite directions from different masses to cancel out if they are arranged just so.

3. It could be a methodology problem. The calculation of the inferred dark matter and velocity dispersion is quite involved and there are lots of instrumental issues and calculation issues that could lead to such an extreme outlier result.

All three possibilities are supported by this description of the galaxy (emphasis added):
In terms of its apparent size and surface brightness it resembles dwarf spheroidal galaxies such as those recently identified in the M101 group at 7 Mpc, but the fact that it is only marginally resolved implies that it is at a much greater distance. Using the I814 band image we derive a surface brightness fluctuation distance of DSBF = 19.0 ± 1.7 Mpc (see Methods). It is located only 14' from the luminous elliptical galaxy NGC 1052, which has distance measurements ranging from 19.4 Mpc to 21.4 Mpc. We infer that NGC1052–DF2 is associated with NGC 1052, and we adopt D ≈ 20 Mpc for the galaxy.
For the Crater II galaxy, a distance of 120 kpc from the Milky Way galaxy led to a Milky Way gravitational field eight times larger than necessary to induce a strong external field effect, and while this dwarf galaxy is about 166 times further from the NGC 1052 as Crater II is from the Milky Way, elliptical galaxies are typically much larger than spiral galaxies, so they have stronger external fields at the same distance.

The Milky Way's mass is about 5.8*10^11 solar masses. NGC1052-DF2 appears to have a mass about 200 times smaller than the Milky Way. Giant elliptical galaxies have up to about 10^13 solar masses. But, the mass of this one has been measured to be only about 1.25 to 4 times larger than the Milky Way (up to almost 6x at two sigma). The estimated mass of NGC1052 (the parent galaxy) is as follows:
Using the kinematic information from the 16 GCs, we can estimate the mass enclosed within the radius of the GC system observed. We use the projected mass estimator (Evans et al. 2003), assuming isotropy and an r−4 distribution, to derive a mass of 1.7 ± 0.9 × 10^12M⊙ within 19 kpc (∼6.5re). The mass estimate error was calculated by bootstrapping the observed velocities and errors. van Gorkom et al. (1986) used HIkinematics to measure a mass of 3.1 × 10^11M⊙ within 23 kpc.
Given the only moderately greater mass and much greater distance, whether or not the external field effect applies here is close thing. If the greater distance reduces the external field strength by less than a factor of 18-54 (284 km/s for the Milky Way external field on Crater II v. 20 km/s for this galaxy scaled by the higher mass of this galaxy; up to about 81 at two sigma for the NGC1052 mass), then the external field effect should be present. But, a distance 166 times further from the dwarf galaxy should reduce the parent galaxy's gravitational field on the dwarf galaxy by more than a factor of 54 (or even the two sigma factor of 81). So, my back of napkin estimate, which could be flawed, suggests that there should be an external field effect from NGC1052 on NGC1052-DF2, or at least, not a full fledged one, unless there is some other source of a stronger external field acting on NGC1052-DF2.

So, spherical symmetry in the Deur paradigm looks like a more likely explanation than the external field effect in MOND, at first glance.

Another possibility is that an unusually rich interstellar gas/dust medium could increase a naive estimate of the strength of local gravitational fields in this system.

Still, this bears further investigation as it is a potentially extremely important data point, which is something I don't have the time to do in depth at the moment.

UPDATE April 2, 2018: This post suggests that the correctly calculated MOND prediction is 14+/- 4 and that the measured value is 8.4 with a 90% confidence interval upper limit of 10. So, it does not disprove MOND, the paper's calculation simply failed to consider the external field effect. The limited data points used in the calculation (ten) also suggests that the measured value is likely to be an underestimate as it was in FORNAX. And, the 20 mpc was distance from Earth, not distance from the dwarf to the elliptical which is about 80 kpc, which is the main reason that my calculation was off.

UPDATE April 3, 2018 (from the comments to the previous link by its author):
On closer reading, I notice in the details of their methods section that the rms velocity dispersion is 14.3 km/s. It is only after the exclusion of one outlier that the velocity dispersion becomes unusually low. As a statistical exercise rejecting outliers is often OK, but with only 10 objects to start it is worrisome to throw any away. And the outlier is then unbound, making one wonder why it is there at all. 
Consider: if they had simply reported the rms velocity dispersion, and done the MOND calculation correctly, they would have found excellent agreement. This certainly could be portrayed as a great success for MOND. Instead, tossing out just one globular cluster makes it look like a falsification. Just one datum, and a choice of how to do the statistics. Not a wrong choice necessarily, but a human choice… not some kind of statistical requirement.
UPDATE April 11, 2018

One of the authors addresses a variety of concerns (of the kind that quite honestly should have been addressed at a pre-print/peer review stage rather than post-publication) (hat tip Backreaction).

In particular, he justifies at great length his velocity dispersion calculation, although the paper really fails seriously in failing to address just how problematic and assumption prone it really is and the reasoning behind the choices made. The uncertainty due to fundamental assumption issues is greatly understated.

He acknowledges that he screwed up the MOND calculation and shifts attention from that mistake to a different dwarf galaxy (Dragonfly 44) where MOND might be off without conclusively showing that this is the case. He states:  "The whole MOND / alternative gravity discussion in the paper rests on a misunderstanding on my part."

He acknowledges the need for more and better data to get a more accurate measurement, some of which can be done quite easily (and really should have been done prior to publication in Nature).

He unconvincingly argues that "lacking" and "without" have different meanings while backpedaling on the "no" dark matter claim, although this criticism isn't honestly such a big deal since other language in the abstract does clarify the point (and indeed highlights that the dark matter a priori prediction was off by a factor of 100 v. a factor of about 0.4 at most for the correctly done MOND prediction).

Bottom line: Nature printed what was really a rough draft with some serious problems as a final and definitive work.

