Friday, January 31, 2020

Not All Experiments Are Created Equal

4gravitons make an interesting analysis of four different kinds of experiments and their respective likelihoods of discovering something interesting.

Some experiments are almost sure to discover something new because we know nothing about something new except that it is out there to measure. Some experiments are strongly expected to reproduce the status quo and are just dotting i's and crossing t's to more fully establish the range of the status quo with the off chance that an unexpected anomaly is discovered. 

In between are theory testing experiments. These can be powerful or merely paradigm confirming, unless a theory can be easily modified to adapt to any set of results, or there are many similar theories, not all of which can be falsified simultaneously.

Thursday, January 30, 2020

The Illinois Confederation Repopulated Cahokia A Century After It Collapsed

I've discussed the Mississippian culture of North America whose capital at its Y1K peak was at Cahokia, now in Southern Illinois, several times at this blog, which a press release at Science Daily sums up as follows:
In its heyday in the 1100s, Cahokia -- located in what is now southern Illinois -- was the center for Mississippian culture and home to tens of thousands of Native Americans who farmed, fished, traded and built giant ritual mounds. By the 1400s, Cahokia had been abandoned due to floods, droughts, resource scarcity and other drivers of depopulation. 
. . .  [M]any studies have focused on the reasons for Cahokia's decline, few have looked at the region following the exodus of Mississippians, whose culture is estimated to have spread through the Midwestern, Southeastern and Eastern United States from 700 A.D. to the 1500s.
But, a new study examines what happened a century after it collapsed. In a nutshell, after a century or so of abandonment, the Native American collection of tribes called the Illinois Confederation moved in for a couple of hundred years until their smaller scale and less urban civilization also collapsed. As the same press release explains (emphasis added):
[A] fresh wave of Native Americans repopulated the region in the 1500s and kept a steady presence there through the 1700s, when migrations, warfare, disease and environmental change led to a reduction in the local population. . . .  
[R]esearchers . . . analyzed fossil pollen, the remnants of ancient feces, charcoal and other clues to reconstruct a post-Mississippian lifestyle. 
Their evidence paints a picture of communities built around maize farming, bison hunting and possibly even controlled burning in the grasslands, which is consistent with the practices of a network of tribes known as the Illinois Confederation. Unlike the Mississippians who were firmly rooted in the Cahokia metropolis, the Illinois Confederation tribe members roamed further afield, tending small farms and gardens, hunting game and breaking off into smaller groups when resources became scarce[.]
The press release "politely" understates the obvious historical fact that the collapse of the Illinois Confederation was proximately caused by the influx of colonists and pioneers with roots in Europe under the organizing principles of the Northwest Ordinance of 1787 adopted under the Articles of Confederation that were in place prior to the adoption of the current United States Constitution in 1789.

There were European hunters, trappers and explorers on the grounds in this part of North American (mostly French) for essentially all of the period during which the Illinois Confederation, which flourished in the post-Columbian era. But, they were thin on the ground and could co-exist with the existing inhabitants, while the settlers who began to move to Southern Illinois in the late 18th century were much more disruptive to the way of life of the existing inhabitants and over the course of a century more or less completely displaced and replaced them.

The Illinois Confederation included the Miami Indians after whom Miami University of Ohio (in and around which I grew up) and the nearby Miami River are named. The Miami Indians who were recently departed when Miami University was founded in the year 1809, but the university now has a treaty relationship with the modern Miami Indian tribe.

The paper and its abstract are as follows (emphasis added):
The occupation history of the Cahokia archaeological complex (ca. AD 1050–1400) has received significant academic attention for decades, but the subsequent repopulation of the region by indigenous peoples is poorly understood. This study presents demographic trends from a fecal stanol population reconstruction of Horseshoe Lake, Illinois, along with information from archaeological, historical, and environmental sources to provide an interpretation of post-Mississippian population change in the Cahokia region. Fecal stanol data indicate that the Cahokia region reached a population minimum by approximately AD 1400, regional population had rebounded by AD 1500, a population maximum was reached by AD 1650, and population declined again by AD 1700. The indigenous repopulation of the area coincides with environmental changes conducive to maize-based agriculture and bison-hunting subsistence practices of the Illinois Confederation. The subsequent regional depopulation corresponds to a complicated period of warfare, epidemic disease, Christianization, population movement, and environmental change in the eighteenth century. The recognition of a post-Mississippian indigenous population helps shape a narrative of Native American persistence over Native American disappearance.
A.J. White, Samuel E. Munoz, Sissel Schroeder, Lora R. Stevens. "After Cahokia: Indigenous Repopulation and Depopulation of the Horseshoe Lake Watershed AD 1400–1900." American Antiquity 1 (2020) DOI: 10.1017/aaq.2019.103

Relevant Prior Posts:

* Poverty Point, Louisiana (a possible ancestral culture to the Mississippians) (March 17, 2017).

