Category Archives: Migration

Y-chromosome validates Bible

Answers to Questions, Bible/Science, Biology, DNA, Migration

 

Foreword

Those who believe the Bible accept it by faith; however, there are many accounts in the Bible that are testable scientifically. One of these accounts is that of Noah having three sons, and these three sons repopulated the entire earth after the flood. This paper provides scientific evidence that all men alive today came from one of three ancient ancestors. Our findings are based on Y-chromosome analysis. The analysis is simple, straightforward, and repeatable; anyone can understand it and repeat it. The data is fully documented herein and generated from mainstream scientific community sources (Reference 1 is the browser and Reference 2 contains the sequences used).

The Bible made the following proclamation thousands of years ago, and now we have the genetic tools to test its validity:

Genesis 9:19  These are the three sons of Noah: and of them was the whole earth overspread.

Genesis 10:32  These are the families of the sons of Noah, after their generations, in their nations: and by these were the nations divided in the earth after the flood. 

Background

We know that the Y-chromosome is passed from father to son, and, in general, each generation passes on a few genetic variants to the next generation. These variants provide genetic markers which are highly valuable for tracking ancestry. Geneticists sort people into groups called haplogroups because they contain like genetic markers. The haplogroups form a family tree for all humanity and allow us to trace ancestry back to our most ancient ancestors.

Former Work

We, at Genesis and Genetics, made a preliminary evaluation of Y-chromosome DNA genetic markers and discovered that all human men on earth came from one of three ancient ancestors (Reference 3). We found that any human man could trace his genetic markers back to one and only one of three ancient ancestors. Any man with a marker ‘A’ at rs9786139 is from one ancient ancestor, a marker ‘A’ at rs17306671 is from another ancient ancestor, and a marker ‘G’ at rs3900 is from the third ancient ancestor. It was easy to associate these three most ancient ancestors with Ham, Shem, and Japheth by looking at Biblical history of migration and nations. Ham had the ‘A’ at rs9786139, Shem had the ‘A’ at rs17306671, and Japheth had the ‘G’ at rs3900.

This former research was based on a study of 57 modern human men. All the men had one, and only one of the three markers stated above.

Note: We use the terms “mutations,” “variants,” and “markers” interchangeably.

Confirmation

Since our original study, we have looked at many more sequences, a total of 1233 Y-chromosome genomes, and found they all conformed to our original findings.  Reference 4  documents the 1233 human genomes and which ones are from each of Noah’s three sons. All 1233 humans had one and only one of the three markers. There were no exceptions. This paper confirms our original findings and compares our Biblical ancestral family tree to that of mainline science.

Comparison to Mainline Science

In general, our analysis agreed with mainstream science concerning haplogroups. Therefore, our family tree uses the same haplogroups as our friends in mainstream science. But they are rooted differently. Here is the secular science tree followed by our family tree. There are several versions of the secular trees (called phylogenetic trees), but we, generally, used the one generated by the International Society of Genetic Genealogy, ISOGG (Reference 5).

 

 

As one can see, the two trees are similar, but the root and flow of genetic markers are different. The secular tree is rooted in haplogroup A, and the Biblical tree is rooted in Noah dividing into three separate haplogroups; one from Ham; one from Shem; and one from Japheth. We do not present Noah’s DNA, but it is simply his three sons’ DNA less their genetic markers.

Finding the Tree Root

Armed with these 1233 diverse genomes, we began our search by noticing that a few mutations/genetic markers, were common in the population;  some were up to 52 percent of the population. It is quite logical to assume that the higher the mutation’s frequency, the better chance that it is at or near the root of our family tree.

For example, if a mutation is in 1/2 of the population, it probably originated when the population was approximately 2 men. If a mutation is in 1/10th of the male population, it probably originated when the male population was approximately 10. And if a mutation is in1/1,000,000), it probably originated when the world population was 1,000,000.

So, we decided that any mutation with a frequency of more than 5 percent could be one of Noah’s three sons. This assumption would allow for some genetic drift and the inability for our 1233 subjects to exactly match the whole world population distribution.

All Men came from three ancient ancestors

Next, we took each of the mutations with frequencies higher than 5 percent and used them to form genetic groups, i.e., haplogroups. Quickly, we realized that every mutation belonged to one and only one of three ancient ancestors.