UPDATE April 14, 2018

A rebuttal paper.

Monday, March 26, 2018

Quantum Mechanical Interpretations

Woit reviews a new book discussing the different prevailing interpretations of quantum mechanics (Copenhagen, Many World, Bohmian, etc.) and in the process does something even more useful. He refers us to an arXiv pre-print, which he finds to be a better treatment of the subject, in addition to being shorter and free and instantly available. He describes the article this way:
For a . . . recent serious take on the issues involved, I’d recommend reading something by Wojciech Zurek, for instance this article, a version of which was published in Physics Today. Trying to figure out what “interpretation” Zurek subscribes to, I notice that he refers to an “existential interpretation” in some of his papers. I don’t really know what that means. Unlike most discussions of “interpretations”, Zurek seems to be getting at the real physical issues involved, so I think I’ll adopt his (whatever it means) as my chosen “interpretation”.
The article opens in this way:
Quantum principle of superposition decrees every combination of quantum states a legal quantum state. This is at odds with our experience (Fig. 1). 
Decoherence selects preferred pointer states that survive interaction with the environment. They are localized and effectively classical. They persist while their superpositions decohere. Decoherence marks the border between quantum and classical, alleviating concern about flagrant and manifestations of quantumness in the macroscopic domain. 
Here we consider emergence of ‘the classical’ starting at a more fundamental pre-decoherence level, tracing the origin of preferred pointer states and deducing their probabilities from the core quantum postulates. We also explore role of the environment as a medium through which observers acquire information. This mode of information transfer leads to perception of objective classical reality.
The arXiv says this about the eight page long pre-print:

Quantum Darwinism, Classical Reality, and the Randomness of Quantum Jumps

Tracing flows of information in our quantum Universe explains why we see the world as classical.
Comments:This manuscript, after cuts and edits to comply with Physics Today limits and style, was published last October. It may have some rough edges, but it also contains technical elaborations omitted from the published version for lack of space that may be of interest to some readers. Thus, while the essence is the same, but there are differences (starting with the title and abstract)
Subjects:Quantum Physics (quant-ph)
Journal reference:Physics Today, vol. 67, pp. 44-50 (2014).

Sunday, March 25, 2018

Was The Dali Skull A Denisovan?

Consider the Dali skull in China from 209,000 +/- 23,000 years ago. 

Was it a Denisovan? As one person in the linked twitter thread notes:

It is not a Neanderthal and and too recent for Homo heidelbergensis. It is almost as old as the oldest trace of modern humans in Africa, and it is about 100,000 years older than the oldest Out of Africa modern human known from any other source.

We don't have ancient DNA from this 1978 discovery or several other ill classified old hominin fossils from China.

Wikipedia notes that:
The Dali cranium is interesting to modern anthropologists as it is possibly a well-preserved example of archaic Homo sapiens; it has a mixture of traits from Homo erectus and Homo sapiens.The details of the face and skull are however distinct from European Neanderthals and earlier European hominids, such as remains found in Petralona cave and Atapuerca. . . . 
There has been considerable debate regarding how to classify the fossil in terms of species, with some anthropologists insisting it to be a regional variant of Homo heidelbergensis and others categorizing it as an early representative of Homo sapiens, and as such there is no current consensus on the species status of the Dali fossil. Some anthropologists, notably many Chinese representatives, cite the characteristics of the Dali cranium and other similar Chinese fossils of that era as evidence for genetic continuity in modern H. sapiens today, as Dali's traits are commonly found in modern Chinese H. sapiens populations. . . . 

An assortment of primitive Homo skulls have tentatively been placed with the Dali find. The Maba Man, a 120 to 140 000 year old fragmentary skull from Guangdong in China shows the same general contours of the forehead. A partial female skeleton with skull from Jinniushan (also China) seems to belong to the same group, characterized by a very robust skull cap but less robust skull base. A possibly fourth member could be the Narmada skull from the Madhya Pradesh in India, consisting of a single robust cranial vault
The Denisova hominin, represented by a very robust finger bone found in the Altai mountains in Russia is quoted as likely linked to the Dali people. DNA studies show the bone belong to a woman, with Mitochondrial DNA linking it to a very deep split in the human tree, at around 1 million years old. This would make the DNA erectus rather than heidelbergensis or other more recent splits. However, the analysis of the nuclear DNA points to a sister group relationship with the neanderthals.
Even one DNA match to Denisovans from any of the skulls in this category could make a very strong case for the classification of all of them.

A related question is whether Dali-hominins replaced Homo erectus in China, co-existed with Homo erectus in China, or evolved from Homo erectus in China. 

Thursday, March 22, 2018

The Impossible Early Galaxy Problem

This paper and its proposed solution is less notable than its discussion of the problem with the standard model of cosmology, which is known as the "impossible early galaxy problem". In general, modified gravity theories lead to earlier structure development in cosmology, so this problem favors such theories relative to dark matter, although modified gravity isn't necessarily the only possible solution.
To understand the formation and evolution of galaxies at redshifts z < 10, one must invariably introduce specific models (e.g., for the star formation) in order to fully interpret the data. Unfortunately, this tends to render the analysis compliant to the theory and its assumptions, so consensus is still somewhat elusive. 
Nonetheless, the surprisingly early appearance of massive galaxies challenges the standard model, and the halo mass function estimated from galaxy surveys at z > 4 appears to be inconsistent with the predictions of LCDM, giving rise to what has been termed "The Impossibly Early Galaxy Problem" by some workers in the field. A simple resolution to this question may not be forthcoming. 
The situation with the halos themselves, however, is more straightforward and, in this paper, we use linear perturbation theory to derive the halo mass function over the redshift range z < 10 for the R_h=ct universe. We use this predicted halo distribution to demonstrate that both its dependence on mass and its very weak dependence on redshift are compatible with the data. 
The difficulties with LCDM may eventually be overcome with refinements to the underlying theory of star formation and galaxy evolution within the halos. For now, however, we demonstrate that the unexpected early formation of structure may also simply be due to an incorrect choice of the cosmology, rather than to yet unknown astrophysical issues associated with the condensation of mass fluctuations and subsequent galaxy formation.
Manoj K. Yennapureddy, Fulvio Melia, "A Cosmological Solution to the Impossibly Early Galaxy Problem" (March 19, 2018).

