The Interpreter; Bayes Theorem; Nephites and Mayans

[_Lemmie]

Regarding Mr Stak's point about re-stating how to map the information without limiting it to being a fact; even with that fix, another large problem arises.

Let me try again…

The axioms of subjective probability have the comparable probability relation > being defined as a set of boolean algebra א (Not the usual symbol but I was getting an SQL ERROR with doublestrokes so I just went with alef ) with all A events and B events being subsets. The empty event is ∅ and the universal event is Ω. So for every A event in א would mean ∅ ⊆ A ⊆ Ω. On any probability measures on א, only P(Ω) is going to equal 1 and nothing else.

I totally get that they wrote this in such a fashion that it commits them to some stupid stuff, but I think they are going to be more committed to the aforementioned axioms than their own stylistic word choices.

Except that their errors are not just stylistic. The authors specifically ruled out the universal event Ω being considered by their own definitions, in fact, they stated it would be dishonest to extend their set beyond A, which they are defining and therefore limiting to a subset of the universal event that is only found in Coe's book. Moreso, they are specifying that they are only considering elements of that subset A that they consider to be true. Defining an element of subset A as true a priori, and then determining that only those true elements of subset A are being considered does NOT allow for the possibility of considering the effect of an untrue element A after the initial conditions are set, nor does it allow for ANY consideration of an element of the universal set outside of A.

They set up their parameters, Stak. If they want to expand them, they need to re-write the paper.

[Guest]

The Book of Ether alone is absolutely fatal to the credibility of the Book of Mormon, with or without the damning, contrary DNA evidence. It is a slam dunk certainty that there could not ever have been a world wide flood that wiped out every single land species of fauna on earth, including humans, that were not on a single, large wooden boat, or that all mankind spoke a single language until the time the Tower of Babel was supposed to have occurred. The evidence against that myth is at least as strong as the DNA evidence.

Over on the Interpreter comments page for the Dale & Deal article, Arc posted the words of Jeffrey R. Holland concerning not only the lack of human habitation in the Americas before the arrival of the Book of Mormon migrations, but also claiming that the continents of the western and eastern hemispheres separated to form the Atlantic basin in accordance with the word of the Lord less than 10,000 years ago.

Arc was reminded by Theodore Brandley that many LDS scholars do not believe in the universal flood (even though the Book of Mormon mentions it), and then stated that the debate was not 'on topic' for discussion the Dale & Dale paper.

Meanwhile, in response to "Mr. Blanco's" comments on the Interpreter article, Hoosier defended Ugo Perego's rationalization for the lack of any middle eastern DNA in the Amerindian genome, while admitting that he/she didn't know much about genetics. Hoosier believes that the extinction of middle eastern DNA was aided by the population bottleneck that occurred during the population-thinning epic battles described by Joseph Smith Jr. in the Book of Mormon.

The following compilation of Simon Southerton's comments on the Book of Mormon DNA problem is too long to post over there. It is posted here because there seems to be members and lurkers alike who are reading both here and over on the Interpreter site regarding the Dale & Dale paper. This was originally written as a response to Philo Sofee and is posted here with the permission of Dr. Southerton.

____________________

Simon Southerton Responds to Apologists Regarding the Book of Mormon DNA Problem

Brief: This documents Dr. Simon Southerton's response to Kerry Shirts regarding Kerry's question, in November of 2017, about a 2014 piece in the Interpreter claiming that it is not reasonable to expect Lehite DNA to be detected in the genomes of modern descendants of pre-Columbian Amerindians.

Kerry,

I was preoccupied with work at the time Perego and Ekin’s Interpreter piece was written in 2014, so didn’t really look closely at it. Here are some thoughts on the article.

There are a couple of recent advances that I should mention at the outset that have some bearing on the paper. The famous X2a mitochondrial DNA lineage, which is present at about 3% in North American Indians, was recently discovered in the ancient remains of Kennewick Man which were retrieved from the banks of the Columbia River near Kennewick, Washington. This skeleton is over 8,000 years old, so the discovery confirms the lineage entered the Americas over 15,000 years ago and has nothing to offer the apologists. (Rodney Meldrum’s empire is built on his X lineage lies and this completely undermines him.)

I should also mention that Perego’s specialty is clearly mitochondrial DNA and he makes no mention of the powerful whole genome research which is now being published. This type of research can reveal in great detail where the European and African DNA found in Native Americans (about 1%) came from and the time it arrived in the New World.

