Thursday, February 23, 2017

Smallpox And Salmonella Did More To Wipe Out Native Americans Than Genocide

Something like 95% of Native Americans died when Europeans arrived in the New World.

But, in North America, at least, the leading cause of death was an epidemic of smallpox from 1775 to 1782 that raced ahead of European colonists from the Atlantic Coast to the Pacific Coast. 

This epidemic was not intended by the colonists as a means of destroying the existing population, nor was it even really well understood. While the germ theory of disease had been proposed at that point, it was not widely accepted.

This isn't to say that Europeans did right by Native Americans before or after this epidemic. But, the bulk of the Native American deaths caused by the Europeans in North America were due to the inadvertent spread of diseases to which Native American populations never exposed to them were far more vulnerable than Europeans who had 8,000 years or so of natural selection at work building their immune systems' ability to defend against these diseases. And, the military superiority of Europeans in the century or so of conquest called "the Indian Wars" that followed, had as much to do with the residual impacts of this devastating loss of life due to new infectious diseases as it did to do with weapons or tactics.

According to the linked Wikipedia article:
The 2010 census found 2,932,248 Americans who identified themselves as being Native American (or Alaskan Native), about 0.9% of the U.S. population. No consensus exists on how many native people lived in the Americas before the arrival of Columbus, but extensive research has been and continues to be conducted. Estimates on the population of pre-Colombus North America range from a low of 2.1 million (Ubelaker 1976) to 7 million people (Russell Thornton) to 18 million (Dobyns 1983).
As the direct result of infectious diseases, conflict with Europeans, wars between tribes, assimilation, migration to Canada and Mexico, declining birth rates, the numbers of Native Americans dropped to below half a million in the 19th century. Scholars believe that the overwhelming main causes were new infectious diseases carried by European explorers and traders. Native Americans had no acquired immunity to such diseases, which had been chronic in Eurasian populations for over five centuries. For instance, some estimates indicate case fatality rates of 80–98% in Native American populations during smallpox epidemics.
The United States Census Bureau (1894) provided their estimate of deaths due specifically to war during the 102 years between 1789 and 1891, including 8,500 natives and 5,000 whites killed in "individual affairs": 
The Indian wars under the government of the United States have been more than 40 in number. They have cost the lives of about 19,000 white men, women and children, including those killed in individual combats, and the lives of about 30,000 Indians. The actual number of killed and wounded Indians must be very much higher than the number given... Fifty percent additional would be a safe estimate.
One important matter attributable to neither combat death nor disease that none of the sources above address is the loss of life, loss of land, loss of culture, and general privation associated with the relocation of Native Americans to reservations far less desirable to them than their ancestral lands, mostly during the 19th century. Such as the relocation of the Cherokee Nation by Andrew Jackson in 1838 and 1839 known as the Trail of Tears.

In a similar vein, another European disease spread long before the germ theory of disease was understood probably causes massive deaths among the people of what is now Mexico. According to Scientific American magazine, hard evidence now linked the collapse of Aztec society following first contact with Spanish conquistadors with an outbreak of Salmonella, to which that society was not adapted either in food preparation methods or in their immune systems.
One of the worst epidemics in human history, a sixteenth-century pestilence that devastated Mexico’s native population, may have been caused by a deadly form of salmonella from Europe, a pair of studies suggest. 
In one study, researchers say they have recovered DNA of the stomach bacterium from burials in Mexico linked to a 1540s epidemic that killed up to 80% of the country's native inhabitants. The team reports its findings in a preprint posted on the bioRxiv server on February 8. . . .
In 1519, when forces led by Spanish conquistador Hernando Cort├ęs arrived in Mexico, the native population was estimated at about 25 million. A century later, after a Spanish victory and a series of epidemics, numbers had plunged to around 1 million. The largest of these disease outbreaks were known as cocoliztli (from the word for ‘pestilence’ in Nahuatl, the Aztec language). Two major cocoliztli, beginning in 1545 and 1576, killed an estimated 7 million to 18 million people living in Mexico’s highland regions. 
“In the cities and large towns, big ditches were dug, and from morning to sunset the priests did nothing else but carry the dead bodies and throw them into the ditches,” noted a Franciscan historian who witnessed the 1576 outbreak. 
There has been little consensus on the cause of cocoliztli—although measles, smallpox and typhus have all been mooted. In 2002, researchers at the National Autonomous University of Mexico (UNAM) in Mexico City proposed that a viral haemorrhagic fever, exacerbated by a catastrophic drought, was behind the carnage. They compared the magnitude of the 1545 outbreak to that of the Black Death in fourteenth-century Europe.

