Thursday, April 27, 2017

Ancient DNA From Cave Dirt

Usually, ancient DNA samples come from the interior of teeth for tooth enamel protects them from the elements for thousands or even tens of thousands of years. But, improved methods are making it possible to recover ancient DNA from less well guarded sources. Basically, scientists can now do CSI class forensic DNA work from scenes that are up to 240,000 years old.

The fragments, predominantly of mtDNA, aren't necessarily good enough to do much more than identify a species of the contributing source of the DNA. But, these scraps can put better definition on the geographic and temporal range of hominin and other mammal species.

This is particularly notable in the case of the Denisova cave, where these scraps add considerably to the time period in which we can document the existence of the archaic hominin species named after the cave, even though we will don't know what Denisovans looked like because we have no reasonably complete skeletal remains.
Slon’s work continues that tradition—she found Denisovan DNA in sediment that’s far older than any of the unearthed fossils. “It’s evidence that Denisovans occupied the cave for tens of thousands of years earlier than we thought,” she says.
The quotation above is from a story in The Atlantic that profiles the results in the Science article from a layman's perspective. The Denisovan bones that were found in 2008 were 30,000 to 50,000 years old. The new Denisovan ancient DNA was found in a Middle Paleolithic layer (MP) as opposed to a Lower Paleolithic layer (LP). 

Conventionally, the Upper Paleolithic is about 50,000 to 10,000 years ago (corresponding to pre-farming Out of Africa and behaviorally modern humans more generally), the Middle Paleolithic is about 300,000 to 50,000 years ago (basically, the Neanderthal years in Europe and the rise of modern humans in Africa), and, the Lower Paleolithic is about 3,300,000 to 300,000 years ago (basically, the pre-Neanderthal, pre-modern human time period in which there were still archaic hominids of some kind). 

The dawn of farming in the Neolithic era marks the end of the Upper Paleolithic era, which yields to the Chalcolithic era (the Copper Age) (ca. 3600 BCE to ca. 2500 BCE), the Bronze Age (ca. 2500 BCE to 1200 BCE), the Iron Age (ca. 1200 BCE to 500 CE), the Middle Ages (ca. 500 CE to 1500 CE), and the Modern Period (ca. 1500 CE to the present). These technologically defined time periods, however (especially the Neolithic Revolution which takes about 4000 years to spread from its point of inception in the Fertile Crescent to the farthest reaches of Europe) reach different places at different times.

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.
Viviane Slon, et al., "Neandertal and Denisovan DNA from Pleistocene sediments" Science (April 27, 2017).

A Map Of Ancient Lower Egypt

Lower Egypt refers to altitude, not north-south latitude. This is a map showing the Nile and major cities and sites of the Dynastic period (ca. 3150 BCE to 30 BCE).

From here.

Wednesday, April 26, 2017

A Pre-Homo Sapiens Hominin Presence In California? Probably Not.

Archaeologists found mastodon bones in San Diego, California that were revealed in connection with road work, that were uranium isotype dated to 130,700 years old plus or minus 9,400 years. So far, unsurprising and nothing different from the kinds of finds that have been coming out of the Le Brea tar pits not far from there for decades.

What is surprising is the claim that has been made about these bones:
Based on several lines of evidence—the way the bones are broken, the way they lay, the presence of large stones that show curious patterns of wear and are out-of-place in the surrounding sediment—the team think that early humans used rocks to hammer their way into the mastodon’s bones. That wouldn’t have been contentious in itself, but the team also claims that the bones from the “Cerruti Mastodon” are 130,000 years old. That would push back the earliest archaeological evidence for humans in North America by a whopping 115,000 years. . . .
To put that in perspective, for decades, the first American settlers were thought to be the Clovis people, who arrived 13,000 years ago. But by discovering older sites with strong evidence of human activity, archaeologists confirmed that the continent had a pre-Clovis presence that dates back 14,600 years—or perhaps even further. Genetic studies have also suggested that modern humans entered America from Asia even earlier, around 23,000 years ago. . . .
They found the mastodon’s bones in a couple of concentrated clusters rather than in a scattered mess. The tops of both thigh-bones had broken off and were lying side-by-side, amid a concentration of other bones. One of the tusks was lying horizontally in the sediment, the other was sticking up vertically. The team think that the remains of a naturally decaying mastodon wouldn’t have ended up in such distinctive patterns—and the bones of nearby bones of wolves and horses certainly didn’t.

And although fragile bones like ribs and vertebrae were still intact, stronger ones like molars and thigh-bones were broken. The fractures aren’t consistent with chewing teeth or trampling feet; instead they look like the breaks you get when you deliberately smash a still-living bone. The team even tried doing this: they smacked modern elephant and cow bones with rocks, and got fractures very similar to the ones on the Cerruti mastodon.

At the site, the team found five large stones (cobbles) amid their clusters of bones, which could have acted as hammers and anvils. These rocks sat in a layer of fine, silt-like sediment, and were far bigger and harder than anything around them. “How did they get there?” says Deméré. “They weren’t being transported by flowing water at the same time as the silt.” Instead, he suggests that they were carried to the site and used to infiltrate the mastodon bones—presumably to get at the marrow within. Sure enough, the rocks showed signs of impact, and the team even managed to fit several detached flakes back onto the “parent” stones.
The gap between the genetic date and the archaeological one is attributed to the "Beringian standstill theory" which holds that the founding population of the Americas entered Beringia around 23,000 years ago, couldn't go further to enter North America from this location due to massive glaciers at the peak of the Last Glacial Maximum, and then started to migrate south to the Americas starting around 15,000 years ago when a gap in the ice emerged.

A date 130,000 years ago would make this find contemporaneous with, or even a few thousand years earlier than, the earliest modern human presence outside of Africa in the Levant and Arabia, and long before any evidence that modern humans had managed to get as far as what is now Turkey, Iran, Pakistan or India.

In other words, if it was a hominin at all, it would probably have to be an archaic hominin, such as Homo Erectus, a Neanderthal, a Denisovan, or a "Hobbit". But, to make the trip to from Siberia to the Pacific Coast of California, you have to pass through the Arctic and near Arctic territory in that vicinity which there is no evidence that "Hobbits" or Homo Erectus ever could.

Now, there is evidence that there were Neanderthals in the Altai Mountains at the Southern rim of Siberia, as late as 100,000 years ago, and Denisovans would also have been in that vicinity in roughly the right time frame, and either of them could have chased herds of megafauna that led them to North America. But, there is no definitive evidence of either Neanderthals or Denisovans east of the Altai, and certain no evidence of either of them in the Americas at any time.

And, they would have to get there at just the right time. Beringia is only a passable land bridge during major global ice ages. So, they would have had to make the trek sometime before 130,000 years ago during an ice age as severe as the Last Glacial Maximum of 20,000 years ago.

There were indeed some ice ages in the relevant time period.

