Sunday, December 29, 2019

The Testimony Of Chewing Gum

A new paper managed to extract a lot of information out of a single sample of very old chewing gum - a date, a complete human genome of the person who used it, ancient DNA that showed what she was eating at the time, and the microbiome of her mouth including a disease that she was fighting at the time similar to mono.

This rich time capsule of ancient DNA comes from a time period when hunter-gatherers who started to repopulate Europe from European refugia around 14,000 years ago, when glaciers had receded after the Last Glacial Maximum ca. 20,000 years ago, co-existed with the first farmers of Europe who migrated in slowly advancing waves along watersheds (mostly in whole family units with only modest admixture with local hunter-gatherers) ultimately from Anatolia (i.e. modern Turkey) who had just started to arrive within a few centuries of that time of this sample.

An artist's recreation of the woman who used the chewing gum based upon her DNA (from here). 

The image above is our best estimate of what Western European hunter-gathers looked like before farming and herding were introduced based upon their DNA. 

This woman's appearance lacks the phenotypic changes in typical Europeans that arose with the first farmers of Europe who descended from Anatolian first farmers (who in turn, were descendants of Fertile Crescent hunter-gatherers).

The modern Scandinavian and Northern European phenotype (i.e. visible traits arising from one's genes) most notably characterized by very light colored skin, hair and eyes, didn't come into existence until the Bronze Age when Anatolian farmers and metal using Ukrainian horsemen admixed. 

The share of Western European hunter-gather ancestry in modern Europeans is quite modest and mostly comes indirectly from early farmers who admixed with the hunter-gatherers who preceded them in places they moved (often limited to places with good water supplies and fertile soils while hunter-gatherers remained dominant or adopted herding only on less prime farming land). 

(Ironically, European hunter-gathers ca. 3700 BCE would look to modern eyes more "African" at first glance than Egyptians of that time period.)
During excavations on Lolland, [Denmark] archaeologists have found a 5,700-year-old type of "chewing gum" made from birch pitch. In a new study, researchers from the University of Copenhagen succeeded in extracting a complete ancient human genome from the pitch. It is the first time that an entire ancient human genome has been extracted from anything other than human bones. . . . [Scientists] also retrieved DNA from oral microbes and several important human pathogens, which makes this a very valuable source of ancient DNA, especially for time periods where we have no human remains[.]
Based on the ancient human genome, the researchers could tell that the birch pitch was chewed by a female. She was genetically more closely related to hunter-gatherers from the mainland Europe than to those who lived in central Scandinavia at the time. They also found that she probably had dark skin, dark hair and blue eyes.
The birch pitch was found during archaeological excavations at Syltholm, east of Rødbyhavn in southern Denmark. . . . Syltholm is completely unique. Almost everything is sealed in mud, which means that the preservation of organic remains is absolutely phenomenal[.]  It is the biggest Stone Age site in Denmark and the archaeological finds suggest that the people who occupied the site were heavily exploiting wild resources well into the Neolithic, which is the period when farming and domesticated animals were first introduced into southern Scandinavia[.] 
This is reflected in the DNA results, as the researchers also identified traces of plant and animal DNA in the pitch -- specifically hazelnuts and duck -- which may have been part of the individual's diet.

In addition, the researchers succeeded in extracting DNA from several oral microbiota from the pitch, including many commensal species and opportunistic pathogens . . . The researchers also found DNA that could be assigned to Epstein-Barr Virus, which is known to cause infectious mononucleosis or glandular fever.  
Birch pitch is a black-brown substance that is produced by heating birch bark. It was commonly used in prehistory for hafting stone tools as an all-purpose glue. The earliest known use of birch pitch dates back to the Palaeolithic.  
Pieces of birch pitch are often found with tooth imprints suggesting that they were chewed. As the pitch solidifies on cooling, it has been suggested that it was chewed to make it malleable again before using it for hafting etc. Other uses for birch pitch have also been suggested. For example, one theory suggests that birch pitch could have been used to relieve toothache or other ailments as it is mildly antiseptic. Other theories suggest, people may have used it as a kind of prehistoric tooth brush, to suppress hunger, or just for fun as a chewing gum.
From hereThe source paper is: 

Theis Z. T. Jensen, et al., "A 5700 year-old human genome and oral microbiome from chewed birch pitch." 10(1) Nature Communications (2019). DOI: 10.1038/s41467-019-13549-9

More coverage at Bernard's Blog.