In an attempt to settle the question, a team led by evolutionary geneticist Johannes Krause at the Max Planck Institute for the Science of Human History in Jena, Germany, extracted and sequenced DNA from the teeth of 29 people buried in the Oaxacan highlands of southern Mexico. All but five were linked to a cocoliztli that researchers think ran from 1545 to 1550. 
Ancient bacterial DNA recovered from several of the people matched that of Salmonella, . . . Further sequencing of short, damaged DNA fragments from the remains allowed the team to reconstruct two genomes of a Salmonella enterica strain known as Paratyphi C. Today, this bacterium causes enteric fever, a typhus-like illness, that occurs mostly in developing countries. If left untreated, it kills 10–15% of infected people. . . . 
Krause and his colleagues’ proposal is helped by another study posted on bioRxiv . . . which raises the possibility that Salmonella Paratyphi C arrived in Mexico from Europe. A team . . . collected and sequenced the genome of the bacterial strain from the remains of a young woman buried around 1200 in a cemetery in Trondheim, Norway. It is the earliest evidence for the now-rare Salmonella strain, and proof that it was circulating in Europe . . . 
The existence of Salmonella Paratyphi C in Norway 300 years before it appeared in Mexico doesn’t prove that Europeans spread enteric fever to native Mexicans, says Schroeder, but that hypothesis is reasonable. A small percentage of people infected with Salmonella Paratyphi C carry the bacterium without falling ill, so apparently healthy Spaniards could have infected Mexicans who lacked natural resistance. Paratyphi C is transmitted through faecal material, and a collapse of social order during the Spanish conquest might have led to the poor sanitary conditions that are ripe for Salmonella spread, Krause and his team note in the paper. 

Even in modern times, mass deaths on this scale usually accompanies first contact experiences of "uncontacted peoples" such as certain remaining Amazonian tribes. 

Harappan Y-DNA Leak

Ancient Harappan DNA is being analyzed right now for publication later this year. Leaks from the lab about the Y-DNA type of these samples (for what reliability one is inclined to give them) are as follows:
Over at Anthrogenica, there's now two members who say they've heard from people associated with the Rakhigarhi investigation that the Rakhigarhi aDNA samples were overwhelmingly L-M20. . . .
"So I don't know if this has been discussed, but I heard from somebody who knows an archeologist at the Rakhigarhi site. 
They are going to release a paper later in the year and 80-90% of the samples were y-HG L-M20. 
I will inquire for more details. I can't verify the authenticity of the man's claims.". . .
Khanabadoshi's choice of expression has got me confused. Eurogenes had mentioned 12 ancient samples were genotyped from the Rakhigarhi site. Neither 80% nor 90% thereof produce very round figures, at 9.6 to 10.8 ancient persons. Does it imply the remaining 10-20% samples were female, so that all ancient males were L-M20. Or does it mean that oddly all of the samples are exclusively male, with the remaining 1-2 ancient people being some other Y haplogroup? (Since Chad Rohlfsen has said L and R2 above, though it's not clear if the R2 is meant predictively or based on a rumour or leak. Razib Khan had predicted H and L a couple of years back.)
Y-DNA haplogroup L-M20 is reasonably common Y-DNA haplogroup in parts of Pakistan and India where the Harappan civilization once thrived, this is is not a stunning result, although peak frequencies in that region today are only about 25%, and are between 10% and 20% for most of the former Indus River Valley civilization area.  (Of course, there is a very good chance that this is not an "independent random" sample and may include distantly related individuals, which would naturally tend to skew towards one haplogroup being dominant.)

Y-DNA haplogroup L is a sister clade to Y-DNA haplogroup T.

Y-DNA haplogroup R1a is fairly common in the region today and widely attributed to Indo-Aryan invaders, so it shouldn't be found in these samples. 