A related issue is that we don't know how black holes got so big so fast under existing cosmology models.

Metal enrichment in the intergalactic medium in the very early universe also challenges our models.

Wednesday, March 21, 2018

More Archaic Admixture Data

More Ancient Neanderthal Genomes

An article in Nature provides great understanding of Neanderthal admixture by adding five new autosomal Neanderthal genomes to our pool of knowledge:
Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. 
Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. 
Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.
The bottom line is that most Neanderthal admixture in modern humans can be traced to the Out of Africa era in a population that would have been basal to almost all non-African modern humans, even Papuans who together with Australian Aborigines who diverge from other non-African modern humans at the most basal point, probably around 65,000-70,000 years ago. If modern humans made it into Asia and Europe before then, and Altai Neanderthal admixture dated to ca. 100,000 years ago suggests that this did happen somewhere, they have not left much of a genetic trace in modern humans.

This makes sense. First wave modern humans in Europe and Siberia mostly went extinct in an ice age about 20,000 years ago, so any subsequent admixture in the Neanderthals European homeland would have been lost. By the time that modern humans recolonized Europe, Neanderthals were extinct.

Inferred Archaic Admixture In Africans

There is essentially no Neanderthal admixture or Denisovan admixture in sub-Saharan Africans that can't be traced to Eurasian back migration to Africa. But, that doesn't mean that the ancestors of today's sub-Saharan Africans didn't also experience admixture with archaic hominins. It just means that they admixed with different hominins from whom we have no ancient DNA, in part due to poor conditions for preserving it, and in part due to insufficient resources devote to looking for potential samples.

But, it is possible to reliably estimate ancient admixture from "ghost populations" of hominins by statistically analyzing patterns in the genomes of people who are alive today and these methods have been validated by comparing their results to those obtained from direct comparisons to ancient homin genomes.

What have scientists found?

According to a new preprint at bioarXiv that largely confirms a couple of prior studies along the same lines:
Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. 
While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals.  
Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR [false discovery rate] ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.
This admixture percentage rivals that of Papuans and aboriginal Australians. It is equivalent to a situation at the time shortly after archaic introgression had ceased, in which the average person had 1.5 great-grandparents who were archaic hominins. This is roughly four times the archaic admixture proportion found in Europeans, and a somewhat lower multiple of Asians who have no Papuan ancestry. It is similar to the total amount of archaic admixture in Papuans. 

But, in this case, it involves West Africans who, unlike early of of Africa modern human populations and proto-Papuan populations, did not experience a really severe population bottleneck in their demographic history that the other populations did.

The study controlled for admixture with highly diverged African populations like Biaka Pygmies.

It is kind of nuts that we can see this huge amount of archaic admixture, and yet have no meaningful idea what kind of hominin was those source of this admixture, just as it is pretty crazy that we can document Denisovan admixture so well while having no real idea what a Denisovan looked like.

As in other cases of archaic admixture, with Neanderthals and Denisovans, it also appears that natural selection has weeded out archaic ancestry from our genomes in areas where modern human genes provide a fitness advantage relative to archaic hominins, who were, on average, less fit than modern humans. But, as in other cases of archaic admixture, there are a few loci where archaic admixture is elevated, suggesting that the introgressed genes provided their descendants with selective advantages involving those loci.

Other studies have found a distinct source of archaic admixture in a different sub-Saharan African Paleo-African population.

While this method was superior in identifying particular loci where archaic introgression did or did not take place, unlike prior studies of this type, the paper does not expressly identify how deeply diverged the archaic population is from the modern humans who admixed (other than that they are much more diverged than the most divergent modern human populations), nor does it identity how long ago this admixture event probably took place, something that prior studies have put shortly before the Holocene era (i.e. more than 10,000 years ago, but not that much earlier than that; certainly in the Upper Paleolithic era).

A finding for the West African Yoruba has wide relevance to sub-Saharan Africa because almost all populations except for a handful of relicts, gained substantial Bantu admixture in the mid-Holocene era, and the Bantu have origins geographically close to that of the Yoruba.

Linguistic Analysis Argues For Expansion Of Proto-Dravidian With South Indian Neolithic

Languages attested in writing more than 950 years ago shown in bold.

A new linguistic analysis argues that the Dravidian languages arose ca. 2500 BCE, the same time as the South Indian Neolithic Revolution. This is one very plausible date, although other studies have argued for a more recent origin on linguistic grounds (and one study argued, implausibly, for a 13000 years BP date). If this is the date of origin it pre-dates the arrival of Indo-Europeans in India by 500-1000 years, and precedes the arrival of Indo-Europeans in the Dravidian linguistic area by a bit longer than that.

The study is an honest effort, but not necessarily terribly reliable as any study is only as good as its assumptions and methods, which aren't terribly convincing, and no serious effort is made in  the paper to validate the assumptions they use or even to clearly describe those assumptions. The methods used are fairly reliable for creating a branching phylogeny of the language family (something that has never been in serious doubt), but is less reliable for purposes of estimating time depth.

For example, the analysis puts all Dravidian languages on an equal footing based upon a Swaedesh vocabulary list, but really, to do it right, they should be limiting themselves to what can be determined from the historic content of the four Dravidian languages that are attested earliest. And, they should be pretty much ignoring North Dravidian languages for which there is a strong case to be made that they didn't arise until about 1000 CE, entirely.