* Cahokia Explained (December 15, 2016) (also referencing three prior posts on the subject).

Wednesday, January 29, 2020

About Fleas

The word for the bug called the flea in English is the same in both Latin and Korean, a fact noted by published linguists as far back as 1923. The reason for this is unclear and a subject of hot linguistic debate.

Tuesday, January 28, 2020

ΛCDM Predicts The Wrong Mix Of Dark Matter Halos

Stacy McGaugh has another enlightening article at his blog on the discrepancies between the ΛCDM model prediction and the empirical evidence that has been apparent since the 1990s and not resolved within the ΛCDM model.

In a nutshell, if you try to apply the ΛCDM[1] to predict the "halo mass function" which is the mix of dark matter halos in the universe by mass, scaled to the proper quantity of dark matter overall, the ΛCDM prediction is wrong.

ΛCDM basically predicts a steady power law relationship between halo masses of a given size at all scales. But, if you interpret the observational data on galaxies (e.g. their luminosity and rotation speed) in a model dependent way to fit a dark matter particle paradigm, you see a steep drop off in observed very large halos in real life that is not predicted by the theory. In real life there are also too few small dark matter halos which should manifest as dwarf and satellite galaxies, relative to the theoretical expectation.

Incidentally, power law relationships with a sharp drop in frequency above a certain maximum threshold, similar to the ΛCDM prediction for the halo mass distribution, but tweaked to have the cutoff scale observed empirically, are quite common in ordinary life. For example, this describes the relationship between magnitude and frequency of earthquakes, floods and tornadoes on Earth.

Some of the key summaries of the data are in the charts below:

Note the logarithmic scale. Thus, the predicted frequency in the chart (the solid line) above of 1,000,000,000 solar mass halos (eyeballing it), is about 500 times too high relative to the observed data (blue squares and purple triangles). The solid prediction line is too high across the board and is too steep at low masses and too shallow at high masses.

The discrepancy is less serious at low masses, but remains profoundly off for high mass halos, even when halos mass is estimated directly using rotational velocity as show below (which isn't very informative for very low mass galaxies because its sample doesn't include them), which is a more direct calculation than the luminosity based estimates shown above.

We can fit a "Schechter function" to the actual data, but that is not a principled theoretical prediction drawn from first principles and is instead merely an empirical phenomenological fit to the data (much like MOND, which works the vast majority of the time over a broad range of applicability from solar system scales to large single galaxy scales but fails in galactic clusters, but is just an observed fit to the data without an underlying theoretical mechanism).

The ΛCDM model predicts that the most massive galaxies should be several hundred times more common than they are and it is harder for astronomers to miss hundreds of huge galaxies than it is for them to miss large numbers of tiny ones. In fairness to the ΛCDM model, however, none of its serious competitors does a particularly good job of explaining why we observe no galaxies with masses in excess of 10,000,000,000,000 solar masses either (although this issue hasn't been seriously analyzed one way or the other, for lack of a sufficient group of scientists actively investigating alternatives, for many of the non-paradigm alternatives). Stacy McGaugh answered my question at his blog regarding the best available hypothesis for why this is the case, stating:
The predominant idea for this goes back to the mid-70s, and essentially says that the gas cooling time has to be shorter than the gravitational collapse time. Basically, there has to be time for the gas to collapse. This comes out to about the right upper mass limit for individual galaxies, but is rather crude in many respects – the cooling time is very sensitive to the metallicity of the gas; a spherical cow that ignores hierarchical substructure is assumed, and so on. Still, that’s the best I’ve heard.
There is also an outstanding issue regarding whether the largest halos ought to be associated with structures like galaxy clusters, rather than individual galaxies, that complicates the analysis.

Other issues with the ΛCDM model.

A review article from 2017 cited in the blog post linked above examines more problems with the "Standard Model of Cosmology."
The dark energy plus cold dark matter (ΛCDM) cosmological model has been a demonstrably successful framework for predicting and explaining the large-scale structure of Universe and its evolution with time. Yet on length scales smaller than 1 Mpc and mass scales smaller than 1011M, the theory faces a number of challenges. For example, the observed cores of many dark-matter dominated galaxies are both less dense and less cuspy than naively predicted in ΛCDM. The number of small galaxies and dwarf satellites in the Local Group is also far below the predicted count of low-mass dark matter halos and subhalos within similar volumes. These issues underlie the most well-documented problems with ΛCDM: Cusp/Core, Missing Satellites, and Too-Big-to-Fail. The key question is whether a better understanding of baryon physics, dark matter physics, or both will be required to meet these challenges. Other anomalies, including the observed planar and orbital configurations of Local Group satellites and the tight baryonic/dark matter scaling relations obeyed by the galaxy population, have been less thoroughly explored in the context of ΛCDM theory. Future surveys to discover faint, distant dwarf galaxies and to precisely measure their masses and density structure hold promising avenues for testing possible solutions to the small-scale challenges going forward. Observational programs to constrain or discover and characterize the number of truly dark low-mass halos are among the most important, and achievable, goals in this field over then next decade. These efforts will either further verify the ΛCDM paradigm or demand a substantial revision in our understanding of the nature of dark matter.
James S. Bullock, Michael Boylan-Kolchin, "Small-Scale Challenges to the ΛCDM Paradigm" (July 13, 2017, last updated September 2, 2019) arXiv 1707.04256