Saturday, December 28, 2019

Mayan Temple Discovered Near Cancun

The find isn't terribly unexpected or paradigm breaking. But, it illustrates that there is still plenty of relatively low hanging fruit out there to be discovered by archaeologists in much of the world. 
Archeologists have discovered a large palace likely used by the Mayan elite more than 1,000 years ago in the ancient city of Kuluba, near the modern day tourist hot spot of Cancun in eastern Mexico, Mexican anthropology officials said. 
The remains of the six-meter high building, 55 meters (180 feet) long and 15 meters wide, suggest the palace was inhabited for two long periods between 600-1050 A.D., the National Institute of Anthropology and History (INAH) said in a statement. 
The Mayan civilization reached its peak between 250 and 900 A.D., when it ruled large swaths of what is now southern Mexico, Guatemala, Belize and Honduras.
From here

Friday, December 27, 2019

Human Evolution Happened In The Old World 122 To 329 Times In The Last 100,000 Years

A "selective sweep" is basically a discrete instance of a gene variant's frequency changing due to some form of natural selection (including reproductive partner selection, fertility rates, and death effects). A new study discussed below looked at genetic evidence of such sweeps in 5 populations each in Africa, Europe and Asia over the last 100,000 years which is about 3,500 generations based upon modern genomes from a pre-existing database. The populations studies were as follows:

The accuracy of the method was confirmed, among other reasons, because the blind statistical methods used located the most famous and intense selective sweeps previously known to have occurred. As the body text explains:
We found that the most enriched genomic regions contain multiple iconic examples of positive selection, e.g., the LCT region in northern Europeans, EDAR in all Asian populations and TLR5 in Africa, as well as various other examples including genes associated with lighter skin pigmentation. This indicates that the information underlying our estimations corresponds to genomic signals in line with natural selection.
Africa has had fewer selective sweeps, instances of gene frequency rate changes not caused by mere random drift, in the last 100,000 years than Europe, which has in turn had fewer selective sweeps than Asia. As the body text explains:
We also found a trend toward more sweeps among non-African populations, particularly in Asia. For example, we estimated 68 [CI:46-91] and 165 [CI:119-211] sweeps in average in Africa and Asia respectively when including complete sweeps in our model.
This is, in part, due to the fact that Africa has had fewer and less intense population bottlenecks in this time frame. It is also due, in part, to the fact that humans, who evolved in the first place in Africa, needed fewer evolutionary adaptations to continue to live there than to live elsewhere where different environmental conditions were present. 

Most selective sweeps have been limited to particular continents, and not global, but have been continent-wide. As the body text of the paper explains:
We found virtually no overlap between populations from different continents, with some exceptions. 
In contrast, the most enriched regions tend to be shared across populations from the same continent. These results indicate that the total number of sweeps in humans should be close to the summation of the mean X computed per continent; i.e., 221 [CI:122-329], a first order approximation neglecting some selection signals shared across continents and considering sweeps are highly shared within continents.
Figure 4C below shows the results graphically with margins of error for Europe and Asia. Below that is a similar figure for five African populations from the Supplemental Materials. The abstract for the paper and its citation follow.

Over the last 100,000 years, humans have spread across the globe and encountered a highly diverse set of environments to which they have had to adapt. Genome-wide scans of selection are powerful to detect selective sweeps. However, because of unknown fractions of undetected sweeps and false discoveries, the numbers of detected sweeps often poorly reflect actual numbers of selective sweeps in populations. The thousands of soft sweeps on standing variation recently evidenced in humans have also been interpreted as a majority of mis-classified neutral regions. In such a context, the extent of human adaptation remains little understood. 
We present a new rationale to estimate these actual numbers of sweeps expected over the last 100,000 years (denoted by X) from genome-wide population data, both considering hard sweeps and selective sweeps on standing variation. We implemented an approximate Bayesian computation framework and showed, based on computer simulations, that such a method can properly estimate X. We then jointly estimated the number of selective sweeps, their mean intensity and age in several 1000G African, European and Asian populations. 
Our estimations of X, found weakly sensitive to demographic misspecifications, revealed very limited numbers of sweeps regardless the frequency of the selected alleles at the onset of selection and the completion of sweeps. We estimated ∼80 sweeps in average across fifteen 1000G populations when assuming incomplete sweeps only and ∼140 selective sweeps in non-African populations when incorporating complete sweeps in our simulations. The method proposed may help to address controversies on the number of selective sweeps in populations, guiding further genome-wide investigations of recent positive selection.
Guillaume Laval, et al., "A genome-wide Approximate Bayesian Computation approach suggests only limited numbers of soft sweeps in humans over the last 100,000 years" bioRxiv (December 23, 2019) doi:

Tuesday, December 24, 2019

Quarks Within Protons Are Entangled

A proton is a composite particle made up of three valence quarks (two up quarks and one down quark) and myriad "sea quarks" which are "confined" by gluons in a coherent and discrete unit. 

