Tuesday, August 30, 2022

Protons Still Don't Decay

Many grand unified theories of physics propose that protons, while long lived, decay eventually. So far, experimental measurements find no evidence of this happening, as the Standard Model of Particle Physics predicts (by virtue of the requirement of conservation of baryon number).

In particular, this rules out many SU(5) GUT theories, including the simplest ones.

We searched for proton decay via pμ+K0 in 0.37 Mtonyears of data collected between 1996 and 2018 from the Super-Kamiokande water Cherenkov experiment. The selection criteria were defined separately for K0S and K0L channels. No significant event excess has been observed. As a result of this analysis, which extends the previous search by an additional 0.2 Mtonyears of exposure and uses an improved event reconstruction, we set a lower limit of 3.6×1033 years on the proton lifetime.
Super-Kamiokande Collaboration, "Search for proton decay via p→μ+K0 in 0.37 megaton-years exposure of Super-Kamiokande" arXiv:2208.13188 (August 28, 2022).

The universe is about 1.37 x 10^10 years old. This limitation means that we would expect that not more than about 2 in 10^23 protons would have decayed so far, everywhere in the universe, for all time. And, of course, this is just a lower bound on the proton lifetime.

The hypothesis that the proton is completely stable seems far more plausible.

Monday, August 29, 2022

A Proposed Observational Test Of Deur's Gravity

There is a fairly straightforward way to distinguish between Deur's approach to gravity and alternative explanations of dark matter phenomena.

Look at the strength of the gravitational field of a spiral galaxy, above or below the disk of the galaxy, by a distance, for example, equal to the distance from the center of the galaxy to its rim.

In a Navarro-Frank-White (NFW) dark matter halo model, or in MOND, the strength of the gravitational field above or below the disk of the galaxy at that distance should be the same as it is at the rim, because those are both spherically symmetric solutions.

But, in Deur's approach to gravity, the strength of the gravitational field above or below the disk of the galaxy at that distance should be weaker than it would be with purely Newtonian gravity in the absence of any dark matter, in an amount that ought to be possible to calculate rather precisely (and to make more precise by calibrating it with the strength of the gravitational field at the rim of the spiral galaxy).

It might be somewhat harder to distinguish, for example, an inferred prolate dark matter halo (which observational evidence strongly favors over a NFW shaped inferred dark matter halo) from Deur's approach to gravity. But, even a prolate dark matter halo should still be stronger than purely Newtonian gravity in the absence of any dark matter above or below the disk of the galaxy at that distance.

This seems like something that could be done by looking at "stray" tracers in the form out of plane stars or satellite galaxies or intergalactic medium, above or below the disk of a spiral galaxy, perhaps also considering the escape velocity of such stars or satellite galaxies in that location, or by considering gravitational lensing of photons in those locations.

Ideally, one would look somewhat off-center of the center of the galaxy to avoid confounds from ultrafast outflows from the center of a spiral galaxy.

If the observations confirm Deur's prediction and are contrary to dark matter particle and MOND theories that could be distinguished from this prediction even without all that great precision, that would be very convincing and striking evidence from an ex ante, untested theoretical prediction of Deur's approach.

This might also distinguish GEM GR effects from gravitational self-interaction effects, although I am less confident of that conclusion. GEM GR effects, since they only work in rotationally supported galaxies, also shouldn't be able to explain inferred dark matter phenomena in galaxy clusters, unlike Deur's approach.

Thursday, August 25, 2022

The Origins Of Malaysian Indigenous Populations

A new study of the genetics of indigenous Malaysians finds that their ancestry is a mix of Hoabinhian hunter-gatherers, Neolithic farmers (probably from Southern China), and Austronesian speakers (a maritime population derived from an ancestral population from Taiwan with some Papuan admixture at some point), with some possible infusion also of people from the vicinity of India.
Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. 
Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). 
Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

The introduction to the paper, as is often the case, provides some useful context:
Southeast Asia (SEA) has rich demographic, linguistic, and genetic diversity. The region is home to around 1249 ethnic groups belonging to five language families. Despite this fascinating diversity, the genetic history of the region remains under-studied and several outstanding gaps regarding the peopling of this region by anatomically modern humans (AMH) still exist. The four most-debated issues concerning the history of AMH in SEA relate to 1—The timing of their arrival in SEA; 2—Origins of hunter-gatherer populations in SEA and their relationship to the Hoabinhian culture; 3—Process of transition from foraging to farming lifestyle, and 4—Development of the cultural groups today recognized as Austroasiatic and Austronesian. According to archeological and early mitochondrial (mt) DNA investigations, the presence of AMH in SEA dates back to around 70–50 k years ago (kya). Later, genome-wide and ancient DNA studies postulated that the AMH entered the region following the “Out-of-Africa” human migration, perhaps via the southern coastal route, and subsequently spread into East Asia (EA), Papua New Guinea, and Australia. Subsequently, migrations from EA during the late-Pleistocene and Holocene, and population movements within the region, have shaped today’s population structure of SEA. The geographical location of Malaysia, a country that is physically split between mainland Asia and Borneo with significant population diversity, provides us with an opportunity to study the population history in SEA.