A date 130,000 +/- 9,400 years ago could have been in the period immediately following an ice age that peaked around 145,000 years ago followed by rapid warming. An ice age peak 340,000 years ago (which may not have been severe enough to give rise to a land bridge) and an ice age peak about 430,000 years ago (which would have been comparable to the Last Glacial Maximum) may have been severe enough to give rise to passable land bridges from Siberia to North America. But before that, there probably wouldn't have been a Eurasian hominin species that could have made the trek.

The trouble is that no one has ever found any hominin or even great ape remains in North America or South America that are not modern human, no one has found any hominin remains (or other other clear traces like footprints) in North America or South America that old, and no one has found any convincingly hominin made tools that old in North America or South America, at least until now.

There are alternative potential explanations. Maybe giant sloths or bears figured out how to use very primitive tools. Maybe the bones really were 130,000 years old, but the hominins who tried to break them up and process them with large stones came along 115,000 years later. Maybe the stones were formed by natural processes and the beast that took them down was a bit OCD. But, the huge gap in the archaeological record until this find appears prompts the maxim that extraordinary claims require extraordinary evidence, while the evidence at this sight is highly indirect, highly inferential, and ultimately pretty marginal.

While this is an interesting hypothesis to entertain, and this find is enough to form the basis of a legitimate scientific hypothesis, ultimately, it is too little to support such an extraordinary paradigm shift by itself.

Tuesday, April 25, 2017

Are Ergative Languages A Sign Of An Ancient And Now Diminished Language Family?

Before being displaced by Semitic and Indo-European languages, most of the languages of Mesopotamia (e.g. Sumerian), the highland of West Asia (e.g. Elamite, Kassite, Hurrian), Anatolia (Hattic, Urartian, Kaskian), and the Caucasus mountain region (almost all Northwestern, Northeastern and Southern Caucasian languages) were ergative languages, a linguistic feature related to verb tense that is not notable for historic linguistic purposes for being a deep structural grammatical feature of certain languages than it is for the details of how it works when you are using the language.

There are also a few outlier ergative languages that exist today of uncertain provenance. Basque is ergative. A couple of Western Berber languages seem to have an ergative substrate.

I suspect that many pre-IE Aegean languages, including Minoan and a Peloponnese language which is a substrate in Greek share this grammatical trait.

I also suspect that the Harappan language shares this trait (and FWIW, I strongly suspect that the Harappans did not speak a language in the same family as Dravidian with one source of evidence being the nature of the apparent substrate in Vedic Sanskrit - an interesting article on Vedic Indian is here). One clue: "A lot of Indo-Iranian languages are partially ergative as well, with the Kurdish languages, Pashto, and Baloch". This is suggestive of an ergative substrate in the Harappan trade zone which makes sense given that Elamite of West Asia is ergative and that Harappans have trade ties to Sumeria and probably arrives as West Asian farmers from the Fertile Crescent where their agricultural package was developed over Persia to the Indus River Valley. (Notably, there appears to be genetic continuity between early West Asian farmers and modern Iranian Zoroastrians).

It is possible, even likely, that this was also a feature of the language of the early Caucasian Farmers even pre-Uruk.

Kurdish, an Indo-European language spoken in a historically ergative language region, has ergative traits. Related is that: "There is also ergativity in Northeastern Neo-Aramaic dialects, which I’m pretty sure is the only case in the whole Semitic family. Probably the result of Kurdish influence (1,000-2,000 years of diglossia, in some cases)—but possibly a direct holdover from the Iron Age ergative highlands?" Again, substrate or strong areal influences.

I also suspect that there was an early metal age migration from the Caucasus/Armenia region into Anatolia, possibly elite led, that gave rise to the Hattic culture from there, the Minoan culture, that was in place before the rise of the Indo-European Hittites there, which replaced the first wave Neolithic culture of Anatolia that had probably prevailed until then.

It is also possible that this was true even of the early Anatolian farmers although the Anatolian farmer possibility is more of a stretch, but there are plausible alternative sources for ergative languages in Anatolia since then. But, if it was true, then the language of Early European Farmers (LBK and CP) was probably ergative and the possibility of Basque being a language of the first farmers acquired by migrant men in Iberia from their local wives, rather than a transplant from a homeland where an ergative language was spoken. If not, Basque must have been part of a language family that was ergative spoken near where Y-DNA R1b and steppe ancestry were common - a metal working, cow husbandry utilizing civilization that is genetically very much like the proto-Indo-Europeans, but was linguistically very different.

Linguists studying these languages tend to be splitters and not lumpers. But, my own strong intuition is that all of these languages have a common linguistic family relationship, although perhaps at a sufficient time depth that it is difficult to reconstruct a proto-language using the strict comparative method, especially when many of the languages in question are dead and only attested in a fragmentary manner. They have too many features in common and are too distinct, while in close geographic proximity to each other, not to be related.

One plausible means by which this language family may have spread is via the Uruk colonies established in the South and North Caucasus ca. 3500 BCE to 3100 BCE discussed here. It isn't clear when the first farmers reached these areas, but their elaborate phonetics and grammar suggest that these language have had few new language learners or outside influences for many thousands of years. They are relict languages. Razib explains that he is: "alluding to the period between 3500 and 3100 BCE in the Near East when the city of Uruk was the nexus for and a source of a massive cultural and mercantile expansion. I’ll quote Wikipedia:"
Around 3600 BC, during the Middle Uruk period, Uruk trade networks started to expand to other parts of Mesopotamia, and as far as North Caucasus. According to archaeologist Konstantine Pitskhelauri, this expansion started even earlier, at the end of the 5th millennium BC, and continued in the 4th millennium. 
Large masses of Uruk migrants settled in the South, and later in the North Caucasus. The sites in this general area include Habuba Kabira in Syria, and Arslantepe in Turkey. Uruk expansion to the northeast included sites like Godin Tepe in Iran. Tepe Gawra, in northwest Iraq, is another important site with deep stratigraphy that includes the Uruk period in later layers. Hamoukar is a large site in northeastern Syria that has been recently excavated; it includes Uruk and pre-Uruk layers. 
Uruk enclaves have also been identified at Tell Brak and Nineveh in northern Mesopotamia, and on the Syrian Euphrates at Qrayya, and Jebel Aruda. On the Euphrates in Anatolia, Uruk enclaves were found at Hassek Hoyuk, Samsat, and Tepecik (Elazığ Province, near Keban Dam).
Razib suggests that these were Roman-like colonies of migrants, rather than being integrated with local peoples other than through treaties with local tribal chiefdoms and trade. They vanished as completely as they arose.

Monday, April 24, 2017

65,000 Years Of Beringia In Maps

The linked post shows images of how Beringia looked on a map at regular intervals over the last 65,000 years. The land bridge was more long lived than usually recognized.

Saturday, April 22, 2017

Hobbits Are Not Dwarf H. Erectus

Most people had already rejected the theory that H. florensiensis (Hobbits) were diseased humans. But, this new physical anthropology study rules out the possibility that they are derived from H. erectus, because their bones show more primitive and basal features.