The article is based on the premise that the small founding populations described in the Book of Mormon met and then integrated into large native populations while they themselves never became numerically significant. Lots of excuses are given for why Lehite/Mulekite/Jaredite DNA may not be found including things like bottleneck effect, genetic drift and natural selection. Somehow the Lehite/Mulekite/Jaredites, while having unlucky DNA, managed to rule native populations for a thousand years. But the authors say nothing about how this farcical takeover was peacefully achieved. Next to nothing is written about how members need to interpret the Book of Mormon text to fit with this vanishing geography. You are left to wonder why God allowed the Book of Mormon narrative to completely fool all the prophets, including Joseph Smith, and millions of honest and sincere readers of the text for almost 200 years. Silly God.

The article skims over the Native American data. Several times the authors say 95% of the DNA is Asian, presumably because you can park faith more comfortably in 5%. I’ve gathered data from over 100 research papers where the authors were specifically studying the origins of native tribes and deliberately excluding people with known European/African ancestry. Of the 15,555 individuals studied 99% have an Asian mtDNA lineage and 1% have either a European or African lineage.

Whenever scientists have taken the time to see where these European lineages came from, they invariably find a match in an individual in Western Europe. Not a single individual among the 15,555 (0.0%) has been identified with a Middle Eastern DNA lineage. Over 600 Mayans have been tested and 99% had an Asian lineage and 1% an African lineage. Yet just a couple of years ago BYU Mesoamerican apologists were weeping about the amazing linguistic and archaeological evidence for the Book of Mormon in Mesoamerica. All evidence mainstream science completely rejects by the way.

The whole genome data sheds further light on the origin of the European DNA in Native Americans. To study the whole genome, scientists use about 700,000 DNA markers scattered across all of the chromosomes. Subsets of these markers are specific to particular populations, e.g, Greeks, Druze, French etc. Genomic markers can therefore be used to track where European and African DNA in Native Americans came from. The following link will take you through to a map that allows you to track where the European and African DNA in the Maya and Pima came from. In both cases, it virtually all came from Western European countries or Sub-Saharan Africa and none came from the Middle East.

http://admixturemap.paintmychromosomes.com/

(Click on the Pima and Maya populations to see where their DNA came from.)

The authors make the point that it’s not possible to distinguish between pre (3000 BCE) and post Columbus European DNA because mtDNA accumulates new mutations at a rate of one mutation every 3,000-9,000 years. Here they are making the very hopeful (but mistaken) assumption that Lehite DNA could be among the European DNA. Middle Eastern populations have been largely separated from Western European populations for almost as long as Asians have been separated from Native Americans. 25,000 years is enough time to accumulate 3-8 new mutations. That’s why it is frequently easy to distinguish the two. I personally have an H mtDNA lineage, but the lineage H subgroup I belong too is exclusively found in Western Europe.

The genomic DNA analysis can also shed light on when the European and African DNA arrived in native populations. As our genomic DNA is passed down the generations, the paternal and maternal chromosomes frequently cross over or recombine. This effectively chops each of our chromosomes up into chunks that come from different ancestors. With each passing generations the chunks get smaller and smaller. If your family tree was largely Native American and a European entered it at some time in the past, it's possible to estimate when they entered based on the length of the European chunks. If they entered recently the chunks would be large. If they entered 2000 years ago they would be very small. These sorts of estimates have been made for admixture in Native American populations and the admixed DNA arrived within the last 500 years.

See http://admixturemap.paintmychromosomes.com/

To further cloud the issue, the authors claim that we can’t possibly know what Lehi’s DNA looked like. They even make the absurd claim that “it must still be acknowledged that virtually any individual DNA profile could be found in any population, although at different frequencies.” Given that the Lehite/Mulekite/Jaredite groups all came from the Fertile Crescent region, and the Lehites and Mulekites from Israel, it is perfectly reasonable to assume they carried DNA that is present in contemporary Middle Eastern populations. The authors are arguing that all of the DNA the Book of Mormon people brought with them may have been rare lineages, which may not be present in Middle Eastern groups today.

The most revealing thing about the article is what it doesn’t say. It says essentially nothing about how Mormons need to reinterpret the Book of Mormon narrative to accommodate the territory they have conceded to science. The authors know that after many thousands of DNA tests, Middle Eastern DNA has not been detected. The Lehites were at most a vanishingly small part of New World populations. We are left to wonder why they make absolutely no mention of the massive populations they encountered? Why did those native populations hand over the rule of their civilisations to a small band of Hebrews? Apparently this astonishing capitulation occurred twice, with both the Lehites and Mulekites.

The Book of Mormon was “written to the Lamanites” but now we don’t know where the Lamanites are. Meanwhile the prophets who are meant to interpret scripture stand silently by.
______________________

Our mitochondrial DNA represents a single maternal lineage within our family tree since it is passed from mothers to offspring in each generation. Apologists often make the point that mtDNA lineages get lost and most go extinct. That's true if you focus on the individual, however, the same mtDNA lineage can be passed down by the individual’s sisters, aunties and their daughters, and many other female relatives in previous generations. It ain't all doom and gloom for mtDNA.