Malaysia is divided into a western part comprising Peninsular Malaysia and an eastern part on the Island of Borneo comprising the States of Sarawak and Sabah. Indigenous populations comprise 13.8% of the about 32 million population of Malaysia. The myriad indigenous communities of East and West express high ethno-linguistic and cultural diversity. The indigenous populations of Peninsular Malaysia are known as Orang Asli (“Original People” in the Malay language). They comprise 0.7% of the Peninsular Malaysia population and are divided into 3 major groups including Negrito, Senoi, and Proto-Malay based on their morphological and ethnolinguistic characteristics. 
Malaysian Negrito are hunter-gatherers who reside in the rain-forests of northern Peninsular Malaysia and are proposed to be descendants of the first settlers of Malaysia. They speak the Northern-Aslian dialect of the Austroasiatic (AA) language family, and their tradition involves egalitarianism and a patrilineal descent system. 
Senoi inhabit the central parts of Peninsular Malaysia. They speak the central and southern dialects of the Aslian language, and they traditionally practice slash-and-burn farming. 
Proto-Malay speak the Malay dialect of the Austronesian language family. They mainly live in the southern parts of Peninsular Malaysia. Proto-Malay practice farming and rain-forest harvesting and their traditions involve a marked social hierarchy. 
Each OA group is further subdivided into 6 subgroups, which makes up 18 OA subgroups. In Sarawak, the indigenous people are collectively known as Orang Ulu (“People of up-river land” in Malay) and comprise 40% of Sarawak’s population. The indigenous populations of Sabah make up 58.6% of Sabah’s population and are divided into 39 tribes. Dusun, Murut, Paitan, and Bajau are the major indigenous groups in Sabah.

Early anthropological studies proposed multiple competing theories about the origin of OAs. The “layer-cake” theory postulated that all three OA groups originated outside of Peninsular Malaysia and entered Malaysia at different times. Another theory by Benjamin (1985) proposed an in situ development and diversification of OAs following the first wave of human migration into Asia. 
Bellwood (1993) suggested that the ancestors of today Senois are associated with early Austroasiatic agriculturists who entered Peninsular during mid-Holocene era. Later interactions between these Neolithic farmers and local hunter-gatherers (ancestors of Negritos) resulted in language shift in Negritos as well as intermediate phenotypical features in Senois. He suggested that Proto-Malays originated from Austronesian speaking farmers who migrated to Malaysia during “Austronesian expansion” approximately 5–7 KYA. 
Early mtDNA studies found both haplogroups unique to Peninsular Malaysia, and those stablished in Indochina in OAs which suggest gene flow from neighboring populations in SEA into OAs. 
These studies identified two haplogroups of M21 and R21 in Negrito and Senoi with TMRCA around 30–50 KYA. Higher frequency of these two ancient haplogroups in Negritos could indicate that they are the most direct descendants of the earliest settlers of Peninsular Malaysia. 
Proto-Malay mainly harbor N21 and N22 haplogroups which may be associated with Austronesian expansion via Island Southeast Asia. 
Genotyping studies highlighted genetic affinity between Malaysian Negritos, Andamanese and Filipino Negritos. This may represent an ancient link between these populations. Whole genome-sequencing showed that Malaysian Negritos has the deepest divergence time from EA compared with the other two OA groups. This study also traced some level of gene flow from South Asia in OAs.

To advance our knowledge of the genetic structure and history of Malaysia’s indigenous people explore their relationship with the ancient hunter-gatherer and agriculturist communities of Malaysia, we performed high-coverage whole-genome analysis of 15 Orang Asli and Orang Ulu individuals including Negritos (Jehai, and Mendriq), Senoi (MahMeri), Proto-Malay (Seletar, and Jakun), and Dusun, and report the results of our analysis here.

The body text of the main analysis includes these highlights (with paragraph order and breaks rearranged for easier reading):

PCA and ADMIXTURE analysis. 
(A) ADMIXTURE analysis results at K = 5 of indigenous Malaysians, Andamanese, Malay, and selected HGDP-CEPH population samplesshowes that the ancestral component related to Southeast Asia (blue) is the most pronounced in OAs while ancestral components related to East Asia (yellow) and South Asia (green) are also present in most of OA groups. 
(B) Global PCA with indigenous Malaysian populations, Andamanese, Malay and selected HGDP-CEPH samples showes that OAs are in general genetically closer to East Asians while Malaysian Negritos have tendency towards Andaman islanders. 
(C) PCA representing ancient Southeast Asian with indigenous Malaysian, Andamanese, Malay and HGDP-CEPH populations from East Asia (EA), Central South Asia (CSA) and Oceania (OCE). Most of OAs positioned between Hoabinhian hunter-gatheres and ancient farmers. 
. . .
For mtDNA, we observed five haplogroups including R21, M21a, M13b1, M17a, and F1a1a in Malaysian Negritos. The TMRCAs of the R21, M21a, M17a, and F1a1a haplogroups have been dated to 8, 23, 19 and 8 kya, respectively, and have previously been reported In Malaysian and Thai hunter-gatherers. Haplogroup M13b has been dated to around 31 kya and observed in low frequency in Asia, specifically in Malaysia, Tibet, and Nepal.
MahMeri harbored the N22a haplogroup. Haplogroup N22a which was observed in MahMeri appears to be restricted to Peninsular Malaysia, although N22 has been recorded in low frequency elsewhere in SEA such as Philippine and Sumatra.
all Seletar carried N9a6b.  The N9a haplogroup is widespread in EA, SA, and SEA. However, its sub-clade N9a6 appears limited to mainland Southeast Asia (MSEA) and reaches the highest frequency in Peninsular Malaysia
Jakun carried the E1a2 haplogroup . . . We found two different haplogroups, M7c1c3 and R9c1a, in the Dusuns. The E1a, M711 [sic], R9c1 haplogroups are prevalent in island Southeast Asia (ISEA) and are widely believed to be associated with the Austronesian expansion.
For the Y chromosome, OA harbor the R1a1a1b2a, R2a, K2b, K2b1, and O2b1 haplogroups. 
The K2b haplogroup and its subclade K2b1, which were observed in Malaysian Negrito and Seletar, have been reported in other SEA Negritos and Oceania. 
Interestingly, we found haplotypes R2a and R1a1ab in Malaysian Negrito. Haplogroup R2a is mainly present in SA and at lower frequencies in Central, Southwest, and EA, while the R1a1a1b, and its sub-clades, comprise the major R1a sub-clades in Central and South Asia.

