Quote Of The Day

This paper is both novel and correct, but the novel part is not correct and the correct part is not novel.

From a peer review of an academic journal article attributed to physicist Wolfgang Pauli.

Papuan Demographic History From Modern Genomes

A new pre-print at bioRxiv disputes the status of Papuans (presumably together with aboriginal Australians) as an outgroup to both European and Asian populations. Instead, it positions them as a sister population of other Asian populations.

The demographic history of the Papua New Guinean population is a subject of significant interest due to its early settlement in New Guinea, at least 50 thousand years ago, and its relative isolation compared to other out of Africa populations. This isolation, combined with substantial Denisovan ancestry, contributes to the unique genetic makeup of the Papua New Guinean population. Previous research suggested the possibility of admixture with an early diverged modern human population, but the extent of this contribution remains debated. 

This study re-examines the demographic history of the Papua New Guinean population using newly published samples and advanced analytical methods. Our findings demonstrate that the observed shifts in relative cross coalescent rate curves are unlikely to result from technical artefacts or contributions from an earlier out of Africa population. Instead, they are likely due to a significant bottleneck and slower population growth rate within the Papua New Guinean population. Our analysis positions the Papua New Guinean population as a sister group to other Asian populations, challenging the notion of Papua New Guinean as an outgroup to both European and Asian populations. 

This study provides new insights into the complex demographic history of the Papua New Guinean population and underscores the importance of considering population-specific demographic events in interpreting relative cross coalescent rate curves.

Mayukh Mondal, et al., "Resolving out of Africa event for Papua New Guinean population using neural network" bioRxiv (September 23, 2024) https://doi.org/10.1101/2024.09.19.613861

The introduction to the paper explains that:

The Papua New Guinean (PNG) population is among the most fascinating in the world, owing to its unique demographic history. Following the Out Of Africa (OOA) event, modern humans populated New Guinea at a remarkably early date-at least 50 thousand years ago. Since then, the population has remained relatively isolated compared to other OOA populations (such as European and Asian populations) and has gone through a strong bottleneck. The substantial Denisovan ancestry within the PNG population and the strong correlation between Denisovan and Papuan ancestries, contribute to the genetic distinctiveness of the PNG population. 

Researchers have suggested that the genomes of PNG populations contain evidence of admixture with a modern human population that might have diverged from African populations- around 120 thousand years ago- much earlier than the proclaimed primary divergence between African and OOA populations. However, the extent to which this early diverged population contributed to the genome of PNG populations remains a subject of ongoing debate. Interestingly, this early migration hypothesis is more widely accepted by archeologists. 

Pagani et al supports this hypothesis, notably through Relative Cross-Coalescent Rate (RCCR) analysis. This RCCR analysis suggests that the PNG population diverged from African populations significantly earlier than other OOA populations. They argued that this earlier divergence indicated by the RCCR curve might reflect a contribution from an earlier OOA population specific to PNG. While this shift in the RCCR curve is well-documented, some researchers attribute it to technical artefacts such as low sample sizes and phasing errors rather than genuine demographic events. 

The origins of the primary lineage of the PNG population have also been contested. Some researchers propose that the PNG population is closely related to the Asia-Pacific populations and serves as a sister group to other Asian populations. Conversely, other researchers argue that the PNG population is an outgroup to both European and Asian populations. 

Recent advancements in analytical methods may provide new insights into these debates. For example, Approximate Bayesian Computation with Deep learning and sequential Monte Carlo (ABC-DLS) allows for the use of any summary statistics derived from simulations to train neural networks, which can then predict the most likely demographic models and parameters based on empirical data. Additionally, the Relate software enhances RCCR analysis by employing a modified version of the hidden Markov model, initially used in the Multiple Sequentially Markovian Coalescent (MSMC) method, allowing for the analysis of thousands of individuals with greater robustness. 

In this paper, we re-examine the demographic history of the PNG population using newly published samples combined with data from the 1000 Genome Project and cutting edge methods. This approach has enabled us to address these longstanding questions with greater precision. We first generate new empirical RCCR curves and demonstrate that the previously observed shift is unlikely to be the result of low sample size or phasing errors. Through simulations, we further show that the PNG population is indeed a sister group to other Asian populations and this shift is probably not due to contributions from an earlier OOA population. Instead, it is likely a consequence of a significant bottleneck and slower population growth in the PNG population.