Their own error bars are 1000 BCE to 4500 BCE, with the archaeology of the South Indian Neolithic used to support a mid-range value. The most reliable youngest possible date comes from Dravidian loan words in the Rig Veda:
There is clear evidence of Dravidian loanwords into Old-Indo-Aryan (1750–250 BCE) dating to the middle Rigvedic period (ca 1200 BCE) in a source area that might have been Sindh, contemporary Southwest Pakistan [6], [8, pp. 69ff, 88]. Southworth [8, p. 64] proposes Sindh, Gujarat and eastern Maharashtra as areas where Dravidian would have been spoken at earlier stages.
Thus a range of perhaps 1500 BCE to 2500 BCE is quite plausible.

But, many linguists have doubted that the amount of linguistic diversity really supports a 4500 years time depth, which could be consistent with a bottleneck effect of diversification from surviving dialects after the language family temporarily went extinct in a large part of its range. Indeed, it is very likely that the particular dialect of Dravidian that was the source of the Rig Vedic substrate is extinct.

The study is: Kolipakam et al. A Bayesian phylogenetic study of the Dravidian language family. Royal Society Open Science (2018).

Tuesday, March 20, 2018

More about MOND v. Dark Matter

* MOND solves the Missing Baryon Problem.

* In MOND there isn't a Lithium 7 problem arising from Big Bang Nucleosynthesis, but there is a deuterium problem which is similar in character but smaller in magnitude.

Large scale structure forms sooner in MOND than in lambdaCDM, consistent with new observations of the very ancient universe (also here), although this is much harder to model precisely because it is a non-linear theory.

* MOND is insufficient to replace all dark matter in clusters, but sister theories like MOG and Deur's work do successfully deal with that issue. The Bullet Cluster is more of a problem for dark matter particle theories than it is for modified gravity theories, as a class.

* There are several successful relativistic modified gravity theories, although toy model MOND is not one of them and is not applicable to relativistic conditions. MOND was developed as an alternative to General Relativity in domains of applicability where General Relativity itself is approximated for practical purposes by Newtonian gravity.

* MOND models all galactic rotation curves with a single experimentally determined universal parameter in a fit that is indistinguishable from perfect given measurement errors. Dark matter theories should not have such low scatter and can only come close to this fit with 16 parameter models fine tuned to existing conditions.

* Dark matter can't explain the Crater II galaxy dynamics. MOND predicts an external field effect that is observed but has no place in conventional General Relativity with or without dark matter.

* Dark matter can't explain MOND-like effects observed in wide binary stars.

* MOND has made multiple predictions that have born out. Dark matter has repeatedly failed to make accurate predictions.

* Deur's work explains all or more dark energy phenomena, explains variations in apparent dark matter amounts in elliptical galaxies, and explains cluster phenomena, and ties MOND/dark matter/dark energy phenomena to quantum gravity foundations.

* There aren't great models of what MOND predicts in the CMB, largely because as a non-linear theory it is hard to model. But, MOG fairs pretty well.

* Direct detection experiments and collider experiments have failed to see any experimental evidence of  beyond the Standard Model particles that could be dark matter candidates over a broad swath of parameter space. For example, here.

* Purported dark matter annihilation signals have all turned out to be false alarms with other explanations. For example, here.

* The inferred dark matter distributions rule out a broad swath of parameter space including the parameter space axiomatically assumed in lambda CDM theories, which assume nearly collisionless dark matter despite the necessity that it have interactions with baryonic matter to have distributions so tightly correlated with baryonic matter.

1400 Posts

This is the 1400th post at the Dispatches From Turtle Island blog.

Why Is A GUT Scale Collider Basically Impossible?

In order to create a collider capable of exploring the GUT scale, it would take a "Dyson swarm" around the Sun to get enough energy, would have to be a "photon collider" and would have have a periodic magnetic field of solar system proportions according to an April 14, 2017 paper exploring the concept.

Friday, March 16, 2018

Edo Era Ainu Genetics

The Ainu people of Japan are descendants of the Jomon fishing-gathering people of prehistoric Japan, but also have significant Siberian ancestry.
The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido. 
Materials and methods 
Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations. 
Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. 
Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.
Noboru Adachi, et al., "Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data" American Journal of Physical Anthropology (October 11, 2017).

Hat tip to the Linear Population Model blog.

Thursday, March 15, 2018

Ancient North African DNA

The biggest surprise of new Mesolithic ancient DNA samples from Morocco is that they lack any European hunter-gatherer ancestry, instead deriving from a mix of Levantine hunter-gatherers and sub-Saharan Africans. Sub-Saharan African admixture was not unexpected, but the proportion of sub-Saharan African ancestry in this ancient DNA is higher than expected, implying early, pre-Neolithic contact between the populations.
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
Marieke van de Loosdrecht, et al.,"Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations" Science (March 15, 2018).

A related account of the find is aimed at an educated lay audience. It notes that:
DNA in hand, paleogeneticists Marieke van de Loosdrecht and Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, sequenced it. They were able to analyze genetic material from the cell’s nucleus in five people and the maternally inherited mitochondrial DNA from seven people. But they found no genetic tie to ancient Europeans. Instead, the ancient Iberomaurusians appear to be related to Middle Easterners and other Africans: They shared about two-thirds of their genetic ancestry with Natufians, hunter-gatherers who lived in the Middle East 14,500 to 11,000 years ago, and one-third with sub-Saharan Africans who were most closely related to today’s West Africans and the Hadza of Tanzania. 
The Iberomaurusians lived before the Natufians, but they were not their direct ancestors: The Natufians lack DNA from Africa, Krause says. This suggests that both groups inherited their shared DNA from a larger population that lived in North Africa or the Middle East more than 15,000 years ago, the team reports today in Science. 
As for the sub-Saharan DNA in the Iberomaurusian genome, the Iberomaurusians may have gotten it from migrants from the south who were their contemporaries. Or they may have inherited the DNA from much more ancient ancestors who brought it from the south but settled in North Africa where some of the earliest members of our species, Homo sapiens, have been found at Jebel Irhoud in Morocco.

