Friday, June 29, 2012

Wicked Problems v. Trivial Problems

As my regular readers know, this blog focuses mostly on the broad issues of prehistory and fundamental physics. Why not other areas of science?

A useful way of understanding the class of problems that interest me, at least from a blogging perspective, is that I am interested in what this blog post has called "wicked problems", in contrast with "trivial problems," of the kind that their blog focuses upon.

Two major technical fields I know have areas that call themselves “complexity”—ours and dynamical systems. . . . [Another sense] reflects the way we use “complex” in ordinary speech: big, involved, hard-to-describe, requiring much effort even to comprehend. It included a cool notion that I think you may like called wicked problems . . . . This is different from our notion of a problem being wickedly hard—it has to do with framing the problem itself. . . .
The key is the notion of a wicked problem(WP). It is not that easy to define what they are, but here is the standard list of properties they have:

*The problem is not understood until after the formulation of a solution.
*Solutions to wicked problems are not right or wrong.
*Every wicked problem is essentially novel and unique.
*Every solution to a wicked problem is a “one shot operation.”
*Wicked problems have no given alternative solutions. . . .

In 1967 West Churchman introduced the concept of wicked problems in a journal article. . . . Horst Rittel and Melvin Webber formally described the concept of wicked problems later in 1973 where they contrasted WP’s from “trivial” problems such as those from mathematics, chess, or puzzle solving.

Put another way, I enjoy the unstructured fumbling around trying to figure out how to determine what is going on and how to make sense of it and problem defining part of the process from unstructured or contradictory data, as much as I do the colder and more purely rational process of solving a well defined, but possibly very difficult, problem.  I like big, messy, unsolved "one shot" problems.

Three senses of the word "complexity"

Put another way, the post distinguishes between three kinds of complexity, the first of which is the wicked problem sense (called it "real-world based" complexity) described above.

Their blog focuses on complexity in a second sense of problems that are wickedly hard to solve (generally the address whether it is theoretically possible to solve a kind of problem in a reasonable amount of time defined in a technical way, which is used to evaluate computer algorhythms and cyptography strength) because they are resource intensive to solve:

When we say “complexity” we almost always are referring to the resources needed to compute and solve some problem. The resources measured can be: time, space, randomness, nondeterminism, rounds, quantum operations, or other resources. Indeed sometimes we mix these together to get measures that limit two or more resources.

They also mention a third sense of the term which they call behavior based complexity, which is also a more common sense of the word than theirs, as used by places like the Sante Fe Institute, and which they claim is based upon:

[T]he notion of “a complex system.” . . . When many say complexity theory, they usually are referring to the type of behavior of a system. This type of complexity theory is all about behavior, about prediction, about chaos, about the tremendous forking of paths (bifurcations) that can arise from even simple systems that evolve over time.

I would quibble with their definition here. "Chaos theory" generally refers to deterministic dynamical systems whose outcomes are hard to predict because they are highly sensitive to initial conditions (like the weather), even if you know the often simple equations that govern them exactly, causing their outcomes to seem quasi-random, and happens to be related for non-obvious reasons to fractals.

Complexity theory is a kindred but analytically distinct endeavor (closely aligned with what sociologists and business management professors mean when they talk about "complex organizations"), and while chaos theory typically involves simple underlying equations, complexity theory does not.  Complexity theory involves notions like "emergence," the conditions that cause systems to be complex, and how to apply simply strategies to deal with complex systems.

Still, while I quibble with their definition, I know what they mean and I agree that it is distinct. Indeed, I think that complexity is a pretty poor term to define the study of how intrinsically difficult certain classes of problems are to solve computationally, in terms of the resources necessary to solve them. It is a very valid area of study, but "complexity" theory is a poor name for it, because the problems that are addressed are generally straightforward and well defined.

Tuesday, June 26, 2012

New Ideas On Gluon Spin And Other QCD Topics

On Wednesday . . . one [talk] was delivered by Luigi Capozza on behalf of COMPASS collaboration. . . . Their aim is to take a measurement of the components of the proton spin. These are usually divided in three parts: Quark contribution, gluon contribution and orbital contribution. The striking part of the measurement is that the gluon contribution is compatible with zero! From what we know in the high-energy limit, where the gluon concept is well-defined, these are spin-1 objects and so, it is not so straightforward to have zero contribution from them to the proton spin and indeed this is an important open problem in theoretical physics.

From Marco Frasca reporting on a conference session at QCD@Work (with presentation slides available here).

This result seems to echo others in QCD that seem to suggest that there is some sort of phase change that gluons experience between high energy (UV) states and low energy (IR) states, giving rise to seemingly completely different particles in terms of both spin and mass.  At any rate, mysteries in something so basic as the sources of spin in a proton are themselves reminders that we don't know everything yet.

Another interesting account from the same source regarding the same conference is this one:
I heard the talk from Mirko Serino about a really innovative idea. Mirko is a PhD studend at University of Salento and together with Claudio Coriano, that is his professor, Luigi Delle Rose and Antonio Quintavalle are producing an analytical computation of Standard Model in presence of gravity. This kind of computation is highly non-trivial and quite complicated. The striking result they get is that appears a coupling between a scalar degree of freedom and the gauge field and this appears as a rather interesting new proposal for mass generation. I have talked with the students of Coriano and they were really excited by this result that is indeed really interesting and unexpected.
In a nutshell, Serino devises proposed additional terms in the Einstein-Hilbert actions from quantum mechanical first principles that could provide a phenomenological clue to look for if one is looking for quantum gravity effects.  The paper does not explore what this would imply in practice at a level sufficiently down to earth for a mere human like myself to understand, and to be perfectly honest, I'm not sure that I perfectly understand all of the assumptions that go into the calculation, even though I understand most of them.

There are also suggestions in the final session of the conference (Svjetlana Fajfer , "New Physics in B to D* tau nu decay") that the Belle and BaBar experiments are seeing 3 sigma plus deviations from the Standard Model in B meson decays which could suggest Beyond the Standard Model physics, such as additional Higgs bosons (charged and heavy), since the results seem impossible to explain with any single consistent set of Standard Model CKM matrix values. Then again, maybe there are just flaws in how the theoretical expecations are being calculated.  Having been through multiple CKM matrix can't be reconciled exercises only to find the data confirm it again, I'm more that a bit skeptical of the results from such an exotic decay.  But, given how scarce any more than three sigma BSM experimental results are these days, it bears watching.

Thursday, June 21, 2012

Y-DNA E Didn't Back Migrate To Africa

One theory held by Dienekes and a few others (and a minority of archaegeneticists) is that Y-DNA haplogroup E, the predominant Y-DNA type in Africa (with most of the remainign men having Y-DNA haplogroups A, B, T or R1b-V88) is a back migration to Africa from Eurasia. The points below, originally composed and somewhat edited since, as a comment to a post on his blog that reiterates this claim, sets out the arguments against this conclusion.

Significant Back Migration To Africa Did Happen

There is no real dispute that there has been some back migration from Eurasia to Africa. Y-DNA haplogroups T and R1b-V88 and mtDNA haplogroups M1 and U6, as well as autosomal data for North Africa, Ethiopia and Somolia, for example, all make a very strong case for back migration having taken place. North Africans, generally speaking have automsomal DNA which 80%-90% or so derived from West Eurasia. Most Ethiopian and Somolians have autosomal DNA which is 40%-50% derived from West Eurasia. The Maasai have a lower but significant share of West Eurasian autosomal genetic contributions. Most other sub-Saharan Africans have almost no West Eurasian source autosomal DNA.

The vast majority of Africans with significant back migrating uniparental and autosomal genetic traces (apart from the people of Madagascar who have quite recent Asian genetic origins in addition to their African roots and cases of recent European admixture such as colored South Africans), speak an Afro-Asiatic language, and most of the rest speak a Nilo-Saharan language. Prehistoric Eurasian admixture is almost completely absent in Paleo-African populations (Khoisan, Pygmies, San, etc.), and populations that speak Niger-Congo languages, apart from some small communities near the outer boundaries of the Niger-Congo linguistic region like the Fulani of Northern Cameroon.

There is also good evidence to suggest that there was at least, a relatively recent back migration that gave rise to the Ethio-semitic languages, and a probably also a more ancient back migration. Ancient DNA and the mtDNA mutation rate data (for mtDNA haplogroupds M1 and U6 which have roughly the same age) suggest that this back migration probably sometime in the late Upper Paleolithic or early Neolithic. A good guess might be around 12,000 years ago when North Africa was repopulated in the Mesolithic at the start of a "wet" Sahara period.

A recent study of autosomal genetics in Ethiopia, however, estimates the Eurasian contribution at ca. 3000 years ago, around the time of the Ethiosemitic language subfamily's arrival there as estimated from linguistic evidence.

But, this most recent study but does not show much difference in Eurasian genetic contributions between Ethiosemitic language speakers and populations such as Cushitic language speakers who are known to have preceded Ethiosemitic language speakers in the region, despite an expectation that a three thousand year old contibution of 40%-50% of Ethiopian autosomal genes would show greater percentage contributions in Ethiosemitic language speakers than in earlier Cushitic language family speakers as earlier uniparental genetic studies had suggested might be the case, particularly on the Y-DNA side (suggesting a male dominanted Ethiosemitic colonization event).

When Did The Out of Africa Migration Happen?

There is archaeological evidence for an Out of Africa and into the Near East migration from somewhere around Sudan to Arabia via the Sinai Pennisula around 104,000 years ago. Modern humans aren't found in Eurasia outside the Middle East (at that time, in South Asia) before about 74,000 years ago, however, and there is a gap in the record of modern humans in the Levant from about 75,000 years ago until about 50,000 years ago. At that time modern humans could have retreated to non-Levantine refugia in Eurasia, or could have simply failed only to be demically replaced by a sceond wave of modern human migration.

The case for a Eurasian refugia during modern human's absence from the Levant is the stronger one.

The flat phylogeny (i.e. with many contemporaneous branches dispersed over a very great geographic area) of mtDNA haplogroup M suggests a rapid Southern route expansion when modern humans finally burst into East Eurasia. The youngest archaic hominin remains on the mainland side of the Wallace line in East Eurasia appear to date from around 100,000 years ago, and the well dated appearance of modern humans in Australia and Melanesia around 45,000 years ago bounds the modern human expansion into East Eurasia from South Asia to sometime before that date. An expansion of modern humans into East Eurasia from South Asia around the time of the Toba explosion, 74,000 years ago, would be a fairly good match to the available genetic based dates from the Y-DNA CF branch, and from the mtDNA M and N derived haplogroups found in East Eurasia, and would also be consistent with the rather thin early archaeological record in East Eurasia from that time period.

As I explain at greater depth below, the distribution of Y-DNA haplogroup D suggests that it was a maritime secondary Out of Africa wave, rather than being part of the initial Southern route expansion Out of Africa, or the migration of modern humans into Europe.

Y-DNA Haplogroup E is not derived from a back migration to Africa

The case for a back migration of Y-DNA haplogroup E, the African branch of Y-DNA clade DE, is not well supported, however.

Y-DNA Haplogroup E as a clearly African rooted distribution.

Y-DNA haplogroup E is the predominant Y-DNA haplogroup in most of Africa. Y-DNA haplogroup E is common in three of the four major linguistic groups of Africa (Afro-Asiatic, Nilo-Saharan, Niger-Congo) and is present in all of them, unlike back migrating Y-DNA haplogroups T and R1b-V88, and back migrating mtDNA haplogroups M1 and U6, all of which are principally found in Afro-Asiatic language speakers. Auotosomal genetic components from West Eurasia in Africa likewise are predominantly found in Afro-Asiatic speakers, while they are nearly absent in West African Niger-Congo speakers.