See also:
We present rotation curve fits to 175 late-type galaxies from the Spitzer Photometry & Accurate Rotation Curves (SPARC) database using seven dark matter (DM) halo profiles: pseudo-isothermal (pISO), Burkert, Navarro-Frenk-White (NFW), Einasto, DC14, cored-NFW, and a new semi-empirical profile named Lucky13. We marginalize over stellar mass-to-light ratio, galaxy distance, disk inclination, halo concentration and halo mass (and an additional shape parameter for Einasto) using a Markov Chain Monte Carlo method. We find that cored halo models such as the DC14 and Burkert profiles generally provide better fits to rotation curves than the cuspy NFW profile. The stellar mass-halo mass relation from abundance matching is recovered by all halo profiles once imposed as a Bayesian prior, whereas the halo mass-concentration relation is not reproduced in detail by any halo model. We provide an extensive set of figures as well as best-fit parameters in machine-readable tables to facilitate model comparison and the exploration of DM halo properties.
Pengfei Li, Federico Lelli, Stacy McGaugh, James Schombert, "A comprehensive catalog of dark matter halo models for SPARC galaxies" (January 28, 2020). arXiv 2001.10538

Other phenomena that are hard to explain with the ΛCDM model are (1) dwarf galaxies with almost no apparent dark matter (which MOND predicted in the early 1980s and explains with the external field effect), (2) the behavior of wide binary star systems in which the stars appear to be bound by a gravitational force stronger than predicted by general relativity, (3) the fact that inferred dark matter halo shapes differ from the theoretically predicted NFW distribution, and (4) the fact that inferred dark matter distributions are tightly linked in a predictable manner to observed ordinary matter distributions even at a fine scaled level that is basically impossible to explain with truly collisionless dark matter particles that interact exclusively through gravity in a manner prescribed by General Relativity.

This tends to imply that dark matter particles, if they exist, must either be subject to a force that acts between dark matter particles (self-interacting dark matter), probably (based on cluster collision data) with a coupling strength on a order similar to that of the electromagnetic force, or a small in coupling strength fifth force governing interactions between dark matter and ordinary matter, or both. So, viable dark matter particle theories need one or two new forces (presumably with at least one beyond the Standard Model non-graviton carrier boson each) in addition to at least one new, beyond the Standard Model, non-graviton dark matter particle. All of these possibilities are significant extensions of the ΛCDM model that materially impact what it would predict. 

There are also some issues with the ΛCDM model when compared with observational data at the larger cosmology scale. Most notably, (1) galaxies form too quickly (the impossible early galaxies problem), (2) 21cm wavelength radiation data that demonstrates the temperature of the universe at 180 million to 280 million years after the Big Bang, seems inconsistent with the model because the universe was much colder than predicted and is instead consistent with a no dark matter hypothesis, and (3) the velocity of colliding galaxy clusters is also too often higher than it predicts.

There are also serious concerns about the cosmological constant part of the ΛCDM model which may be overestimated or non-existent due to several methodological issues with how the value of this parameter is determined based upon the available data. See, e.g., a post at this blog here. The jury is out regarding whether these concerns are well founded or lead to the conclusions that the people proposing them have suggested. This is a fairly recent and still hotly debated issue in cosmology and astronomy, and beyond the scope of this post.

In fairness, while the ΛCDM model is contradicted by the observational evidence at small scales in many respects, it is still a decent zeroth order approximation of reality, that could conceivably be tweaked to better fit observation through some mass assembly process that is currently not understood and by factors such as gravitational interactions with distributions of ordinary matter, although this possibility looks quite doubtful given everything we know so far.

Most strongly supporting it, the ΛCDM model compares favorably in predicting the dynamics of particles near the fringes of spiral galaxies that are outside the main plane of the spiral, relative to many leading modified gravity theories. 

What the does the ΛCDM model gets right?

The ΛCDM model does do an excellent job of predicting the nature of the cosmic microwave background radiation (which has slight warm and cold spots) that is observed, although it turns out that this is easier to fit than one might naively assume. This is because some of the parameters are determined relative to other parameters, rather than being truly independent of each other, so fewer degrees of freedom involved that have to be fit than one would expect just looking at the raw data in a superficial manner.

The ΛCDM model also does a decent job of explaining why observable matter has a web-like or cell-like structure at the largest scales with filaments of higher matter density surrounding comparative voids of matter.

What observational data sometimes touted as a problem for dark matter particle theories does not materially undermine the ΛCDM model?