Scientists studying human populations (doing population genetics!) are not focusing on the DNA of individuals (funny how a dumb "non-population geneticist" needs to remind the apologists). They are looking at the DNA of populations. Instead of looking at individual mtDNA "haploypes" they are looking at "haplogroups" which are collections of related haplotypes. The A,B,C,D and X mtDNA classes are haplogroups, and within each haplogroup there are many haplotypes. Haplogroups tend not to go extinct and this is the case in the Americas. Virtually all of the ancient remains tested in the Americas have an A,B,C,D or X mtDNA lineage. Also, the A,B,C,D and X lineages are still present today at about 50% collectively in Central and North Asian populations.

Our Genomic DNA, however, represents 99.99% of our DNA and comes from many more of our ancestors. A lot of whole genome research has been published in the last few years and it hasn't been addressed by the apologists. It's much harder to argue for extinction with Genomic DNA; that's why they are starting to claim the Lehites were never numerically significant to begin with.

[_Gadianton]

I finally sat back over a couple of tacos last night and began to read the actual article.

In the Book of Mormon we read:

Book of Mormon: There shall come over the whole earth an intense darkness lasting three days and three nights. Nothing can be seen, and the air will be laden with pestilence which will claim mainly, but not only, the enemies of religion. It will be impossible to use any man-made lighting during this darkness.

Mormon Interpreter: One example of Bayesian “strong” evidence is the remarkably detailed description of a volcanic eruption and associated earthquakes given in 3 Nephi 8. Mesoamerica is earthquake and volcano country, but upstate New York, where the Book of Mormon came forth, is not. If the Book of Mormon is fictional, how could the writer of the Book of Mormon correctly describe a volcanic eruption and earthquakes from the viewpoint of the person experiencing the event? We rate the evidentiary value of that correspondence as 0.02. We assume a piece of evidence is “unusual” if it gives facts that very probably were not known to the writer, someone living in upstate New York in the early 19th century, when virtually nothing of ancient Mesoamerica was known.

What can I say. How could he have known?

[_Physics Guy]

I looked up the paper on Interpreter and it looks really long. I'm afraid I don't have time to pore through it all.

One thing that caught my eye was that they count the flood myth as a hit against Smith having made up the Book, as if Smith were an alien visitor to Earth, totally ignorant of human cultures in general, making random guesses about Mayan culture. Who the hell has ever suggested that, though? The alternative to historical authenticity for the Book of Mormon is not random guessing on Smith's part. It's systematic copying of the Bible, which includes a flood, for Noah's sake.

If the Mayans also had a flood myth, then maybe that's surprising as a common feature of two ancient cultures, but it is NOT evidence in favor of authentic Mesoamerican history against Bible fan fiction, because a Bible-copier and a Mesoamerican historian would be equally bound to mention a flood. And this is precisely the kind of point that Bayesian inference is all about; the only way to overlook it is to have no grasp of Bayesian inference at all.

I was hoping to find a subtle error that intelligent people could have overlooked, yet be intelligent enough to recognize if it were clearly pointed out. Now it looks instead as though the problems with this paper may be more tedious to explain than that. I don't have time, I'm afraid.

[_SteelHead]

I finally sat back over a couple of tacos last night and began to read the actual article.

In the Book of Mormon we read:

Book of Mormon: There shall come over the whole earth an intense darkness lasting three days and three nights. Nothing can be seen, and the air will be laden with pestilence which will claim mainly, but not only, the enemies of religion. It will be impossible to use any man-made lighting during this darkness.

Mormon Interpreter: One example of Bayesian “strong” evidence is the remarkably detailed description of a volcanic eruption and associated earthquakes given in 3 Nephi 8. Mesoamerica is earthquake and volcano country, but upstate New York, where the Book of Mormon came forth, is not. If the Book of Mormon is fictional, how could the writer of the Book of Mormon correctly describe a volcanic eruption and earthquakes from the viewpoint of the person experiencing the event? We rate the evidentiary value of that correspondence as 0.02. We assume a piece of evidence is “unusual” if it gives facts that very probably were not known to the writer, someone living in upstate New York in the early 19th century, when virtually nothing of ancient Mesoamerica was known.

What can I say. How could he have known?

Where does the Book of Mormon mention a volcanic erruption? ............. Oh....... it doesn't? Strong correlation of an event not in the book. WINNING!