The concluding discussion notes that: 

Archeological and genetic evidence shows that the presence of AMH in Malaysia dates back to at least 40 kya. Between 13 to 3 kya Hoabinhian hunter-gatherers occupied the Peninsular. The Hoabinhian culture with a stone tool industry characterized by unifacial pebble tools, are believed to originate from south China and spread throughout mainland Southeast Asia (MSEA) and island Southeast Asia (ISEA). Since 4 kya, this South East Asian nation also witnessed at least two waves of migration from Neolithic farmers and Austronesian speakers.  . . .

While indigenous Malaysians are genetically closer to EA populations, consistent with previous studies, our new ADMIXTURE analysis revealed traces of South Asian ancestral component in OAs of Peninsular Malaysia. We could not detect this component in Dusun in Borneo. The presence of SA ancestral component in OAs has been previously reported. This ancestral component might be attributed to the first wave of human migration into SEA via the southern coastal route or later gene flow from SA during the expansion of Indian culture into Peninsular Malaysia in the first century A.D. Archeological sites in the state of Perak provide evidence of Hindu civilization. Being on the maritime route between China and South India, the Malay peninsula was involved in this trade. The Bujang Valley, being strategically located at the northwest entrance of the Strait of Malacca as well as facing the Bay of Bengal, was continuously frequented by Chinese and south Indian traders. Such was proven by the discovery of trade ceramics, sculptures, inscriptions and monuments dated from the 5th to fourteenth century CE. . . .

Analysis of OAs with ancient DNA from the Gua Cha revealed the contribution of populations genetically close to these samples into the Malaysian Negritos gene pool. The Gua Cha site is a rock shelter in northern Peninsular Malaysia. Based on Sieveking (1954), two archeological phases are recognizable at this site. The Hoabinhian phase when the shelter was used for habitation and occasionally for burial, and the Neolithic phase when it functioned as a cemetery. Radiocarbon dating showed that the Hoabinhian occupied the Gua Cha from 9 kya and later the Neolithic farmers used this site from 3 kya. Our outgroup-f3 analysis is consistent with the archeological findings regarding the transition from hunting-gathering to farming lifestyle in the Gua Cha cave. While the Ma911 (Hoabinhian layer) shared most alleles with the Malaysian Negritos, the Ma912 (Neolithic farmer) was closer to the Senoi agriculturists. Our results confirm that modern Malaysian Negritos have been derived genetically from two ancient populations: the Hoabinhian hunter-gatherers and the Neolithic farmers who originated from South China or MSEA.

Our analysis detected gene flow between different OA tribes, notably between Malaysian Negritos, with MahMeri and Jakun tribes. The admixture between neighboring OA tribes or between OAs and the Malay population has been reported previously. For example, Jinam et al. (2013) reported recent admixture between Jehai and their neighboring Malay, whereas such admixture was absent in Kensiu (another Negrito group). We did not find any traces of Negrito or Hoabinhian ancestry in Dusun. Likewise, Yew et al. (2018) reported the absence of Negrito ancestry in North Borneo, Dayak, and Bidayuh populations. Considering the demographical and archeological evidence which supports the presence of Austro-Melanesian people on Borneo Island, the best explanation for the absence of Negrito ancestry in Borneo could be the replacement of initial Austrolo-Melanesian inhabitants of the island by the Austronesians.

Interestingly, all the Seletar samples carried mtDNA N9a6b haplogroup. N96a haplogroup seems to be confined to the ISEA and reaches the highest frequency in Malaysia. Our results are consistent with Jinam et al. (2012) who reported only 4 mtDNA haplogroups (with N9a6b making up of 71% of mtDNA haplogroup frequency) in Seletar. Seletar are sea nomads who live along the strait of Johor (a waterway that separates Malaysia from Singapore). The history of Seletar is not well-documented. They are usually associated with the Orang Laut (“Sea people” in Malay), a conglomerate of sea nomad tribes who occupied the strait of Melaka. Our TreeMix and ROH results indicate that the Seletar are genetically closer to the Austronesian speakers, but they experienced severe genetic drift.

Tuesday, August 23, 2022

A Hypothetical Pre-Big Bang Universe And More Conjectures

There are at least three plausible solutions to the question of why we live in a matter dominated universe when almost all processes experimentally observed conserve the number of matter particles minus the number of antimatter particles. 

One is that the initial Big Bang conditions were matter dominated (as our post-Big Bang universe almost surely was a mere fraction of a second after the Big Bang). There is no scientific requirement that the universe had any particular initial conditions.

A second is that there are new, non-equilibrium physics beyond the Standard Model that do not conserve baryon and lepton number and are strongly CP violating at extreme high energies. No new physics is necessary for the Standard Model to continue to make mathematical sense to more than 10^16 GeV, known as the grand unified theory (GUT) scale. And, there is no evidence of such physics yet. But the most powerful particle colliders and natural experiments that function as particle colliders have interaction energies far below the 10^16 GeV. The most powerful man made collider, the Large Hadron Collider (LHC), is probing energies on the order of 10^4 GeV, about a trillion times lower than those of the immediate vicinity in time of the Big Bang.

A third is that matter, which can be conceived of as particles moving forward in time, dominates our post-Big Bang universe, while there is a parallel pre-Big Bang mirror universe dominated by antimatter, which can be conceived of as particles moving backward in time. To the extent that this calls for beyond the Standard Model physics, the extensions requires are very subtle and apply only at the Big Bang singularity itself. 