The lack of direct detection of dark matter particles in dark matter detection experiments confirms that if dark matter particles exist that they do not have meaningful electromagnetic, weak force, or strong force interactions with other particles of ordinary matter, but this is entirely consistent with the standard, unmodifed ΛCDM model. 

The direct dark matter detection experiments do tell us that any interaction that dark matter particles have with ordinary matter must be much weaker than the weak force of the Standard Model between ordinary matter particles (which is mediated by Z boson exchange). 

The observed frequency of decay products of Higgs bosons, W and Z bosons likewise supports the hypothesis that if dark matter particles exist, dark matter particles do not decay via the weak force if individual particles have a mass of 62.5 GeV or less (with the available galaxy dynamics data favoring a dark matter particle mass on the order of 1-10 keV over heavier masses if dark matter is created through the most popular thermal freeze out hypothesis). 

Given evidence that dark matter particles, if they exist, are stable or metastable over time lines comparable to the age of the universe (or are created and destroyed at almost exactly identical rates, perhaps due to some sort of conservation law), the lack of weak force decays is also unsurprising.

Likewise, because the ΛCDM model takes no position on how dark matter particles come into being, whether they decay, or how it can be destroyed, the lack of dark matter annihilation signal detections and the lack of collider signatures of dark matter neither contradicts nor supports the ΛCDM model.

The available data does not clearly favor models in which dark matter particles are fermions, over models in which dark matter particles are bosons, but the ΛCDM model is agnostic on that issue.

[1] Pronounced lambda "C" "D" "M", in which lambda is the cosmological constant, and CDM stands for "Cold Dark Matter" but really means "warm" or "cold" dark matter which is "nearly" collisionless with ordinary matter and other dark matter and hence has dynamics that are predominantly a function of gravity alone.  The aggregate amount of CDM in the model is fixed from moments after the Big Bang to the present, while the amount of dark energy (described by the cosmological constant) is proportional to the spatial volume of the universe at any given point in time, and hence grows over time. This model is also known as the Standard Model of Cosmology and is the prevailing paradigm, despite an ever growing list of discrepancies with the empirical evidence. ΛCDM has a good (but not perfect) track record relative to observational data at scales larger than galaxy clusters, but a very poor track record at scales of galaxies and smaller systems.

Friday, January 24, 2020

About Blue Eyes

This isn't new (the paper is twelve years old), but it caught my eye today.

The time frame for the initial mutation spans the late Mesolithic era, an era during which hunter-gatherers from Southern Europe repopulated the rest of the continent as glaciers from the last major ice age retreated to the north, and the early Neolithic era. It predates the Copper, Bronze and Iron ages. The authors of the paper on the genetics of eye color believe that the blue eye color gene is genetic fitness neutral. As a press release on the study explains in a conclusion stronger than the study itself really supports given its limited sample size and diversity:
New research shows that people with blue eyes have a single, common ancestor. Scientists have tracked down a genetic mutation which took place 6,000-10,000 years ago and is the cause of the eye color of all blue-eyed humans alive on the planet today.
The mutation is similar to an albinism mutation but more targeted and less complete.
"Originally, we all had brown eyes," said Professor Hans Eiberg from the Department of Cellular and Molecular Medicine. "But a genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a "switch," which literally "turned off" the ability to produce brown eyes." The OCA2 gene codes for the so-called P protein, which is involved in the production of melanin, the pigment that gives colour to our hair, eyes and skin. The "switch," which is located in the gene adjacent to OCA2 does not, however, turn off the gene entirely, but rather limits its action to reducing the production of melanin in the iris -- effectively "diluting" brown eyes to blue. The switch's effect on OCA2 is very specific therefore. If the OCA2 gene had been completely destroyed or turned off, human beings would be without melanin in their hair, eyes or skin colour -- a condition known as albinism. 
Variation in the colour of the eyes from brown to green can all be explained by the amount of melanin in the iris, but blue-eyed individuals only have a small degree of variation in the amount of melanin in their eyes. "From this we can conclude that all blue-eyed individuals are linked to the same ancestor," says Professor Eiberg. "They have all inherited the same switch at exactly the same spot in their DNA." Brown-eyed individuals, by contrast, have considerable individual variation in the area of their DNA that controls melanin production. 
Professor Eiberg and his team examined mitochondrial DNA and compared the eye colour of blue-eyed individuals in countries as diverse as Jordan, Denmark and Turkey. 
The abstract and citation to the paper are as follows:
The human eye color is a quantitative trait displaying multifactorial inheritance. Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we fine mapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. By association analyses, we identified two SNPs within this region that were perfectly associated with the blue and brown eye colors: rs12913832 and rs1129038. Of these, rs12913832 is located 21.152 bp upstream from the OCA2 promoter in a highly conserved sequence in intron 86 of HERC2. The brown eye color allele of rs12913832 is highly conserved throughout a number of species. As shown by a Luciferase assays in cell cultures, the element significantly reduces the activity of the OCA2 promoter and electrophoretic mobility shift assays demonstrate that the two alleles bind different subsets of nuclear extracts. One single haplotype, represented by six polymorphic SNPs covering half of the 3′ end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.
Hans Eiberg, et al., "Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression." 123(2) Human Genetics 177 (March 2008). DOI: 10.1007/s00439-007-0460-x