Furthermore, Neanderthal DNA, which is found at about the same percentage frequency in all Eurasians, is absent from most African populations who are overwhelming Y-DNA haplogroup E bearers. Thus, back migrating early Y-DNA haplogroup DE* or haplogroup E bearers, if they existed, would have had to do so prior to Neanderthal admixture which appears to have happened before or at around the same time as West Eurasian and East Eurasian populations became distinct (and certainly prior to 45,000 years ago, as Australian Aborigines and Papuans have the same levels of Neanderthal admixture as other Eurasians). Indeed, even if the YAP mutation that defined Y-DNA macrohaplogroup DE actually did take place in Eurasia, the circumstantial evidence would suggest that this would have had to have taken place before these people developed most of the genetic features that make Eurasians genetically distinct from Africans - call them "pre-Eurasians" in Eurasia, perhaps.

Y-DNA haplogroup E subhaplogroups that do not appear to have a source in Bantu introgression are found in African pygmies, whose population genetic split from other Africans is one of the most basal dating to perhaps 70,000 years ago, and who were believed to have been linquistically distinct prior to Bantu introgression. This points to its African antiquity.

Africa also has basal branches of Y-DNA hg E not found anywhere else (e.g. E2). The most basal lineages, paragroup E*, have been found in a single Bantu-speaking male from South Africa, amongst pygmies and Bantus from the Cameroon/Gabon region, and in two individuals from Saudi Arabia. The distribution of Y-DNA haplogroup E overall in Africa is continuous throughout Northern and Subsaharan Africa, and is terrestrial.

All of the basal branches of Y-DNA haplogroup E are found in Africa, including Y-DNA subhaplogroup E2, some major lineages within subhaplogroup E1, and parahaplogroup E* that are found only in Africa. In contrast, all of the subhaplogroups of Y-DNA haplogroup E which are found in West Eurasia are from phylogenies rooted in Africa. Moreover, the SW European and SE European Y-DNA haplogroup E subhaplogroups don't have a common European source - their phylogeny reveals separate West Asian and Northwest African origins for Y-DNA haplogroup E in Europe with European specific lineages within these African rooted clades that are comparatively recent.

Inconsistently with a back migrating Y-DNA haplogroup, Y-DNA haplogroup E is less common in East Africa, where Y-DNA haplogrups A and B (found only in Africa and basal to both Y-DNA macrohaplogroups DE and CF) are more common, than Y-DNA haplogroup E is in most of the rest of Africa. All other back migrating uniparental markers and automomal genetic clines display the opposite trend in their distributions.

Y-DNA Haplogroup D has a sporadic East Eurasian distribution.

Y-DNA D is a rare haplogroup that has a sporadic Asian distribution with a deep rooted divide between D2 a Japanese subhaplogroup, and D*, D1 and D3 found in a network centered on the Andaman Islands and Tibet, with low frequencies in Eastern India and Southeast Asia, and seeps out from Tibet at low frequencies into Central Asia. Y-DNA haplogroup D is absent from Africa (including Madagascar), Oceania (which was colonized first by Austronesians), Europe, other parts of West Eurasia, the Americans, Melanesia and Australia.

It appears from the mtDNA make up of populations where Y-DNA haplogroup D is found that the earliest Y-DNA haplogroup D populations in East Eurasia probably had female counterparts who were part of mtDNA M (excluding later separately named mtDNA haplogroups) which is found only in East Eurasia, with no counterparts who were from mtDNA haplogroup N and its decendants that are found in both West and East Eurasia.

The geography of D is consistent with long range maritime migration to successive uninhabited islands or unoccupied areas in the wake of migrations occupying most territory by CF clade members. It may represent a secondary Out of Africa migration.

Modern humans did not arrive in Japan until about 30,000 years ago, the likely root of the Y-DNA D2 subhaplogroup which is restricted almost entirely to Japan or in much lower frequencies adjacent areas traceable to Japanese migration, so Y-DNA haplogroup D in East Eurasia can be no younger. The Andaman islands may not have had modern human occupants until about 20,000 years ago. Tibet had modern human occupants prior to 20,000 years ago, but possibly not much before 30,000 years ago.

Despite the fact that modern humans were in South Asia at the time of the Tobu erruption, 74,000 years ago, Y-DNA D is not distributed widely throughout South Asia. It is instead geographically limited to areas with high levels of Ancestral South Indian (ASI) admixture (which has its closest extant match in the Andaman islanders), but the distribution of Y-DNA D in India is more localized than the ASI autosomal genetic component in India and Y-DNA haplogroup D is uncommon even in mainland India.

Modern humans arrived in Europe around 40,000 years ago and it lacks Y-DNA haplogroup D. Australia and New Guinea were first occupied by modern humans around 45,000 years ago and lack Y-DNA haplogroup D. Denisovian autosomal DNA does not overlap with the populations where Y-DNA haplogroup D is found (basically Melanesians, Aborginal Australians and to a lesser extent Philippino Negritos), suggesting that Y-DNA haplogroup D populations probably didn't co-exist with the archaic hominin Denisovians for any prolonged period of time, if at all. Thus, there is strongly suggestive circumstantial evidence to suggest that Y-DNA haplogroup D dispersed after 40,000 years ago, but before 30,000 years ago, long after the initial Out of Africa migration, and close in time to when the Neanderthals began the downward spiral into extinction in West Eurasia.

The Americas, which lack Y-DNA haplogroup D, were mostly first occupied by modern humans starting around 14,000 years ago via the Bering Strait from Siberia (in mainland East Eurasia), although that founding population could have arrived in Beringia as soon as about 22,000 years ago. The Beringian first Native American founding population, among other things, supported itself by hunting mammoths. And, the earliest modern human migrants to the Americas from Beringia probably didn't have boating capabilities on a part with Y-DNA haplogroup D dominanted peoples who first settled the Andaman Islands and Japan, since if they did, the North American glaciers of the last glacial maximum would not have presented a serious barrier to their migration into the rest of the Americas. Later circumpolar populations in the Americas who did have solid maritime abilities arrived in the Americas many thousands of years later than 14,000 years ago.

Of course, the population bottleneck associated with the founding population of the Americas, which may have numbered in the hundreds on a census basis, could easily have excluded many Y-DNA lineages present on the East Eurasian mainland and could even have omitted many Y-DNA lineages that were present at low frequences in the founding population of Berginia before it expanded into the rest of the Americas as these lineages could have been lost due to genetic drift. Still, it is safe to say that the founding population of the Americas was probably not derived from a population in which Y-DNA haplogroup D was predominant, and Native American population genetics show more affinity to Siberia than Japan or Tibet, where Y-DNA haplogroup D is common.

The confined distribution of Y-DNA haplogroup D bearers to places that were probably either completely or nearly completely unpopulated by modern humans when they arrived, whille they are absent from places were Y-DNA clade CF bearers were already present in any great numbers, also disfavors the notion that an offshoot of their particular culture took Africa by storm in a way that made Y-DNA haplogroup E the predominant patriline genetic source for all of Africa, displacing all of its predecessors and being found in all of Africa's major language family populations.

The split of Y-DNA D and E took place long before the other back migrations to Africa sometime after men with Y-DNA in pre-split haplogroup DE left Africa.

There are just eight known cases of individuals from paragroup DE*, two in Tibet, and six from West Africa, although they may be some in the Andaman Islands. This implies that the dispersal of bearers of pre-split y-DNA haplogroup DE split between Asian and African populations, wherever it happened, took place at some point shortly before, rather than after the DE split.

The YAP mutation that defines DE and associated hinted at research from the 1000 Genomes project suggest that DE's divide is vary ancient, dating to roughly the Out of Africa era, or at the latest, early Upper Paloelithic. Mutation rate evidence that Y-DNA haplogroup D is older than Y-DNA haplogroup E has been contradicted by later research by some of the same investigators.

While mutation dating is problematic, it isn't so irrelevant and inaccurate that one cannot say that the DE divide is much more ancient than the mtDNA M1/mtDNA U6/Y-DNA T/Y-DNA R1b-V88 backmigrations or events giving rise to Ethiosemitic languages.

The timing of the Y-DNA DE split is at an age roughly contemporaneous with the split of the Khoisan and Pygmy populations from other Africans, the most basal population split in African population genetics.

The timing of the haplogroup D expansion suggested by the geographic distribution of Y-DNA haplogroup D is much younger than the date suggested by mutatioon rates which indicate that Y-DNA haplogroup D is only a bit younger than the root of Y-DNA macrohaplogroup CF, which is the dominant non-African Y-DNA clade and the only one found at any great distance from Africa in East Eurasia other than much more rare Y-DNA haplogroup D. The date implied by the mutation rates is on the order of twenty thousand to thirty thousand years more recent than the best estimate of the date at which Y-DNA macrohaplogroup DE split into Y-DNA haplogroups D and E.

A back migration of people with Y-DNA haplogroup E to Africa, in addition to preceding Neanderthal admixture with non-Africans, would also have to have been made up exclusively of men and of women with mtDNA haplogroup L3, the only African mtDNA lineage that is a source for non-African mtDNA lineages, because mtDNA haplogroup M1, the only potentially East Eurasian origin mtDNA lineage in Africa, arrived in Africa scores of millennia later. But, there are no indigeneous populations of East Eurasia who had mtDNA haplogroup L3 prior historic or almost historic era migrations (i.e. prior to 6,000-7,000 years ago).

A more plausible possibility that could explain this gap is that a small group of pre-split haplogroup DE bearing men from Africa either migrated to a refugium (perhaps in somewhere Arabia that subsequently became too arid to leave a remnant population in Arabia, or perhaps in South India) where they were part of a small endogameous community until their maritime expansion into East Eurasia that wasn't swept up in the initial Southern route expansion out of Africa, much later.

Alternately, this small endogamous community of pre-split haplogroup DE men could have existed for tens of thousands of years somewhere in Africa, only to be totally replaced within Africa during the more successful expansion of haplogroup E within Africa sometimes between then and the Bantu expansion, leaving only a handful of of descendents who ultimately ended up in West Africa behind, and leaving no surviving members who had been part of a D lineage that emerged in Africa.


After considering all of the evidence, it becomes clear that a scenario in which Y-DNA haplogroup E back migrates from Eurasia to Africa is grossly implausible, even though it is possible to imagine highly contrived and unprecedented set of events. It might not be proof beyond a reasonable doubt, but there is surely clear and convicing evidence that Y-DNA haplogroup E has its origins entirely in Africa.

Also, even if Y-DNA haplogroup E did back migrate from Eurasia to Africa, this would have had to have happened so early on in the Out of Africa migration process that its place of emergence would not different in practical observable implications in any meaningful way from an African origin, because it would have had to have predated the point at which the Out of Africa population had become very distinct genetically from Eurasians.

None of this is highly controversial. All of the facts, although not quite all of the connecting of the dots made in this post, is derived from peer reviewed published scholarly journal articles, either directly, or as citation support for my sources. I haven't taken the time to annotate this post (although I aspire to at some point), but have read almost all of those articles and blogged many of them.

The last published paper to argue seriously for a non-African origin of Y-DNA haplogroup E in Africa was published in 2007, and many of the sources I am relying upon in this post (including all of the Neaderthal DNA work and a lot of the detailed subtyping of Y-DNA haplogroup D and Y-DNA haplogroup E in Europe and Ethiopian DNA and much of the automsomal work, in general) has been published since then. The Asian origin for Y-DNA haplogroup E was a distinctly minority view in 2007, was disavowed by one of its original proponents based upon new evidence in 2008, and has almost surely lost informed supporters based upon the increasing weight of the evidence against this theory since then. I wouldn't yet call the theory pseudo-science, but it is starting to approach that threshold as our picture of humanity's genetic prehistory grows clearer.

We also know from recent research on Y-DNA haplogroup E in Europe, which I've previously blogged, that most of the Y-DNA haplogroup E in Europe has African sources in the Holocene era and in many cases much more recent African origins.

One important consequence of an African origin for Y-DNA haplogroup E (or at least a very early back migration that left no traces behind in Eurasia), is that it allows us, as we try to glean humanity's prehistory with archaeogenetics, to focus our attention entirely on Africa, with significant back migration from Europe taking place only fairly late in the game and probably in at most just a few main waves (Epipaleolithic, Neolithic, Ethiosemitic, and some historic era migration).