The paper then defines the demographic models that the paper analyzed at a broad brush level:

To explore the demographic processes causing the observed RCCR shift, we tested five plausible demographic scenarios labelled A, O, M, AX and OX. In Model A, the PNG and East Asian populations are sister groups. Model O positions the PNG population as an outgroup to both European and East Asian populations. Model M combines elements of both A and O, suggesting that the PNG population arose from admixture between a sister group of the Asian population and an outgroup of European and Asian populations. Model AX postulates that the PNG population is a sister group to the Asian population but received input from an earlier OOA population. Finally, in Model OX, the PNG population receives a contribution from an earlier OOA population, while remaining ancestry came from an out group to the European and East Asian populations. . . .  

The best-fitting parameters for Model A largely correspond with the previously established OOA model, with some deviations specific to the inclusion of the PNG population. 

Our model suggests that all OOA populations, including PNG, diverged from African populations (represented by Yoruba) around 62.4 (62- 62.8) thousand years ago, experiencing a significant bottleneck. Approximately 52 (51.6- 52.8) thousand years ago, Neanderthals contributed around 3.7% (3.59- 3.85%) of the genome to these OOA populations. Shortly thereafter, Europeans and East Asians diverged from the PNG populations around 51.2 (50.8- 51.6) and 46.2 (45.9- 46.5) thousand years ago, respectively. The PNG population then mixed with Denisovans around 31.2 (31.1- 31.5) thousand years ago, contributing approximately 3.16% (3.05- 3.21%) to the genome of PNG. 

Our analysis also shows that the PNG population experienced a more severe bottleneck (674 [663- 689] of effective population size) than other OOA populations (i.e. Europeans 3512 [3423- 3589] and East Asians 1771 [1730- 1799] of effective population size), with growth rates significantly lower than those of other OOA populations, consistent with previously published data. 

While our parameter inference is generally robust within the individual model, substantial changes occur when the underlying model is altered. Given that determining the precise demographic model for human populations is an ongoing effort, parameter estimates should be considered supplementary to the model rather than independent results. 

The concluding discussion of the results notes that:

We successfully replicated the shift observed by Pagani et al., confirming its presence in both physically mapped and statistically phased sequences, which involved over 100 PNG samples. This consistency suggests that the shift is reproducible, though its underlying cause may differ from the original interpretation of Pagani et al.. 

Our analysis using ABC-DLS supports a simpler demographic model for PNG populations, proposing them as a sister group to Asians with no substantial detectable contribution from an earlier OOA population. Interestingly, our simulated models reveal that a stronger bottleneck with a lower growth rate could produce a similar shift in RCCR analysis and potentially be misinterpreted as a signal of an earlier population separation. While RCCR is a valuable proxy for estimating the separation time between populations, it is not without biases. The shift could result from various factors, including earlier divergence times, admixture with earlier diverged populations, or even a bottleneck in one of the populations, as demonstrated in our study. Interestingly this demographic history of stronger bottleneck with slower growth rate was also experienced by the Andamanese population, which explains the shift found in the Andamanese population as well. Thus, using RCCR analysis to rebuild the tree of divergence might need to be revised.

The observed shift in the RCCR curve suggests that a recent bottleneck can impact estimates of effective population size in the distant past. Notably, in our simulations, the Papua New Guinean bottleneck occurred much later (around 46.2 thousand years ago) than the observed shift (peaking around 100 thousand years ago) with a population (Yoruba) that separated a long time ago. This finding implies that the estimation of effective population size and cross-coalescent rates may not be entirely independent, potentially affecting RCCR analysis in its current form. Further analysis suggests that the estimation of coalescent rate was affected earlier than true changes of effective population size, which shifts the RCCR curve as RCCR is a ratio of coalescent rates. Additionally, this shift was absent in simulations involving populations that separated 300 thousand years ago, akin to the San population, indicating that the bottleneck effect diminishes over longer separation times.