Fun With Archaic Admixture Analysis

Archaegenetics is not a reductionist field and the more we know the more intricate the tapestry of human ancestry becomes.
Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. 
We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

All of these Eurasian and New World populations have a bottom right cluster in the images below that corresponds to Neanderthal ancestry.

The Papuan (bottom right in the image below) sample also has a center-left cluster that corresponds to Deniovan ancestry. A less pronounced center-left cluster indicating a smaller amount of ancestry from the same population is found in East Asia, Southeast Asia and South Asian individuals middle two rows of the image below. 

The big reveal in this study is that the East Asian individuals, in particular, seem to have two distinct clusters of Denisovan ancestry, with a small secondary top left cluster in each suggesting a second admixture event with genetically diverged Denisovan populations.

Denisovan ancestry is absent, however, in European individuals (top row) and in New World individuals (bottom row except the Papuan). Pontus Skoglund also notes that:
There is an undiscussed but potentially explosive implication of this paper: the 2nd Denisovan gene flow signal in East Asia seems to be absent from Native American ancestry--could Denisovans have survived after the isolation of these lineages <30 kya??
For what it is worth, I don't think that Skoglund's hypothesis is correct. I think it is more likely that the primary Denisovan admixture event reflects admixture of Southern route modern human migrants with Denisovans and that the secondary Denisovan admixture event (which is absent in Papuans) reflects admixture of a subset of Northern route modern human migrants who followed more or less what is now known as the Silk Road, and was distinct from the small founding population of the Americas.

This data point also strengthens the hypothesis that very old, non-Homo erectus hominin remains found in China with a mix of archaic and modern features are either Denisovan or hybrid Denisovan-modern human individuals.

Figure 4: Contour Density Plots of Match Proportion of Introgressed Segments to the Altai Neanderthal and Altai Denisovan Genomes

The match proportion is the proportion of putative archaic-specific alleles in a segment that match the given archaic genome, excluding alleles at positions masked in the archaic genome sequence. Segments with at least ten variants not masked in the Neanderthal genome and at least ten variants not masked in the Denisovan genome are included. Numbers inside the plots indicate the height of the density corresponding to each contour line. Contour lines are shown for multiples of 1 (solid lines). In addition, contour lines for multiples of 0.1 between 0.3 and 0.9 (dashed lines) are shown for additional detail. European populations are given in the first row, East Asian populations in the second row, South Asian populations in the third row, and American and SGDP Papuan populations in the final row. Additional information about the populations can be found in Table 1.

Wednesday, March 14, 2018

How Did One Language Family Come To Dominate Australia Prior To European Contact?

It remains a mystery how Pama–Nyungan, the world’s largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social or technological advantages allowed rapid language replacement from the Gulf Plains region during the mid-Holocene. Others have proposed expansions from refugia linked to climatic changes after the last ice age or, more controversially, during the initial colonization of Australia. Here, we combine basic vocabulary data from 306 Pama–Nyungan languages with Bayesian phylogeographic methods to explicitly model the expansion of the family across Australia and test between these origin scenarios. We find strong and robust support for a Pama–Nyungan origin in the Gulf Plains region during the mid-Holocene, implying rapid replacement of non-Pama–Nyungan languages. Concomitant changes in the archaeological record, together with a lack of strong genetic evidence for Holocene population expansion, suggests that Pama–Nyungan languages were carried as part of an expanding package of cultural innovations that probably facilitated the absorption and assimilation of existing hunter-gatherer groups.
Remco R. Bouckaert, Claire Bowern & Quentin D. Atkinson "The origin and expansion of Pama–Nyungan languages across Australia" Nature Ecology & Evolution (March 12, 2018).

Skepticism is in order because New Zealander Quentin D. Atkinson has a history of relying on math that fails to honor existing linguistic knowledge resulting in clearly wrong predictions. But, his hypothesis here is, at least, strongly conventional wisdom confirming.

My strong suspicion is that the key cultural innovation was the integration of the Dingo into Australian society after ca. 50,000-60,000 previous years without dogs. The epicenter of this expansion coincides perfectly with the expected location of an introduction of the Dingo into Australia, and the Dingo is also known to have resulted in a second wave of mass extinctions of local fauna in Australia.

More Trouble For Dark Matter

An analysis of ambient radio wave activity at particular frequencies provides a window into the nature and temperature of the universe very early in its existence. What does it show?
The profile is largely consistent with expectations for the 21-centimetre signal induced by early stars; however, the best-fitting amplitude of the profile is more than a factor of two greater than the largest predictions. 
This discrepancy suggests that either the primordial gas was much colder than expected or the background radiation temperature was hotter than expected. Astrophysical phenomena (such as radiation from stars and stellar remnants) are unlikely to account for this discrepancy; of the proposed extensions to the standard model of cosmology and particle physics, only cooling of the gas as a result of interactions between dark matter and baryons seems to explain the observed amplitude. The low-frequency edge of the observed profile indicates that stars existed and had produced a background of Lyman-α photons by 180 million years after the Big Bang. The high-frequency edge indicates that the gas was heated to above the radiation temperature less than 100 million years later.
Of course, the (literally) defining property of dark matter in the standard model of cosmology (called ΛCDM for a cosmological constant with "cold dark matter") is that dark matter is completely or almost collisionless with respect to ordinary baryonic matter . . . . dots that this abstract refrains from connecting.

What correctly predicts what is observed?