I tend to favor this quite elegant approach, although the evidence is hardly unequivocal in favoring it over the alternatives, and it may never be possible to definitively resolve the question.

The introduction to a new paper and its conclusion, below, explain the features and virtues of this third scenario. 

The paper argues that the primary arrow of time (since fundamental physics observes CPT symmetry to high precision) is entropy as one gets more distant in time from the Big Bang, that cosmological inflation and primordial gravitational waves is not necessary in this scenario, and in this scenario, it makes sense that the strong force would not violate CP symmetry, despite the fact that there is an obvious way to insert strong force CP violation into the Standard Model Lagrangian. 

In contrast, cosmological inflation is quite an ugly theory, with hundreds of variants, many of which can't be distinguished from each other with existing observations.

In a series of recent papers, we have argued that the Big Bang can be described as a mirror separating two sheets of spacetime. Let us briefly recap some of the observational and theoretical motivations for this idea. 

Observations indicate that the early Universe was strikingly simple: a fraction of a second after the Big Bang, the Universe was radiation-dominated, almost perfectly homogeneous, isotropic, and spatially flat; with tiny (around 10^−5 ) deviations from perfect symmetry also taking a highly economical form: random, statistically gaussian, nearly scale-invariant, adiabatic, growing mode density perturbations. Although we cannot see all the way back to the bang, we have this essential observational hint: the further back we look (all the way back to a fraction of a second), the simpler and more regular the Universe gets. This is the central clue in early Universe cosmology: the question is what it is trying to tell us. 

In the standard (inflationary) theory of the early Universe one regards this observed trend as illusory: one imagines that, if one could look back even further, one would find a messy, disordered state, requiring a period of inflation to transform it into the cosmos we observe. 

An alternative approach is to take the fundamental clue at face value and imagine that, as we follow it back to the bang, the Universe really does approach the ultra-simple radiation-dominated state described above (as all observations so far seem to indicate). Then, although we have a singularity in our past, it is extremely special. Denoting the conformal time by τ , the scale factor a(τ) is ∝ τ at small τ so the metric gµν ∼ a(τ)^2ηµν has an analytic, conformal zero through which it may be extended to a “mirror-reflected” universe at negative τ. 

[W]e point out that, by taking seriously the symmetries and complex analytic properties of this extended two-sheeted spacetime, we are led to elegant and testable new explanations for many of the observed features of our Universe including: (i) the dark matter; (ii) the absence of primordial gravitational waves, vorticity, or decaying mode density perturbations; (iii) the thermodynamic arrow of time (i.e. the fact that entropy increases away from the bang); and (iv) the homogeneity, isotropy and flatness of the Universe, among others. 

In a forthcoming paper, we show that, with our new mechanism for ensuring conformal symmetry at the bang, this picture can also explain the observed primordial density perturbations. 

In this Letter, we show that: (i) there is a crucial distinction, for spinors, between spatial and temporal mirrors; (ii) the reflecting boundary conditions (b.c.’s) at the bang for spinors and higher spin fields are fixed by local Lorentz invariance and gauge invariance; (iii) they explain an observed pattern in the Standard Model (SM) relating left- and right-handed spinors; and (iv) they provide a new solution of the strong CP problem. . . . 

In this paper, we have seen how the requirement that the Big Bang is a surface of quantum CT symmetry yields a new solution to the strong CP problem. It also gives rise to classical solutions that are symmetric under time reversal, and satisfy appropriate reflecting boundary conditions at the bang. 

The classical solutions we describe are stationary points of the action and are analytic in the conformal time τ. Hence they are natural saddle points to a path integral over fields and four-geometries. The full quantum theory is presumably based on a path integral between boundary conditions at future and past infinity that are related by CT-symmetry. The cosmologically relevant classical saddles inherit their analytic, time-reversal symmetry from this path integral, although the individual paths are not required to be time-symmetric in the same sense (and, moreover may, in general, be highly jagged and non-analytic). 

We will describe in more detail the quantum CT-symmetric ensemble which implements (12), including the question of whether all of the analytic saddles are necessarily time-symmetric, and the calculation of the associated gravitational entanglement entropy, elsewhere.

The paper and its abstract are as follows:
We argue that the Big Bang can be understood as a type of mirror. We show how reflecting boundary conditions for spinors and higher spin fields are fixed by local Lorentz and gauge symmetry, and how a temporal mirror (like the Bang) differs from a spatial mirror (like the AdS boundary), providing a possible explanation for the observed pattern of left- and right-handed fermions. By regarding the Standard Model as the limit of a minimal left-right symmetric theory, we obtain a new, cosmological solution of the strong CP problem, without an axion.
Latham Boyle, Martin Teuscher, Neil Turok, "The Big Bang as a Mirror: a Solution of the Strong CP Problem" arXiv:2208.10396 (August 22, 2022).

Some of their key earlier papers by some of these authors (which I haven't yet read and don't necessarily endorse) are: "Gravitational entropy and the flatness, homogeneity and isotropy puzzles" arXiv:2201.07279, "Cancelling the vacuum energy and Weyl anomaly in the standard model with dimension-zero scalar fields" arXiv:2110.06258, "Two-Sheeted Universe, Analyticity and the Arrow of Time" arXiv:2109.06204, "The Big Bang, CPT, and neutrino dark matter" arXiv:1803.08930, and "CPT-Symmetric Universe" arXiv:1803.08928.

Moreover, if Deur's evaluation of gravitational field self-interactions (which is most intuitive from a quantum gravity perspective but he claims can be derived from purely classical general relativity) is correct, then observations attributed to dark matter and dark energy (or equivalently a cosmological constant) in the LambdaCDM Standard Model of Cosmology, can be explained with these non-Newtonian general relativity effects in weak gravitational fields, predominantly involving galaxy and galaxy cluster scale agglomerations of matter. 