Our results also reveal that when the contribution from an earlier OOA population is between 1-5%, our neural analysis misclassifies the Model AX to be Model A at a higher rate. We found that when the contribution from an earlier OOA population is set between 1-5%, our ABC-DLS analysis tends to misclassify the Model AX as Model A at a higher rate. A similar issue arises with Model M, where a low contribution (less than 5%) from an outgroup Eurasian population can still be misclassified as Model A. Thus our analysis does not work for less than 5% contribution from these unknown ghost populations, though Model OX does not show a similar phenomenon with Model A misclassification. While we cannot completely rule out the possibility of a small contribution from these populations, our analysis suggests that such models are not necessary to explain the RCCR shift as previously proposed.

Interestingly, our results position PNG as a sister group to Asian populations rather than an outgroup of European and Asian. The primary difference between those models and ours lies in the migration rates between populations. Previous models that incorporated significant migration rates between populations were found to have confounded results, leading us to avoid including migration rates in our models. Without migration, our Model O closely resembles the previous models of PNG. Given that those models used substantial migration rates, they are not directly comparable to our models without migration rate. Indeed with high migration rates, our approach failed to distinguish between Model A and O with high certainty. Still our work suggests that the main lineage of PNG is coming from a sister group of Asia, which was not confounded by a convoluted migration rate patterns between populations.

Our parameter estimation suggests that the PNG population separated from other populations around 46.2 (45.9 - 46.5) thousand years ago, a timeline that aligns with archaeological estimates of when the ancestors of PNG reached the ancient continent of Sahul, the landmass that once connected New Guinea and Australia. 

Additionally, our Relate analysis indicates that the separation time between PNG and European populations was the longest observed among OOA populations. However, as our model suggests, this is likely a bias caused by the bottleneck of PNG. This bottleneck may lead to an overestimation of the separation time, particularly in RCCR analysis. In reality, it is more likely that PNG and East Asian populations separated later than the divergence between PNG and European populations. 

In conclusion, our study provides compelling evidence that the unique demographic events—specifically, a significant bottleneck and slower population growth—within the PNG population are key factors influencing the observed shifts in RCCR curves. These findings not only refine our understanding of PNG's demographic history but also emphasise the necessity of accounting for population-specific demographic events when interpreting RCCR curves. 

Semi-Recessive Genes

Some genes classified as recessive genes that have their main phenotypical effects only when both copies of it are present, are actually only "semi-recessive" and have much milder versions of the same phenotypic effects in "carriers" with only one copy of the gene.

A new pre-print at bioRxiv demonstrates this by looking at 1929 genes considered recessive in the British UK Biobank database which includes 378,751 unrelated European individuals, singling out carriers of recessive genes associated with intellectual disabilities, who exhibit below average intellectual abilities themselves, as an example.

The abstract explains that:

The genetic landscape of human Mendelian diseases is shaped by mutation and selection. Selection is mediated by phenotypic effects which interfere with health and reproductive success. Although selection on heterozygotes is well-established in autosomal dominant disorders, convincing evidence for selection in carriers of pathogenic variants associated with recessive conditions is limited, with only a few specific cases documented.

We studied heterozygous pathogenic variants in 1,929 genes, which cause recessive diseases when bi-allelic, in a cohort of 378,751 unrelated European individuals from the UK Biobank. We assessed the impact of these pathogenic variants on reproductive success. We find evidence for fitness effects in heterozygous carriers for recessive genes, especially for variants in constrained genes across a broad range of diseases. Our data suggest reproductive effects at the population level, and hence natural selection, for autosomal recessive disease variants. We further show that variants in genes that underlie intellectual disability are associated with reduced cognition measures in carriers. In concordance with this, we observe an altered genetic landscape, characterized by a threefold reduction in the calculated frequency of biallelic intellectual disability in the population relative to other recessive disorders. The existence of phenotypic and selective effects of pathogenic variants in constrained recessive genes is consistent with a gradient of heterozygote effects, rather than a strict dominant-recessive dichotomy.