A universe with no dark matter where the matter in the universe is entirely made up of baryonic matter (i.e. a modified gravity hypothesis), as explained in a readable two page (exclusive of references) paper supplementing the paper in the journal Nature linked above, that accepts virtually all of its data, theoretical framework and equations. It merely connects the dots that the paper in Nature didn't. They money language:
Equation 1 then predicts a maximum absorption of  
T21, max = −0.24 K for fb = 0.16; (2)  
T21, max = −0.60 K for fb = 1. (3)  
The observed value is T21 ≈ −0.5 K (Bowman et al. 2018), and appears from their Fig. 2 to be closer to −0.55 K. Such a strong signal is expected in a baryonic universe, but is unobtainable in ΛCDM. 
Figure 1 of the supplemental paper shows that a naive, unmodified ΛCDM prediction (as opposed to the maximal possible variation of it) is T21 ≈ −0.05 K, about 9% of the observed value, as opposed to 92% of the value predicted in a purely baryonic scenario (the exact margin of error isn't stated).

Once again, modified gravity theorists have correctly predicted the results of future experimental observations and dark matter theories made the wrong prediction, on a matter independent of previous predictions that have been confirmed.

McGaugh's linked supplement paper also makes some further predictions that new data can test:
1. Strong 21cm absorption will also be observed during the dark ages (z > 30).  
2. The 21cm power spectrum will show pronounced baryonic features.  
3. Large galaxies and the cosmic web emerge earlier than anticipated in ΛCDM (Sanders 1998; McGaugh 2015).  
The first two predictions stem simply from a universe made of baryons. Only the third prediction is model-specific; some hints of large early structures already exist (e.g., Steinhardt et al. 2016; Franck & McGaugh 2016). This implies that structure grows nonlinearly, erasing baryonic features at late times through mode mixing (McGaugh 1999).

UPDATE March 16, 2018: A completely separate paper constrains dark matter models via metal enrichment in very old galaxies.

UPDATE: March 20, 2018: Virtually all of the scatter in the radial acceleration relation observed in galaxies can be explained by measurement error - the residual scatter after estimating the effects of various forms of measurement error is about 3%.

These tweets from Federico Lelli explain the paper's significance:
In and we show that baryons and dynamics are tightly linked in galaxies at a *local* level: the observed acceleration (from the gas rotation curve) correlates with that expected from the distribution of baryons (using Newton's law).
At high accelerations gobs=gbar because baryons fully dominate the dynamics. These data come from the central parts of massive galaxies where there is no need for dark matter. At low accelerations, the data deviates from the 1:1 line. That's the classic indication of dark matter! 
We were expecting something like this! @DudeDarkmatter did a similar work back in 2004: … What really shocked us was the tightness of the relation! The deviations from the mean relation (aka "scatter") are of the order of 30%! 
This scatter is absurdly small for the (poor) standards of galactic astronomy. So we did a simple math exercise: let's propagate the errors on the measurements and compare the resulting expected scatter from errors (black) with the observed scatter (red). The two are consistent!
This means that the relation is consistent with NO intrinsic scatter. The width of the relation can be fully explained by observational errors. In general this happens only when you deal with Laws of Nature, like Kepler's laws. This is a big deal, so we further looked into it. 
The problem is that errors in Astronomy are a mess. We don't have complete control on them as Physicists can have with their experiments in their labs. Our lab is the Universe and the Universe doesn't care about what we wanna do. And here comes Pengfei's paper. 
There are three main sources of error on gobs and gbar: the galaxy distance, the galaxy inclination, and the conversion from stellar light to stellar mass. If you got them a bit wrong, the galaxy will shift perpendicularly or horizontally from the mean relation, adding scatter. 
The fact that the observed scatter is only 30% means that we did a pretty good job in estimating these quantities. But now we want to know whether this 30% can completely disappear when the errors are taken into account. 
To do this, Pengfei used Bayesian statistics and a technique called Markov Chain Monte Carlo (MCMC). Essentially you can fit the mean relation to individual galaxies, allowing the light-to-mass conversion, distance, and inclination to vary a little, within the observed errors. 
This is an example of how good the fits can be. They are not all this good. But if we measure the mean deviation from the fits for all galaxies, the resulting number is ridiculously small: 13%. We have a recipe that explains rotation curves better than 13% using only baryons!
When we optimize distance, inclination, and mass-to-light conversion, the radial acceleration relation becomes extremely tight. This didn't necessarily have to happen because we are varying *global* quantities while looking at a *local* relation, connecting different galaxy radii. 
If you are still following me, you may wonder what drives the remaining 13% scatter. Well, part of it could be intrinsic, but most of it must surely come from errors on the rotation velocities (due to non-circular motions and other nuisances) which are indeed of the order of 10%. 
To summarize: we have a relation which is very tight for astronomical standards. The deviations from the mean can all be explained by measurement errors. The relation is consistent with no intrinsic scatter. So is this a Law of Nature? Or just another galaxy scaling relation? 
Ops! I forgot to add the key plot. Here you see the radial acceleration relation using best-fit distance, inclination, and mass-to-light ratio. The tiny residuals need two tiny Gaussians, but we think we understand why this happens. It's likely how velocity errors are estimated.

The paper's abstract and citation are as follows:
Galaxies follow a tight radial acceleration relation (RAR): the acceleration observed at every radius correlates with that expected from the distribution of baryons. We use the Markov Chain Monte Carlo method to fit the mean RAR to 175 individual galaxies in the SPARC database, marginalizing over stellar mass-to-light ratio (Υ⋆), galaxy distance, and disk inclination. Acceptable fits with astrophysically reasonable parameters are found for the vast majority of galaxies. 
The residuals around these fits have an rms scatter of only 0.057 dex (∼13%). This is in agreement with the predictions of modified Newtonian dynamics (MOND). 
We further consider a generalized version of the RAR that, unlike MOND, permits galaxy-to-galaxy variation in the critical acceleration scale. The fits are not improved with this additional freedom: there is no credible indication of variation in the critical acceleration scale. The data are consistent with the action of a single effective force law. The apparent universality of the acceleration scale and the small residual scatter are key to understanding galaxies.
Pengfei Li, Federico Lelli, Stacy McGaugh, James Schormbert, "Fitting the Radial Acceleration Relation to Individual SPARC Galaxies" arXiv (February 28, 2018).