This would dispense with the need for any new particle content in a theory of everything beyond the almost universally predicted, standard, plain vanilla, massless, spin-2 graviton giving rise to a quantum gravity theory that could be theoretically consistent with the Standard Model. 

It would also imply that there are no new high energy physics that need to be discovered apart from one at the very Big Bang singularity itself where matter and antimatter pairs created according to Standard Model physics rules segregate between the post-Big Bang and pre-Big Bang universe at this point of minimum entropy, to explain all of our current observations. 

We would need no dark matter particles, no quintessence, no inflatons, no axions, no supersymmetric particles, no sterile neutrinos, no additional Higgs bosons, and no new forces.

We aren't quite there. We have some final details about neutrino physics to pin down. Our measurements of the fundamental particle masses, CKM matrix elements, and PMNS matrix elements need greater precision to really decisively support a theory behind the source of these physical constants. We have QCD to explain hadrons but can't really do calculations sufficient to derive the spectrum of all possible hadrons and all of their properties yet, even though it is theoretically possible to do so. And, of course, there are lots of non-fundamental physics questions in both atomic and larger scale lab physics and in the formation of the universe that are almost certainly emergent from these basic laws of physics in complex circumstances, which we haven't yet fully explained.

There would also be room for further "within the Standard Model" physics to derive its three forces plus gravity, and couple dozen physical constants from a more reductionist core, but that is all. And, there is even some room in the form of conjectures about variants on an extended Koide's rule and the relationship between the Higgs vacuum expectation value and the Standard Model fundamental particles to take that further.

It is also worth noting that even if Deur's treatment of gravitational field self-interactions is not, as claimed, possible to derive from ordinary classical General Relativity, either because it is a subtle modification of Einstein's field equations, or because it is actually a quantum gravity effect, there is still every reason to prefer his gravitational approach, that explains all dark matter and dark energy phenomena and is consistent with astronomy observations pertinent to cosmology (for example, explaining the CMB peaks and resolving the impossible early galaxy problem) with a simple and elegant theory, neatly paralleling QCD, that has at least two fewer degrees of freedom than the LambdaCDM Standard Model of Cosmology despite fitting the observational data better at the galaxy and galaxy cluster scales.

And, Deur's approach is pretty much the only one that can explain the data attributed to dark energy in a manner the does not violate conservation of mass-energy (a nice compliment to a mirror universe cosmology that is time symmetric since conservation of mass-energy is deeply related to time symmetry).

Deur's paradigm has the potential to blow away completely the Standard Model of Cosmology, and the half century or so of astronomy work driven by it and modest variation upon it, in addition to depriving lots of beyond the Standard Model particle physics concepts of any strong motivation.

Milgrom's Modified Newtonian Dynamics (MOND) has actually done a lot of the heavy lifting in showing that observational data for galaxies can be explained, for observations within this toy model theory's limited domain of applicability, without dark matter. 

But Deur's theory, by providing a deeper theoretical justification for the MOND effects that it reproduces, by extending these observations of galaxy clusters and cosmology scale phenomena, by making the theory naturally relativistic in a manner fully consistent with all experimental confirmations of General Relativity, and by providing an elegant solution to observations seemingly consistent with dark energy or a cosmological constant, unifies and glows up MOND's conclusions in a way that makes a gravitational explanation of dark matter far more digestible and attractive to astrophysicists who have so far clung to the increasingly ruled out dark matter particle hypotheses.

A mirror universe cosmology, likewise, has the potential to stamp out the theoretical motivation for all sorts of new physics proposals that simply aren't necessary to explain what we observe as part of a new paradigm of the immediate Big Bang era cosmology.

We are now in a position where physicists can see fairly clearly what the metaphorically promised land of a world where the laws of physics are completely known, even if the scientific consensus hasn't yet caught up with this vision.

It turns out that many of the dominant topics of theoretical physics discussion over the last half-century, from dark matter, to dark energy, to cosmological inflation, to supersymmetry, to string theory, to the multiverse, to cyclic cosmologies, to the anthropic principle, to technicolor, to multiple Higgs doublets, to a grand unified theory or theory of everything uniting physics into a single master Lie group or Lie algebra, do not play an important role in that future vision. Likewise, this would dispense with the need for the many heavily analyzed, but less subtle than Deur's variations on Einstein's Field Equations as conventionally applied, which are the subject of regular research.

If the scientific method manages to prevail over scientific community sociology, in a generation or two, all of these speculative beyond the Standard Model physics proposals will be discarded, and we will be left with a moderately complicated explanation for the universe that nonetheless explains pretty much everything. 

I may not live to see that day come, but I have great hope that my grandchildren or great-grandchildren might live in this not so distant future when humanity has grandly figured out all of the laws of physics in a metaphysically naturalist world.

Exotic And Heavy Hadron Mass Predictions

A new paper uses an improved neural network method to estimate the masses of various exotic hadrons (i.e. tetraquarks and pentaquarks) and doubly charmed and bottomed three valence quark baryons. It achieves results comparable to a couple of other analytical QCD methods and significantly improves on prior neural network methods.

The paper illustrates that while it is possible to make "reasonable predictions" of hadron masses, most of the approximations are quite crude compared to the experimental data, and even state of the art and computationally demanding lattice QCD methods still only approach parts per two thousand claimed accuracy.

A cynical person could argue that this method is merely trend fitting and doesn't reflect the underlying QCD physics that give rise to the result in any theoretically justifiable way, but given the great uncertainties and immense calculation efforts that go into theoretically justified QCD calculations of hadron masses with current methods and the fact that this approach can distinguish between hadrons that some of the alternatives cannot, this shortcoming is excusable for the time being.