The is notable because it also largely rules out the theory that Hobbits are a subtype of Denisovans or H. heidelbergensis. Instead, it seems likely that they left Africa before or contemporaneously with H. erectus and are closer to H. habilis than any other known species of Homo.
The most comprehensive study on the bones of Homo floresiensis, a species of tiny human discovered on the Indonesian island of Flores in 2003, has found that they most likely evolved from an ancestor in Africa and not from Homo erectus as has been widely believed. The study by The Australian National University (ANU) found Homo floresiensis, dubbed "the hobbits" due to their small stature, were most likely a sister species of Homo habilis -- one of the earliest known species of human found in Africa 1.75 million years ago. 
Data from the study concluded there was no evidence for the popular theory that Homo floresiensis evolved from the much larger Homo erectus, the only other early hominid known to have lived in the region with fossils discovered on the Indonesian mainland of Java. . . .
Homo floresiensis is known to have lived on Flores until as recently as 54,000 years ago.
The study was the result of an Australian Research Council grant in 2010 that enabled the researchers to explore where the newly-found species fits in the human evolutionary tree. 
Where previous research had focused mostly on the skull and lower jaw, this study used 133 data points ranging across the skull, jaws, teeth, arms, legs and shoulders. 
Dr Argue said none of the data supported the theory that Homo floresiensis evolved from Homo erectus. 
"We looked at whether Homo floresiensis could be descended from Homo erectus," she said. 
"We found that if you try and link them on the family tree, you get a very unsupported result. All the tests say it doesn't fit -- it's just not a viable theory." 
Dr Argue said this was supported by the fact that in many features, such as the structure of the jaw, Homo floresiensis was more primitive than Homo erectus. 
"Logically, it would be hard to understand how you could have that regression -- why would the jaw of Homo erectus evolve back to the primitive condition we see in Homo floresiensis?" 
Dr Argue said the analyses could also support the theory that Homo floresiensis could have branched off earlier in the timeline, more than 1.75 million years ago. 
"If this was the case Homo floresiensis would have evolved before the earliest Homo habilis, which would make it very archaic indeed," she said. 
Professor Mike Lee of Flinders University and the South Australian Museum, used statistical modeling to analyse the data. 
"When we did the analysis there was really clear support for the relationship with Homo habilis. Homo floresiensis occupied a very primitive position on the human evolutionary tree," Professor Lee said. 
"We can be 99 per cent sure it's not related to Homo erectus and nearly 100 per cent chance it isn't a malformed Homo sapiens," Professor Lee said.
From Science News.
Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. 
We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. 
The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens.
Debbie Argue, Colin P. Groves, Michael S.Y. Lee, William L. Jungers. "The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters." Journal of Human Evolution (April 2017).

UPDATE April 24, 2017:
The [Hobbit] skull was astonishingly small: around just 400 cubic centimetres. This was a good 200cc less than the cranial capacity of any fossils then included in our our genus, Homo. Just for comparison, your brain will measure somewhere between 1,000 and 2,000cc. . . . Earlier Homo erectus specimens were known from east and South-East Asia. Perhaps, suggested some researchers, the Flores hominin was an offshoot of Homo erectus, and had undergone “island dwarfing”. Other experts were not so sure; the anatomy of Homo floresiensis seemed too primitive. . . .The shape of the pelvis and the proportions of the limbs looked primitive – reminiscent of australopithecines, or the earliest of human species, Homo habilis, from around 2-3m years ago. But those hominins only ever lived in Africa … as far as we know. . . .

The Flores hominins were, more clearly than ever, rooted deep in that tree: they could not be descendants of Homo erectus. They came from something more primitive – a close cousin of Homo habilis. But what was an ancient-looking hominin like this doing in Indonesia? 
In the most widely accepted model of human evolution today, the first emergence of hominins out of Africa involved Homo erectus, and happened some time after 2m years ago. But Homo floresiensis raises the tantalising possibility of an earlier expansion of hominins – who were probably not-quite-Homo – out of Africa. 
We know, from reconstructions of ancient climate and geography that it certainly would have been possible for hominins to emerge from Africa as far back as 3m years ago. In fact, other large mammal species – including elephants – did just that.
From The Conversation. Another discussion at the same site notes that a different study found a fit with H. Erectus that this study rejects.

The link on the words "climate and geography" above is to the following review article (whose abstract, unfortunately offers more tease than substance).
The past decade has seen the Pliocene and Pleistocene fossil hominin record enriched by the addition of at least ten new taxa, including the Early Pleistocene, small-brained hominins from Dmanisi, Georgia, and the diminutive Late Pleistocene Homo floresiensis from Flores, Indonesia. At the same time, Asia's earliest hominin presence has been extended up to 1.8 Myr ago, hundreds of thousands of years earlier than previously envisaged. Nevertheless, the preferred explanation for the first appearance of hominins outside Africa has remained virtually unchanged. We show here that it is time to develop alternatives to one of palaeoanthropology's most basic paradigms: ‘Out of Africa 1’.
Robin Dennell and Wil Roebroeks, "An Asian perspective on early human dispersal from Africa", 438 Nature 1099-1104 (December 22, 2005).

Meanwhile the brain of H. Naledi is called tiny but advanced.

UPDATE TWO April 26, 2017:

The following interesting and relevant pre-print was identified by Ryan in the comments:
Introgressions from Neanderthals and Denisovans were detected in modern humans. Introgressions from other archaic hominins were also implicated, however, identification of which poses a great technical challenge. 
Here, we introduced an approach in identifying introgressions from all possible archaic hominins in Eurasian genomes, without referring to archaic hominin sequences. We focused on mutations emerged in archaic hominins after their divergence from modern humans (denoted as archaic-specific mutations), and identified introgressive segments which showed significant enrichment of archaic-specific mutations over the rest of the genome. Furthermore, boundaries of introgressions were identified using a dynamic programming approach to partition whole genome into segments which contained different levels of archaic-specific mutations. 
We found that detected introgressions shared more archaic-specific mutations with Altai Neanderthal than they shared with Denisovan, and 60.3% of archaic hominin introgressions were from Neanderthals. Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes. Above results suggested a complex admixture history among hominins. The proposed approach could also facilitate admixture research across species.
Ya Hu, et al., "Genome-wide Scan of Archaic Hominin Introgressions in EurasiansReveals Complex Admixture History" (2014).

According to the pre-print an introgression from an unknown archaic hominin which diverged from modern humans approximately 859,000 years ago is "close to the reported divergence time between Africans and the ancestors of Neanderthals and Denisovans." It further concluded that "segments bore much higher similarity to Neanderthal than to Denisovan genomes." It goes on to infer that these segments are derived from an archaic hominin species that is a Neanderthal or Neanderthal-like.