To the extent that particular Y-DNA haplogroup E lineages are associated with particular linguistic families or subfamilies in Africa, the populations that expanded and spread those languages expanded and spread those languages from a population that was mostly African in origin, even if there may have been outside thin superstate influences in the initial population from which it expanded.

While not nearly so decisive, this conclusion is also an important clue that tends to favor an African continental, rather than a Levatine origin of the Afro-Asiatic languages, because Semitic language speakers in the Levant have much more frequently bear Y-DNA haplogroup E than other West Eurasian populations. So does the fact that we can historically date the time period when Semitic languages first started to be spoken in the Eastern part of the Fertile Crescent (after about 2000 BCE), and their absence from Anatolia apart from small Akkadian trading colonies and influences from Arabic speakers in the last thirteen hundred years (after about 700 CE).

This conclusion isn't decisive, because it departs from the usual trend in which the first farmers exert cultural dominance over the people they encounter as they expand. But, an emerging picture of the North African Neolithic in which much of the demic influence of West Eurasia on North Africa precedes the Neolithic by a few thousand years as the area is repopulated during a "wet Sahara" climate phase, and North Africans become herders long before becoming farmers in a process that allows for a transition that has a stronger cultural component and a weaker demic component than parallel developments in Europe, weaken the strength of a first farmers paradigm for the linguistics of the Afro-Asiatic language family.

Instead, a scenario in which Afro-Asiatic languages are spread by indigenous hunting and gathering populations who adopted Fertile Crescent herding practices with animals domesticated there, while avoiding a profound introgression of peoples from the Fertile Crescent at that point, seems more plausible. The expansion was probably driven by food production technologies, and individual subfamilies within the Afro-Asiatic language family do show strong signs of demic expansion. But, some of the different linguistic families, at least, probably arose from language shift rather than population replacement, because the Afro-Asiatic language family, while made up of populations that have a number of genetic features distinct for Africa, are not geneticallly homogeneous and can't be linked in any simple phylogenetic tree at a population genetic level.

Wednesday, June 20, 2012

North Africans Consumed Milk Products 7 K.Y.A.

New research confirms an emerging consensus about when and where herding domesticated animals began to replace hunting and gathering in Africa (an activity that included the use of pottery and the collection of wild grains), and expands our understanding of how that herding society worked.

It happened in North Africa (including many places that are now too arid for this activity) and the Nile Valley after similar developments in the Middle East, but at about the same time that herding emerges in Europe. It happened before the main African origin crops were domesticated, and not long after the domestication in Egypt of the donkey. It appears to have involved both dairying and the use of cattle for meat from the start, or from very close to the start of a herding mode of food production.

The New Research

By analysing fatty acids extracted from unglazed pottery excavated from an archaeological site in Libya, the researchers showed that dairy fats were processed in the vessels. This first identification of dairying practices in the African continent, by prehistoric Saharan herders, can be reliably dated to the fifth millennium BC.

Around 10,000 years ago the Sahara Desert was a wetter, greener place; early hunter-gatherer people in the area lived a semi-sedentary life, utilising pottery, hunting wild game and collecting wild cereals. Then, around 7,000-5,000 years ago as the region became more arid, the people adopted a more nomadic, pastoral way of life, as the presence of cattle bones in cave deposits and river camps suggests.

Researchers . . . studied unglazed pottery dating from around 7,000 years ago, found at the Takarkori rock shelter in the Tadrart Acacus Mountains, Libya. Using lipid biomarker and stable carbon isotope analysis, they examined preserved fatty acids held within the fabric of the pottery and found that half of the vessels had been used for processing dairy fats. This confirms for the first time . . . . the importance of milk to its prehistoric pastoral people. . . .

"We already know how important dairy products . . . which can be repeatedly extracted from an animal throughout its lifetime, were to the people of Neolithic Europe, so it's exciting to find proof that they were also significant in the lives of the prehistoric people of Africa. . . .

[T]hese results also provide a background for our understanding of the evolution of the lactase persistence gene which seems to have arisen once prehistoric people started consuming milk products. The gene is found in Europeans and across some Central African groups, thus supporting arguments for the movement of people, together with their cattle, from the Near East into eastern African in the early to middle Holocene, around 8,000 years ago."

"While the remarkable rock art of Saharan Africa contains many representations of cattle -- including, in a few cases, depictions of the actual milking of a cow -- it can rarely be reliably dated. Also, the scarcity of cattle bones in archaeological sites makes it impossible to ascertain herd structures, thereby preventing interpretations of whether dairying was practiced."

From here.

The paper is: Julie Dunne, Richard P. Evershed, Mélanie Salque, Lucy Cramp, Silvia Bruni, Kathleen Ryan, Stefano Biagetti, Savino di Lernia. First dairying in green Saharan Africa in the fifth millennium bc. Nature, 2012; 486 (7403): 390 DOI: 10.1038/nature11186

The abstract of the paper notes that: "In the prehistoric green Sahara of Holocene North Africa—in contrast to the Neolithic of Europe and Eurasia—a reliance on cattle, sheep and goats emerged as a stable and widespread way of life, long before the first evidence for domesticated plants or settled village farming communities."

Other Evidence Regarding The Arrival Of The Neolithic Revolution In Africa

Notably, the find comes from the central Saharan highlands, not the Mediterranean coast or what is currently the African Sahel.  The find comes not from the "wet Sahara" period itself, but from the period when the Sahara was becoming increasingly arid.  There is an implication on the narrative from the press release journalism at Science Daily quoted above, that pastrolism may have not had much of an advantage over hunting and gathering until an increasingly arid climate in the Sahara tipped the scales in favor of pastoralism.

This date is older by more than a thousand years than the oldest reliably dated Central Saharan find of cattle bones.

The new research adds to the context provided by archaeological evidence of cattle bones in Africa, and insights provided by animal genetic data about the domestication of sheep and goats in Africa.

Cattle bones have been found at Nabta Playa, in the Eastern Sahara near the Middle Nile, dated to roughly the same time period as the evidence of dairy products in the most recent report in the central Saharan highlands.

There is archaeological evidence for cattle ca. 8,000 BCE in the Upper Euphrates Valley. Morphologically altered domestic cattle are not found in Central Anatolia until after 6,500 BCE, although morphological change appears empirically to follow domestication by about a thousand years in most cases. This Saharan find is roughly contemporaneous with the earliest evidence for dairying in Europe.

A 5000 BCE date would be after the domestication of the donkey in Egypt (camel domestication comes much later, probably after 1000 BCE).  As noted in the prior post on cattle domestication, around 5000 B.C.E. (i.e. at the same time as the milk residue find), "the remains of small livestock (sheep or goats) appear in several Middle Neolithic sites at Nabta. Because there are no progenitors for sheep or goats in Africa, these caprovines were almost certainly introduced from southwest Asia."  Another source puts caprovines in the region as much as a thousand years earlier.  That post also noted that:

[D]omestic cattle were present in coastal Mauritania and Mali around 4,200 years ago and at Capeletti in the mountains of northern Algeria about 6,500 years ago. At about that same time, they may have been present in the Coastal Neolithic of the Maghreb. Farther south in the Central Sahara, domestic cattle were present at Meniet and Erg d’Admco, both of which date around 5,400 years ago, and at Adrar Rous, where a complete skeleton of a domestic cow is dated 5,760 +/- 500 years B.P ].

Domestic cattle have been found in western Libya at Ti-n-torha North and Uan Muhuggiag, where the lowest level with domestic cattle and small livestock (sheep and goats) dated at 7,438 t 1,200 B.P. At Uan Muhuggiag, there is also a skull of a domestic cow dated 5,950 +/- 120 years. In northern Chad at Gabrong and in the Serir Tibesti, cattle and small livestock were certainly present by 6,000 B.P. and may have been there as early as 7,500 B.P. We are skeptical, however, about the presence of livestock at Uan Muhuggiag and the Serir Tibesti before 7,OO0 B.P., when small livestock first appear in the Eastern Sahara, if we must assume that these animals reached the central Sahara by way of Egypt and the Nile Valley. This also casts doubt on the 7,500 B.P. dates for cattle in these sites.

The earliest domestic cattle in the lower Nile Valley have been found at Merimda, in levels that have several radiocarbon dates ranging between 6,000 and 5,400 B.P. and in the Fayum Neolithic, which dates from 6,400 to 5, 400 B.P. These sites also have domes-tic pigs and either sheep or goats. In Upper Egypt, the earliest confirmed domestic cattle are in the Predynastic site of El Khattara, dated at 5,300 B.P. However, domestic cattle were almost certainly present in the earliest Badarian Neolithic, which dates before 5,400 B.P. and possibly were there as early as 6,300 B.P. Farther south, in Sudan near Khartoum, the first domestic cattle and small livestock occurred together in the Khartoum Neolithic, which began around 6,000 B.P.

Sorghum and pearl millet, two of the characteristic African domesticated plants were probably domesticated at least a thousand years after this earliest evidence of dairying in the Sahara. But, there is some evidence for at least proto-farming or intense collection of wild types of these plants are far back as 6000 BCE.  Arguably domesticated cattle bones are found in the Middle Nile as far back as 7000 BCE, but a few hundred years before that in the Middle Nile, ca. 7300 BCE, the evidence supports a hunting and gathering lifestyle rather than one associated with herding.

I have not focused recently on the dating of the arrival of Southwest Asian domesticated plants from the Fertile Crescent Neolithic into Africa in general, and North Africa in particular. 

A map in Fuller (2007) suggests the arrival of wheat and barley in Egypt ca. 5000 BCE-4000 BCE (after domestication in the Fertile Crescent ca. 7000 BCE), and in Nubia ca. 3000 BCE.  This would be well after the most recent dates for the arrival of pastoralism involving sheep, goats and cows in Africa.  Nothing in the report on the Takarkori rock shelter find suggests that evidence of pastrolism was accompanied by evidence of wheat and barley cultivation which one would expect to find in the same kinds of places that pottery relics disclosing milk storage or processing are found.

Also per Fuller (2007), pottery is found in both the Central Saharan highlands, where this find was made, and up and down the Nile basin, before 6800 BCE.

Evidence for Demic Diffusion?

One of the core debates in prehistory, which may have different answers in different places, is the extent to which the arrival of herding and farming that was derivative of the Neolithic revolution in the Fertile Crescent was spread via a process of demic diffusion (i.e. mostly through the migration of new peoples to those areas from Southwest Asia), or cultural diffusion (i.e. mostly through the adoption of the technologies by the indigeneous people in the areas to which the Neolithic revolution spread).

The new research does not offer very strong support, by itself anyway, for the assertion of one of the researchers quoted above that the arrival of dairying in the Sahara had a human component that was largely demic, as opposed to mostly involving merely cultural transmission of the knowledge necessary to carry on a pastoralist (i.e. herding) lifestyle.

The evidence from modern ethnographies and historic adoptions of pastoralism by hunting and gathering populations like the African San people, the Navajo, and the Australian aborigines, suggest that herding is a way of life that is more easily transmitted culturally to hunting and gathering peoples than farming. Indeed, one can make the case that early cultural adoption of herding before farming took hold in a region is critical to the continued vitality of populations ancestral to the early hunting and gathering populations that took up herding.

One can propose some general rules:

* Peoples who are hunters and gatherers when they first encounter farmers are mostly wiped out.
* Peoples who are hunters and gatherers who encounter herders who are not farmers have a decent chance of surviving as a people by becoming herders through cultural diffusion rather than demic diffusion. But, if they don't transition to herding, they will be wiped out unless they live someplace so marginal for farming and herding that no one wants to migrate into their territory.
* Peoples who are farmers persist genetically, even when they are conquered by outside pastoralists and swiftly assimilate the pastoralist superstate to their way of life.
* Peoples who are wiped out linguistically and/or culturally in a demographic transition leave stronger matriline traces than they do patriline traces.
* Peoples who rely on fishing for most of their sustainance are an intermediate case between terrestial hunters and gatherers, who have less staying power, and herders, who have more staying power, vis-a-vis farmers.