It appeared that we found Shem, Ham, and Japheth. There was a Shem haplogroup, a Ham haplogroup, and a Japheth haplogroup. All 1233 genomes fit into one and only one of the three. There were no exceptions. The three root mutations had frequencies of 10%, 38%, and 52%. And, as expected, they added up to 100% of the population. Furthermore, Shem, Ham, and Japheth were associated with the three ancient ancestor mutations easily by looking at the geographical locations of each group and comparing them to Bible history. Ham went south and east; Japheth went north and east, and Shem populated the Near East and Europe.

Noah’s Y-chromosome is impossible to find directly. The reason is that he is the origin of all male humanity and he had, by definition, no genetic markers. Therefore, the way to find Noah’s Y-genome is by determining the genomes of his sons and deleting all their mutations.

The true root of humanity was Adam. Adam’s DNA went through the bottleneck of Noah. So we all came from Adam, and we all came from Noah. Adam is the root of all humanity, and Noah is the root of post-flood humanity.

Genetic Mutations/Markers Flow in One Direction

Just as water flows downstream, so do genetic markers. Genetic markers flow from most ancient ancestors to modern ancestors. For instance, your great-grandfather passed markers to your grandfather who passed additional markers to your father. Your father passed his additional markers to you. And if you are a man, you too will pass new markers to your sons. Lineage flows downstream. More and more new markers appear in offspring as the generations pass. However, the original markers of your ancestors remain in your genome. A key point here is that as the markers flow away from the root, the new markers divide the offspring into sub-haplogroups. This dividing into sub-haplogroups shows the direction of the genetic marker flow.  Distant branches have only the markers close to the root but are missing many of the markers in their cousins, second cousins, etc.

Therefore, as expected, the data shows that markers flow from Noah’s three sons to their sub-haplogroups. Consider just haplogroup K. Everyone from haplogroup K has the rs3900 G marker. Likewise, the sub-haplogroups have additional markers that show they are later generations forming smaller haplogroups such as M, N, O, P, Q, R, S, and T. T must come from K, but K cannot come from T.

Since genetic mutations/markers flow downstream, it is not possible that the root of the Y-chromosome family tree is rooted in a marker with a small frequency. In order for that to happen, it would take many bottlenecks, overwrites, drift, and other genetic contortions.

Full Population Representation

The three adjacent haplogroups, IJ, IJK, and K contain 100 percent (Ham 38%, Shem 10%, and Japheth 52%) of the 1233 genomes analyzed. In other words, they are the source of all modern humans. Take any other combination of the other haplogroups and mix and match them; they do not represent all humanity; they do not add up to 100 percent. The only way you get one hundred percent is to use IJ, IJK, and K.

Biblical and Secular History

The haplogroups IJ, IJK, and K comprise people from Mid-East, West Asia, and Near East. According to the Biblical narrative, all humanity came from the Armenian mountains which are in West Asia and close to the Near East and the Mid-East. In short, these haplogroups locations fit nicely into Biblical history.

The historical age began in Mesopotamia, shortly after the flood. These earliest writings document a worldwide flood and the world populated by flood survivors. Nowhere do these legends and writings record mankind originating from other parts of the world.

Summary

The Y-chromosome DNA is the perfect vehicle for scientifically testing the portion of the Bible that says all modern human men were born of three ancient men. The Y-chromosome data of 1233 genomes corroborates the Biblical account. We now have a Biblical family tree and can trace our ancestry to the Biblical sons of Noah.

Future Work

We are in the process of identifying the DNA of Noah’s 16 grandsons in the family tree.

 

References:

  1. http://useast.ensembl.org/info/about/publications.html
  2. https://www.genome.gov/27528684/1000-genomes-project
  3. https://www.genesisandgenetics.org/2021/04/16/y-chromosome-migration-and-the-biblical-phylogenetic-tree-or-finding-ham-shem-and-japheth-via-y-chromosome/
  4. https://www.genesisandgenetics.org/Ancient.xlsx
  5. https://docs.google.com/spreadsheets/d/1Y0GXjhazYa46u0EpPA9b0Y0RVWuh5lDzww_o979mbjQ/edit#gid=1904113265
  6. https://useast.ensembl.org/index.html