The internal structure of a proton is a matter of ongoing investigation and one insight reached recently based upon experimental data is that quarks within protons, as previously suspected, appear to be "entangled" which is to say that their behavior is correlated, rather than being independent of each other.

The investigators think that the quantum entanglement may help to explain why quarks and gluons are always confined in composite particles.

[D]ata from the Large Hadron Collider hint that protons’ constituents don’t behave independently. Instead, they are tethered by quantum links known as entanglement, three physicists report in a paper published April 26 at  
Quantum entanglement has previously been probed on scales much larger than a proton. In experiments, entangled particles seem to instantaneously influence one another, sometimes even when separated by distances as large as thousands of kilometers (SN: 8/5/17, p. 14). Although scientists suspected that entanglement occurs within a proton, signs of that phenomenon hadn’t been experimentally demonstrated inside the particle, which is about a trillionth of a millimeter across. 
“The idea is, this is a quantum mechanical particle which, if you look inside it, … it’s itself entangled,” says theoretical physicist Piet Mulders of Vrije Universiteit Amsterdam, who was not involved with the research. 
In the new study, the team analyzed collisions of protons, which had been accelerated to high speeds and slammed together at the Large Hadron Collider in Geneva. Using data from the CMS experiment there, the researchers studied the entropy resulting from entanglement within the proton. Entropy is a property that depends on the number of possible states a system can take on, on a microscopic level. An analogy is a deck of cards: A shuffled deck has multiple ways that it could be ordered, whereas an ordered deck has only one, so the scrambled cards have higher entropy. 
If entanglement exists within a proton, there will be additional entropy as a result of those linkages. That entropy can be teased out by counting the number of particles produced in each collision. The amount of entropy the researchers found agreed with that expected assuming the quarks and gluons were entangled, the physicists report in their paper[.]
From Science News. The paper is:

Z. Tu, D. Kharzeev and T. Ullrich. The EPR paradox and quantum entanglement at sub-nucleonic scales. arXiv:1904.11974 (April 26, 2019).

Monday, December 23, 2019

You Can't See The Brightest Star In The Sky

NASA's Fermi Gamma-ray Space Telescope has discovered a faint but sprawling glow of high-energy light around a nearby pulsar. If visible to the human eye, this gamma-ray 'halo' would appear about 40 times bigger in the sky than a full Moon.
From here

"Biggest" would be more accurate than "Brightest", but I claim poetic license for the post title. Gamma rays are in the deep ultraviolet beyond the wavelengths of visible life, which is why you can't see it.

Indian Ocean Sea Level Is A Near A Record High (In Recorded History)

Sea levels are nearing an all time high due to global warming.
[S]ea levels in the central Indian Ocean have risen by close to a meter in the last two centuries. . . .

"We know that certain types of fossil corals act as important recorders of past sea levels. By measuring the ages and the depths of these fossil corals, we are identifying that there have been periods several hundred years ago that the sea level has been much lower than we thought in parts of the Indian Ocean." . . .
if such acceleration continues over the next century, sea levels in the Indian Ocean will have risen to their highest level ever in recorded history.
From here based upon this paper:

Paul S. Kench, et al. "Climate-forced sea-level lowstands in the Indian Ocean during the last two millennia." Nature Geoscience (2019); DOI: 10.1038/s41561-019-0503-7

Munda Origins In South Asia Better Understood

There is no serious doubt that the Munda languages of South Asia arrived starting around 3000 BCE from Southeast Asia via rice farmers. A new paper whose abstract and citation appears below fills in some of the details of how that happened.

At least three patrlineal founders over a period of time, differentiated between North Munda and South Munda and Khasi were involved, and Tibeto-Burman Y-DNA O2a-M95 came separately with a different founding population. They did not experience a language shift from Austroasiatic languages in South Asia.