With regard to the mysterious Class 3 segments that have the much older divergence date, the paper notes that:
Class3 segments were those most distantly related to the African genome, with a divergence (3,464 kya) about the time of, or earlier than, the exodus of Homo erectus out of Africa. The probability that a segment was not broken by recombination, assuming a hypothetical African origin (ρ- value in Table 1), was low in class3 segments; thus, it was unlikely that class3 segments were derived from the African genome. 
Overall, 37.1% of class3 segments were adjacent to a class2N segment. Simulation results did not support the hypothesis that class3N and class2N introgressed independently into the Eurasian genome (see Material and Methods). A majority (86.5%) of the class3N segments bore high similarity (>80%) to the Neanderthal genome. Thus, our results suggested that the class3N segments of unknown archaic hominins introgressed into the Eurasian 7 genome via the Neanderthal genome introgression, together with the class2N segments. 
The class3 segments that were not adjacent to class2 segments (denoted as class3E segments) accounted for 0.35% of the genome. These segments were flanked by AMH segments with low E-allele rates and low similarity with the Neanderthal genome. Furthermore, they were significantly shorter than the class2N segments (1:10 on average, p<2.2×10-16), which suggested that class3E segments existed in modern humans earlier than the time that Neanderthal genomic segments entered the Eurasian genome. These results indicate that class3E segments could also be derived from unknown archaic hominins, but probably not from Neanderthal introgression. Interestingly, 28.5% of class3E segments overlapped with at least one class3N segment; thus, those segments were unlikely to have been derived from independent origins (p<2.2×10^-16). 
We observed only one module (close to a similarity=1) in the distribution of pairwise similarities among the overlapping segments of class3. This finding suggested that class3 segments could be attributed to a single archaic hominin, which we refer to as hominin-E. We hypothesized that four possible models might explain the introgression from hominin-E to modern humans and Neanderthals (see Discussion). The most parsimonious model held that a single introgression occurred from hominin-E to the ancestors of modern humans and Neanderthals. This explanation was consistent with the reported results that an archaic hominin (Tafr>1 Mya) contributed to the Denisovan genome. . . .
Hominin-E genetically diverged from the Africans very early (~3 Mya). One possible source of hominin-E is Homo erectus, which migrated out of Africa at ~1.7 Mya. Another possible source could be the australopithecines, which inhabited Africa; it was proposed that those hominins might have migrated out of Africa at ~3 Mya. 
There are seven possible scenarios that might explain the history of genomic admixtures between hominin-E and other hominins. Class3N segments were derived from the hominin-E introgression in Neanderthals, and class3E segments were derived from the hominin-E introgression in modern humans. Because class3N and class3E segments accounted for only a small proportion of the genome (0.04% and 0.35%, respectively), the probability that 28.5% of class3E segments might overlap with class3N segments was less than 2.2×10-16, when they were derived from different origins. 
Therefore, the observed overlapping class3N and class3E segments could be derived from a hominin-E introgression, which occurred before the divergence of modern humans and Neanderthals. Thus, the scenarios described in Figures S9A, S9B, and S9C are unlikely, because they could not explain the overlapping regions between class3N and class3E segments. Because 32.1% of class3N did not overlap with class3E and 71.5% of class3E did not overlap with class3N, modern humans and Neanderthals might have received an additional hominin-E introgression after their divergence. Therefore, the scenarios in Figures S9E, S9F, S9G are possible. Furthermore, the scenario in Figure S7D is also possible, because the non-overlapping regions of class3N and class3E segments could be explained by genetic drift after the divergence of modern humans and Neanderthals. 
[Ed. The figures are on page 38 of the preprint and actually labeled S7. As referred to above: Figure S9A is an introgression to modern humans but not Neanderthals after the two split, S9B is an introgression to Neanderthals but not modern humans after the two split, S9C involves independent introgressions to modern humans and Neanderthals after the two split. Figure S9D is a single introgression to the pre-split ancestor of modern humans and Neanderthals. Figure S9E adds an additional separate introgression into modern humans but not Neanderthals post-split to S9D. Figure S9F adds an additional separate introgression into Neanderthals but not modern humans post-split to S9D. Figure S9G adds additional independent separate introgressions in modern humans and Neanderthals post-split to S9D.]
For what it is worth, Figure S9D (a single introgression to the pre-split ancestor of modern humans and Neanderthals) seems more plausible to me than the scenarios in Figures S9E, S9F and S9G which involve that pre-split introgression and a subsequent direct introgression into one or both post-modern human/Neanderthal split lines. This is because we already know that the divergence between modern humans and Neanderthals was sufficient to give rise to the effects of Haldane's law of partial hybrid incompatibility at an 800,000 to 900,000 year divergence date. The divergence between the archaic hominin associated with Class 3 genes and the ancestor of Neanderthals, Denisovans and modern humans is 2,600,000 to 2,700,000 years and would be even greater for the derived Neanderthal/modern human offshoots involved.

An introgression from an archaic hominin which diverged from modern humans 3,464,000 years ago that contributed to the genomes of the common ancestors of modern humans and Neanderthals would be consistent with an introgression of Homo habilis genes into H. heidelbergensis which may have been ancestral to both modern humans and Neanderthals.

In late breaking news: The Homo naledi find has been determined to be just 200,000 to 300,000 years old according to a National Geographic interview with the investigator, although the formal journal paper setting forth the methodology by which this was determined has not been released. Also, an independent Homo naledi site has been found not far from the original one. This is much later than anticipated based upon the extent to which the remains appeared to be basal as opposed to derived relative to other archaic hominin finds.

Friday, April 21, 2017

Oldest Temple In World May Have Been Built In Reaction To A Comet Impact

From the LGM to the Younger Dryas

The Last Glacial Maximum (LGM) was the low point of the last major ice age and took place ca. 18,000 BCE. At that time, most of Europe, Siberia and North America were covered with thick glaciers, human in Europe were confined to three small refugia.

The water used in the glaciers and associated polar ice packs greatly lowered the sea level on Earth, connecting the British Isles and Continental Europe with a land bridge; giving rise to a land bridge across the Bering Strait; connecting many islands in island Southeast Asia to each other and the mainland; connecting Papua New Guinea, Australia and the island of Tasmania; making the water passage to the Andaman Island from mainland Southeast Asia much less daunting; and making it easier to reach Japan from mainland East Asia.

As the Earth warmed up again following the LGM, sea levels rose and the glaciers retreated. This allowed the founding population of the Americas expanded from Beringia into North and South America (ca. 12,000-13,000 BCE), and hunter-gatherers from the European refugia and the Near East repopulated Europe, while those hunter-gatherers and others from Asian refugia repopulated Siberia. Populations in the Americas were isolated from the rest of the world. Island Southeast Asians were isolated from mainland Asia and each other. Papua New Guinea was isolated from Australia. And, the Andaman Islands and Japan became more inaccessible from the mainland. Proto-farming was starting to develop in the Fertile Crescent in the Near East (Mesopotamia, Anatolia and the Levant).

Just as the climate was becoming tolerable for farming in many places, the Younger Dryas event occurred. This was a sudden, global, extreme cooling event that started around 10,800 BCE and lasted about 1400 years. This plunged the world into another severe ice age, although not quite as deep an ice age as the LGM. As noted by an author of a paper discussed last month at this blog:
"[T]he Younger-Dryas coincides with the end of Clovis culture and the extinction of more than 35 species of ice-age animals. Moore says while evidence has shown that some of the animals were on the decline before Younger-Dryas, virtually none are found after it. Moore says that would indicate an extinction event for North America." The animals that went extinct included the mastodon, mammoth and saber-toothed tiger.
So climate change, as well as overhunting, appears to have played an important part in the North American megafauna extinction.