Another important shortcoming of this method, however, is that the uncertainty in the estimates is not well quantified, although comparing experimental results to the predictions made can allow for a reasonable guess as to its order of magnitude (1%-11%), which is indeed competitive with alternative approaches that are currently viable such as older neural network methods, the Gaussian process method, and a Constituent Quark model approach. Also, the claimed error of some of the other predictions is not consistent with the experimental results.

The tables reprinted below also compactly review the valence quark structure of these hadrons (notwithstanding the fact that there is not complete consensus on this point) and the literature measuring and estimating their masses.

Deviation of prediction from best fit experimental results in MeV:

X(3872)  -44.5
Z(3900)  189.1
Z(4020)  273.8
Z(4430)    42.0
Y(4260) -180.9
Y(4360) -477.4
Y(4660) -530.1
P(4312) -140.9
P(4440) -292.4
P(4457)   -91.4
Z(100610) -204.1
Z(100650) -81.4

In the one experimental result (below) that can be compared to its doubly charmed and bottomed baryons, the error relative to the best fit value is 52.5 MeV high (better than 2% accuracy). 

Where only lattice QCD predictions are available for doubly charmed and bottomed baryons, three of the seven best fit values are consistent at the two sigma level (or at least very close) with the lattice QCD predictions, which implies that this method has significantly more uncertainty than lattice QCD.
The paper and its abstract are as follows:
Recently, there have been significant developments in neural networks; thus, neural networks have been frequently used in the physics literature. This work estimates the masses of exotic hadrons, doubly charmed and bottomed baryons from the meson and baryon masses using neural networks. Subsequently, the number of data has been increased using the artificial data augmentation technique proposed recently. We have observed that the neural network's predictive ability increases using augmented data. This study has shown that data augmentation techniques play an essential role in improving neural network predictions; moreover, neural networks can make reasonable predictions for exotic hadrons, doubly charmed, and doubly bottomed baryons. The results are also comparable to Gaussian Process and Constituent Quark Model.
Huseyin Bahtiyar, "Predicting Exotic Hadron Masses with Data Augmentation Using Multilayer Perceptron" arXiv:2208.09538 (August 19, 2022).

Monday, August 22, 2022

Diet Drives Height

Individual variation in height, like individual variation in IQ, is strongly influenced by genetics. But, population level variations in height (between populations or over time) is profoundly influenced by environment, rather than genetic legacies. There is a good case to be made that the same is true of IQ.

This paradox is also seen, for example, in modern Japan and South Korea where height is closely correlated with year of birth, with children born later in more economically prosperous times with less food scarcity ending up taller.

This also provides a food production counterpart to the "coal curse" by which regions with particularly great coal resources lagged in later economic development as the natural resource based economy fostered by rich coal resources prevented other forms of economic production from thriving, which mattered when coal became less economically important.
In the late nineteenth century, the North American bison was brought to the brink of extinction in just over a decade. We demonstrate that the loss of the bison had immediate, negative consequences for the Native Americans who relied on them and ultimately resulted in a permanent reversal of fortunes. Once amongst the tallest people in the world, the generations of bison-reliant people born after the slaughter lost their entire height advantage. By the early twentieth century, child mortality was 16 percentage points higher and the probability of reporting an occupation 29.7 percentage points lower in bison nations compared to nations that were never reliant on the bison. Throughout the latter half of the twentieth century and into the present, income per capita has remained 28 percent lower, on average, for bison nations. This persistent gap cannot be explained by differences in agricultural productivity, self-governance, or application of the Dawes Act. We provide evidence that this historical shock altered the dynamic path of development for formerly bison-reliant nations. We demonstrate that limited access to credit constrained the ability of bison nations to adjust through re-specialization and migration.
Donn. L. Feir, Rob Gillezeau & Maggie E.C. Jones, "The Slaughter of the Bison and Reversal of Fortunes on the Great Plains" NBER Working Paper 30368 (August 2022), DOI 10.3386/w30368

Tuesday, August 16, 2022

What Killed The Megafauna?

We've seen a mass extinction of megafauna worldwide since humans started to develop technologies like bows and arrows and make their first forays out of Africa. 

How much was climate responsible for this shift and how much was due to overhunting by modern humans?

A new paper makes the case for overhunting as the dominant cause of megafauna extinction worldwide. But I'm not convinced that there is a single answer. The paper itself observes that there are regional differences and then largely ignores this observation:
Population declines varied across ecological realms, with Australasia and the Neotropics experiencing the least severe declines over the Quaternary period (95% HPDI: [-0.244, 0.044] and [-0.228, -0.070], respectively), compared to Indomalaya and Nearctic (95% HPDI: [-0.458, -0.299] and [-0.410, -0.227], respectively). 
Separation of species according to the biome they occupy resulted in the largest discrepancy of population size decline between polar (95% HPDI: [-0.317, 0.037]) and temperate-adapted species (95% HPDI: [-0.460, -0.296]), while insectivores (95% HPDI: [-0.228, 0.201]) experienced a small and non-significant decrease compared to hypercarnivores (95% HPDI: [-0.394, -0.223]). 
Lastly, species with ranges overlapping regions where Homo sapiens was the first and only hominin present, tend to have the lowest decline (95% HPDI: [-0.269, -0.155]), compared to species in regions where archaic Homo species arrived early (95% HPDI: [-0.380, -0.290]). 
Generally, non-African temperate regions with a relatively long history of hominin activity experienced the largest decrease in megafauna population sizes. In contrast, and with the exception of polar species, warmer biomes with only H. sapiens activity seem to have declined the least. 
However, this observation is most likely driven by an increase of megafauna population sizes in Neotropics and Australasia between 1.25 million and 100,000 years ago, prior to human arrival. Notably, population decline starting at approximately 100,000 years ago, and continuing towards the present, is ubiquitous across realms.
In the Americas and especially in North America, the Younger Dryas climate event appears to have been a powerful driver of species extinction relative to the overhunting that had occurred by then. 