The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested structure of South Asian branches within the larger tree, predominantly present in East and Southeast Asia. However, it had previously been unclear how many founders brought the haplogroup O2a-M95 to South Asia. On the basis of the updated Y chromosomal tree for haplogroup O2a-M95, we analysed 1,437 male samples from South Asia for various downstream markers, carefully selected from the extant phylogenetic tree. 
With this increased resolution, we were able to identify at least three founders downstream to haplogroup O2a-M95 who are likely to have been associated with the dispersal of Austroasiatic languages to South Asia. 
The fourth founder was exclusively present amongst Tibeto-Burman speakers of Manipur and Bangladesh. 
In sum, our new results suggest the arrival of Austroasiatic languages in South Asia during last five thousand years.
Prajjval Pratap Sing, et al., "Counting the paternal founders of Austroasiatic speakers associated with the language dispersal in South Asia" bioRxiv (November 18, 2019) (emphasis added).

Background from the Introduction (emphasis added):

Among the four major language families present in South Asia, the Austroasiatic language family has the smallest number of speakers. Nevertheless, its geographical location and exclusive distribution amongst tribal populations make Austroasiatic one of the most intriguing language families in the context of the Subcontinent where it is represented by the major Mundari and minor Khasi branches. The advancement of technology has helped to resolve the long standing debate about the arrival of Austroasiatic (Mundari) speakers to South Asia. The three types of genetic markers (mtDNA, Y chromosome and autosomes) revealed the extraordinary migratory phenomenon. Because of the incompatible histories of their paternal and maternal ancestries, the origin and dispersal of Austroasiatic language in these populations had remained a debatable issue for many years. For Mundari speakers, the exclusive South Asian maternal ancestry pinpointed their origin in South Asia, whereas their overwhelming East/Southeast-Asian-specific paternal ancestry associated with haplogroup O2a-M95 suggested a dispersal from East to West. Another Austroasiatic branch, Khasi, evinced mixed ancestries for both the paternal and maternal lines. Over a century of ethnographical and Indological scholarship had identified Austroasiatic language communities as representing the earliest settlers of South Asia, so that this view represented the consensus. Then, the increasing resolution of the Y-chromosomal tree and Y-STR-based coalescent calculations began to challenge our view of these populations. Despite the problems with STR-based coalescent calculations, the Y-STR variance for haplogroup O2a-M95 was consistently reported to be significantly higher in Southeast Asia. 
With the technological advancement, a much clearer picture has now emerged, showing a strong association of largely male mediated gene flow for the dispersal of Mundari speakers from Southeast Asia to South Asia. The autosomal data showed a bidirectional gene flow between South and Southeast Asia. In addition, the global distribution and internal phylogeny of Y-chromosomal haplogroup O2a-M95 decisively demonstrated that this language dispersal transpired from Southeast Asia to South Asia. In a recent genome-wide study of a large number of South and Southeast Asian populations, Dravidian speakers of Kerala and Lao speakers from Laos were found to be the best ancestral proxies for Mundari speakers. The admixture dates for these ancestries were estimated to be between 2-3.8 kya. Moreover, this study also found clear-cut genetic differentiation between North and South Munda groups.
Based on the prevalence of haplogroup O2a-M95, the arrival of Mundari speakers to South Asia was shown to have been largely male-mediated. However, it remained unclear how many paternal founders had brought this haplogroup to South Asia. The recent admixture time estimated through autosomal data has now narrowed down the arrival of Mundari ancestors to South Asia. Therefore, a marker such as M95, which originated >12 kya, would not help us to understand the most recent founding lineages. The association of haplogroup O2a-M95 with the arrival of Mundari speakers has been explored previously in detail. However, the lack of downstream markers made it impossible to discern the number of most recent founders who had originally borne the language to South Asia. Moreover, previous studies on Tibeto-Burman populations of Northeast India and Bangladesh also reported this same haplogroup, giving rise to the contentious question as to whether the expansion of Tibeto-Burmans could have involved the assimilation of Austroasiatic populations. 
Therefore, we took advantage of recent technological advancements and extracted the downstream SNPs associated with Munda-related populations from one of our recent studies. We genotyped these SNPs for large number of Mundari, Tibeto-Burman and Bangladeshi population groups and reconstructed the phylogeographical distribution of downstream branches of haplogroup O2a-M95 in South Asia.
From the body text (emphasis added):

The diverse founders as well as the large number of unclassified samples (41% for Mundari, 38% for Khasi and 1% for Tibeto-Burmans) suggest that the migration of Austroasiatic speakers to South Asia was not associated with the migration of a single clan or a drifted population. 
Neither does the contrasting distribution of various founders discovered in this study amongst both Mundari and Tibeto-Burman populations support the assimilation of the former to the latter. 

Youngest Homo Erectus Remains Are About 100,000 Years Old

This reaffirms the paradigm and status quo, that Homo erectus had a million year run in Asia and vanished shortly (percentage-wise) before modern humans arrived.