Two subsequent papers have favored a somewhat earlier Mesolithic European hunter-gatherer origin for the genes, rather than a Neolithic one, and have refined the genetic model to include a few more genes. As Wikipedia explains:
People of European descent show the greatest variety in eye color of any population worldwide. Recent advances in ancient DNA technology have revealed some of the history of eye color in Europe. All European Mesolithic hunter-gatherer remains so far investigated have shown genetic markers for light-colored eyes, in the case of western and central European hunter-gatherers combined with dark skin color. The later additions to the European gene pool, the Early Neolithic farmers from Anatolia and the Yamnaya Copper Age/Bronze Age pastoralists (possibly the Proto-Indo-European population) from the area north of the Black Sea appear to have had much higher incidences of dark eye color alleles, and alleles giving rise to lighter skin, than the original European population.
The two  more recent papers cited are:

Mathieson, Iain (2015). "Eight thousand years of natural selection in Europe". bioRxiv 016477.

Neanderthals probably had blue eyes, light colored hair and light colored skin, while the modern humans who co-existed and encountered with them at the end of the Upper Paleolithic era would have had brown eyes, dark hair and dark colored skin. But, genes for light pigmentation in modern humans alive today arose from mutations that took place roughly 20,000 years after Neanderthals were extinct and were not derived from Neanderthal admixture.

Monday, January 20, 2020

Climate Was Pivotal To Out Of Africa Migration

Deserts were major barriers to human migration in the pre-Holocene era and deserts waxed and waned based upon shifts in climate over time historically. This is entirely expected, but important. 

Whilst an African origin for Anatomically Modern Humans is well established 1, the timings of their expansions into Eurasia are the subject to heated debate, due to the scarcity of fossils and the lack of suitably old ancient DNA 2. Here, we estimate potential timings and routes out of Africa by deriving anthropologically and ecologically plausible precipitation requirements for human existence, and applying them to high-resolution palaeoclimate reconstructions for the past 300k years. We find that exit routes and timings previously suggested based on archaeological and genetic evidence coincide precisely with the presence of sufficiently wet corridors into Eurasia, while the gaps between the proposed exit timings co-occur with periods of insufficient rainfall. This demonstrates the key role that palaeoclimatic conditions played for out-of-Africa expansions. The challenging environmental conditions outside of Africa that occurred between windows of potential contact, coupled with the lack of a demographic rescue effect from migration and possible competition with other hominins, likely explain the demise of early colonists prior to the large-scale colonisation of the world beginning from ∼65kya.
Robert M. Beyer, Mario Krapp, Anders Eriksson, Andrea Manica,"Windows out of Africa: A 300,000-year chronology of climatically plausible human contact with Eurasia" BioRxiv (January 14, 2020). doi:

From the main text, which reasonably fairly sums up the evidence, omitting a couple of old dates in India (pre-dating the Toba eruption) and Myanmar and Indonesia (shortly after the Toba eruption), however.
The dating of most out-of-Africa fossils, and the dating of the split between Eurasian and African populations based on mitochondrial and whole-genome data 3,4 point to a major exit ∼65k years ago. However, archaeological findings in Saudi Arabia dated to at least 85k years ago 5, in Israel to at least ∼90k years ago 6, possibly ∼194k years ago 7, and in Greece dated back to ∼210k years ago 8 point to previous excursions from Africa, which might have reached as far as China 9. 
These, or another previous waves, might have also left a small genetic contribution (∼1%) found in modern inhabitants of Papua New Guinea 10. Further evidence for a possibly earlier exit comes from traces of geneflow from AMHs into Neanderthal, genetically dated to before 130k years ago, but could be as old as 270k years ago 11. Thus, AMHs likely had repeated periods when they were able to leave Africa, even though the timing and fate of those early waves is unclear.

Friday, January 17, 2020

Human Genetics 201

The rules of human genetics you learned in high school are a good first order approximation of how human genetics work. But, as we look closer, we are actually learning that human genetics are more complex.

* Some men are genetically pre-disposed to have more sons. There are genes that determine the sex ratio of a man's sperm output. So, some men are genetically pre-disposed to have sons, and other men are genetically pre-disposed to have daughters. This explains, for example, why after a war, more boys than girls are born. 
In many of the countries that fought in the World Wars, there was a sudden increase in the number of boys born afterwards. The year after World War I ended, an extra two boys were born for every 100 girls in the UK, compared to the year before the war started. The gene, which Mr Gellatly has described in his research, could explain why this happened. 
As the odds were in favour of men with more sons seeing a son return from the war, those sons were more likely to father boys themselves because they inherited that tendency from their fathers. In contrast, men with more daughters may have lost their only sons in the war and those sons would have been more likely to father girls. This would explain why the men that survived the war were more likely to have male children, which resulted in the boy-baby boom.
Also the natural sex ratio in humans is not 50-50 but 105-100, because the balances boys being more prone to die as children than girls, historically.)