In Australia, we see one wave of mass megafauna extinction when modern humans arrive and a secondary wave when the dingo enters the Australian ecosystem.

In Africa, where modern humans originated and to a lesser extent in tropical Southeast Asia, megafauna extinction was more measured.

In Northern Eurasia, the Last Glacial Maximum ice age surely played some part in extinguishing megafauna and modern humans alike from the region and resulted in a global reduction of modern human effective population size almost everywhere in the world.

This paper's bottom line conclusion may be correct, but I'm not convinced that the story can be completely told at this level of generality.
The worldwide loss of large animal species over the past 100,000 years is evident from the fossil record, with climate and human impact as the most likely causes of megafauna extinctions. To help distinguish between these two scenarios, we analysed whole-genome sequence data of 142 species to infer their population size histories during the Quaternary. 
We modeled differences in population dynamics among species using ecological factors, paleoclimate and human presence as covariates. We report a significant population decline towards the present time in more than 90% of species, with larger megafauna experiencing the strongest decline. We find that population decline became ubiquitous approximately 100,000 years ago, with the majority of species experiencing their lowest population sizes during this period. 
We assessed the relative impact of climate fluctuations and human presence on megafauna dynamics and found that climate has limited explanatory power for late-Quaternary shifts in megafauna population sizes, which are largely explained by Homo sapiens arrival times. 
As a consequence of megafauna decline, total biomass and metabolic input provided by these species has drastically reduced to less than 25% compared to 100,000 years ago. These observations imply that the worldwide expansion of H. sapiens caused a major restructuring of ecosystems at global scale.
Juraj Bergman, et al., "Worldwide late-Quaternary population declines in extant megafauna are due to Homo sapiens rather than climate" bioRxiv (August 15, 2022). doi: https://doi.org/10.1101/2022.08.13.503826

Monday, August 15, 2022

Hard Physical Evidence Shows Arrival Of Greeks In Crete When Expected

In the late Bronze Age, specifically during a time period called Late Minoan IIIB from about 1350 BCE to 1100 BCE, around the time of "Bronze Age collapse" (from roughly 1200 BCE to 1150 BCE), the non-Indo-European Minoan civilization on the island of Crete, which used a Linear A script (presumably to record Minoan language content), was replaced by the Mycenaean Greek (linguistically Indo-European) population that started to use the Linear B script (which is believed to have used the same symbols to phonetically record Mycenaean Greek content) and left distinctive Mycenaean artifacts and architecture. An earlier study also found a person with steppe autosomal DNA absent in earlier Minoans in the same necropolis that produced "newcomer" results in this study.

Unsurprisingly, a new study looking at remains from Crete from the appropriate era, found mostly human and animals remains of local origins with typical Minoan mtDNA. But, four remains from around the time of the transition at the same necropolis, all with the same mtDNA (of a haplogroup also found in Minoans), showed non-local origins based upon non-genetic chemical indicators, and a fifth grave in the same complex (from which no chemical samples of remains could be retrieved) had Linear B writing. A few animal remains at that location in that time frame also had non-local origins.

The non-local origins were found at a Late Minoan IIB era necropolis at location "3" on the map below:

Regional map via Wikipedia.

This is, of course, exactly what you would expect. It confirms the paradigmatic narrative of this transition with chemical evidence from human and animals remains. On the other hand, the study, which did not include ancient DNA other than mtDNA (despite mentioning a single prior autosomal DNA sample from a previous paper), does not really resolve any of the outstanding seriously controversial questions about the nature of that transition that it poses in its own introductory material.

The purely local origins of all other remains fits the paradigm of stasis during the Minoan era itself (following another clear cut transition from the Neolithic era to the Minoan era, starting around 3500 BCE. The Neolithic (i.e. farmer and herder) culture on Crete dates to about 6000 BCE.

The timing of the Minoan-Mycenaean transition also further confirms that Minoan civilization survived the eruption of the Thera volcano on what is now the island of Santorini (which took place in 1628 BCE give or take a year or two) through its population continuity after that date.

Some highlights from the introduction and discussion portions of the paper state:

Archaeological research of the Neolithic and Bronze Age periods on Crete has a long history, starting in the 19th century, and remains a vibrant research area today. It is likely that Crete was first substantially settled in the Neolithic period, with Neolithic levels (especially Late Neolithic) being found at palace sites such as Knossos, where the earliest Neolithic levels have recently been radiocarbon dated. There has been substantial research on the Late Neolithic-Early Bronze Age transition in Crete, especially in looking for the origins of what would be a unique later Bronze Age (Minoan) material culture, including the first use of a novel pottery firing technology.

The site of Knossos has a long sequence of occupation levels, spanning the early (aceramic) Neolithic, final Neolithic and Early, Middle and Late Bronze Age. The separation into different time periods at the site by Arthur Evans led to the widely use terminology for the chronological sequences on Crete, specifically the use of the term ‘Minoan’ for the Bronze Age levels which is divided into Early, Middle and Late Minoan periods, largely based on pottery typologies. An alternative terminology focusses more on the sequences of the formation and abandonment of the palace sites on Crete and is termed the pre-,proto-,neo- and post-palatial periods. Here, we generally follow the site chronologies used by the site excavators, which use the Evans ‘Minoan’ terminology.