Razib reminds us that there were many archaic hominin species in Asia contemporaneously with Homo erectus, including Neanderthals, Denisovans, the "hobbits" of Flores, and an additional species or three in the Philippines and possible China too. Modern humans reached Sumatra no later than 70,000 years ago, immediately after the Toba eruption.

It wouldn't be surprising to find new Homo erectus remains later, or new modern human remains earlier, that would narrow the gap between the two species or possible leave evidence of a brief overlap like the 1,000 years overlaps characteristic of Europe at a local level.

This species diversity may have flowed from topographies and ecologies that created many separate and independent ecological micro-niches that could not be sustained, for example, on a broad flat plain or in an area with thin trees cover and rolling hills.

My personal conjecture is that the Toba eruption resulted in temporary ecological changes that devastated the already low density H. erectus population and cleared the way for an influx of modern humans from South Asia via Myanmar. Modern humans eventually killed almost all of the stragglers, although relict populations of H. erectus may have survived many thousands or tens of thousands of years past first contact and I don't rule out the possibility that there is still a small relict population of archaic hominins or archaic hominin hybrids deep in some Indonesian jungle. If archaic hominins continue to exist anywhere, it is probably there.  
Homo erectus is the founding early hominin species of Island Southeast Asia, and reached Java (Indonesia) more than 1.5 million years ago. Twelve H. erectus calvaria (skull caps) and two tibiae (lower leg bones) were discovered from a bone bed located about 20 m above the Solo River at Ngandong (Central Java) between 1931 and 1933, and are of the youngest, most-advanced form of H. erectus. Despite the importance of the Ngandong fossils, the relationship between the fossils, terrace fill and ages have been heavily debated. 
Here, to resolve the age of the Ngandong evidence, we use Bayesian modelling of 52 radiometric age estimates to establish—to our knowledge—the first robust chronology at regional, valley and local scales. We used uranium-series dating of speleothems to constrain regional landscape evolution; luminescence, 40argon/39argon (40Ar/39Ar) and uranium-series dating to constrain the sequence of terrace evolution; and applied uranium-series and uranium series–electron-spin resonance (US–ESR) dating to non-human fossils to directly date our re-excavation of Ngandong.
We show that at least by 500 thousand years ago (ka) the Solo River was diverted into the Kendeng Hills, and that it formed the Solo terrace sequence between 316 and 31 ka and the Ngandong terrace between about 140 and 92 ka. Non-human fossils recovered during the re-excavation of Ngandong date to between 109 and 106 ka (uranium-series minimum) and 134 and 118 ka (US–ESR), with modelled ages of 117 to 108 thousand years (kyr) for the H. erectus bone bed, which accumulated during flood conditions These results negate the extreme ages that have been proposed for the site and solidify Ngandong as the last known occurrence of this long-lived species.
Yan Rizal, et al., "Last appearance of Homo erectus at Ngandong, Java, 117,000–108,000 years ago" Nature (December 18, 2019). doi:10.1038/s41586-019-1863-2

Tuesday, December 3, 2019

Astronomy Observations Supporting Dark Energy's Existence May Actually See Large Scale Structure

Executive summary

Is dark energy the dominant kind of stuff in the universe? 

Maybe not. 

A credible analysis of a data set much larger than the on supporting the existence of dark energy when it was proposed imply that the fact that the data supporting the existence of dark energy comes from supernovae which have a skewed distribution favoring certain parts of the sky suggest that what looked like dark energy may actually be an observation of large scale structure in the universe.


The Standard Model of Cosmology

The "Standard Model of Cosmology" also known as the ΛCDM model, where Λ (pronounced "lambda") is the cosmological constant of General Relativity, and CDM stands for "cold dark matter" (confusingly a term defined in a manner consistent with both "warm dark matter" and "cold dark matter" in non-cosmology contexts).

The ΛCDM model is the leading overarching framework for understanding the structure and logic of our astronomy observations at the sale of the universe as a whole and its large scale structure. Its prominence derives from the fact that it can be fit consistently to astronomy observations of very large cosmological scales with just seven or so parameters determined based upon astronomy observations. 

The ΛCDM model also provides a plausible framework that could produce sometimes reasonable similar to the structure of the existing universe at the scale of galaxies and galaxy clusters, although fitting the astronomy data to observations at this scale has been more problematic.