Hila Fridman, et al., "Reproductive and cognitive effects in carriers of recessive pathogenic variants" bioRxiv (October 1, 2024). https://doi.org/10.1101/2024.09.30.615774

Dark Matter Is Still Probably The Wrong Answer

Stacy McGaugh has a reaction blog post to the Scientific American article "What if We Never Find Dark Matter?" by Slatyer & Tait.

It nicely sums up the sociological conundrum in astrophysics that has led the discipline to throw a lot of weight and support behind a deeply flawed dark matter particle hypothesis with a particle that hasn't been detected and no hypothetical particle that can fit the astronomy observations and no theory that has made many significant ex ante predictions, rather than MOND and modified gravity that is a much better fit to the astronomy observations and has made many significant ex ante predictions.

He is spot on. Some good quotes:

In the 1980s, cold dark matter was motivated by both astronomical observations and physical theory. Absent the radical thought of modifying gravity, we had a clear need for unseen mass. Some of that unseen mass could simply have been undetected normal matter, but most of it needed to be some form of non-baryonic dark matter that exceeded the baryon density allowed by Big Bang Nucleosynthesis and did not interact directly with photons. That meant entirely new physics from beyond the Standard Model of particle physics: no particle in the known stable of particles suffices. This new physics was seen as a good thing, because particle physicists already had the feeling that there should be something more than the Standard Model. There was a desire for Grand Unified Theories (GUTs) and supersymmetry (SUSY). SUSY naturally provides a home for particles that could be the dark matter, in particular the Weakly Interacting Massive Particles (WIMPs) that are the prime target for the vast majority of experiments that are working to achieve the exceptionally difficult task of detecting them. So there was a confluence of reasons from very different perspectives to make the search for WIMPs very well motivated.

That was then. Fast forward a few decades, and the search for WIMPs has failed. Repeatedly. Continuing to pursue it is an example of the sunk cost fallacy. We keep doing it because we’ve already done so much of it that surely we should keep going. So I feel the need to comment on this seemingly innocuous remark:

although many versions of supersymmetry predict WIMP dark matter, the converse isn’t true; WIMPs are viable dark matter candidates even in a universe without supersymmetry.

Strictly speaking, this is correct. It is also weak sauce. The neutrino is an example of a weakly interacting particle that has some mass. We know neutrinos exist, and they reside in the Standard Model – no need for supersymmetry. We also know that they cannot be the dark matter, so it would be disingenuous to conflate the two. Beyond that, it is possible to imagine a practically infinite variety of particles that are weakly interacting by not part of supersymmetry. That’s just throwing mud at the wall. SUSY WIMPs were extraordinarily well motivated, with the WIMP miracle being the beautiful argument that launched a thousand experiments. But lacking SUSY – which seems practically dead at this juncture – WIMPS as originally motivated are dead along with it. The motivation for more generic WIMPs is lacking, so the above statement is nothing more than an assertion that runs interference for the fact that we no longer have good reason to expect WIMPs at all. . . . 

I can save everyone a lot of time, effort, and expense. It ain’t WIMPs and it ain’t axions. Nor is the dark matter any of the plethora of other ideas illustrated in the eye-watering depiction of the landscape of particle possibilities in the article. These simply add mass while providing no explanation of the observed MOND phenomenology. This phenomenology is fundamental to the problem, so any approach that ignores it is doomed to failure. I’m happy to consider explanations based on dark matter, but these need to have a direct connection to baryons baked-in to be viable. None of the ideas they discuss meet this minimum criterion.

Of course it could be that MOND – either as modified gravity or modified inertia, an important possibility that usually gets overlooked – is essentially correct and that’s why it keeps having predictions come true. That’s what motivates considering it now: repeated and sustained predictive success, particularly for phenomena that dark matter does not provide a satisfactory explanation for. . . . 

The equation coupling dark to luminous matter I wrote down in all generality in McGaugh (2004) and again in McGaugh et al. (2016). The latter paper is published in Physical Review Letters, arguably the most prominent physics journal, and is in the top percentile of citation rates, so it isn’t some minuscule detail buried in an obscure astronomical journal that might have eluded the attention of particle physicists.