 

 

Finding Ham, Shem, and Japheth via the Y-Chromosome

Answers to Questions, Bible/Science, DNA, Migration

 

Introduction

At Genesis and Genetics, we have examined Y-chromosome genomes searching for Noah and his three sons, Ham, Japheth, and Shem. They were easy to find.  According to our analysis, if you have the rs17306671 Y-chromosome mutation nucleotide A you are from Shem. If you have the rs9786139 Y-chromosome mutation nucleotide A you are from Ham. If you have the rs3900 Y-chromosome mutation nucleotide G you are from Japheth. If you are a woman, you will have to check your father’s y-chromosome. Women don’t have the y-chromosome.

Background

Here is a bit of background: Y-chromosome DNA is exclusively found in males; it is inherited from one’s father. The Y-chromosome has approximately 60 million base pairs, each of which is subject to mutations. Mutations develop in the Y-chromosome, typically at the rate of 2 mutations per generation. This is based on a mutation rate of 1.0*10^-9 mutations /nucleotide/year (Reference 1) and 30 years per generation. These mutations allow us to track ancestry. If one man populated all the earth, all males would have his Y-chromosome, and if this man had two sons, one would expect that roughly half of the world would have one son’s mutations and the other half would have the other son’s mutations. Furthermore, if our original ancestor had 10 grandsons, one would expect that each grandson would have mutations that would each exist in approximately 10 percent of the male population. Successive generations would continue to generate new mutations that would form a human family tree, known as a phylogenetic tree to geneticists.

Easy to follow logic

The following presents the easy-to-follow logic and analysis which anyone can repeat. Our findings are consistent with the Bible and modern science raw data.

In our research, we used the above principles in tracking our most ancient ancestors. We made no assumptions and shelved our preconceived ideas. We wanted to see where the data led us. Appendix A shows the precise method we used to extract the data. Our strategy was simple; we gathered the Y-chromosome mutations, which are seen in more than 5 percent of human males, and entered them into a spreadsheet. We looked for patterns and color-coded the resulting groups. Please consider doing one Y-chromosome example yourself using Appendix A as a guide, or if you have your Y-chromosome data, you can trace it back to your most ancient ancestor/ancestors. You will see the ancient ancestor to whom you are related.

Sources

The data used in this research came from the 1000 genomes project (Reference 2) and retrieved using the Ensembl browser (Reference 3). The data appeared to be correct with no errors. No data was eliminated due to suspect errors, and no data was “cherry-picked” to suit any preconceived ideas. Our thanks to the great effort of those who did the sequencing and publishing of the raw data. We also greatly appreciate that it was made available to the public.

We started by taking 57 Y-genomes of diverse people (Americas, East Asia, Europe, South Asia, and Africa). Next, we gathered mutations that were in at least 5 percent of the world’s male population. The technical term for this is those with a Mean Allele Frequency (MAF) greater than or equal to 0.05 (5 percent). These mutations are the most interesting; any smaller MAF mutation is a subset of those greater than 5%.

Results

The spreadsheet below provides 57 rows (individual male humans) and 30 columns (mutations over 5 percent of the population). Each column element of the matrix was color-coded to show us whether the individual had the mutation or not. We noticed patterns beginning to form (you can CLICK HERE to see the EXCEL copy.)

Next, we switched columns and rows to form groups. The groups were obvious. We also took each group and moved the columns so that the columns for each group with the largest MAF were on the left. Now we can see a clear pattern in the figure below. We see that each individual fits into just one group and had no mutations in any other group. Also, we see that every individual in the group has the mutation with the greatest MAF; this is the mutation of the most ancient ancestor of that group. Here is what the spreadsheet looks like after grouping: Note: you can CLICK HERE to see the matrix in EXCEL.

Looking at the matrix above, we see that each group has one maximum MAF. The yellow is .38, the red is 52, and the green is .10. They add up to 100 percent.

Consistent with the Bible

Now that we have shown that our most ancient ancestor had three sons, we can state that this finding is consistent with the Bible. The three groups are consistent with the three sons of Noah: Ham, Shem, and Japheth. The Bible states that, generally, those from Ham went south to Africa and southern Asia, those from Japheth went north to northern Europe and northern Asia, and those from Shem stayed in the Caucuses, the Near East, and North Africa. Therefore, one could easily conclude that Ham is the yellow group, Shem is the green group, and Japheth is the red group. Note: Noah’s Y-chromosome is also known since it would be that of the three sons with all mutations removed.