Even at the cosmological level, the ΛCDM model has critics who are credible, smart, well-qualified PhD astronomers, astrophysicists and cosmologists, who argue that new data requires modification of this model. This post is about one such criticism.

Dark Energy

In General Relativity with a cosmological constant, the cosmological constant is a constant baseline amount of mass-energy per volume of spacetime that exists in a vacuum (in models where this mass-energy is something separate from the spacetime itself this is most often called "quintessence" or "dark energy". In this model, the universe constantly expands in volume from a mere volumeless point at the moment of the Big Bang and expands at the speed of light, and the amount of dark energy in the universe is proportionate to the volume of the universe. 

Dark energy violates conservation of mass-energy in the ordinary sense by increasing as the volume of universe expands.

Ordinary matter and dark matter

In contrast, in the ΛCDM model, the aggregate amount of ordinary matter and cold dark matter in the universe is constant, so the density of ordinary matter and cold dark matter in the universe declines as a function of one over the age of the universe (currently about 14 billion years in round numbers).

Ordinary matter, cold dark matter (and also all forms of mass-energy in the universe other than dark energy, such as kinetic energy and photons), perfectly obeys the conservation of mass-energy (although quantum mechanics allows mass-energy to be temporarily "borrowed" in non-observable intermediate steps of physics phenomena making possible phenomena like quantum tunneling which is necessary, for example, for transistors to work as they do, something that would be impossible in the classical electromagnetic theory summarized in Maxwell's equations). 

Everything other than dark energy in the universe is constantly expanding in all directions with the momentum of the Big Bang modified by gravitational pulls in all directions from everything else in the universe, although everything other than massless particles (basically photons) is doing this at less than the speed of light. So, clumps of matter like galaxies constant get more distant from each other, on average.

In the absence of dark energy, the average rate of this expansion would be constant, driven at first order by the momentum of the Big Bang, and modified up or down at second order (in an amount hat would average out over time), by the proximity of other ordinary matter, dark matter and radiation in its vicinity.

The phenomenological implications of dark energy

But, in the ΛCDM model, the constant increase in the aggregate mass-energy of the universe, by continually adding dark energy at the outer boundary of the universe as the volume of space in the universe expands at the speed of light away from the Big Bang, causes the rate at which ordinary matter and dark matter in the universe expands away from other ordinary matter and dark matter in the universe to accelerate because the newly created dark energy is pulling it outward.

Dark energy's existence is inferred in the ΛCDM model when the the rate at which ordinary matter and dark matter in the universe expands away from other ordinary matter and dark matter in the universe to accelerates.

Measuring dark energy

This acceleration can be inferred from astronomy observations because the finite speed of light means that our astronomy observations of things that are further away (something that can be determined using a phenomena known as "red shift") are further back in time. So, if the rate at which distant objects of expanding away from each other is slower than the rate at which close objects are expanding away from each other, then we can use the difference between those rates to determine the cosmological constant and the amount of dark energy as a proportion of the total mass-energy of the universe at the present time.

Using astronomy observations to determine the relative amounts of dark energy, cold dark matter and ordinary matter in the universe, in a model dependent way using the ΛCDM model, implies that right now, 14 billion years after the Big Bang, dark energy accounts for about 70% of the aggregate mass-energy of the universe at the present time, while about 30% of the aggregate mass-energy of the universe at the present time is other stuff, mostly ordinary matter (about 5% in round numbers) and dark matter (about 25% in round numbers).

The main astronomy observation we use to estimate the amount of dark energy in the universe is the distribution of Type Ia supernovae in the observable universe. These supernovae produce a very distinctive electromagnetic signal which is consistent among supernovae of this type that makes it possible to accurately determine their distance and hence how long ago they occurred based upon how redshifted the electromagnetic signal (mostly with visible light, but also with other wavelengths of light), which can be combined with the location in the sky where it is observed to mark a four dimensional Type Ia supernovae map from which expansion rates can be determined. (These supernovae also happen a predictable rates in a well understood astrophysical process.)

Similarly, according to the ΛCDM model, a little more than 7 billion years ago, about 34% of the mass energy of the universe was dark energy, about 11% was ordinary matter, and about 55% was cold dark matter.

Isotropy v. Anisotropy

But, in order to accurately calculate the amount of dark energy in the universe we have to make some key assumptions which we use to fit our astronomy observations to the ΛCDM model.

One of the key assumptions that goes into converting astronomy observations into a cosmological constant value (which combined with the age of the universe can be used to determine the amount of dark energy in the universe), is that the universe is isotropic. This means that at cosmological scales (i.e. the scale of large chunks of the entire universe), that the observable properties of any given large chunk of the universe is basically identical and symmetrical. 