This successfully replicates and improves upon a finding from a December 14, 2015 paper.

And, don't forget the stunning case of the Crater II galaxy where MOND accurately predicted an outlier result that could not be obtained with a dark matter model.

Crater II isn't completely independent of the low scatter result but tests the same thing in very different domains of applicability in different ways. And the other empirical datasets discussed above are completely independent of these results.

A 2016 paper with overlapping authorship with this one shows that observation is not consistent with dark matter that does not interact with baryonic matter is not consistent with observation, a finding that another independent study has replicated.
Cosmological N-body simulations predict dark matter (DM) haloes with steep central cusps (e.g. NFW, Navarro et al. 1996). This contradicts observations of gas kinematics in low-mass galaxies that imply the existence of shallow DM cores. 
Baryonic processes such as adiabatic contraction and gas outflows can, in principle, alter the initial DM density profile, yet their relative contributions to the halo transformation remain uncertain. 
Recent high resolution, cosmological hydrodynamic simulations (Di Cintio et al. 2014, DC14) predict that inner density profiles depend systematically on the ratio of stellar to DM mass (M∗/Mhalo). Using a Markov Chain Monte Carlo approach, we test the NFW and the M∗/Mhalo-dependent DC14 halo models against a sample of 147 galaxy rotation curves from the new Spitzer Photometry and Accurate Rotation Curves (SPARC) data set. These galaxies all have extended H{\small I} rotation curves from radio interferometry as well as accurate stellar mass density profiles from near-infrared photometry. 
The DC14 halo profile provides markedly better fits to the data compared to the NFW profile. Unlike NFW, the DC14 halo parameters found in our rotation curve fits naturally fall within two standard deviations of the mass-concentration relation predicted by ΛCDM and the stellar mass-halo mass relation inferred from abundance matching with few outliers. 
Halo profiles modified by baryonic processes are therefore more consistent with expectations from Λ cold dark matter (ΛCDM) cosmology and provide better fits to galaxy rotation curves across a wide range of galaxy properties than do halo models that neglect baryonic physics. Our results offer a solution to the decade long cusp-core discrepancy.

Tuesday, March 13, 2018

Sabine Hossenfelder (and others) On Naturalness

A Power Point presentation (converted to pdf form) on Naturalness from a recent conference presentation by Sabine Hossenfelder explains why Naturalness is not a legitimate hypothesis generator in physics. The straight forward reasoning is solid and she's right. Eventually, the rest of the discipline should come around, although they've wasted a generation ignoring this common sense.

Another presenter (Fred Jegelehner) at the same conference explains how, from other perspectives than the conventional one, there is nothing unnatural about the Higgs boson mass and the conventional "hierarchy problem" is misguided.

Meanwhile Jester comes out of a long hibernation at his blog to say this:
The clear message from the LHC is that the dominant paradigms about the physics at the weak scale were completely misguided. The Standard Model seems to be a perfect effective theory at least up to a few TeV, and there is no indication at what energy scale new particles have to show up. . . . The naturalness problem of the cosmological constant and of the Higgs mass may suggest some fundamental misunderstanding of quantum field theory on our part.
He offers sensible suggestions about new directions that experimenters and theorists in physics should consider as a result - something many of us have been preaching as voices in the wilderness for some time now. 

He cites Sabine's blog, a pre-print on the "Post-Naturalness" era, and an article at the Economist citing people including Woit (of "Not Even Wrong" fame).

Monday, March 12, 2018


For what it's worth, the analytics for this blog indicate that there has been some SEO mischief going on, although I can't figure out what it is really trying to accomplish, or how it is done. I police comment spam quite thoroughly, so whoever you are out in cyberspace screwing around with this, you have nothing to gain here.

Quick Hits

Europe and Northern Asia

* From Davidski at Eurogenes: 
the remains of this individual (sampled by Mathieson et al. 2018, see here) are from a cemetery of the Sredny Stog culture, which, based on historical linguistics and archaeological data, has already been posited to have been a Proto-Indo-European (PIE) culture. . . Ukraine_Eneolithic I6561 is the oldest recorded individual belonging to Y-haplogroup R1a-M417 . . . Ukraine_Eneolithic I6561 is the oldest sample with UDG-treated genome-wide data to carry the 13910*T lactase persistence allele, which reaches its maximum frequency in Northwestern Europe, and is also relatively common amongst Indo-European-speaking South Asians, but not Middle Easterners . . . based on historical linguistics data, the Proto-Indo-Europeans are generally regarded to have been foragers turned pastoralists, rather than farmers, but nevertheless, pastoralists familiar with farming, and indeed Ukraine_Eneolithic I6561 appears to be mostly a mixture of Eastern European and Caucasus Hunter-Gatherers (EHG and CHG, respectively), but with around 30% input from early European farmers.
Somebody has to be the first Indo-European-like ancient genome. But, this case offers a potential resolution of a key disputed historical mystery. Did the 13910*T lactase persistence allele arise in Indo-Europeans (in whom it was later strongly selected for) or in situ in Northwest Europe? 

This find strongly makes the case for a proto-Indo-European Ukrainian origin.

This doesn't refute the evidence of strong selective fitness for the LP allele, but the fitness coefficient doesn't have to be nearly as high if you start with an allele that is present at low frequency in a source population that is already growing rapidly for other reasons which may have strong founder effects, as it does if you start from a single mutation in Northwest Europe's early European farmer population that is otherwise shrinking or stagnating.