Global deposits of rare elements at the time of the Younger Dryas event similar to those found at the CT boundary created by the comet that destroyed the dinosaurs ca. 65 million years ago have made it increasingly clear that the Younger Dryas event was also caused by an extraterrestrial impact, probably by a comet or asteroid about two-thirds of a mile (one kilometer) in diameter, probably originating in the the Taurid meteor stream given its timing, which has now been established quite precisely.

The place where the Younger Dryas object hit the Earth has not yet been identified. This is in some ways a more difficult task because the impact was smaller, but this difficulty is compensated for, in part, because the Younger Dryas impact was much more recent.

Göbekli Tepe

A National Geographic artists impression of Göbekli Tepe shortly after it was completed.  

The Göbekli Tepe in Southeast Anatolia is a sophisticated stone edifice with carved imagines on it that is arguably the earliest temple or astronomical monument in the world. It is located atop a mountain ridge in the Southeastern Anatolia Region of modern-day Turkey, approximately 12 km (7 mi) northeast of the city of Şanlıurfa, not far north of the middle of the border between Syria and Turkey. The tell has a height of 15 m (49 ft) and is about 300 m (980 ft) in diameter. It is approximately 760 m (2,490 ft) above sea level. It is near the northern peak of the Fertile Crescent.

This is particularly notable because it was built by hunter-gathers before crops or farm animals had been domesticated (although domesticated dogs did exist by that point). Its construction coincides with the Younger Dryas event and it was used for about 2,000 years thereafter (i.e. until about 8,000 BCE) this time period corresponds the the archaeological periods in the Near East known as Pre-pottery Neolithic A (PPNA) and Pre-pottery Neolithic B (PPNB).

A new study suggests that the timing of its construction very close in time to the Younger Dryas event was no coincidence. Instead, Göbekli Tepe was probably the response of this community of hunter-gatherers to the Younger Dryas event. It was an observatory as much as it was a temple.
We have interpreted much of the symbolism of Göbekli Tepe in terms of astronomical events. By matching low-relief carvings on some of the pillars at Göbekli Tepe to star asterisms we find compelling evidence that the famous ‘Vulture Stone’ is a date stamp for 10950 BC ± 250 yrs, which corresponds closely to the proposed Younger Dryas event, estimated at 10890 BC. We also find evidence that a key function of Göbekli Tepe was to observe meteor showers and record cometary encounters
Indeed, the people of Göbekli Tepe appear to have had a special interest in the Taurid meteor stream, the same meteor stream that is proposed as responsible for the Younger-Dryas event. Is Göbekli Tepe the ‘smoking gun’ for the Younger-Dryas cometary encounter, and hence for coherent catastrophism?
Martin B. Sweatman and Dimitrios Tsikritsis, "Decoding Göbekli Tepe with archaeoastronomy: What Does The Fox Say?", 17(1) Mediterranean Archaeology and Archaeometry, 233-250 (2017).

Hat tip to Dienekes' Anthrpology BlogThe title of the paper is a silly allusion to a cult classic cute little pop song with international distribution by international artist Ylvis, who has an interest in archaeological (having also written a song about Stonehenge), whose lyrics discuss the sounds that various kinds of animals make, as well as a reference to one of the carvings at the monument.

UPDATE May 2, 2017:

The body text associates the Fox in the imagery with the Northern Taurids and the Northern Aquarius constellation and assigns all of the other animals except the snakes and headless human as symbols for either constellations (a.k.a. asterism) or pole stars. The suspected pole stars, with which the site is aligned, were several thousand years past the point when they actually marked true north, suggesting an astronomy tradition that dated back thousands of years. The associations of symbols with constellations is supported by the fact that they appear in astronomical order. "Handbag" symbols are interpreted as sunsets, given the orientation of the stones.

The v shapes and snakes are suspected to be symbols of comets, and in particular, a known comet whose path is discussed. The headless human is associated with a catastrophe at the time of the Younger Dryas and other symbolism is associated with ash clouds blocking the sky.

The lengthy period of about two thousand years over which the site was built and used suggests that the symbols were being used as a form of astronomy protolanguage, and there are allusions to corresponding use of the same symbols at other sites which are not explored in detail.

The overall site suggests a particular concern with the Taurid meteor shower that was probably the source of the Younger Dryas object.

Overall the presentation is quite convincing and also gives you a feel for the motives and worldview of the people who built this observatory/temple. There appear to have been sacrificial offerings of animals corresponding to the constellations in question.

Did Bell Beaker People Introduce Modern European Dogs?

Dogs similar to modern European dog breeds start to appear in Europe in about the same time and places as the Bell Beaker people and in at least one instance, accompanying a Bell Beaker man in his burial.

Thursday, April 13, 2017

Blog Post Results In Revision Of Next Edition Of New Trade Non-Fiction Book!

This is so unprecedented that it is newsworthy.

Sometimes, voices in the wilderness are heard, although it helps to have a voice that is timely, frequently amplified through mainstream media sources, and has a particularly knowledgable interlocutor.
April 7, 2017
The Particle Zoo: The Search for the Fundamental Nature of Reality
By Gavin Hesketh
Paperback Edition
Quercus (15 Jun. 2017) 
A few weeks ago, I reviewed Gavin Hesketh’s book The Particle Zoo. I found his introduction to quantum field theory very well done. Considering that he can’t rely on equations, Hesketh gets across a lot of details (notably, what Feynman diagrams do and don’t depict). 
However, I was quite unhappy with various inaccuracies in the book, particularly concerning the search for physics beyond the standard model. 
But then something amazing happened! Hesketh sent me an email a few days ago, saying he read my review and revised the manuscript for the paperback edition to address the criticism. While the changes between the two editions will not be large, it usually doesn’t take more than a sentence or two to add some context or a word of caution. And so, I’m happy to endorse the paperback edition of The Particle Zoo which (according to amazon) will appear on June 15th. 
Posted by Sabine Hossenfelder at 6:37 AM

Wednesday, April 12, 2017

Connecting IceCube To Sesame Street

The high energy events observed at the IceCube Neutrino Observatory have triggered many investigations interpreting the highly energetic neutrinos detected as decay products of heavy unstable Dark Matter particles. However, while very detailed treatments of the IceCube phenomenology exist, only a few references focus on the (non-trivial) Dark Matter production part -- and all of those rely on relatively complicated new models which are not always testable directly. 
We instead investigate two of the most minimal scenarios possible, where the operator responsible for the IceCube events is directly involved in Dark Matter production. We show that the simplest (four-dimensional) operator is not powerful enough to accommodate all constraints. A more non-minimal setting (at mass dimension six), however, can do both fitting all the data and also allowing for a comparatively small parameter space only, parts of which can be in reach of future observations. 
We conclude that minimalistic approaches can be enough to explain all data required, while complicated new physics seems not to be required by IceCube.
Marco Chianese and Alexander Merle, "A Consistent Theory of Decaying Dark Matter Connecting IceCube to the Sesame Street" (April 11, 2017).