Y-DNA haplogroup R2 is fairly common in the Indus River Valley area are pretty much nowhere else, so its possible absence or low frequency in this sample is notable.

Y-DNA haplogroup H is a leading Y-DNA type in India, widely believed to be autochronous, and showing up in Pakistan as well although with how much antiquity it is hard to know. An absence of Y-DNA haplogroup H would tend to show relative low levels of contact with the southern India, where the Dravidian languages are now spoken.

Wednesday, February 22, 2017

Notable Views Regarding Physics


If you review a large amount of information about a subject and don't have an opinion, you aren't paying attention. Needless to say, I have opinions about a great many matters that I have reviewed at the "tree level" over the years in the area of physics.

If you are a long time reader of this blog, you know the views that I have expressed on a variety of notable issues in physics. But, if you are relatively new to this blog, you might be less familiar with these views. 

It is not my purpose to mislead anyone into thinking that there is a scientific consensus regarding an observation that I make that may be a minority view regarding a controversy or issue, or may even be one that I am the only person currently actively advocating. And, anyone reading this blog should know the assumptions, preconceptions and hypotheses that I come to my coverage holding.

Also, I want to make clear that none of my views on these physics issues are set in stone. They represent my current synthesis of the available evidence. I have changed my mind about some of them in the past, and no doubt will in the future as new evidence becomes available. Each new data point refines the picture, sometimes confirming it with greater certainty, sometimes providing greater detail, and sometimes resulting in a paradigm shift.

This post is a summary of conclusions. It does not purport to even attempt to cite to posts at this blog where I marshal evidence in favor of a view or analyze why I believe it to be correct. This has happened over the course of many hundreds of posts and would be too time consuming and voluminous to include here.

Substance - My Most Notable Views About Physics

I. Gravity, Dark Matter, Dark Energy and Astronomy

A. In my view the most unimportant unsolved problem in fundamental physics is how the phenomena attributed to dark matter arise.

B. There are two primary paradigms: particle based dark matter theories and gravity modification theories. The available evidence does not refute all models advanced in either approach, although much of the potential dark matter parameter space has been ruled out by observation and analysis, and some gravity modification theories have likewise been ruled out.

C. I believe that a gravity modification theory is considerably more likely than a particle based theory to explain dark matter phenomena.

D. I believe, at a lower level of certainty, following the work of Deur, that:

(1) the correct gravity modification arises from a quantum gravity theory that conceptualizes gravity as an exchange of gravitons rather than primarily as a geometric bending of space-time;

(2) this quantum gravity theory differs from the predictions of general relativity predominantly in weak gravitational fields (as opposed, for example, to near the Big Bang or black holes);

(3) the quantum gravity modification largely arises from the failure of general relativity to accurately reflect second and greater order effects arising from graviton interaction with other gravitons in a manner analogous to gluon interactions with other gluons;

(4) in principle this quantum gravity theory introduces no new fundamental constants not found in GR (although it may operationally need one or two constants that are in practice derived even though they could in principle be determined from existing constants);

(5) in this theory the amount of ordinary matter and its geometric shape both impact the second order quantum gravity effects;

(6) much of all of the effects of dark energy result from gravitons being diverted to make gravitational pulls stronger in ways that manifest in dark matter phenomena, leading to gravitational forces between systems that manifest dark matter phenomena to be weaker than they would be without this effect; and

(7) there are solid indications that the amount of dark energy or the size of the cosmological constant, as the case may be, is materially overestimated experimentally, which makes it more likely that substantially all dark energy effects are side effects of dark matter phenomena.

E. If, the less probably case is true and in fact, gravity is not modified and the source of dark matter is a particle:

(1) dark matter phenomena are predominantly the product of not more than two kinds of particles (a fermion singlet (which may or may not be composite) and a boson that interacts only with dark matter), and quite possibly only one kind of particle; 

(2) those particles are warm dark matter scale for the fermion or less; and

(3) the dark matter particles have essentially no non-gravitational interactions with ordinary matter through any of the three Standard Model forces (electromagnetic, strong and weak).