Genetic evidence on that point can, in my humble opinion, be argued both ways.  On one hand, there is evidence that the mostly Eurasian version of the latase persistance gene, which we would expect to spread with the migration of dairying peoples, is found in North Africa.  On the other hand, the population history of North Africa has many layers to it, some much more recent, and some of the important uniparental markers found in modern North African populations are characteristically African and show considerable continuity with the population genetics of pre-Neolithic North African populations revealed by ancient DNA from some North African sites.

Since latase persistance genes can carry a powerful fitness advantage for its carriers in times of food scarcity, a very small number of cases of introgression of this gene into a herding population that acquired herding technology and animals mostly as a result of cultural diffusion and trade could easily have been amplified in its frequency in the population afterwards while leaving only the most trace genetic evidence from selectively neutral sources.

Hat Tips to Dienekes and Maju whose posts I reviewed in preparing this one.

Monday, June 18, 2012

Rumors: Higher Significance Higgs Finding In July

Rumor has it (see here and here) that the statistical significance of experimental evidence for a Higgs boson, at about 125 GeV of mass +/- about 1 GeV, is rising above that reported late last year marching ever forward to towards the five standard deviation (i.e. five sigma) level which is the industry standard in high energy physics for a "Discovery" of a new particle and that this result will be announced at the ICHEP conference in about three weeks.

The Rumors Predict The Obvious.

While the rumors are reportedly based on inside information, their substance is really pretty obvious the same as what one would predict without insider information.

This is not really surprising. The Large Hadron Collider continues to produce more data and all other things being equal the new data from the same experiment to look a lot like the old data from that experiment. If the Higgs boson is there, mathematical projected based upon the rate of LHC data generation that we're experiencing makes it highly likely that a five sigma result will be announced sometime this year. The ICHEP conference next month is one of half a dozen or events left this year where this result would be likely to be announced (big results are usually announced at academic conferences). And, even if there isn't a five sigma announcement at ICHEP, there could easily be a higher sigma Higgs boson data announcement that is short of five sigma, but more significant than the result from last winter (which, given the trend line, would reassure everyone who was worried that last winter's accouncement was just a cruel statistical fluke).

Indeed, if there was announcement that the statistical significant of the apparent Higgs boson find had not increased, that would call the previous result into doubt. For this to happen, the Higgs boson signals seen at the LHC in the last few months would have to be quite a bit weaker than the Higgs boson signals seen in LHC's first few months, indicating that the early result might have been a statistically fluke.

If a Higgs boson is there, it will be a Standard Model Higgs boson.

For reasons that I've discussed previously at this blog, the nature of the search methods used to identify a potential Higgs boson (such as the quantum mechanical limits on the kinds of interactions that can produce diphoton events) tends to strongly imply that any particle discovered i this search has all of the properties of a Standard Model Higgs boson (i.e. an intrinsic spin of zero, zero electromagnetic charge, the predicted quantum number that describes the strength of its weak force interactions, no weak force decay modes into non-Standard Model particles, and no color charge in the sense meant by the quantum chromodynamics theory that describes the nuclear strong force).

Bayseans out there would also give weight to the fact that the Standard Model has been incredibly accurate to date, so the discovery of something that looks a lot like a Standard Model Higgs boson, which is the last undiscovered particle in that model, right where it belongs more or less based on predictions from several decades ago, also gives us confidence that if we have discovered something that it is the Standard Model Higgs boson because it fits appropriately developed prior expectations.

So, don't take the hype about the need for months of additional research to determine if the particle we've found is really a Standard Model Higgs boson very seriously.

The announcement will have few new implications for BSM theories.

Now, it turns out that plenty of beyond the standard model theories, including all variations of SUSY, have more than one Higgs boson, one of which, typically the lightest, looks more or less exactly like the Standard Model Higgs boson. So this discovery doesn't itself exclude them. But, theories that don't have at least one Standard Model Higgs boson that could have a mass in the 124 GeV-126 GeV range (such as most versions of "Technicolor" and "non-linear sigma" models, which were invented in substantial part to hedge against the possibility that no Standard Model Higgs boson would be discovered), of course, are toast.

What helpful new information remains to be discovered?

Since a huge number of physicists already assume that we've discovered the Higgs boson somewhere in a roughly 2 GeV mass range, the speculative implications of new data really boil down to a few points that are still uncertain.

First, the details of the Higgs boson mass still matter. A mass discrepency as subtle as the difference between 124 GeV and 126 GeV turns out to have lots of importance in many beyond the Standard Model theories, for example, having considerable power in determining SUSY parameter space. One extreme is a much more natural number for SUSY, in what is already a liminal mass range for it, than the other (honestly, I don't even recall which is which without looking it up, since I am bearish on SUSY theories for other reasons).

The exact mass number is also relevant in determining if the Higgs boson mass is realy a fundamental constant or can be derived from some formula of other known Standard Model constants. The Standard Model doesn't have such a formula in it, but doesn't preclude the possibility that there are deeper relationships between the constansts that it does have which are being determined with ever greater certainty that makes formulas relating them less and less likely to be numerological coincidences.

Second, are we really seeing just one Higgs boson, or is there more than one kind of Higgs boson each of which has all of the same non-mass properties and each of which has a similar, but not identical mass? Some BSM theories have two nearly indistinguishable Higgs bosons of very similar mass and more data could rule out the possibility that there is both a 124 GeV and a 126 GeV neutral Higgs boson, for example.

Third, what is the "width" of the Higgs boson resonnance (which is a function of its half-life)? There should be a measureable width because Higgs bosons are not stable particles either in theory or as observed in practice, since decays are observed and stable Higgs bosons are not), but the constant is not strongly determined theoretically. Increasingly accurate data about the Higgs boson rest mass should also provide increasingly accurate data about the Higgs boson resonnance width, since generally you use the same data (a measurement of the overall resonnance of the Higgs boson, i.e. hill in the chart), to determine both at the same time.

Resonnance widths have been estimated for all of the quarks, for the charged leptons, and for composite particles made of quarks (although not for neutrinos to any great level of precision so far as I know, as their masses are also not known with much accuracy), but the only bosons for which resonnance widths are known are the W and Z boson widths, which are themselves not independent of each other. The Higgs boson resonnance width is the only boson resonnance width in the Standard Model which is independent of the W and Z boson value, so it might help us to find a pattern more generally.

Knowing this number is also helpful in refining the accuracy of the calculated "Standard Model backgrounds" in high energy physics interactions which physicists aided by computers calculate as a reference point against which the experimental data can be compared to see if there are any statistically significant evidence of beyond the standard model physics in the experimental results. The more accurately the constants of the Standard Model background are known, the more statistical power a set of experiments has to detect deviations from that background expectation (even, in principle, out of data from experiments already concluded and reanalyzed based on new estimates for Standard Model constants to use in calculating background expecations).

Other Unfinished Business: Revisiting High Energy SM Predictions

Scores, if not hundreds or thousands, of physics papers have been written discussing the predictions of the Standard Model at high energies given the then known constants and accepted equations of the Standard Model. But, almost all of those papers were hampered by the need to hedge the question of the mass of the Higgs boson and either made only broad generalizations based upon a wide range of favored masses and made a guess regarding Higgs boson mass which was in most cases wrong.

We also know a whole host of other Standard Model constants more precisely as a result of the work that has been done at the LHC, and the dramatic surge in computing power over the last decade or so has also steadily increased the number of terms that can be calculated from the infinite series approximations used to do calculations within the Standard Model thereby reducing "theoretical" error in these predictions, particularly at higher energies where the higher order terms in the equations used to calculate the approximate numerical results are more important.

The time has come to do another really serious and complete high energy extrapolation of Standard Model predictions, now that much more accurate estimates can be made of all of its parameters, now that more terms can be included in the calculations, and now that we can say with increasing confidence, for example, that there is not a fourth generation of the four kinds of Standard Model fermions out there.

One of the driving forces behind research into beyond the Standard Model physics has been an awareness that at high enough energies, the unmodified Standard Model blows up as its equations start to give unphysical answers (e.g., the sum of the probabilities of all possible events stops adding up to 100% called a violation of unitarity, and vacuum instability). The existence of a Standard Model Higgs boson at 124 GeV +/- has kicked this threshold up significantly from many previous estimates. But, I haven't seen any real definitive efforts to quantify this impact directly integrating all of the new data that LHC has provided.

These problems aren't overwhelming anymore, however.

A Higgs boson mass of 125 GeV implies a "metastable" vaccum (per the link in the paragraph above) at least up to something close to the GUT scale (10^10 GeV at the least optimistic estimate with the lighest experimentally supported Higgs boson mass to 10^18 GeV+ with a Higgs boson mass at the high end of the current range). The GUT scale is often described as 10^16 GeV, and the Planck scale is about 10^19 GeV.

There is also a near complete absence of unitarity problems at the currently favored Higgs boson mass:

[F]or . . . [a] Higgs mass around 125 GeV, which is currently phenomenologically favorable, the quartic coupling remains perturbative at all scales and preserves unitarity at all scales, both at tree level and when electroweak logarithms are included, which suppress amplitude and cross section of longitudinal gauge boson scattering significantly at high energies.

Knowing when this starts to happen and what is driving this mathematically, within the theory, can point us towards the weak spots in the theory that need to be investigated in further experiements (beyond mere brute force higher and higher energy colliders that try to determine what happens directly). If the Standard Model is flawed in some way, it is probably in what ever parts of the model are most strongly driving the unphysical results that are predicted, or because "new physics" is lurking at the relevant energy scale, waiting to be discovered.

Of course, if these problems virtually vanish with the currently favored Higgs boson mass, they perhaps they aren't problems any more and the beyond the standard model theories motivated by a desire to solve these no longer existing problems are no longer well motivated. Indeed, a Higgs boson mass of roughly the measured amount virtually insures that the Standard Model does not break down in theory, at least, at any energy that can be produced in an Earth bound laboratory (where energies are ca. 10^4 GeV with current techologies).

There is also an absence of observable weirdness of the type predicted at high energies if there is a Standard Model breakdown, such as vacuum instability, at the places that are home to the highest energy interactions that can be observed via astronomy, suggesting that to the extent that the Standard Model does break down at extreme high energies this could be due to our own errors in estimating the Higgs boson mass, or flaws in how we extrapolate the Standard Model to very high energies, or to special structural features of those kinds of extremely high energy interactions that make what is theoretically possible unphysical in practice.

Moreover, the current Higgs boson mass estimates suggests that if there does need to be a fix to the Standard Model at very high energies to prevent it from breaking down, that this fix can afford to be very, very subtle with a tweak that is equivalent in impact to the effect of having a Higgs boson mass that is just 1-2% heavier than the current estimate at the highest of available energy scales.

Where Could The Standard Model Be Flawed At High Energies?

What parts of the Standard Model might perform almost perfectly at moderately high energies, but fail catastrophically at higher energies that are not yet succeptible to being produced in experiments or post-Big Bang astronomical events?

I've previously suggested that the unphysical results at high energies might be driven by flaws in describing the "beta functions" that are used to describe the "running of the coupling constants" of the three Standard Model forces (strong, weak and electromagnetic) at different energy levels. Minor flaws in either the form or the constants used in these equations would be almost invisible at low energies but could give rise to dramatic problems at higher energies.

Another plausible place to look for flaws would be in areas where effects from general relativity or quantum gravity might be ignored. The Standard Model is built to accomodate special relativity, but not the additional implications of general relativity, which are usual expected at an order of magnitude level in the systems we study in high energy physics experiements to have a negligible impact even though we can't precisely computer them in a theoretically rigorous way. But, simply ignoring these effects at high energies may be inappropriate.

Asymptotic safety

One of the papers that accurately predicted the Higgs boson mass before it was determined last fall, at least provisionally, assumed a quantum gravitational concept called asymptotic safety (see, e.g., Percacci (2007)) to achieve that result, which suggests that this avenue of inquiry might be fruitful. The notion that the beta function of the gravitational force might have special characteristics that make it renormalizable (despite the fact that gravity is not renormalizable in naiive efforts to express it through quantum mechanical equations) has been kicking around since Weinberg proposed it this as a possibility in 1979, but the relevant mathematical breakthroughs to show that it might be possible to devise a mathematically coherent theory that could act in this manner have surfaced only recently.