The paper is:

Gellatly et al. "Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio Gene." Evolutionary Biology (Dec 11, 2008) DOI: 10.1007/s11692-008-9046-3

* Epigenetic markers can be inherited. The main form of genetic inheritance is in your genes, which are inherited from your ancestors ad infinitum, modified only by genetic mutations. During life, however, an organism's genes are "annotated", which tells those genes how to express themselves, most notably by a process known as DNA methylation. This is critical. The DNA in the cells in your ears need to know not to express as bone tissue, and your red blood cells need to know not to turn into white blood cells, for example, significant environmental exposures in life such as period of famine or intense fear also impact these annotations. Collectively, the annotations in your genome are called, rather unimaginatively, your epigenome.

Jean-Baptiste Lamarck thought that evolution was primarily driven by epigenetic responses to the environment being passed on to the next generation. And, mostly he was wrong. But, it turns out that he was not entirely wrong. The epigenome can be passed on in part to the next generation as well. A recent paper provides an example of this happening.

The paper is:

Sandra Catania, et al., 'Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase." Cell (2020). DOI: 10.1016/j.cell.2019.12.012

* Not all genes mutate at the same rate. We've actually know for a long time that certain parts of your genome (both different parts of your autosomal genome, and different parts of your mitochondrial genome) mutate at different rates. This makes determining the time frame in which two genomes diverged from each other based upon the number of mutations by which they differ much trickier than it was believed to be when this was first attempted.

* It is possible for your genome to change during your life.  An endogenous retrovirus, if you are infected by it, can permanently change your genes in a way that is passed on to your descendants. About 5%-8% of the human genome has its source in ERVs rather than parent to child inheritance. Viral infections with this effect are used for gene therapy. A bone marrow transplant can also change your genome. Also, of course, genetic mutations can arise by pure chance, and the risk of mutations can be enhanced by environmental conditions such as exposures to toxins.

* Not all cells in a person's body are necessarily identical. The phenomena is called genetic mosaicism if it arises in an organism arising from a single egg (often due to a mutation early in the developmental process), and genetic chimerism, in which two or more genotypes arise in one individual from the fusion of more than one fertilized zygote in the early stages of embryonic development (although many reasonably knowledgable people use the terms as interchangeable). Another way it commonly arises is in vitro fertilization. Also, it increasingly appears that when a woman is pregnant that some cells with genes of the fetus survive in the mother (also by implication, leaving cells with some genes that have an origin in the father in the mother.)

* Children do not receive exactly 50% of their genes from each parent, although it is close to 50-50. Some children receive a little more than 50% of their genes from their father, some a little less. You also can't tell which parent a child receives more genes from based upon appearance or other phenotypic traits, because the most obvious traits are governed by a very small share of the total genome. I've seen this, for example, in the genetic testing of my children and in the genetic testing of other siblings which I have seen. To be perfectly honest, I don't fully understand how this happens.

Monday, January 13, 2020

The North Star Was A Different Star When The Egyptians Built Their Pyramids.

The more interesting part of this story, below, is actually old news, while the new part of the story is that the former North star, Thuban, has been recently discovered to be part of a binary star system, something that escaped detection for thousands of years despite the prominence of this star in the sky.
Although it's not the brightest star in the sky, Polaris serves as our guiding North Star. It's a steady star in the Ursa Minor constellation to guide by, remaining constant while the rest of the north sky moves. This is because Polaris is closest to Earth's north pole, so it appears that the other stars in the sky rotate around it. 
But Polaris hasn't always been our North Star. And during the construction of the earliest Egyptian pyramids 4,700 years ago, the pole star was Thuban, or Alpha Draconis, found in the Draco constellation. The star is 270 light-years from Earth. 
There is evidence now that Thuban was used to guide the construction of the pyramids, given how their placement, and even air shafts, align with the stars. 
The North Star changed because Earth's spin axis itself wobbles slowly over the course of 26,000 years, which alters the position of our pole and where it points in the sky.
From here.

Wednesday, January 8, 2020

Thank You Readers For Being So Engaged!

The Readers Of This Blog Comment A Lot

At this blog, there are 1.50 comments per day, on average.

At Wash Park Prophet, there are 0.35 comments per day, on average.

I am very thorough in removing spam comments from both this blog and its sister blog Wash Park Prophet, so these figures reflect only genuine legitimate comments to posts.