Bible in Genesis 10, the Table of Nations, states that all humanity came from these three sons:

Genesis 10:1  Now these are the generations of the sons of Noah, Shem, Ham, and Japheth: and unto them were sons born after the flood.

Genesis 10:32  These are the families of the sons of Noah, after their generations, in their nations: and by these were the nations divided in the earth after the flood.

Analysis

This means that roughly 1/3 of the earth’s male population came from each son, but, since Japheth had 7 sons, Ham had 4 sons, and Shem had 5 sons; therefore, the worldwide distribution should be closer to the following:

Patriarch   Number of sons    % Projected World Population        Observation

Japheth        7 sons                                              43.75                                         52

Ham                4 sons                                              25                                                38

Shem              5 sons                                              31.25                                         10

 

The chart above shows that both the Ham and Japheth results were higher than expected, and Shem was lower than expected. However, this can be explained in at least two ways:

(1) The Ham and Japheth offspring are in the world’s heavily populated areas, namely South and East Asia.

(2) The Thousand Genomes Project did not provide representatives of the Near East, the Mid-East, or Northern Africa, all of which would increase the Shem percentage, thereby decreasing Ham and Japheth’s percentages.

The above two issues are not meant as criticism but offered as an explanation.

Bible, secular history, and genetic diversity

Our findings are consistent with the Bible, secular ancient history, and genetic diversity:

  1. The Bible documents Noah and his family to be the only ones spared from the deluge which flooded the entire earth, and the earth was repopulated through Noah’s three sons.
  2. The historical period began when the Sumerians began writing cuneiform tablets. These early writings documented the kings before and after the flood. Also, the Sumerian legends are consistent with the world being populated by the three sons on the Ark.
  3. According to the Bible and Sumerian history, all humanity came from one family. As they migrated throughout the world, the genetic diversity would be lost from those who separated from the core population; therefore, the most genetic diversity should be where Noah’s family settled, the Near East. Those who migrated to the Americas, Australia, and southern Africa lost some genetic diversity. We can consider two levels of observing genetic diversity, first, what we see and, second, what DNA tells us. We can easily see eye color, skin color, and hair color. Looking at a globe, it is apparent that those with the most visual diversity meet in the Near East, the place of disembarkation from Noah’s Ark. From a DNA standpoint, one can look at the diversity of haplogroups, both Y-chromosomal and mitochondrial. The extremities are South Africa, Australia, and the Americas, which have only a few haplogroups. The location with the most haplogroups is, again, in the Near East.

Summary

(1) From a Y-chromosome perspective, it appears that all humanity came from three male humans.

(2) Item (1) is not proof of the Biblical narrative concerning Noah’s three sons, but it is consistent with it. To prove it, one would have to sequence every human male ever born and analyze his genome. If anyone can trace an individual human Y Chromosome back to some basal mutation other than the three given, please let us know and comment below.

(3) We can now project Noah’s DNA; it is that of his three sons with no mutations.

(4) Our findings are consistent with the Bible, Sumerian history, and our current state of human diversity.

Future analysis It is now possible to know the Y-chromosome DNA of each of Noah’s grandchildren. This is in our job jar.

References:

1 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748900/#:~:text=The%20chromosomes%20were%20separated%20by,7.0%20%C3%97%2010%E2%88%928).

2 https://www.internationalgenome.org/

3 https://useast.ensembl.org/index.html

Appendix A

If you would like to repeat this analysis or add to it, the following is the step-by-step procedure we used.

Let’s start by taking someone from, perhaps, Peru and find out to which group he belongs. Did he come from Shem, Ham, or Japheth?

(1) We open Ensembl (https://useast.ensembl.org/index.html ). Leave everything default and enter rs9786139 in the upper right-hand box—hit enter.

(2) You should get a new window with the following “rs9786139 (Human Variant).” Click on it. Notice that the MAF is .38.