II. Cosmology

A. In my view, the most likely explanation for the matter-antimatter asymmetry in the universe is that there is an antimatter dominated universe "before" the Big Bang in which the second law of thermodynamics runs in the other direction that balances the matter dominated nature of our own universe. This implies that a new source of extreme CP violation is unnecessary. But, I do not hold this view with a high level of confidence.

B. In my view, the evidence to support the events of the early moments of the Big Bang prior to Big Bang nucleosynthesis, including "inflation" is not solid enough to constitute scientific proof and is merely a plausible hypothesis.

C. I believe that the multiverse and anthropic principle are being used in fundamentally unscientific ways at this time.

III. Neutrino Physics

A. I think that neutrinos are very unlikely to have Majorana mass.

B. I think that neutrinos have a "normal" mass hierarchy.

C. I think that cosmology based caps on the sum of the neutrino masses are accurate and can be integrated with other data to accurately estimate the neutrino masses.

D. I think that we don't understand the mechanism of neutrino mass generation or neutrino oscillation beyond the current phenomenological model. But, I think that seesaw models of neutrino mass are almost surely wrong. I think that there is a reasonable possibility that some sort of boson mediates neutrino oscillation.

E. I think that neutrino oscillation almost surely has a CP symmetry violating term.

F. I think that neutrino oscillation does not involve any maximal mixing angles.

G. I think that neutrinoless double beta decay never happens, nor do any other forms of sub-GUT scale lepton number violation or baryon number violation (such a proton decay).

H. I think that there is probably not a right handed neutrino.

IV. Quantum Mechanics And Space-Time

A. Entanglement inherently requires a surrender of at least one of three things: causality, locality and reality. I am not nearly so convinced that causality and locality need to be maintained as many physicists.

B. I think that the non-speed of light paths in the particle propagator of quantum mechanics suggests that the picture of space-time are perfectly smooth and local is likely to be incorrect.

C. I think that the four dimensional nature of space-time may be emergent, but that there are unlikely to be more than four or five dimensions of space-time, and that there are no compactified dimensions.

D. I am not perfectly convinced that quantum mechanical randomness is not just extremely chaotic (in a mathematical sense of a deterministic system highly sensitive to slight changes in initial conditions) rather than truly random behavior.

V. Beyond The Standard Model Theories

A. I believe that some of the most notable experimental anomalies which physics are dealing with today, such as the muon g-2 problem and the muonic proton radius puzzle, are due to some combination of experimental error and a failure to properly apply existing fundamental physical laws to the problems properly, rather than to beyond the Standard Model Physics.

B. I believe that so called "problems" such as the "hierarchy problem" and the "strong CP problem" are not problems at all that need to be solved and are unsound at a basically philosophical level in their very formulation.

C. I believe that there are deeper theories that can explain the relationship of the Standard Model constants, particles and forces to each other from a more fundamental set of rules and constants. For example:

(1) I think that the sum of the square of the fundamental particle masses is functionally related to the Higgs vacuum expectation value.

(2) I think that at least the charged fermion masses relative to each other dynamically through a process that primarily involves W boson interactions and reproduces a relationships approximately captures in Koide's rule.

(3) I think that it is likely that the CKM matrix can accurately be parameterized with one real parameter and one complex parameter.

(4) I think it is plausible that the CKM matrix parameters are related functionally, in some way, to the PMNS matrix parameters.

(5) I think it is plausible that it may be possible to determine the CP violating phases of the CKM matrix and PMNS matrix from first principles.

D. I believe that the barriers to quantum gravity involve more of a shortage of computational tools and lack of creativity, than they do any fundamental theoretical problem.

E. I think that beyond the Standard Model fundamental particles that do not serve merely as preons for Standard Model fundamental particles are generally ill motivated. We might be missing one or two, but if my conjectures regarding dark matter are correct, we don't need any more fundamental particles, and certainly not the multitude suggested by SUSY theories.

F. I think that supersymmetry and supergravity do not accurately describe reality and merely constitute toy models useful for thinking about particle physics to use in more realistic models.

G. I think that there are some operative principles for applying quantum chromodynamics that we do not yet know which are necessary to understand the non-observation of glueballs and the spectrum of scalar and axial vector mesons.

H. I think that string theory is incorrect but may provide valid insights.