Another paper, Peracci (2010) spells out asymptotic safety in the context of Standard Model interactions a bit more specifically:

The strong interactions are already described by an asymptotically safe theory, and there are reasons to believe that this result is not ruined by the coupling to gravity. The electroweak and Higgs sectors of the standard model are perturbatively renormalizable, but some of their beta functions are positive. This means that either new weakly coupled degrees of freedom manifest themselves at some scale, before the couplings blow up, or else the theory is consistent, but in a nonperturbative sense. The simplest realization of the latter behavior is AS [asymptotic safety]. If the world is described by an AS theory, there are two main possibilities: one is that AS is an inherently gravitational phenomenon, in which case AS would manifest itself at the Planck scale; the other is that each interaction reaches the FP [fixed point] at its characteristic energy scale.

For example, the Higgs vacuum expectation value (vev) might run with the energy scale of a system.

For criticism of the asymptotic safety program in quantum gravity, see for example, this July 11, 2009 post by Lubos Motl.

UPDATE June 20, 2012

There is considerable additional discussion in the comments (mostly from me, much of it quoting Matt Strassler's blog), about what kind of experimental outcomes could contradict a conclusion that what has been found so far is a Standard Model Higgs boson, and you can read the comments to follow that analysis.

What is less obvious is that if the particle detected truly is the Standard Model Higgs boson, this is inconsistent with SUSY theories that generically require that the Higgs sector consist of multiple Higgs bosons that collectively give rise to the effects attributed to the Higgs boson.

Moreover, string theory, generically, implies SUSY, although the reverse is not true.

Hence, the LHC, should it establish conclusively that the particle it has found really is the Standard Model Higgs boson has falsified essentially all versions of both SUSY and Sting Theory.

Now, in reality, the LHC is not capable of directly testing every single property of the Higgs boson and comparing it to the Standard Model. Some of the possible decays from a Higgs boson are so rare and subtle that you'd need a collider so powerful it might be impossible to make to test them. But, LHC probably can test enough Higgs boson properties to generically rule out any kind of SUSY theory that a theoretical physicist could ever love. And, as I've noted before another kind of LHC result (the exclusion of like SUSY particle candidates) combined with results from non-LHC experiments related to neutrinoless double beta decay, both of which are unrelated to exploration of the properties of the Higgs boson, are already on the verge of falisfying a huge swath of SUSY theories in a completely independent way. A failure to observe neutrinoless double beta decay in non-LHC experiments that are growing increasingly precise also essentially implies that neutrinos have only Dirac mass.

If the LHC and neutrinoless double beta decay experiments do this, and it will come very close in just a year or two, SUSY and String Theory are dead. If so, there are really no mainstream Beyond the Standard Model Particle Physics theories left to test (the linear sigma and technicolor models, for example, already having been pretty much killed by the discovery of the Higgs boson as well), although there is still room to infer more fundamental theories that reduce to precisely the Standard Model from fewer parameters.

Killing off all of these theories affects more than just the high energy physics community. It also removes almost all of the plausible dark matter candidates from the discussion.

Of course, LHC or neutrinoless double beta decay experiments could find that we haven't found the Standard Model Higgs boson, or that there is a considerable amount of neutrinoless double beta decay. But, the far more likely possibility is that they won't.

Thursday, June 14, 2012

Autosomal Genetic Mutation Rates

Maju takes the occasion of the sequencing of the bonobo genome to succinctly take advantage of a very solid long term calibration point for establishing the mutation rate of the genome in Great Apes as about half as great as indicated in the paper describing the result. This is possible because a reasonable well dated geological event, the formation of the Congo River, is closely associated with the Bonobo-Pan divergence date. One of the authors provides an encouraging comment noting limitations of the date in the paper and the reasons that it is likely wrong in the direction that Maju suggests based on other data sets. Maju concludes:

So unless the geology is wrong, bonobos and chimpanzees diverged 1.5 to 2 million years ago, and not a mere million years ago, as this paper claims.

This has important implications for the Homo-Pan divergence age [i.e. human-chimpanzee], as I have discussed again and again. Assuming that the 4.5:1 ratio estimated in this paper is correct, then the actual Homo-Pan divergence age ranges between 6.8 to 9.0 million years ago (and not a mere 4.5 Ma), with a median of 7.9 Ma, quite similar to the 8 Ma estimate I have been defending since the Caswell paper was published in 2008.

This matters directly, because it strongly influences how we fit archaeologically dated bones into the chain of evolutionary events that gave rise to modern humans. For example, Homo Erectus is about three-quarter of the way from the Homo-Pan divergence to modern humans with an 8 million years ago estimate, but only about half way with a 4.5 million year estimate. Similarly, Ardi is about half way on the timeline from the Homo-Pan divergence to modern humans with the 8 million years ago estimate, but appears almost at the very moment of the Homo Pan divergence with the 4.5 million year estimate.

This also matters because mutation rate date calibration has broad importance for the interpretation of almost all genetically estimated dates in pre-history and ancient history, and a factor of two error rate is easily enough to throw a population divergence date from one historical era to another. The longer the calibrating time period involved, the more likely it is to reflect the long term average and avoid systemic errors in other dates.

Autosomal genomes, because they are some much more data rich and have lots of apparently selectively neutral sequences, are more attractive dating tools than uniparental Y-DNA which has been empirically shone to be incoherent in mutation rate terms, probably because it is subject to so much more selective pressure.

The lack of qualification within the paper on the estimate for the divergence date is really quite unfortunate because, while the sequencing of the bonobo genome has wide relevance in all sorts of areas, the divergence data is one of the most digestable nuggest of knowledge in the paper for an educated layman or for other genetics researchers, and hence one of the most likely to be widely disseminated.

Aliens Prequel Includes PIE Passage

The Language Log blog is hot on the path of deciphering an untranslated passage spoken in a reconstruction of the Proto-Indo-European (PIE) language in the movie Promotheus, which is a prequel to the Alien movie series complete with comments providing hints from the person who wrote the passage for the movie and short sound clips.

One of those hint comments notes that:

Schleichers' Fable is indeed the practice piece used in David's language lesson. Fassbender took, by his own admission, about 17 hours to commit the entire fable to memory - poor man - and RS ended up using only the first line, which runs as follows:

hjewɪs jasmə hwælnə nahəst akʷunsəz dadʳkta (KD

This isn't a million miles away from Kortlandt or Lühr (or, for that matter, Schleicher's original). On the subject of the writing system, let me quash a rumour: it ISN'T of my doing. The use of what resembles a mixed cuneiform/hieroglyphic system, with elements of Eteocypriot and Linear Elamite chucked in for good measure, would not have occurred to me - I'm glad to say. The script comes courtesy of Fox's art department.

Quite a few efforts have been made to reconstruct PIE, so resources for deciphering it are fairly readily available (and the source language is hinted in a way fairly obvious to people familiar with linguistics earlier in the film). But, since the reconstuctions are anything but uniform and the phonetics are unfamiliar to English language speakers, the task is quite daunting, even for the professional and serious amateur linguists who frequent the blog.

Wednesday, June 13, 2012

Prehistory Via The Genetics of Goats and Sheep

Recent studies attempt to fathom the process of goat and sheep domestication respectively using the uniparental genetics of the modern populations of these animals as a tool to achieve this end.

Goat Herding Sailors

The abstract of the goat paper, Pereira (2009), includes the following:

Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East.

It has been previously shown that goats have a weak phylogeographic structure compatible with high levels of gene flow, as demonstrated by the worldwide dispersal of the predominant mtDNA haplogroup A. In contrast, our results revealed a strong correlation between genetic and geographical distances in 20 populations from different regions of the world.

The distribution of Y chromosome haplotypes in Maghrebi goats indicates a common origin for goat patrilines in both Mediterranean coastal regions. Taken together, these results suggest that the colonization and subsequent dispersal of domestic goats in Northern Africa was influenced by the maritime diffusion throughout the Mediterranean Sea and its coastal regions of pastoralist societies whose economy included goat herding. Finally, we also detected traces of gene flow between goat populations from the Maghreb and the Iberian Peninsula corroborating evidence of past cultural and commercial contacts across the Strait of Gibraltar.

The similar conclusion of the abstract of Zeder (2008), on "Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact," also deserves to be restated together with the goat paper:

The past decade has witnessed a quantum leap in our understanding of the origins, diffusion, and impact of early agriculture in the Mediterranean Basin. In large measure these advances are attributable to new methods for documenting domestication in plants and animals.

The initial steps toward plant and animal domestication in the Eastern Mediterranean can now be pushed back to the 12th millennium cal B.P. Evidence for herd management and crop cultivation appears at least 1,000 years earlier than the morphological changes traditionally used to document domestication. Different species seem to have been domesticated in different parts of the Fertile Crescent, with genetic analyses detecting multiple domestic lineages for each species.

Recent evidence suggests that the expansion of domesticates and agricultural economies across the Mediterranean was accomplished by several waves of seafaring colonists who established coastal farming enclaves around the Mediterranean Basin.

This process also involved the adoption of domesticates and domestic technologies by indigenous populations and the local domestication of some endemic species. Human environmental impacts are seen in the complete replacement of endemic island faunas by imported mainland fauna and in today's anthropogenic, but threatened, Mediterranean landscapes where sustainable agricultural practices have helped maintain high biodiversity since the Neolithic.

Genocidal Sheep Farmers

The abstract of the sheep paper, Chessa (2009), which uses a more sophisticated methodology involving genetic traces of ancient retroviruses argues (in part):
The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their “retrotype” and morphological traits dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as well as breeds previously recognized as “primitive” on the basis of their morphology, such as the Orkney, Soay, and the Nordic short-tailed sheep now confined to the periphery of northwest Europe. A later migratory episode, involving sheep with improved production traits, shaped the great majority of present-day breeds.
In short, sheep have experienced a major episode of population replacement sometime after the early Neolithic, leaving only a few relict populations at the European fringe. The result is likely to be less controversial than evidence of human population replacement, of course, because sheep are not people and we expect, or at least do not fault, herders, for consciously practicing sheep eugenics.

Light Dark Matter Parameter Space Narrowed

A clever reworking of the Xenon 10 direct dark matter detection experiment's twelve days of calibration data has excluded a significant share of the MeV scale dark matter parameter space for dark matter that interacts with electrons, something that "weakly interacting particles" (i.e. WIMPS) would not.

The Oldest Domesticated Cattle Bones In Africa

A 2005 report provides the oldest solid evidence of the use of domesticated cattle and associated Neolithic transition in Egypt (no later than 7000 BCE (9000 BP), and no earlier than 7300 BCE (9300 BP) in the Middle Nile) (and for that matter in Africa), although the local variety of wild aurochs from which domestic cattle were domesticated were present (and presumably hunted) at least six thousand years earlier according to newly dated petroglyphs from the same general region.

The Advent Of Middle Nile Neolithic Is Established To Within About 300 Years

Marnie has some notable data points on the archaeology of domesticated cattle in Egypt which he has translated from a Francophone report of a Swiss research team. An excerpt from his translation is below:
The difference between the tombs attributed to the Mesolithic and the cemeteries of the Neolithic are fundamental. . . . In a millennium, Nubian society had completely transformed their social organization. This transformation must have taken place on account of the introduction of domestic cattle, the oldest findings of which are in the Middle Nile at Nabta Playa in Egypt and Kerma. . . . [examination of the Northern Sudanese Middle Nile site of] El Barga . . . confirmed our hypothesis that El Barga is a Neolithic site: a man's grave next to which was deposited the skull of a domestic cattle buried just above the burial of a child. Two carbon 14 dates have given results of approximately 5750 BCE [7762 bp] that make this the oldest Neolithic site in the Nile Valley. . . .