Why Sesame Street (emphasis mine)?
The IceCube Neutrino Observatory, a neutrino telescope located at the Amundsen-Scott South Pole Station, is a unique window to observe highly energetic neutrinos reaching the Earth’s surface, originating from sources as close as the upper regions of the atmosphere up to extra-galactic objects. Its applications to closer sources range from a more precise determination of the atmospheric neutrino flux over measuring the properties of active neutrinos and constraining those of sterile neutrinos to astrophysical findings such as the shadowing effect of the moon on cosmic rays. As for the wider sources, IceCube’s goal is to investigate several types of astrophysical neutrino emitters, its possible applications ranging from astrophysical point sources over Dark Matter annihilation to supernovae. Finally, also certain exotic particles may leave visible signatures in the detector, such as magnetic monopoles.

A big surprise in the data taken between 2010 and 2013 was the detections of three very high energy events. These events have been under such scrutiny and have generated such an amount of interest, that they have even been given names after characters of the Sesame Street for better recognition: Ernie (1.14 PeV), Bert (1.04 PeV), and Big Bird (2.2 PeV).
Sociologically, this makes a bit of sense as a lot of researchers publishing papers in this field are at about the age when they have children watching Sesame Street.

Friday, April 7, 2017

Warm Dark Matter Parameter Space

A new paper reviews the remaining parameter space that could be consistent with a warm dark matter model. The range of possible masses and other parameters of these dark matter candidates is quite narrow.

Tuesday, April 4, 2017

Waiting for Ancient DNA Data

The world is waiting for results from three important ancient DNA studies that could address longstanding open questions in historical population genetics, but limited to arguments around the edges using mostly existing information, until then.

* One is a huge dataset of ancient Bell Beaker DNA and related samples that would cast light on the Bell Beaker ancient DNA.

* One is a report on ancient Harappan DNA, the first major ancient DNA result from South Asia. Rumors have purported to leak one of the study's main findings.

* One, which will be longer in coming, is a major Minoan ancient DNA study.

While on their surface these are ancient DNA studies related to archaeological cultures, important historical linguistic issues are related to each. If you know the genetic source of a prehistoric culture, there are fewer uncertainties involved in making inferences about it linguistically.

Further Analysis

One of today's less notable than anticipated pair of papers is closed access, but some interesting points from other papers are found in the comments at Eurogenes' post on them linked above (edited for formatting and punctuation, emphasis mine) provide some interesting commentary on them:

We now know from whole Y chromosome sequencing studies of modern samples that the coalescent time of the most common European sub-clade of R1b-M269 is shallow, 5–7 thousand years (Batini et al. 2015; Hallast et al. 2015; Karmin et al. 2015; Poznik et al. 2016). 
From the aDNA studies we have learned that the oldest R1b-M343 lineages, including 14 KYA Villabruna Man from Italy (Fu et al. 2016) and three European hunter-gatherers and three early farmer samples (Fig. 7), did not belong to the R1b- M269 sub-clade According to the ancient DNA evidence, affinity in their autosomal genes to the early farmers of Atapuerca from Spain (Gunther et . . . 

Late Neolithic, Early Bronze Age and Iron Age samples from Central and Western Europe have typically the R1b-L11, R1a1-Z283 and R1a-M417 (xZ645) affiliation while the samples from the Yamnaya and Samara neighbourhood are different and belong to sub-clades R1b11-Z2105 and R1a2-Z93 (Allentoft et al. 2015; Cassidy et al. 2016; Haak et al. 2015; Mathieson et al. 2015; Schiffels et al. 2016). 
The R1b11-Z2015 lineage is today common in the Caucasus and Volga-Uralic region while being virtually absent in Central and Western Europe (Broushaki et al. 2016). 
Interestingly, the earliest offshoot of extant haplogroup R1b-M343 variation, the V88 subclade, which is currently most common in Fulani speaking populations in Africa (Cruciani et al. 2010) has distant relatives in Early Neolithic samples from across wide geographic area from Iberia, Germany to Samara (Fig. 7). In a similar way, early offshoots of the R1b and R1a phylogenies, including R1b lineages derived at P297 and ancestral at M269, and R1a lineages which are derived at M459.
To digest this, you need a program explaining how the Y-DNA R1a and R1b clades are related to each other.

On the R1a side:

*R1a-M459 (a.k.a. R1a1) is very basal and includes essentially all extant Y-DNA R1a although there are a few intermediate clades with very few representatives between R1a-M420 at the root of R1a and R1a-M459.

* R1a2-Z93 (a.k.a. R1a1a1b2) found mostly in Asia, is a sister clade to R1a1-Z282 (a.k.a. R1a1a1b1a) found mostly in Eastern Europe, and is not ancestral to the Eastern European clade. Both of these are clades within both R1a-M417 (a.k.a. R1a1a1) and R-Z645 (a.k.a. R1a1a1b).

*R1a-M417 (xZ645) (a.k.a. R1a1a1) is the same branch of R1a that includes the Eastern European and Asian clades minus the subclade (R1a1a1b) that includes both of those clades that make up the lion's share of R1a in West Eurasia.

The key point is that the European steppe ancient Y-DNA R1a individuals come are part of an already differentiated Asian clade of R1a (now found mostly in Central Asia and South Asia) which is a sister clade to the European clades rather than being ancestral to them. Likewise outlier pro-Corded Ware ancient Y-DNA R1a in Europe is from a distantly related basal clade of R1a that is not ancestral to the currently predominant clades of Y-DNA R1a found there. 

On the R1b side:

* R1b-M343 (a.k.a. R1b*) is the most basal root of Y-DNA R1b.

* R1b-V88 is a very basal branch of R1b on a different branch than R1b-M269.

* R1b-M269 (a.k.a. R1b1a1a2) is a quite derived branch found mostly in Western Europe.

* R1b-L11 (a.k.a. R-P310/L11* a.ka. R1b1a2a1a1*) is a derived version of R1b-M269 which a paraclade of R1b-L151/P310 that has three sister clades including two common sister clades:R-U106 (a.k.a. R1b1a2a1a1a) found in Germanic Europe, and R-P312 (a.k.a. R1b1a2a1a1b) found in Iberia, British Isles, Italy and France.

* R1b11-Z2105 appears to be a typo or obsolete classification because R1b-Z2105 is actually R1b1a1a2a2, which is the a2 subbranch of R1b-M269, which is a sister clade to R1b-L151/P310. It appears that this may be the same clade or much more closely related to the clade R-Z2103 (a.k.a. R1b1a2a2) which is found in the Balkans and Turkey.