* I continue to think that the role of Vitamin D may be critical for the role of LP allele selection in Europe. "Normal" vitamin D consumption can reduce early death from cardiovascular disease by 30%, reduces vulnerability to TB, prevent chronic lung diseaseprevents osteomalacia in adults, seasonal flu and cold vulnerability (same link with sources linked therein), seasonal affective disorder vulnerability (same link), and really importantly (same link) prevents pre-eclampsia, gestational diabetes mellitus, preterm birth and first-trimester miscarriage. The health benefits for adults and especially pregnant women of not having a Vitamin D deficiency which is especially common in high latitudes where there is less sunlight much of the year in an already growing population with above average levels of the allele could be great.

Lot of deaths during famines are really compound with dietary deficiency leading to vulnerability to diseases that well nourished people would weather, which leads to death whose cause is really both disease and malnutrition. Also, an appearance of lower vulnerability to non-deadly diseases is something that sexual selection can also act upon. A guy (or gal) who more often suffers from colds and flus and is down emotionally in winter months is less sexy and less attractive as a mate.

* A lengthy lay audience oriented paper on Finnish genetic origins in Finnish.

It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto-Uralic people, was brought into the Carpathian Basin by the Hungarian Conquerors. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. 
In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. 
Phylogenetic and population genetic analysis indicated that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Huns. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe, which area was part of the later European Hun empire. Our data give support to the Hungarian Hun tradition and provides indirect evidence for the genetic connection between Asian and European Huns. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin, raising doubts about the Conqueror origin of Hungarian language.
I am inclined to think that the linguistic and interpretative gloss placed on the genetic data in this bioXriv preprint is weak, even though the genetic data do accurately indicate a more complex population history of the Conquerors than had been previously been acknowledged. The failure of the study to take a more interdisciplinary approach to an event in the historic era is also disappointing.

Africa, Middle East and Southern Asia

* Sheep and goats were domesticated close in time and place to each other.

* Turkey started as early Anatolian but had multiple waves of introgression, most recently a moderate Turkish one, but earlier Greek and Armenia ones with the Greeks having somewhat more impact.

* Ancient artifacts and structure in Nubian funerary complexes reveal a blending of Egyptian and local traditions, and a strong role for women as bearers of family reputations and extended family identity.

* The Toba eruption did not cause a volcanic winter in East Africa and hence wasn't a push factor for migration Out of Africa which some genetic data hints should have taken place around then. But, this doesn't resolve the question of whether the eruption may have thinned jungles and local hominin populations that could have prevented modern human migration out of India until then. There is documented modern human associated tool use both before and after the Toba eruption in India. More analysis of this issue from a South African perspective is found in a new article at Nature.

* Paleoclimate and East African hominin evolution.

* Climate change in India relevant to Harappan civilization:
Our record reveals that relatively wet conditions prevailed at the northern edge of Rajasthan from ~5.1 ± 0.2 ka BP, during the beginning of the agricultural-based Early Harappan phase of the Indus Civilization. Monsoon rainfall intensified further between 5.0 and 4.4 ka BP, during the period when Indus urban centres developed in the western Thar Desert margin and on the plains of Haryana to its north. Drier conditions set in sometime after 4.4 ka BP, and by ~3.9 ka BP an eastward shift of populations had occurred. Our findings provide evidence that climate change was associated with both the expansion and contraction of Indus urbanism along the desert margin in northwest India.
* The climate change associated with its impact on the decline of Harappan civilization was fairly gradual. More on the timing of the death of the mighty Sarasvati River here. More research on this question (not necessarily mainstream in its conclusions).

* The Painted Gray Ware culture in NW India may be older than conventionally assumed.

* Steppe, Harappan and BMAC cultures compared.

* There were diverse, probably contemporaneous cemetery practices in Harappan society at a single cemetery.

* Indus seals probably regulated ownership and control of high value goods rather than being used for routine ration system administration. IVC script was probably written right to left.

* Does the Rig Veda recount Indian Ocean navigation at an earlier date than attested in existing Greco-Roman sources? Indus pottery has been found in Oman.

* What was the range of Neanderthals in South Asia?

* Were there Mousterian tools in North China briefly during the Upper Paleolithic era?

New World

Native Americans in California used nicotine: "the Ohlone tribe in San Francisco Bay to extract plaque from the teeth of eight individuals, buried between 6,000 and 300 years ago, and analyze it for nicotine. . . . Among the samples they analyzed, two tested positive for nicotine, demonstrating for the first time that the drug can survive in detectable amounts in ancient plaque. One of these individuals, an adult man, was also buried with a pipe. A surprise came from the molar of an older woman, which also tested positive for nicotine.The individuals who used it were pre-Columbian. The paper is: Jelmer W. Eerkens, et al. "Dental calculus as a source of ancient alkaloids: Detection of nicotine by LC-MS in calculus samples from the Americas." 18 Journal of Archaeological Science: Reports 509 (2018).

* If you've read Jared Diamond's classic "Guns, Germs and Steel", you know that there were a number of independently domesticated crops in what is now the American South, which went into disuse when a better package of crops developed in Meso-America reached the area. Researchers have unearthed evidence of the cultivation of that first wave of American original domesticates from 2000 years ago. The story follows the not uncommon path of a result that is well known in local museums disconnected from larger scientific networks finally connecting with the larger scientific discourse.

* Using new LIDAR tools, researchers have found evidence that a densely populated classical Mayan civilization full of cities had 10-15 million people in an area comparable to medieval England at its peak around 800 CE, which is two to three time the most optimistic earlier estimates, in places whose habitability had been doubted because it is currently so swampy.

* People were eating wild potatoes in Utah (and processing it into potato flour) ca. 10,900 years ago.