[T]he cemetery shows technical and social transformations that had already taken place and one can't doubt that the introduction of pastoralism had occurred at an earlier time. The discovery of two sites located five kilometers from El Barga confirmed this hunch. . . . The sites . . . contain the bones of domestic cattle. Some of the remains were dated by radiocarbon dating to approximately 7000 BCE [9000 bp].
The study classifies a nearby site 300 years earlier as Mesolithic (7300 BCE; 9300 BP), pin pointing the Mesolithic to Neolithic transition at this location well down the Nile, at least insofar as cattle herding is concerned (but also in the overall cultural transformation that results from the transition), quite precisely.

Marnie also notes that in another post that the dating of "Egyptian rock art drawings of aurochs at Qurta on the Upper Nile . . . . [which] indicate that aurochs (bos primigenius) were present south of the First Cataract, earlier than 15,000 years ago."

To the best of my knowledge, the oldest archaeological evidence for the domestication of cattle (or for that matter, the oldest reliably dated evidence of the Neolithic revolution generally) in Africa is in Egypt, so this very precisely establishes the latest possible date for the arrival of the Neolithic in the Middle Nile, while also bracketing out the earliest possible date for its arrival there.


The study, as translated, correctly on this point, I think, states: "The sites . . . contain the bones of domestic cattle. Some of the remains were dated by radiocarbon dating to approximately 7000 BCE [9000 bp]."  This has some weasle wording, implying that domestic cattle probably go back to 7000 BCE in continuity with the remains at the site generally as part of a common culture, but not saying anything nearly that definitive.  This language wouldn't be inconsistent with a reading in which the domestic cattle bones in the neighboring sites really back pack only to 6000 BCE, and that the earlier remains were associated with a continuous somewhat advanced for a Mesolithic society proto-Neolithic culture (a goats and sheep without cattle culture, for example), and that it is premature to state that the Neolithic transition in the Middle Nile dates to 7000 BCE rather than 6000 BCE.  I think that the authors intend a stronger reading that that, which their juxtaposition of findings and strong implications suggest, but that they don't feel that their evidence is so definitive that they can truly commit to a more explicit conclusion yet.

I couldn't locate information on error bars on the dates cited in the translation in the original, but perhaps an informed commenter could provide information on how accurate carbon-14 dating is at this time depth or call attention to the pertinent language in the paper or its supplemental materials.

Also, I have assumed, but not confirmed that the carbon-14 dates cited in the paper are calibrated dates rather than crude ones, a distinction that is material to the tune of something on the order of low single digit centuries at this time depth. At the very least, one ought to assume that the dates discussed in the paper, whether calibrated or not, were at least compared with dates in the same units from the literature given the claim that this is the oldest such site.

Implications For The Big Neolithic Transition Picture

The study does not appear to distinguish the domesticated cattle bones found in the Middle here from Near Eastern domesticates from a thousand years earlier in the Upper Euphrates Valley. As Marnie noted in another post citing Zeder (2008):

"Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion and impact" has these domestication dates BP: sheep 11,000; goats 11,000; pigs 10,500; cattle 10,000 (Upper Euphrates Valley). However, she states that morphologically altered domestic cattle are not found in Central Anatolia until after 8,500 BP.
Thus, this new data is consistent with the most widely accepted (although, of course, not universally accepted) narrative in which the primary domestication of cattle in the Fertile Crescent ca. 8000 BCE (10000 BP) which has spread to the Middle Nile in Upper Egypt and Northern Sudan roughly 800 to 1000 years later via migrating pastoralists rather than a local domestication in Egypt.

Open Questions Requiring Further Investigation

This analysis still leaves open questions and room for controversy (although some questions left open by this report's conclusion and mentioned below may have actually already been resolved with other research):

Why Did Cattle Domestication Leap Frog From The Fertile Crescent To The Middle Nile?

You can't get to the Middle Nile without going through the Sinai, and either the Lower Nile or the Eastern Sahara immediately to the West of the Nile River Valley (which had a climate more favorable for cattle herding then than it does now). So, where isn't aren't their older domesticated cattle skulls in the Lower Nile, for example, than there are in Middle Nile?

Marnie has suggested that there may have been an independent cattle domestication from Egyptian aurochs, something that may have been favored everywhere aurochs were found at the time by large scale climate shifts in the entire region, and perhaps mere culture transmission of the idea of domesticating aurochs in general from travelers who did not bring the animals and the entire cultural package with them in a demic migration. He notes in support of this the somewhat distinctive character of domesticated cattle in Africa. I tend to disfavor this interpretation, mostly because a technology transfer scenario is consistent with the known dates and has been documented fairly persausively for most of the rest of the world where the Fertile Crescent package (or other Neolithic packages) arrived.

Other possibilities are that as of ca. 7800 BCE to 7000 BCE:

(1) archaeological preservation conditions then and in the millennia that followed may not have been as good in Lower Nile as in the Middle Nile, destroying the evidence of an earlier Lower Nile Neolithic transition (this could be due, for example, (A) to continuously high populations densities in the Lower Nile with later populations defiling older remains, (B) to greater practical use and recycling of bones by people in the Lower Nile, (C) to more dramatic flooding, (C) to higher groundwater levels, (D) to temperatures more favorable to decomposition, or (E) to poorer soil, moisture and temperature conditions for preservation enhancing mud packs and clays), or

(2) conditions for cattle herding may have been better in the Middle Nile than the Lower Nile, perhaps due to elevation or localized flooding concerns (the even later appearance of domesticated cattle in Central Anatolia which was closer to the site of the earliest known auroch domestication, however, tends to disfavor a scenario in which highland river basins are favored ecology for cattle herding; but the fact that cattle seem to have been domesticated in the Upper Euphrates Valley rather than the Euphrates Delta, suggests that maybe Lower Egypt wasn't an optimal ecology for cattle herding; perhaps it one goes too far into the highlands, such as Central Anatolia and Ethiopia, the evenings get too cold in the winter or the grasses don't get enough moisture to be as thick and reliable), or

(3) existing populations may have posed less of a barrier to the introduction of cattle herding in the Middle Nile than the Lower Nile, either because:

(A) the Lower Nile people were so prosperous in hunting and gathering at the time that they resisted encroachment and innovation from cattle herders, or because

(B) a society involving semi-sedentary fishing, pre-farming of wild crops and undomesticated animals, pottery making, and short range hunting and gathering in a confined and abundant territory gave rise to a society more capable of rapidly and voluntarily (or with minimal coercion from a thin superstate class) integrating Fertile Crescent cattle herding into their way of life even though this earlier collection of intermediate innovations towards sedentary society was less transformative and less dynamic.

The (3)(B) scenario is quite similar to Marnie's hypothesis, but would attribute modern domestic cattle distinctiveness in Egypt to admixture of imported domesticated cattle with wild aurochs over the millennia until the wild aurochs were extinct in the region, or to the introgression and genetic influence in Indian cattle in the Bronze Age, rather than to an independent domestication.

Of course, for either of the claims in possibility (3) to hold up, one must first establish from the archaeological record that there were strong cultural distinctions between the Lower Nile and Middle Nile in the 8th millennium BCE.

What Else Accompanied Domestic Cattle To The Middle Nile?

To what extent was the Neolithic transition in the Middle Nile a population replacement phenomena and to what extent was it was culturally adoption phenomena, and how gender biased was the demic impact that did result whatever its magnitude? The male and female uniparental and the autosomal genetics of North Africa and East Africa all make clear that there were one or more demic back migrations from the Near East to that region. What particular components of the modern population genetic mix arrived in this cattle herding wave relative to Upper Paleolithic back migrations and later back migrations? What did the Middle Nile look like from a population genetic perspective in the Mesolithic before Fertile Crescent food production techniques arrived?

Were the dramatic societal changes observed in cemeteries home grown or do they represent adoption of a Fertile Crescent cattle herding culture?

At what time did sheep, goats, and Fertile Crescent farming crops arrive at which places relative to the arrival of domesticated cattle?   Did they arrive all at once after consolidating into a complete Neolithic package in the Near East, or did they arrive in multiple closely successive waves?  See, e.g., here and here. See also, here (citing Dillon (2007) which argues that "The domestication of sorghum has its origins in Ethiopia and surrounding countries, commencing around 4000–3000 BC.")

It is generally accepted that the donkey was domesticated in Egypt. The usual chronology is to assume that this happened sometime after Fertile Crescent domesticated animals arrived (I've seen 6000 B.C.E. proposed as a domestication date). Where did this happen and is that the right chronology? What evidence supports that conclusion?

When do we start to see cultural innovations from the Fertile Crescent package, in general, in the Nile, and what particular innovations do we see? Do those innovations show continuity from a Mesolithic substrate in Egypt, or are they something genuinely new under the sun?

Taking it as a given that the oldest evidence for the Fertile Crescent Neolithic in Africa is found in the Middle Nile at this location, do subsequent dates from elsewhere in Africa allow us to develop an empirically grounded picture of when and where it spread from that African epicenter? To the extent that this picture is consistent with one or more of multiple possible scenarios for the expansion and spread of the Afro-Asiatic and Nilo-Saharan languages, those scenarios are favored relative to the alternatives.


This is a bit of a raw data dump, but is included for convenience and future reference. The narrative part of the post ends above. This is one big footnote.

In general, what is notable is that the currently available evidence suggests that the domestication of plants used in Sahel agriculture was surprisingly recent (with pearl millet only just barely domesticated in Africa before it was exported to India), that the evidence for an independent African domestication of cattle is shallow, that sheep and goats arrived in African, if anything after if not simultaneously with, cattle herding, rather than before it, and that the human presence in East African was intermittent with modern humans frequently banished from the region for centuries by prolonged arid periods.

Domestication dates and climate in North Africa

Selective domestication and climate data points from here (citing "Are the early Holocene cattle in the Eastern Sahara domestic or wild?" Fred Wendorf & Romuald Schild (Evolutionary Anthropology 3(4), 1994)):

Eastern Sahara

The Eastern Sahara near Upper Egypt has been repeatedly abandoned and repopulated in response to shifting climate conditions during the Holocene era. It provides a latest possible introduction date for sheeps and goats which quite possibly post-date the widespread use of cattle as a food source.

[T]here is no evidence of human presence [in the Eastern Sahara near Upper Egypt] before 9,500 B.P. except for a radiocarbon date of around 10,000 years ago from a hearth west of Dakhla. The earliest sites with large bovid remains are imbedded in playa sediments that overlay several meters of still older Holocene playa deposits. . . [of] Middle Paleolithic artifacts[.]. . .

These assemblages have been classified as the El Adam type of the Early Neolithic. Several radiocarbon dates place the complex between 9,500 and 8,900 B.P. There is no evidence that there were wells during this period. It is assumed, then, that these sites represent occupations that took place after the summer rains and before the driest time of the year when surface water was no anger available. Three of these sites . . . have yielded, through excavation, more than 20 bones and teeth of large bovids that have been identified as Bos. These occurred along with several hundred bones of gazelle (Gazella dorcas and G. dama) and hare (Lepus capensis); a few bones of jackal (Canis aureus), turtle (Testudo sp.); and birds (Otis tarda and Anas querquedula); the large shell of a bivalve (Aspatharia rubens), probably of Nilotic origin; and various snail shells (Bulinus truncatus and Zoorecus insularis).

After a period of aridity around 8,800 years ago, when the desert may have been abandoned, the area was re-occupied by groups with a lithic tool-kit that emphasized elongated scalene triangles. The grinding stones, scrapers, and rare pieces of pottery that are present characterize the El Ghorab type of Early Neolithic and have been dated between 8,600 and 8,200 B.P. Oval slab-lined houses occur during this phase. all of them located in the lower pans of natural drainage basins. However, there are no known wells, suggesting that the desert still was not occupied during the driest part of the year. Faunal remains are poorly preserved in these sites and. indeed, only one bone of a large bovid was recovered from the four sites with fauna. in these sites the Dorcas gazelle is the most numerous, followed by hare, together with single bones of wild cat (Felis silvestris), porcupine (Hystrix cristata), desert hedge-hog (Paraechinus aethiopicus) an amphibian, and a bird.