Bonus quote from the comments:

It’s exactly the same crap as with string theory, and supersymmetry, and inflation, and dark sectors, and many other research bubbles in the foundations of physics. It is mathematical fiction; it’s nothing to do with reality any more.

- Sabine Hossenfelder (YouTube link).

A New Published Koide Triple Paper

Arivero at the Physics Forums (who comments here from time to time) has gotten his article on Koide Triples published:

I had put in a preprint some calculations of Koide masses using the original composite idea and they have happened to be published as Eur. Phys. J. C 84, 1058 (2024). https://doi.org/10.1140/epjc/s10052-024-13368-3, so as a collateral effect we now have another published paper that mentions:

• the waterfall, in a footnote.
• the tuples (0ds), (scb) and (cbt).
• the relation sum(scb) = 3 sum (leptons).

It is nice to see this promising line of inquiry advanced. The preprint linked and its abstract are as follows:

We propose an interpretation for the adjoint representation of the SO(32) group to classify the scalars of a generic Supersymmetric Standard Model having just three generations of particles, via a flavour group SU(5). 

We show that this same interpretation arises from a simple postulate of self-consistence of composites for these scalars. The model looks only for colour and electric charge, and it pays the cost of an additional chiral +4/3 quark per generation.

Alejandro Rivero, "An interpretation of scalars in SO(32)" arXiv:2407.05397 (July 7, 2024). The published version is open access and was published on October 15, 2024.

Bonus: The article contains a cute "Turtles All The Way Down" illustration, which we here on Turtle Island, appreciate.

Atomic Nuclei Described At Quark-Gluon Level

Context

Once of the things that physicists can do, even if our understanding of the laws of physics is complete, is to formally derive the properties of more complex structures, like atoms, from the fundamental laws of physics found in the Standard Model. 

We understand the structure of atoms mostly in the context of a simplified proton-neutron-electron model, that is used in chemistry and even, for the most part, in nuclear physics, with a simplified (mostly experimentally fit) binding energy description of how protons and neutrons are held together in atomic nuclei that describes the residual strong force that holds protons and neutrons in the atom together in a nucleus (that we know is mediated mostly by composite pions as force carriers and to a secondary extent by force carrying composite kaons, rather than directly by gluons). 

The Standard Model of Particle physics provides a more fundamental description of protons, neutrons, and their interactions in terms of quarks and gluons with its model of the strong force that binds quarks and gluons to each other that is mediated by force carrying gluons. This theory is called quantum chromodynamics (QCD) because the analogy to electric charge for the strong force is called "color charge". Quarks can have one of three color charges, and gluons come in eight combinations that involve pairs of color charges.

The New Paper

Half a century after the Standard Model was devised, a new paper has made a major breakthrough at advancing the unfinished project of explaining atomic nuclei in terms of quarks and gluons, rather than in terms of composite protons and neutrons bound by the residual strong force.

The new paper accurately reproduces the structure of 18 atomic different nuclei with quantum chromodynamics (the theory of the Standard Model strong force that binds quarks and gluons to each other).

The parton distribution functions (PDFs) describe the structure of a composite particle in terms of quarks and gluons. PDFs can be calculated, in theory, from first principles in the Standard Model without any experimental input beyond the values of the two dozen or so experimentally measured physical constants of the Standard Model. 

But until less than a decade ago, in practice, parton distribution functions were almost always created by a vast statistical data dump from billions of collisions to which a mathematical function was fitted, that were very particular to particular particles at particular energy scales. These were updated from time to time with new data from more collisions. 

When it has been done previously from first principles, this has mostly been confined to individual protons, neutrons, or other simple hadrons such as pions (hadrons are composite particles whose particles are bound by gluons), not to multi-hadron atoms.

The new paper make some big leaps beyond that, advancing the project of rigorously demonstrating what we had merely assumed (for some good reasons) for the last fifty years: that the structure of atomics can be described fully from first principles using the Standard Model.

I quote at length from a secondary source account of what the paper is doing, because the paper itself is too technical for a general audience and what the paper is doing is sufficiently technical that I don't want to mangle it in my paraphrased retelling of it.