This is true despite the fact that Wash Park Prophet has about 45% more page views per month than Dispatches From Turtle Island. A reader at this blog is about six and a half times as likely to leave a comment after viewing a page as at Wash Park Prophet (about one comment is posted per 155 page views at this blog).

This blog averages about 310 page views per day, although it is prone to spikes when I make a popular post that is referred by other blogs or social media or is on a hot topic, and when I make multiple posts in a short period of time, and lulls at other times.  

This is true even though it is consistently the case that I make more posts per year at Wash Park Prophet. For example, in the years when both blogs have been in place for a full year (2012-2019) the annual number of posts at each blog have been as follows:

Year       Wash Park Prophet     Dispatches From Turtle Island         Total   
2019       192                                    173                                           365

2018       226                                    213                                           439

2017       294                                    244                                           538

2016       414                                    210                                           624

2015       300                                    176                                           476

2014       205                                    126                                           331

2013       292                                    168                                           460

2012       376                                    222                                           598

I can only conclude that readers of Dispatches From Turtle Island are much more engaged with the content at this blog, which is certainly a good thing.

My Audience

Also, while I like comments, I am also delighted to have readers who very rarely comment but appreciate the content here. 

If you are a regular reader who very rarely comments, feel free to "delurk" in the comments at this post, just so that I can know that you are out there.  

I always like to better understand my audience.

Fun Fact: About 9% of my readers are in Russia, the #2 location from which this blog is read after the United States (which accounts for about 43% of my readers). 

Most of the rest of my readership is from other European countries (Western and Eastern Europe), from Canada, and from Australia (although I know I have several regular readers in New Zealand, where I lived for a year myself as an exchange student), as well. I do have readers in Latin America and Asia, but apparently considerable fewer of them on a country by country basis.

About 60% of my readers use Windows, about 17% use Macs, about 7% use Linux, and the other 18% read this blog on their phones.

Other Blogs Compared

Certainly, there are other blogs which a much more engaged audience, Eurogenes, Backreaction, The Reference Frame, Not Even Wrong, and Razib Khan's Gene Expression blog and his contributions to the Brown Pundits blog, for example.

Also, just to toot my own horn a little, while the number of posts at this blog isn't huge, only a handful of single author science blogs that do any meaningful analysis in the entire blogosphere are updated as regularly as this one.

This remains true in the separate domains of science covered by this blog even if you break this blog up into its two subcomponents, with almost 50% of the posts having math and/or physics tags (837 out of 1741 posts), and about 50% of the posts being about anthropology, historical linguistics, genetics, biodiversity, evolution and the history of the distant past, with only slight overlap (usually involving ancient astronomers).

I also aim to make about 3% of the posts at this blog humorous and I am currently two posts over that quota (54 humorous posts v. a quota of 52). Somewhat surprisingly, posts tagged humor are frequently also about mathematics.

John Baez's blog, Azimuth blog, and Lubos Motl's The Reference Frame are only ones that comes to mind on the math and physics side, although 4gravitons, which updates consistently once a week on average, comes close. 

Razib Khan's collection of blogs is the only example that comes to mind on the subject of the other half of what this blog covers.

I'm sure that I've missed a few frequently updated single author science blogs with meaningful analysis in the fields that this blog addresses, but I'd hazard to guess, not all that many. If you know of some, please let me know so that I can add them to my blogroll.

Tuesday, January 7, 2020

The Real Butterfly Effect

Chaos and fractals were the youngest fields of math that I studied in college (operations research was a close runner up). But, it was also among the most fascinating and profound. 
The name “Butterfly Effect” was popularized by James Gleick in his 1987 book “Chaos” and is usually attributed to the meteorologist Edward Lorenz. But I recently learned that this is not what Lorenz actually meant by Butterfly Effect. . . . 
Lorenz, in this [1969] paper, does not write about butterfly wings. He instead refers to a sea gull’s wings, but then attributes that to a meteorologist whose name he can’t recall. The reference to a butterfly seems to have come from a talk that Lorenz gave in 1972, which was titled “Does the Flap of a Butterfly’s Wings in Brazil set off a Tornado in Texas?” 
The possibility that a small change in initial conditions can lead to a massively different outcome somewhere (the contemporary meaning of the phrase), was actually not the strongest claim made in the 1969 paper.
How well can you make predictions using the data from your measurements? You have data on that finite grid. But that does not mean you can generally make a good prediction on the scale of that grid, because errors will creep into your prediction from scales smaller than the grid. You expect that to happen of course because that’s chaos; the non-linearity couples all the different scales together and the error on the small scales doesn’t stay on the small scales. 
But you can try to combat this error by making the grid smaller and putting in more measurement devices. 
For example, Lorenz says, if you have a typical grid of some thousand kilometers, you can make a prediction that’s good for, say, 5 days. After these 5 days, the errors from smaller distances screw you up. So then you go and decrease your grid length by a factor of two. 
Now you have many more measurements and much more data. But, and here comes the important point: Lorenz says this may only increase the time for which you can make a good prediction by half of the original time. So now you have 5 days plus 2 and a half days. Then you can go and make your grid finer again. And again you will gain half of the time. So now you have 5 days plus 2 and half plus 1 and a quarter. And so on. 
Most of you will know that if you sum up this series all the way to infinity it will converge to a finite value, in this case that’s 10 days. This means that even if you have an arbitrarily fine grid and you know the initial condition precisely, you will only be able to make predictions for a finite amount of time. 
And this is the real butterfly effect. That a chaotic system may be deterministic and yet still be non-predictable beyond a finite amount of time.
Sabine Hossenfelder tells the entire story in more depth at her blog, Backreaction. 