Another brief period of aridity between 8.200 and 8,100 B.P. coincides with the end of the El Ghorab type of Early Neolithic in the desert. With the return of greater rainfall about 8,100 B.P., a new variety of Early Neolithic, the El Nabta type, appeared in the area. . . . Radiocarbon dates place the El Nabta sites between 8,100 and 7,900 B.P. . . . Beside each house was one or more bell-shaped storage pits; nearby were several deep (2.5 m) and shallow (1.5 m) water-wells. This site, located near the bottom of a large basin, was flooded by the summer rains. The houses were repeatedly used, probably during harvests in fall and winter. Several thousand remains of edible plants have been recovered from these house floors. They include seeds, fruits, and tubers representing 44 different kinds of plants, including sorghum and millets. All of the plants are morphologically wild, but chemical analysis by infrared spectroscopy of the lipids in the sorghum indicates that this plant may have been cultivated. Of the four El Nabta sites that have yielded fauna, two contained bones of a large bovid identified as Bos. The faunal samples from the other two sites are very small.

Another brief period of aridity separated the El Nabta Early Neolithic from the succeeding Middle Neolithic, which is marked by the much greater abundance of pottery. In addition, each piece of pottery is decorated over its entire exterior surface with closely packed comb- or paddle-impressed designs. Some of the pots are large, and analysis of the clays indicates that they were made locally. There were also some changes in lithic tools. More of them were made of local rocks, but there was sufficient continuity in lithic typology to suggest that the preceding Nabta population was also involved.

Radiocarbon dates indicated an age for the Middle Neolithic between 7,700 and 6,500 B.P. The sites from the early part of this period range from one-or-two house homesteads in some of the smaller playas to multi-house villages in the larger basins. There is also one very large settlement along the beach line of the largest playa in the area, as well as, small camps on the sandsheets and the plateaus beyond the basins. . . . All of the sites have large, deep walk-in wells and storage pits. Except for the small camps, most of the sites appear to have been reused many times, with new house floors placed on top of the silt deposited during the preceding flood.

Excavations at five Middle Neolithic sites have yielded more than 50 bones from large bovids. Most of these bones came from the large “aggregation” site at the margin of the largest playa in the area and from the early Middle Neolithic site, dated before 7,000 B.P., which is located on a dune adjacent to another large playa. Each of the other three Middle Neolithic sites yielded only one to three large bovid bones.

Around 7,000 B.P., the remains of small livestock (sheep or goats) appear in several Middle Neolithic sites at Nabta. Because there are no progenitors for sheep or goats in Africa, these caprovines were almost certainly introduced from southwest Asia. . . . the paucity of the fauna and the absence, except for cattle and small livestock, of animals that require permanent water suggests a rather poor environment, most likely comparable to the northernmost Sahel today with about 200 mm of rain or less annually.

The Middle Neolithic was brought to an end by another major but brief period of aridity slightly before 6,500 B.P., when the water table fell several meters and the floors of many basins were deflated and reshaped, The area probably was abandoned at this time. . . .

With the increase in rainfall that began around 6,500 years ago. human groups again appeared in the area, but this time with ceramic and lithic traditions that differed from those of the preceding Middle Neolithic. This new complex, identified as Late Neolithic, is distinguished by pottery that is polished and sometimes smudged on the interiors. This pottery resembles that found in the slightly later (about 5,400 or, possibly, 6,300 B.P.) Baderian sites in the Nile Valley of Upper Egypt. It seems likely that an as yet undiscovered early pre-Badarian Neolithic was present in that area and either stimulated or was the source of the Late Neolithic pottery in the Sahara. It is unlikely, however, that this hypothetical early Nilotic Neolithic will date much earlier than 6,500 B.P. There are terminal Paleolithic sites along the Nile that are dated to around 7,000 B.P. and it is highly improbable that two such different life-ways could co-exist exist for long in the closely constrained environment of the Nile Valley.. . . The end of the Late Neolithic in the Eastern Sahara is not well established.The period may have tasted until around 5,300 B.P. when this part of the Sahara was abandoned.

Due to poor preservation faunal remains in Late Neolithic sites are not as abundant as those from the Middle Neolithic. However, the Late and Middle Neolithic samples generally include the same animals suggesting that the environment was also generally similar during these periods. Although large bovids are also present in three Late Nealithic sites, and more frequently than in the faunal assemblages of the preceding period, they still are a minor component of the sample.

The Late Neolithic Nabta is marked by interesting signs of increased social complexity, including several alignments of updght slabs (2 x 3 m) imbedded in, and sometimes almost covered by, the playa sediments. Circles of smaller uptight stabs may calendrical devices. Stone-covered tumuli are also present; two of the smaller ones contain cow burials, one in a prepared and sealed pit. . . .

Even the earliest of these early Holocene Eastern Sahara sites have been attributed to cattle pastoralists. It is presumed that these Early Neolithic groups came into the desert from an as yet unidentified area where wild cattle were present and the initial steps toward their domestication been taken. This area may have been the Nile Valley between the First and Second Cataracts, where wild cattle were present. Moreover, lithic industries were closely similar to those in the earliest Saharan sites. . . . It is assumed, because of the apparrent absence of wells at the earliest sites, that the first pastoralists used the desert only after the summer rains, when water was still present in the larger drainage basins. After 8,000 years ago, when large, deep wells were dug, the pastoralists probably resided in the desert year-round.

Other Parts of North Africa:

The antiquity of the known domestic cattle elsewhere in North Africa does not offer much encouragement with regard to the presence of early domestic cattle in the Eastern Sahara.

Gautier recently summarized the available data, noting that domestic cattle were present in coastal Mauritania and Mali around 4,200 years ago and at Capeletti in the mountains of northern Algeria about 6,500 years ago. At about that same time, they may have been present in the Coastal Neolithic of the Maghreb. Farther south in the Central Sahara, domestic cattle were present at Meniet and Erg d’Admco, both of which date around 5,400 years ago, and at Adrar Rous, where a complete skeleton of a domestic cow is dated 5,760 +/- 500 years B.P ].

Domestic cattle have been found in western Libya at Ti-n-torha North and Uan Muhuggiag, where the lowest level with domestic cattle and small livestock (sheep and goats) dated at 7,438 t 1,200 B.P. At Uan Muhuggiag, there is also a skull of a domestic cow dated 5,950 +/- 120 years. In northern Chad at Gabrong and in the Serir Tibesti, cattle and small livestock were certainly present by 6,000 B.P. and may have been there as early as 7,500 B.P. We are skeptical, however, about the presence of livestock at Uan Muhuggiag and the Serir Tibesti before 7,OO0 B.P., when small livestock first appear in the Eastern Sahara, if we must assume that these animals reached the central Sahara by way of Egypt and the Nile Valley. This also casts doubt on the 7,500 B.P. dates for cattle in these sites.

The earliest domestic cattle in the lower Nile Valley have been found at Merimda, in levels that have several radiocarbon dates ranging between 6,000 and 5,400 B.P. and in the Fayum Neolithic, which dates from 6,400 to 5, 400 B.P. These sites also have domes-tic pigs and either sheep or goats. In Upper Egypt, the earliest confirmed domestic cattle are in the Predynastic site of El Khattara, dated at 5,300 B.P. However, domestic cattle were almost certainly present in the earliest Badarian Neolithic, which dates before 5,400 B.P. and possibly were there as early as 6,300 B.P. Farther south, in Sudan near Khartoum, the first domestic cattle and small livestock occurred together in the Khartoum Neolithic, which began around 6,000 B.P.

It is probably significant that none of the early Holocene faunal assemblages in the Nile Valley from the Fayum south to Khartoum that date between 9,000 and 7,000 H.P contains the remains of cattle that have been identified as domestic. It is this ab-sence of any evidence of recognizable incipient cattle domestication in the Nile Valley or elsewhere in North Africa that cautions us to consider carefully the evidence of early domestic cattle in the Eastern Sahara. . .

Equus, even in the Late Paleolithic, seems to have been confined to the Red Sea Hills and the east bank of the Nile. . . .

[Did] the first steps toward cattle domestication began in the Nile Valley, perhaps during the Late Pleistocene, when there is so little faunal evidence to support that hypothesis? The answer may lie in the identification of the cattle remains found in the Late Paleolithic sites in Sudanese and Egyptian Nubia. It has been suggested that it would be very difficult to separate the bones of the incipiently domestic cattle from those of wild cattle.

More On African Cattle Domestication

See also here:

The problem of cattle domestication in Northeastern Africa is considered and hopefully ‘‘solved’’ in the light of new mtDNA evidence which suggest an early late Pleistocene split between African, Asian, and Eurasian wild Bos populations.

The Grigson’s study concluded cattle from all periods at Nabta Playa were morphologically wild (2000).

Smith’s study: morphologically wild prior to and including the El Nabta/Al Jerar Maximum (7050 – 6150 BC), but domesticated from the Ru’at El Ghanam phase (5900 – 5500 BC) onward.

More on Sorghum Domestication With A Barley Footnote

From the same source:

One of these sites yielded charred seeds of wild millet and two varieties of legumes (Wasylikowa, report to F. Wendorf 1996)

It also has a reference to possible early domesticated sorghum. Although again the case is bit weak. There’s more reference to it here. The seeds don’t appear to resemble any kind of cultivated sorghum though. They did seem to be harvesting and storing them in large amounts; some of the houses had storage pits for the grains.

Preliminary chemicalanalyses by infrared spectroscopy of the lipids in the archaeological sorghum show closer resemblance to some modern domestic sorghum than to wild varieties (Wasylikowa et al. 1993)

In a later publication (97) Wasylikowa describes the Sorghum as more likely to be wild, after another study of the seeds showed them to be typically wild seeds.

Smaller grain size and the lack of any spikelets containing attached branchlets of the inflorescence or rachis fragments suggest that the material harvested and eaten at the Nabta Playa site were of a wild type.

This sorghum doesn’t seem to ‘spread out’, as farmers tend to expand massively into their hunter gatherer neighbours very rapidly. The expansion of domesticated sorgum doesn’t seem to begin until the expansion of the domesticated donkey, which parallels it’s spread into Asia quite well, and the donkey seems to have been domesticated about 6,000 BP.

The barley recovered from this site during the 1977 excavations (Hadidi in Wendorf and Schild 1980: 347) is regarded as intrusive. . . .

Around 8000 cal B.P. there was an important new addition to the food economy of the Middle Neolithic. Domestic caprovids, either sheep or goat, or both, were introduced from Southwest Asia, probably by way of the Nile Valley (although the oldest radiocarbon dates now available for the Neolithic along the Nile are about 500 years later)

See also here (citing Dillon (2007) (who in turn seems to be replying on the book C. Wayne Smith, Richard A. Frederiksen, "Sorghum: Origin, History, Technology, and Production" (2000) in the vicinity of pages 26-39, which in turn cites Murdock (1959) (Mande in West Africa ca. 4500 BCE and then to Sudan ca. 4000 BCE); Ehret (1988) (Lake Chad 4000 BCE); Shaw (1976) citing Clark (Adrair Bous 2000 BCE); J.R. Harlan (1976; 1989; 1995) (3000 BCE in Africa since in India by 2000 BCE or even as early as 3000 BCE; Doggett (1988) (3000 BCE); Mann (1983) (6000 BCE); Fred Wendorf (1984)(not 8000 BCE); Stemler (Sahara and Nile 1000 BCE); Wigboldus (1990) (after 0 CE); Rowley-Conwy 1997; 1999) (relatively recently); A. A. Magid (1989; 1995) (relatively recently in Nile Valley); Barnett (1997) (relatively recently in Ethiopia); R. Haaland (1995; 1998) (wild sorghum introduced to India, domesticated there and reintroduced to Africa; notably, none of the book's sources argue for an Ethiopian sorghum domestication ca. 4000 BCE-3000 BCE):

Arthropological evidence suggests that hunter-gatherers consumed sorghum as early as 8000 BC. The domestication of sorghum has its origins in Ethiopia and surrounding countries, commencing around 4000–3000 BC. Numerous varieties of sorghum were created . . . . These improved sorghum types were spread via the movement of people and trade routes into other regions of Africa, India (approx. 1500–1000 BC), the Middle East (approx. 900–700 BC) and eventually into the Far East (approx. AD 400).