In contrast, if the universe is anisotropic, then there is very large scale structure in the universe (presumably an imprint of trends put in place by the way that random outcomes of very early events in the universe, possibly at a quantum mechanical level in the first few seconds of the universe even, turned out).

An anisotropic universe isn't a horribly outrageous or absurd idea. At the scale of our local few dozen galaxies, the universe is undeniably anisotropic. There are big clumps of matter that make up galaxies and galaxy clusters, and vast comparatively empty spaces with only a little hydrogen gas and dust and a few stray isolated stars and rocks in them. And the number of galaxies in each spatial direction is not the same.

Whether the universe is isotropic or anisotropic at the cosmological scale of the entire observable universe is, in principle at least, a question that doesn't have a Platonically right or wrong answer as a matter of pure reason that can be determined empirically from astronomy observations.

The New Paper

A six page paper published in a peer reviewed scientific journal two weeks ago suggests that the astronomy observations suggesting that the rate at which the ordinary matter and cold dark matter in the universe is expanding is accelerating is just an optical illusion arising from the fact that the universe is actually anisotropic at cosmological scale. 

As a result, from our vantage point on Earth, we may actually be seeing the large scale structure of the universe and misinterpreting those observations as the acceleration of the universe due to dark energy. The paper asserts that this happens because we are using the ΛCDM model to fit our observations because the ΛCDM model counterfactually assumes that the universe is isotropic. 

While this would be bad news for a core tenant of the ΛCDM model and mean that everything we've been told about cosmology for decades is significantly inaccurate, this could be good news for fundamental physics. This is because there are deep problems involved in figuring out the fundamental laws of physics in models where the core law of conservation of mass-energy is not observed globally by gravity, even though the Standard Model of Particle Physics obeys this law and all local observations of gravity obey this law. And, the assumption of isotropy which is displaced is an assumption about empirical reality, rather than itself being a fundamental law of physics that needs to be true.

In particular, it is much easier to devise a model of quantum gravity in which gravity observes the same law of conservation of matter-energy that the Standard Model does, than it is to do so in which some gravitational phenomena does not observe that law.

The abstract of the paper and its citation are as follows:
Observations reveal a “bulk flow” in the local Universe which is faster and extends to much larger scales than are expected around a typical observer in the standard ΛCDM cosmology. This is expected to result in a scale-dependent dipolar modulation of the acceleration of the expansion rate inferred from observations of objects within the bulk flow.

From a maximum-likelihood analysis of the Joint Light-curve Analysis catalogue of Type Ia supernovae, we find that the deceleration parameter, in addition to a small monopole, indeed has a much bigger dipole component aligned with the cosmic microwave background dipole, which falls exponentially with redshift z: q0 = qm + qd.n̂ exp(-z/S). The best fit to data yields qd = −8.03 and S = 0.0262 (⇒d ∼ 100 Mpc), rejecting isotropy (qd = 0) with 3.9σ statistical significance, while qm = −0.157 and consistent with no acceleration (qm = 0) at 1.4σ. Thus the cosmic acceleration deduced from supernovae may be an artefact of our being non-Copernican observers, rather than evidence for a dominant component of “dark energy” in the Universe.
Jacques Collins, et al., "Evidence for Anisotropy of cosmic acceleration", 631 Astronomy and Astrophysics L13 (November 20, 2019) DOI:

Hat tip to Backreaction. As Sabine Hossenelder explains in this blog post:
The most important evidence we have for the existence of dark energy comes from supernova redshifts. Saul Perlmutter and Adam Riess won a Nobel Prize for this observation in 2011. . . . They used the distance inferred from the brightness and the redshift of type 1a supernovae, and found that the only way to explain both types of measurements is that the expansion of the universe is getting faster. And this means that dark energy must exist. 
Now, Perlmutter and Riess did their analysis 20 years ago and they used a fairly small sample of about 110 supernovae. Meanwhile, we have data for more than 1000 supernovae. For the new paper, the researchers used 740 supernovae from the JLA catalogue. But they also explain that if one just uses the data from this catalogue as it is, one gets a wrong result. The reason is that the data has been “corrected” already.

This correction is made because the story that I just told you about the redshift is more complicated than I made it sound. That’s because the frequency of light from a distant source can also shift just because our galaxy moves relative to the source. More generally, both our galaxy and the source move relative to the average restframe of stuff in the universe. And it is this latter frame that one wants to make a statement about when it comes to the expansion of the universe.