The later Bronze Age, usually labelled the Late Minoan period (corresponding to the final Neopalatial and Postpalatial periods) is an area of particularly intensive study and interest. One of the long-standing areas of interest in Bronze Age Cretan Minoan studies is the end of the period, where many sites were abandoned, and the archaeological record changes to include archaeological material culture and architecture stylistically similar to forms used on the Greek mainland, where the Late Bronze Age is commonly termed ‘Mycenaean’. This is also the period where there is the appearance of Linear B script in Crete, which was widely used in mainland Greece in the Mycenaean period, and the end of the use of the (still untranslated) Linear A writing common in Minoan sites on Crete. The end of the Minoan period is also characterised by the abandonment of palace sites, which often have a ‘destruction layer’ coinciding with the end of the use of these sites. The search for causal factors leading to the end of the Minoan period have been discussed at length since the early days of archaeological studies in Crete. There is an argument that there was a natural disaster, such as an earthquake or volcano, that coincided with this time period, while others have argued that Crete (and the surrounding region) was perhaps violently invaded at this time by external invaders, including the so-called ‘sea peoples’. There is also the discussion that the island of Crete was settled by Myceneans from the mainland, also perhaps violently, or as new settlers arriving in a perhaps de-populated Crete. 

In this paper we sought to explore evidence of mobility in Crete, with an emphasis on sites dating to the Late Minoan periods using biomolecular methods (isotope and DNA analysis). Our study employed a range of isotopic measurements (carbon, nitrogen, strontium, sulphur) of humans and animals from Neolithic and Bronze Age sites across Crete. The isotopic measurements on animals were to establish local baselines for the different regions of the island, and the human isotope values were compared with the local baseline isotope values to see if they were consistent with them living their lives in Crete, and local to the site and region where they were buried. Any humans that had isotope values that were markedly different from the baseline (faunal) values were considered to be ‘non-local’ and most likely from mainland Greece or the Eastern Mediterranean. Mitochondrial DNA was also sequenced from eight individuals and their sequences were compared to larger scale-studies of the region to look for evidence of possible movements of people between Crete and surrounding regions. . . .

The biomolecular evidence presented here strongly points to little movement of people between Crete and the surrounding regions during the Neolithic and Bronze Age periods. However, at the end of the Bronze Age, in the postpalatial Late Minoan period (LMIII) we found four individuals with non-local isotope values suggesting they may have originated from outside of Crete and were then buried in the Late Minoan cemetery of Armenoi.

The site of Armenoi dates to the Late Minoan IIIB (LMIIIB) period and contains over 230 burial features. It has been excavated by Y. Tzedakis over a period of more than 40 years, first starting in 1969 and has many rock-cut burial features (chamber tombs) of different sizes. Some of the larger tombs contained grave goods including pottery and burials in large free-standing ceramic larnakes. Many of the other tombs also contained pottery, and some of the smaller ones had no grave goods at all. These chamber tombs usually contained either multiple or single burials. Most of the pottery dates to the LMIIIB period, and there is the remarkable find of a pottery vessel (stirrup jar) from tomb 146 (which has DNA results presented in this paper, but we were unable to measure isotope values of humans from this tomb) that is inscribed with Linear B script (the inscription is ‘wi-na-jo’). 
The Linear B writing script was not in use in Early or Middle Bronze Age Crete (which instead used Linear A script), but it was in widespread use at Late Bronze age Mycenaean sites on the Greek mainland. Therefore, Armenoi (and some of the palace sites, such as Knossos, where this new Linear B script is the main script used on tablets in the Late Bronze Age) may have been settled by people from the mainland who used this Mycenaean script or may have been imported from the mainland through trade or other contacts and was then locally adopted as the main script.

It is possible then that the four individuals with ‘non-local’ sulphur isotope values (two of these individuals also had higher strontium isotope values than the marine strontium value and our bioavailable faunal baseline average value) were new Mycenaean settlers or traders (especially the two individuals with both strontium and sulphur outlier values) from the mainland that settled at or near to Armenoi and the existing cemetery was used for burials of these newcomers.

While the mtDNA sequences do not offer conclusive evidence for the origins of the studied individuals, previously published nuclear DNA data from Armenoi specimen 503 showed that this individual was genetically distinct from preceding Cretans, and in her genetic profile more similar to contemporaneous Myceneans from the mainland in that she also harbored ancestry derived from Bronze Age steppe pastoralists that Minoans pre-LMIII lacked.

The paper and its abstract are as follows:

We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age (‘Late Minoan’) period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to determine the local baseline values. We then measured the strontium and sulphur values of humans from Late Neolithic and Bronze Age sites. 
Our results indicate that most of the humans have sulphur and strontium isotope values consistent with being local to Crete, showing no evidence for a wide-scale movement of people from the Greek mainland or other areas away from Crete in these time periods. 
However, we found four individuals from the late Bronze Age (Late Minoan III) cemetery of Armenoi with sulphur isotope values not typically found in Crete and are instead consistent with an origin elsewhere. This cemetery at Armenoi also has one of only a few examples of the newly adopted Mycenaean Linear B script on Crete found outside of the palace sites, pointing to an influence (trade and possible migration) from the mainland, which may then be the place of origin of these four individuals. 
DNA (mtDNA) studies of eight Late Bronze Age individuals from Armenoi have results consistent with people living in Aegean region at this time and cannot be used to distinguish between individuals from Crete (‘Minoans’) and the Greek mainland [‘Mycenaeans’]).

Michael Richards et al, "Finding Mycenaeans in Minoan Crete? Isotope and DNA analysis of human mobility in Bronze Age Crete." PLOS (2022). 

Hat tip to Bernard's Blog.