[_Analytics]

Another fundamental problem is how they came up with comparing the Book of Mormon to the Mayan in the first place. Joseph Smith didn't claim to be trying to describe the Mayan. The reason the LGT folks chose that time and place is because that is where the book fits the best. The reason the story is imagined to take place in Mayan lands is because that is where things like "Large-scale public works" were located.

Joseph Smith shot a shotgun in the dark, and the apologists drew a circle around where it hit. Now Dr. Dale and Dr. Dale are pretending that is what he was aiming for and are asking "what are the odds?"

Of course that analogy isn't perfect--they didn't really hit the Mayans that much. The Book of Mormon is full of all sorts of things that are totally anachronistic in Mayan civilization (e.g. Jesus!). An honest and competent analysis would take those things into account and would ask questions like, "Assuming the Book of Mormon is a accurate translation of an ancient Mayan manuscript written on golden plates, what is the probability that we'd have no evidence of Mayans writing in Egyptian on Golden plates?" (Answer: 0.00001 or something smaller). And the companion question, "Assuming the Book of Mormon was made up, what is the probability that we'd have no evidence of Mayans writing in Egyptian on Golden plates?" (Answer: 0.999999 or something bigger).

Limiting the analysis to the mundane things that Coe put into his book was a clever trick to avoid the scores of anachronisms throughout the book that discredit it.

[_Analytics]

I finally sat back over a couple of tacos last night and began to read the actual article.

In the Book of Mormon we read:

Book of Mormon: There shall come over the whole earth an intense darkness lasting three days and three nights. Nothing can be seen, and the air will be laden with pestilence which will claim mainly, but not only, the enemies of religion. It will be impossible to use any man-made lighting during this darkness.

Mormon Interpreter: One example of Bayesian “strong” evidence is the remarkably detailed description of a volcanic eruption and associated earthquakes given in 3 Nephi 8. Mesoamerica is earthquake and volcano country, but upstate New York, where the Book of Mormon came forth, is not. If the Book of Mormon is fictional, how could the writer of the Book of Mormon correctly describe a volcanic eruption and earthquakes from the viewpoint of the person experiencing the event? We rate the evidentiary value of that correspondence as 0.02. We assume a piece of evidence is “unusual” if it gives facts that very probably were not known to the writer, someone living in upstate New York in the early 19th century, when virtually nothing of ancient Mesoamerica was known.

What can I say. How could he have known?

Are we sure Dr. Dale and Dr. Dale are real believers who really wrote this? This is the kind of article a clever anti-Mormon would write as a spoof to mock gullible Mormons who are desperate for a win.

[Guest]

Another fundamental problem is how they came up with comparing the Book of Mormon to the Mayan in the first place. Joseph Smith didn't claim to be trying to describe the Mayan. The reason the LGT folks chose that time and place is because that is where the book fits the best. The reason the story is imagined to take place in Mayan lands is because that is where things like "Large-scale public works" were located.

Joseph Smith shot a shotgun in the dark, and the apologists drew a circle around where it hit. Now Dr. Dale and Dr. Dale are pretending that is what he was aiming for and are asking "what are the odds?"

Of course that analogy isn't perfect--they didn't really hit the Mayans that much. The Book of Mormon is full of all sorts of things that are totally anachronistic in Mayan civilization (e.g. Jesus!). An honest and competent analysis would take those things into account and would ask questions like, "Assuming the Book of Mormon is a accurate translation of an ancient Mayan manuscript written on golden plates, what is the probability that we'd have no evidence of Mayans writing in Egyptian on Golden plates?" (Answer: 0.00001 or something smaller). And the companion question, "Assuming the Book of Mormon was made up, what is the probability that we'd have no evidence of Mayans writing in Egyptian on Golden plates?" (Answer: 0.999999 or something bigger).

Limiting the analysis to the mundane things that Coe put into his book was a clever trick to avoid the scores of anachronisms throughout the book that discredit it.

You could apply this methodology to any number of places and it would work - like the one guy who stops by from time to time and argues that the Book of Mormon took place in Malaysia. If you applied the same study, but swapped Maya lands for Malaysia and ran the numbers what happens? Bet the odds improve, as there were actually horses and silk, and metalworking in Malaysia. What does that mean about the validity of the study?

[_DrW]

Are we sure Dr. Dale and Dr. Dale are real believers who really wrote this? This is the kind of article a clever anti-Mormon would write as a spoof to mock gullible Mormons who are desperate for a win.

Analytics,

Let me assure that you are not the only one who has considered this possibility.

[_SteelHead]

Well Carrier used Bayesian methodology to prove that Jesus isn't historical, and these Dales use it to prove the Book of Mormon is.................. Which is dependent on Jesus.......


Somebody just divided by 0.