The atomic nucleus is made up of protons and neutrons, particles that exist through the interaction of quarks bonded by gluons. It would seem, therefore, that it should not be difficult to reproduce all the properties of atomic nuclei hitherto observed in nuclear experiments using only quarks and gluons. However, it is only now that an international team of physicists has succeeded in doing this. . . .

This long-standing deadlock has only now been broken, in a paper published in Physical Review Letters. Its main authors are scientists from the international nCTEQ collaboration on quark-gluon distributions.

"Until now, there have been two parallel descriptions of atomic nuclei, one based on protons and neutrons which we can see at low energies, and another, for high energies, based on quarks and gluons. In our work, we have managed to bring these two so far separated worlds together," says Dr. Aleksander Kusina, one of the three theoreticians from the Nuclear Physics of the Polish Academy of Sciences (IFJ PAN) participating in the research. . . .

Experiments . . . show that when electrons have relatively low energies, atomic nuclei behave as if they were made of nucleons (i.e. protons and neutrons), whereas at high energies, partons (i.e. quarks and gluons) are "visible" inside the atomic nuclei.

The results of colliding atomic nuclei with electrons have been reproduced quite well using models assuming the existence of nucleons alone to describe low-energy collisions, and partons alone for high-energy collisions. However, so far these two descriptions have not been able to be combined into a coherent picture.

In their work, physicists from the IFJ PAN used data on high-energy collisions, including those collected at the LHC accelerator at CERN laboratory in Geneva. The main objective was to study the partonic structure of atomic nuclei at high energies, currently described by parton distribution functions (PDFs).

These functions are used to map how quarks and gluons are distributed inside protons and neutrons and throughout the atomic nucleus. With PDF functions for the atomic nucleus, it is possible to determine experimentally measurable parameters, such as the probability of a specific particle being created in an electron or proton collision with the nucleus.

From the theoretical point of view, the essence of the innovation proposed in this paper was the skillful extension of parton distribution functions, inspired by those nuclear models used to describe low-energy collisions, where protons and neutrons were assumed to combine into strongly interacting pairs of nucleons: proton-neutron, proton-proton and neutron-neutron.

The novel approach allowed the researchers to determine, for the 18 atomic nuclei studied, parton distribution functions in atomic nuclei, parton distributions in correlated nucleon pairs and even the numbers of such correlated pairs.

The results confirmed the observation known from low-energy experiments that most correlated pairs are proton-neutron pairs (this result is particularly interesting for heavy nuclei, e.g. gold or lead). Another advantage of the approach proposed in this paper is that it provides a better description of the experimental data than the traditional methods used to determine parton distributions in atomic nuclei.

"In our model, we made improvements to simulate the phenomenon of pairing of certain nucleons. This is because we recognized that this effect could also be relevant at the parton level. Interestingly, this allowed for a conceptual simplification of the theoretical description, which should in future enable us to study parton distributions for individual atomic nuclei more precisely," explains Dr. Kusina.

The agreement between theoretical predictions and experimental data means that, using the parton model and data from the high-energy region, it has been possible for the first time to reproduce the behavior of atomic nuclei so far explained solely by nucleonic description and data from low-energy collisions. The results of the described studies open up new perspectives for a better understanding of the structure of the atomic nucleus, unifying its high- and low-energy aspects.

From Phys.org. The paper and its abstract are as follows:

We extend the QCD Parton Model analysis using a factorized nuclear structure model incorporating individual nucleons and pairs of correlated nucleons. Our analysis of high-energy data from lepton deep-inelastic scattering, Drell-Yan, and 𝑊 and 𝑍 boson production simultaneously extracts the universal effective distribution of quarks and gluons inside correlated nucleon pairs, and their nucleus-specific fractions. Such successful extraction of these universal distributions marks a significant advance in our understanding of nuclear structure properties connecting nucleon- and parton-level quantities.

A. W. Denniston, et al, "Modification of Quark-Gluon Distributions in Nuclei by Correlated Nucleon Pairs", 133 Physical Review Letters 152502 (October 11, 2024). DOI: 10.1103/PhysRevLett.133.152502

An earlier pre-print related to this paper can be found at arXiv, but the open access version of this paper is not yet available at arXiv.