How do you even make such a correction? Well, you need to have some information about the motion of our galaxy from observations other than supernovae. You can do that by relying on regularities in the emission of light from galaxies and galaxy clusters. This allow astrophysicist to create a map with the velocities of galaxies around us, called the “bulk flow” . 
But the details don’t matter all that much. To understand this new paper you only need to know that the authors had to go and reverse this correction to get the original data. And then they fitted the original data rather than using data that were, basically, assumed to converge to the cosmological average. 
What they found is that the best fit to the data is that the redshift of supernovae is not the same in all directions, but that it depends on the direction. This direction is aligned with the direction in which we move through the cosmic microwave background. And – most importantly – you do not need further redshift to explain the observations. 
If what they say is correct, then it is unnecessary to postulate dark energy which means that the expansion of the universe might not speed up after all. 
Why didn’t Perlmutter and Riess come to this conclusions? 
They could not, because the supernovae that they looked were skewed in direction. The ones with low redshift were in the direction of the CMB dipole; and high redshift ones away from it. With a skewed sample like this, you can’t tell if the effect you see is the same in all directions. 
What is with the other evidence for dark energy? 
Well, all the other evidence for dark energy is not evidence for dark energy in particular, but for a certain combination of parameters in the concordance model of cosmology. These parameters include, among other things, the amount of dark matter, the amount of normal matter, and the Hubble rate. 
There is for example the data from baryon acoustic oscillations and from the cosmic microwave background which are currently best fit by the presence of dark energy. But if the new paper is correct, then the current best-fit parameters for those other measurements no longer agree with those of the supernovae measurements. This does not mean that the new paper is wrong. It means that one has to re-analyze the complete set of data to find out what is overall the combination of parameters that makes the best fit.
The post there concludes as follows:
This paper, I have to emphasize, has been peer reviewed, is published in a high quality journal, and the analysis meets the current scientific standard of the field. It is not a result that can be easily dismissed and it deserves to be taken very seriously, especially because it calls into question a Nobel Prize winning discovery. This analysis has of course to be checked by other groups and I am sure we will hear about this again, so stay tuned.

This is basically a rehash of an analysis previously published by an overlapping group of authors in 2016. A more technical discussion of the 2016 paper can be found at 4gravitons. 

There is also an unrelated major 2015 paper revealing a systemic issue involved in dark energy calculations, which is that there are basically two kinds of type Ia supernovae which have to be distinguished and that grouping them in one pool of data undermines its precision and reliability. I summarized that paper in the linked post as follows:
It turns out that there are two different subtypes of type 1a supernovas, with one more common in the early universe, and the other more common recently. They are very hard to distinguish in the visible light spectrum, but have clear differences in the UV spectrum. As a result, the rate at which the universe is expanding, if indeed it is expanding, and the amount of dark energy in the universe, are systemically overestimated by a significant amount. 
Less dark energy may, however, mean that another cosmology mystery is more profound. This could bring the relative amounts of dark matter and dark energy in the universe closer together, something that is already called the cosmic coincidence problem because there is no obvious theoretical reason for the two dark components of cosmology to be so similar in aggregate amount.
It isn't clear to me if the 2016 and 2019 paper account for the issue discovered in the 2015 paper. If they don't, the case for there not being net dark energy may be even stronger. 

Monday, December 2, 2019

European Barbarians Had Varied Y-DNA Within Populations

I'll comment more if I have time, but the headline points out what I think is the most notable point. This kind of Y-DNA diversity doesn't happen overnight. It takes generations. This points to a diversity of ancestry among discrete groups of "barbarians" in Europe that is greater than usually appreciated and a more cosmopolitan culture among these groups than is often appreciated.

Also, while the Hungarian example is usually considered an extreme counterexample of demic diffusion of language, with language shift secured despite minimal genetic introgression, there is lots of Uralic Y-DNA (see also Eurogenes) in this ancient DNA sample from Hungary.

Via Bernard's Blog. From that post (translated by Google from the French original):
Endre Neparáczki and his colleagues have just published a paper entitled: Y-chromosome haplogroups from Hun, Avar and conquering Hungarian nomadic period people of the Carpathian Basin. They analyzed the Y chromosome haplogroups of several individuals from 8 cemeteries in Hungary hosting Hungarian conquerors but also individuals from the previous Hun and Avar periods. The authors also tested some autosomal markers associated with eye, hair and skin color, and lactose tolerance. The authors obtained results for 46 men including three from the Hun period and 14 from the Avar period.