By the time sorghum was transported to America during the late 1800s to early 1900s, the diversity of new sorghum types, varieties and races created through the movement of people, disruptive selection, geographic isolation and recombination of these types in different environments would have been large. . . . Sorghum is the closest cultivated relative of sugarcane.

The book notes (at 30) that wild types are now found in the Eastern Sahara-Nile area, Lake Chad, and the inland Niger delta, and that the earliest uncontested evidence of crop cultivation in North Africa comes from Mauritania (Amblard 1996); the Fezzan 2600 BCE-2500 BCE of Libya (van der Veen (1995) neither of which has sorghum. Wendorf and Schlid (1980); A. Gautier (1980, 1984), Kuper (1981); and Pachur and Roper (1984) found wild sorghum in the Nile Valley in anticipation of the creation of the Lake Nassar Reservoir from 8000 BCE to 9000 BCE. Domesticated sorghum has been found in Southern Sudan at the confluence of the Blue Nile and Atbara Rivers at the Shaqadud cave complex which are dated to 2173 BCE +/- 83 years and 2109 +/-65 years by L. Constantini (1983) (1500 years before Stemler (1976) and Haaland (1987). Klee and Zach (1999) claim 4000 years of domestication of grasses and tending of wild grasses in Northeast Nigeria at early Neolithic sites. Neumann (1999) argues for the spread of African domesticate agriculture from Saharan out-migrations starting 3000 BCE. G. Connah (1981) documents native versions of modern African domesticated crops and useful trees in savannas of the Sudan, the Sahel and Lake Chad. A. E. Close and F. Wendorf (1992) discuss some of their relevant excavations. Rowley-Conwy has reported samples of domesticated Sorghum from 1000 BCE that become abundant by 800 BCE, and historic attestations from the 700s BCE by Assyrians in Egypt. The Middle Nile Valley has no date from about 3000 BCE to 1000-500 BCE, but older finds appear consistent with wild type sorghum in high frequency but low volume. Neumann (1999) states that as late as 2700 BCE, the residents of the Lake Chad basin relied on wild millet and other wild grasses rather than domesticated cereals with gathering of wild plants forming a dominant part of the economy that also produced pottery impressed with wild grass patterns. Dates of Arabian and Indian finds as far back as 4000 BCE (Qurm, wild); Hili (3090 BCE (repudiated by authors) and 2500-2400 BCE, wild), Pirak (1600 BCE, domesticated). Inamgao in Deccan India ca. 1600 BCE-700 BCE has a variety of foreign plants some African, but not sorghum and only in a minor way per Kajale (1977, 1991). Rojdi, India has samples of both sorghum and pearl millet as far back as 2000 BCE in some abundance although Weber (1991) and Meadows (1996) have somoe doubts about some species identifications. Hulas, India has both African and Near Eastern crops in association with Late Harappan (1700 BCE to 1000 BCE) cultural finds.

The book recites at 64-66 that Zhijun Zhao (2000) reports sorghum finds in China from 5000 BP (Donghuishan, Ganzu Province), 3000 BP (Niazipoo, Shaanxi Province) and the Western Zhou dynasty 1100-771 BCE (Sanlidun, Jiangsu Province) while Underhill (1997) makes a non-definitive claim for sorghum in China as early as 3500 BCE to 3800 BCE in the East Central Yellow River Valley The early sites all involve Northern China's Yellow River and not the Southern Chinese Neolithic. To find an African crop in China so early, and before any parallel instances in India is remarkable.

The book also notes that R.H. Meadow (1996) finds African domesticated sorghum in the Indus River Valley in the late third millennium and early second millennium. Kajale (1991) discusses a possible later arrival; A. de Maigret (1986); Mercy (1991); and Clieuziou and Tosi (1989) discuss a possible late third millenium arrival. Doggett (1988) suggests a route from Somolia and East Africa via Aden to Baluchistan continuing Sumerian trade routes in place in 2800 BCE. Constantini (1984) and Potts (1994) document evidence of trade between Yemen and Ethiopia/Sudan in the Bronze Age from African origin botanical remains. Edens and Wilkinson (1998) see a Bronze Age complex civilization in the Yemen highlands ca. 3600 BP-2600 BP possibly as a Sabaean civilization precursor with strong ties to the Horn of African and Ethiopia and Punt, even pre-Iron Age. Pickersgill (1983) (based on historical sources) likewise argues for a pre-second millenium B.C.E. trade route connecting Yemen to East Africa and on to India. Fattovich (1997) argues that the trade is at least as old as the Iron Age. Harappan trade with the Sumerians is documented prior to 2500 BCE.

The book reaches some overall analysis at 70+ with domesticated sorghum speculated to have been used in the Nile earlier than any finds to date, and a possible back migration of a second domesticated version from India also considered a provacative, but real possibility. The Tarim basin is identified as a fruitful place to look for sorghum trade with China. The Sahara may have been more of a barrier than it is now prior to camel domestication. A rapid demic diffusion of sorghum cultivation is offered as an explanation of why it is hard to localize its geographic origins between the West Africian Sahel and Sudan. New discoveries about Bronze Age Yemen and Southern India that are older than current finds are anticipated. F. Allard (1998 Int. J. Hist. Archaelogy, 1999 Antiquity) is looking at these nearly contemporaneous with India connections from China to Africa that could have been by land or sea with a land route somewhat favored. The book predates ancient DNA evidence from these plants or even really definitive modern phylogenies of old strains. At 74, the book references (without citation on that page) an old Indian tribal story about an African queen or king sending a group of people to colonize and trade with the Deccan pennisula.

More On Ethiopian Agriculture

More on early Ethiopian agriculture here (citing Blench, Enset culture and its history in highland Ethiopia):
Cultural and linguistic evidence concerning the origin and distribution of enset culture seem to point generally in the same direction. Enset was part of a widespread and ancient system of cultivation of vegetative crops formerly distributed much more widely through the Ethiopian highlands. The main cultivators of enset were Omotic-speakers, though it was probably adopted early by some groups of Cushitic-speakers.

However, when the Ethio-Semites entered Ethiopia bringing seed agriculture and the plough, enset and other root crops such as yams (Dioscorea spp.) and the Labiates (Coleus spp.) were pushed into residual cultivation, except where the terrain was so highly dissected that ploughing was effectively impossible. In this situation, notably in the southwest, the Gurage Semitic-speakers adopted enset and it became central to their production system, permitting the expansion of population to levels such that no other crop would support comparable densities in similar terrain.

Blench's contention that Cushitic has origins in the Neolithic is also referenced, although the purely linguistic argument (the existence of a shared proto-word for sheep and goats) is rather flacid. Among other reasons, a loan word could easily have accompanied the introduced domesticated animal where ever it went, something observed in the cases, for example, of tea and bananas. Also, if the original domestication of the loan word was into one Cushitic language, and the original borrower of the domesticated animal modified the word in a characteristically Cushitic fashion and was the source of the domesticated animal's spread to with its Cushitically adapted name to other Cushitic populations, the common loan word would even look Cushitic in a particularlized way, and secondary dispersion of ideas and technologies is likely to occur preferrentially with people who speak languages related to one's own.

More On Pearl Millet Domestication

Dorian Fuller (2007) has written the definitive review of what science knows about pearl millet domestication in West Africa, one of the most important African specific domesticates, given current knowledge (comprehensive citations and references to omitted figures not included):

Sites with early pearl millet are numbered: 1, Dhar Tichitt sites; 2, Dhar Oualata sites; 3, Djiganyai; 4, Winde Koroji; 5, Karkarichinkat; 6, Ti-n-Akof; 7, Oursi; 8, Birimi; 9, Ganjigana; 10, Kursakata. Historical sites with pearl millet metrical data: 11, Arondo; 12, Jarma; 13, Qasr Ibrim.

Pearl millet domestication is inferred from two sets of evidence. First, there was loss of natural seed shedding, which is linked to the shift from sessile involucres to development of a non-dehiscent peduncle. This shift is already evident from ceramic impressions of pearl millet chaff by 1700–1500 BC in Mauretania, and slightly later in Nigeria. Pearl millet shows a subtle but clear change in grain shape, becoming apically thicker and more club-shaped than its wild counterpart, i.e. an increased thickness/breadth ratio. However, a major increase in seed size appears delayed. . . .

Early West Africa averages (Birimi, 1700–1500 BCE; Kursakata, 1500–800 BCE) fall in the wild zone although ranges extend into the larger domesticated zone. The earliest finds in India (Surkotada, approx. 1700 BCE) are close to these as are Early Historic (200 BCE–300 CE) Nevasa in southern India. North Indian Narhan (1400–800 BCE) shows a marked shift towards larger sizes comparable with modern domesticates, as does early medieval Qasr Ibrim (Egypt, approx. 450 CE: this find is preserved by dessication and has been reduced to be comparable with carbonized material). Jarma in south-west Libya may show an apparent shift towards somewhat larger grains during the early first millennium CE, comparable with the size found in medieval Senegal at Arundo. Later Medieval Jarma has shifted back towards to near wild size range.

Of note is that early West Africa populations, from the second and first millennia BC, have their averages firmly in the wild size range, although there are long tails of variation that extend into the larger size range (e.g. at Birimi). One of the earliest finds of pearl millet from India comes from Surkotada, Gujarat, approx. 1700 BC, which can be seen to fall with these early domesticated African populations. By contrast, a rather later, Gangetic population from Narhan is markedly larger, suggesting selection for larger-grained pearl millet. In Africa larger grained populations appear in the first millennium AD, represented by finds from Nubia and Libya, as well as Medieval Senegal. However, the continued small-grained populations in Early Historic South India (Nevasa) and apparent reversion in later Medieval Libya suggests that there may be factors that work against gigantism in pearl millet, and in the absence reinforcing selection populations may tend towards the smaller size ranges. . . .

As both Libya and South India lack wild populations, this cannot be attributed to cross-pollination with wild types. There may be some constraints particular to this crop, as one experiment indicates that optimal germination occurred under higher temperatures that resulted in lower average grain weights. In addition, pearl millet involucres are polymorphic in grain count with the vast majority producing two grains, a large minority with one larger grain, and a further minority producing 3–9 grains, which are necessarily smaller. Thus, selection for higher grain counts, and more reliable germination, might conflict with selection for larger seed sizes. Nevertheless as a working hypothesis, I would propose that, as with pulses, there is a deeper burial threshold that selected for gigantism in pearl millet at some times and in some locations. In that regard it might be noted that the larger grain populations in Libya and Nubia, like that in Gangetic India, are associated with more intensive plough cultures, whereas ards were not present in West Africa and may have declined in post-Garamantean Libya. Thus, we can hypothesize that large-grained varieties evolved under plough systems and then dispersed back to West Africa at a later date. If so, this would imply separate events of grain enlargement in India and north-eastern Africa. While initial cultivation must have selected for non-shattering, and slight changes in grain weight and shape (the club shape), serious gigantism may have required a stronger selection pressure and therefore evolved later: a millennium or more later in India, and two millennia later in Africa. . . .

[W]e would predict that pearl millet cultivation began by 3200–2700 BC.
Even if pearl millet was cultivated as a crop a thousand years before the date estimated, this pillar of locally domesticated crops in Sahel agriculture is still domesticated long after the Fertile Crescent package of crops arrived in the parts of Africa where they were viable, and probably after Sorghum as well. Fuller's account also suggests that Pearl Millet may have made made its way to India almost as soon as it had been domesticated in Africa, rather than in a transfer of a crop which had long been cultivated there, although the possibility of a reversion to a wild type under selection pressure in an increasingly arid Sahel environment is also a possibility.