Monday, January 6, 2020

Large Southeast Asian Meteor Impact Location From 790,000 Years Ago Found

The details of a meteor impact that caused global climate changes that may have been pivotal in hominin evolution are now known with much more specificity. 

[T]he impact point of a meteorite that struck the Earth approximately 790,000 years ago lies buried beneath a volcanic field in southern Laos. . . . .  
Prior research has shown that approximately 790,000 years ago, a large meteorite (the largest known young meteorite impact) struck Earth in the Eastern Hemisphere. So great was the impact that debris was strewn across a tenth of the entire planet's surface. Scientists know about the impact because of bits of glassy clasts known as tektites have been found in places like Antarctica, Australia and Southeast Asia. Prior evidence also suggested the impact site was likely somewhere in Southeast Asia, but until now, the exact location has been unknown. In this new effort, the researchers have found evidence that suggests the reason the crater has not been found is that it is hidden beneath a volcanic field—and they provide four lines of evidence to back up their claim. 
From here. The paper and its abstract are as follows:
A field of black glassy blobs, strewn across about 20% of Earth’s Eastern Hemisphere, resulted from the impact of a large meteorite about 790,000 y ago. The large crater from which these tektites originated has eluded discovery for over a century, although evidence has long pointed to a location somewhere within Indochina, near the northern limit of the strewn field. We present stratigraphic, geochemical, geophysical, and geochronological evidence that the ∼15-km diameter crater lies buried beneath a large, young volcanic field in Southern Laos.  
The crater and proximal effects of the largest known young meteorite impact on Earth have eluded discovery for nearly a century. We present 4 lines of evidence that the 0.79-Ma impact crater of the Australasian tektites lies buried beneath lavas of a long-lived, 910-km3 volcanic field in Southern Laos: 1) Tektite geochemistry implies the presence of young, weathered basalts at the site at the time of the impact. 2) Geologic mapping and 40Ar-39Ar dates confirm that both pre- and postimpact basaltic lavas exist at the proposed impact site and that postimpact basalts wholly cover it. 3) A gravity anomaly there may also reflect the presence of a buried ∼17 × 13-km crater. 4) The nature of an outcrop of thick, crudely layered, bouldery sandstone and mudstone breccia 10–20 km from the center of the impact and fractured quartz grains within its boulder clasts support its being part of the proximal ejecta blanket.
Kerry Sieh et al., "Australasian impact crater buried under the Bolaven volcanic field, Southern Laos," Proceedings of the National Academy of Sciences (2019) (open access). DOI: 10.1073/pnas.1904368116 (Companion commentary from PNAS here).

Why Care?

This impact was the most notable climate event on Earth prior to the Holocene (i.e. the last 10,000 years) at a time the coincides with several key moments in hominin evolution.

The meteorite impact in question pre-dates the evolution of modern humans and either precedes or coincides with the evolution of our archaic hominin sister species Homo neanderthalensis, Homo denisova, and Homo heidelbergensis (possibly the direct evolutionary ancestor of modern humans and a mother species rather than a sister species, the exact relationship is unclear). It wouldn't be unreasonable to conjecture that the global climate impact that arose from this impact was a major factor that lead to the evolution of the shared predecessor of these two species. (I side with those who consider Neanderthals to be a separate species from modern humans in the same genus, rather than a subspecies of modern humans based on evidence of hybrid incompatibility between modern humans and Neanderthals when they admixed.)

It also is close in time to the earliest evidence of the archaic hominin Homo floresiensis (a.k.a. "hobbits") on the island of Flores in Indonesia. It wouldn't be an unreasonable conjecture that this impact was pivotal in the event that cause H. florensiensis to migrate to the island of Flores.

H. florensiensis, however, is probably much more basal in the hominin evolutionary tree even than Homo erectus (which evolved around 2 million years ago in Africa and had spread to Asia many hundreds of thousands of years before this meteorite impact).

It is also close in time to the earliest evidence of archaic hominin species in the Philippines, Homo luzonensis (whose existence was just confirmed in 2019 with bones from this species). It wouldn't be an unreasonable conjecture that this impact was pivotal in the event that cause H. luzonensis to migrate to the Philippines. Limited information makes classification of H. luzonensis in a hominin evolutionary tree difficult.