The key point is that the Y-DNA R1b clades found in the ancient DNA of the Yamnaya and Samara are closely related sister clades of those found in Western Europe, rather than being ancestral to them. Likewise, the early outlier instances of ancient Y-DNA R1b in ancient DNA from Europe involves basal sister clades to the predominant R1b-M269 rather than ancestral clades of Y-DNA R1b.

The bottom line is that modern Europeans while related fairly closely to people bearing Y-DNA R1a and R1b on the European steppe identified to date, and in old outlier samples from Europe, and in modern Y-DNA R1b-V88 people mostly in North Africa, are not direct descendants of any of these populations and their clades expanded much more recently and very rapidly.

Another comment states:
Archaeological part (CWC) is actually quite good.
Here is a hint what will BBB show: 
"Bell Beaker groups had by now also emerged on the scene, introducing metallurgy, and they further complicated the mix of cultures and people." 
There are two key-words here - emerged and metallurgy. The first one suggest a rather local development. The second a connection to an originally non-IE way of life, as in this sentence: 
"Extensive exchange systems linked different groups together and secured access to products outside the pastoral economy, such as metal." 
Now we can connect this with the old-new slide about mobility, which also showed that CE BB were less mobile than CWC (you can't be more mobile than shepherds if you're "introducing metallurgy", because metal deposits don't have legs like cows; you can eventually jump from one ore mine to another). 
Another interesting thing is about pottery:

"Corded Ware pottery appeared later in Northern Europe, and we may suggest that this did not happen until women with ceramic skills married into this culture and started to copy wooden, leather and woven containers in clay."

Monday, April 3, 2017

Predicting The Higgs Mass With A Slight SM Extension

A clever new paper makes a slight tweak to GR (a running cosmological constant) and a slight tweak to the Standard Model (adding one massless real scalar boson), and uses it to correctly post-dict the 125 GeV Higgs boson mass, to make the theory fit the cosmology data better, and to solve other theoretical pathologies.

Overall this plan of attack for BSM physics looks promising.

The Long Tail Is Still Making Important Discoveries In Mathematics

AS HE WAS brushing his teeth on the morning of July 17, 2014, Thomas Royen, a little-known retired German statistician, suddenly lit upon the proof of a famous conjecture at the intersection of geometry, probability theory, and statistics that had eluded top experts for decades. 
Known as the Gaussian correlation inequality (GCI), the conjecture originated in the 1950s, was posed in its most elegant form in 1972 and has held mathematicians in its thrall ever since. “I know of people who worked on it for 40 years,” said Donald Richards, a statistician at Pennsylvania State University. “I myself worked on it for 30 years.” 
Royen hadn’t given the Gaussian correlation inequality much thought before the “raw idea” for how to prove it came to him over the bathroom sink. Formerly an employee of a pharmaceutical company, he had moved on to a small technical university in Bingen, Germany, in 1985 in order to have more time to improve the statistical formulas that he and other industry statisticians used to make sense of drug-trial data. In July 2014, still at work on his formulas as a 67-year-old retiree, Royen found that the GCI could be extended into a statement about statistical distributions he had long specialized in. On the morning of the 17th, he saw how to calculate a key derivative for this extended GCI that unlocked the proof. “The evening of this day, my first draft of the proof was written,” he said.
From here.

Sunday, April 2, 2017

Higgs Boson Decays To Tau Leptons Confirm Standard Model

The Standard Model Higgs boson is predicted to sometimes decay to tau leptons (third generation electrons and positrons), at a frequency that is a function of their mass. The Standard Model Higgs boson is also predicted to have no CP violation at leading order.

Both of these predictions hold true experimentally, although neither exclusion of beyond the Standard Model hypotheses is ultra-precise, even though these are the best exclusions available.

The Latest Results

A March 29, 2017 pre-print combining the ATLAS and CMS data from Run-I at the Large Hadron Collider (LHC) on the topic found that the Higgs boson coupling to the tau lepton (which had a 5.5 sigma signal in the combined data) was consistent with the Standard Model prediction to within the limits of experimental error, and that there was no CP violation observed to within the limits of experimental error. The abstract is vacuous, so I'll quote some highlights from the body text instead:
The search for CP violation in the interactions of the newly discovered Higgs boson with the other Standard Model (SM) particles is motivated by the lack of sources of CP violation to explain the baryon asymmetry observed in the Universe. In the SM, no effect of CP violation is expected at LO in the production or decay of the SM Higgs boson. Hence, an observation of CP violation involving the observed Higgs boson would be a strong sign of physics beyond the SM. The H → ττ final state is very powerful for studies of CP invariance of the Higgs boson couplings. It is one of the most sensitive channels for the Vector Boson Fusion (VBF) Higgs boson production and it is the most sensitive for the Higgs boson decay into fermions. With H → ττ events, it is possible to probe the CP structure of both the HVV couplings to gauge bosons in VBF events and also of the H f f couplings to fermions. . . .
In combination with the ATLAS and CMS results in the other Higgs boson decays, these two analyses lead to the observation of the H → ττ decays at 5.5σ and µ = 1.11+0.24 −0.22. From this combination, the signal strengths for the ggF and VBF productions measured in the H → ττ decays are 1.0 +0.6 −0.6 and 1.3 +0.4 −0.4, respectively. . . .
Investigations of CP-violating Higgs boson couplings in the decays into pairs of massive gauge bosons show no deviation from SM. . . .
The observable is a CP-odd Optimal Observable built from the leading-order matrix element for the VBF production. An effective Lagrangian is used to include CP-violating effects from operators with mass dimension up to six in the HVV couplings. The effective Lagrangian assumes that the same coefficient is multiplying the CP-odd structures for the HW+W−, HZZ and Hγγ vertices and that all other couplings are as predicted in the SM. Under these assumptions, the matrix element M is the sum of the SM CP-even contribution MSM and a CP-odd contribution Mcp−odd from the dimension-six operators parametrised by the parameter d˜: 
M = MSM + d˜ · Mcp−odd. 
The Optimal Observable OO is defined as the ratio of the CP-odd interference term between MSM and Mcp−odd to the SM contribution. . . .
Since the Optimal Observable is CP-odd, a non vanishing mean value (OO) not equal to 0 is an indication of CP violation.  
The observed mean values (OO) in the data selected in the signal regions are 0.3 ± 0.5 in the ll channel and −0.3 ± 0.4 in the lh channel. Both results are consistent with zero within uncertainties and show no hints for CP violation. 
Limits on the CP-odd couplings are set based on a combined maximum-likelihood fit to the Optimal Observable distributions in data both in the ll and lh channels. Fig 2 shows the result of this fit for the SM d˜ = 0 hypothesis and the best-fit µ = 1.55+0.87 −0.76 in the lh signal region. The regions d˜ < −0.11 and d˜ > 0.05 are excluded at 68% CL. These intervals are an order of magnitude better than those obtained by ATLAS using the Higgs boson decays into gauge bosons. The analysed data does not provide enough sensitivity to set 95% CL intervals though. 
Bottom Line

The experimentally observed Higgs boson continues to be consistent with the predictions of the Standard Model for the Higgs boson in the face of all experimental tests to date through the completion of Run-I and preliminary partial data from Run-II of the LHC.

Implications For Beyond The Standard Model Physics

Implications Of The Tau Coupling Measurement For BSM Physics

The measurement of the tau coupling is important not just because it shows the Higgs boson is as predicted, but because the properties of the Higgs boson are globally sensitive to the properties of the entire matter content of the Standard Model. This is true because all of the fundamental particles of the Standard Model derive their masses from interactions with the Higgs boson in the Standard Model. 

If there were other fundamental particles that derived their masses from the Higgs boson, the properties of the Higgs boson in its decays that are observed experimentally would be different. The experimental data would be particularly sensitive to any missing heavy fundamental particles, which are the hardest to exclude by other methods. 

For example, if there were another particle that derived its mass from the Higgs boson with a mass greater than the 1.776 GeV of the tau lepton and less than or equal to half of the Higgs boson mass of about 62.5 GeV, this would cause the tau lepton signal strength to be much different than the observed signal. Yet, any deviation from the Standard Model signal strength of more than 59% greater than the Standard Model signal or more than 33% less than the Standard Model signal strength is ruled out with 95% confidence by the Run-I data.

A new heavy particle with a mass between 1.776 GeV and 62.5 GeV would tend to make the tau lepton signal weaker. A new light particle with a mass under 1.776 GeV would tend to make the tau lepton signal stronger. Both these kinds of deviations from the Standard Model are disfavored pretty much to the point of being ruled out, except for a possible new very light particle that derives its mass from Higgs boson interactions, by this measurement.

Of course, none of this is terribly earth shaking news. Any particle interacting with weak force interactions via W boson or Z boson with a mass of under 45 GeV have been ruled out since the LEP experiment operated at the LHC's location before it was dismantled in 2001 to make room for the LHC. And, other data from experiments including Tevatron and the LHC have ruled out new particles in the 45 GeV to 62.5 GeV range long ago.

New particles with masses more than 62.5 GeV that derive their mass from Higgs boson interactions might also impact the Higgs boson signal strength of the tau lepton, but I don't have the expertise to say that with confidence. Apparently percent level deviations in couplings can arise from multi-TeV scale new physics.

Of course, if beyond the Standard Model particles derived their mass entirely via mechanisms that don't involve the Higgs boson, this limitation would no longer apply. The trouble is that most two Higgs doublet models with five Higgs bosons rather than one, or more arcane models with even more Higgs bosons, don't interact with new particles in a manner entirely independent of the Standard Model Higgs boson. So, the tighter the fit of the experimentally observed Higgs boson to the Standard Model Higgs boson is, the less room there is for beyond the Standard Model theories with additional Higgs bosons as well.

What If There Is A New Physics "Desert"?

A scenario in which any beyond the Standard Model high energy physics manifest only at many orders of magnitude above the "electro-weak scale" of a hundreds of GeVs, after a "desert" of new physics, becomes more likely with each passing month as new LHC results are released.

If this is the case, we will probably never be able to observe beyond the Standard Model high energy physics in man-made particle colliders.

Even most "natural experiments" in the vicinity of high energy events related to stars and black holes would not have high enough energies to display beyond the Standard Model physics.

For example, it is a hundred times too cold in the hottest parts of the Sun (about 15,000,000,000 degrees Kelvin, to reach the temperatures where a high energy phenomena predicted by the Standard Model, called quark-gluon plasma, can occur (1 GeV per cubic femtometer, which is equivalent to a temperature of about 2,000,000,000,000 degrees Kelvin), even though this energy level has been reached and this phenomena has been observed, in Earth bound particle accelerators.

The first time humans were able to artificially create these energy densities (a.k.a. temperatures) was in 2015 at the Large Hadron Collider (although non-definitive hints that we might have done it were seen at other colliders as early as 2005). Nothing in the solar system had ever been that hot previously at any time in the four or five billion years since it came into existence. The temperatures reached in Run-II of the LHC on Earth are already hotter than those found in a supernova.

If there is a "desert" before beyond the Standard Model high energy physics, it could easily take temperatures on the order of 200,000,000,000,000,000,000 degrees Kelvin or more to see even a definitive experimental hint of this high energy new physics. There may not be any place in nature in the last 13.5 billion years (i.e. in any directly observable period of time since the Big Bang) that has been that hot. At best, we might find indirect evidence in gravity waves discernible in the cosmic background radiation of the universe that might suggest new physics at those temperatures.

Indeed, if there is a "desert" of beyond the Standard Model high energy physics, the details of these physics would be relevant only philosophically and for cosmology applications, since the vicinity of the Big Bang is the only time those physics would come into play.

Implications Of The Lack Of CP Violation For Cosmology

While the data aren't inconsistent with zero CP violation, the exclusions aren't terribly strong. But, the exclusions are still strong enough, and robust enough since they confirm finding from a different measurement of CP violation by the Higgs boson, to make the Higgs boson a poor candidate to explain the matter-antimatter asymmetry observed in the universe. This key cosmology question, therefore, remains an open one.

The Standard Model has only one source of CP violation (a phase in the CKM matrix) which is small δ13 = 1.20 ± 0.08 radians, when maximal CP violation would be π, commonly approximated as 3.14159 and is insufficient by itself to explain the matter-antimatter asymmetry in the universe. The observed CP violating phase for the W boson interactions of quarks is about 40% of the maximal CP violating phase.

There is almost certainly a second source of CP violation in the Standard Model extended to accommodate neutrino masses (a phase in the PMNS matrix of neutrino oscillation) which is believed to be much larger and near maximal based upon preliminary measurements with large error margins. But, without a bridge that does not exist in the Standard Model between neutrinos, where the CP violation probably occurs, and quarks, where the matter-antimatter asymmetry of the universe is observed, the cosmology problem remains and initial conditions of the universe in which the matter-antimatter asymmetry already exists are necessary.

Weird Polish Trees

I wasn't inspired to do anything for April Fool's Day this year, but here's a stranger than fiction tidbit of reality.

In Poland’s Krzywy Las, or Crooked Forest, the pine trees look like potbellied stick figures. On some 400 trees, the trunks buckle out 90 degrees, creating bark-covered bellies that drag just above the earth, oddly, all pointing in the same direction — north. 
No one knows for certain what caused this unusual stand of trees in a protected forest, just outside the town of Gryfino, Poland. The town was mostly destroyed during World War II, and the truth of the forest was lost with it. . . .
The pine trees, thought to have been planted in the early 1930s, bend at the trunks, and some extend outward around three to nine feet before zipping back up into the air. The trees — around 50 feet high at their tallest — were probably damaged at an early age, causing them to permanently grow this way. But how? . . .
It’s possible that a heavy snowfall covered the trees and continued to weigh them down through spring, when buds sprouted up and grew from the snow-covered trunk. But this wouldn’t explain the straight pines that surround this patch of bent ones.

The prevailing hypothesis is that farmers manipulated the trees in the 1930s to use their bent wood for furniture or ship building, but that the war prevented them from following through.
From the New York Times.