(3) Click on the ICON that says, “population genetics.” Scroll down to find “AMR” and the subgroup “PEL.” Click on the “PEL.” You can see that 95 percent of this group has a “G,” and 5 percent of the population have an “A.” Next, go to the far right of the “PEL” row and click on “show.” Each of the rows of this screen is an actual human being. You will notice that most of this group has a “G,” but a few have an “A.”

(4) Looking at the population genetics of those from PEL, Peru, you can see that a few Peruvians are from Ham, but most are from someone else. You can find out who by entering the defining mutations for Shem and Japheth. If you enter all the mutations and analyze the same Peruvian, you will see all his mutations are in one group or another. If you look at rs3900, you will see that most Peruvians are from Japheth.

(5) continue entering the mutations one by one, and you will see that our Peruvian is only from one group and has no mutations from any other group. If you do a significant number of individuals, please sent them to us.

 

Fertile Crescent, Nimrod, and Confusion of Language – Human Migration Part 2

Migration, Uncategorized

Overview

At Genesis and Genetics, we take secular science findings and use them to defend the Bible. In the case of the fertile crescent archaeology, we have found much information concerning human migration, Nimrod, and the confusion of tongues. We found the following:
* The oldest vineyards in the world are in ancient Armenia, as documented in our former blog Noah’s wine country.

* As Noah’s offspring spread out, they settled in the fertile crescent. This was before the migration into the “Land of Shinar.” The reason for this is that the Land of ShinarEarly migration (Lower Mesopotamia) was underwater. Presently, much of Lower Mesopotamia is less than 60 feet above sea level. For instance, presently the elevation of Babylon is 7 feet, Ur is 59 feet, Uruk is 52 feet, and Eridu is 23 feet.

* A portion of the fertile crescent is to the East of the Land of Shinar in the foothills of the Zagros Mountains. According to the Bible, those who settled in the Land of Shinar “came from the East.” This means that only a portion of Noah’s offspring settled in the Land of Shinar. The Bible says that those who settled in the Land of Shinar wanted to “make a name for themselves.” If they were the only civilization on the earth, they wouldn’t have to make a name for themselves.

* Shortly after the arrival in the Land of Shinar (Sumer), a sophisticated society began, and an Empire arose from the city of Uruk (Biblical Erech). This empire spread out into the fertile crescent.  The secular archaeologists refer to it as the Uruk Expansion. The Emperor/ruler/king was a man called Enmerkar. He is a prime candidate, and our pick, for the Biblical Nimrod.

* Enmerkar enjoyed great success until the language was confused. There are many historical references to the confusion of language, and in the “legend of Enmerkar and the Lord of Aratta,” Enmerkar is blamed for the confusion of tongues.

* Enmerkar (Nimrod) lost his empire due to the confusion of tongues. He lost his ability to communicate with his outposts, trade partners, and clans in the empire.

* Enmerkar was credited for being the first to use written language. Written language arose quickly after the Uruk Empire collapsed. Possibly, Enmerkar attempted to restore his empire by introducing writing and using it and scribes to renew the empire. But it didn’t work. Shortly after the collapse of the Uruk empire, the dynastic period began. Each language group had a king. The confusion of tongues accomplished God’s purpose in that the people were divided.

* Enmerkar (Nimrod) was shamed and fell into obscurity.

Details

Noah and his family disembarked in ancient Armenia. Modern archeology tells us that the most ancient vineyards are in ancient Armenia. This is also the point of origin of most domestic grapes. So, all humanity and domestic grapes migrated from ancient Armenia (Noah’s Wine Country), consistent with the Bible.

As Noah’s children multiplied, they sought new lands and adventure. Some migrated North and East to Asia, and some migrated South to the fertile crescent, including Egypt. At this time, the waters were still receding from the flood, and lower Mesopotamia (the Land of Shinar) was still underwater. As the waters receded, those in the fertile crescent East of the Land of Shinar moved into the rich alluvial plain, which became Sumer and Akkad. Here is some Biblical proof that only a portion of Noah’s offspring migrated to the Land of Shinar:

Genesis 11:4  And they said, Go to, let us build us a city and a tower, whose top may reach unto heaven; and let us make us a name, lest we be scattered abroad upon the face of the whole earth.

They wanted to do two things, first, make a name for themselves, and two, they wanted to disobey the command of God to scatter, i.e., migrate. If they continued with their goals, God would lose the hope of having a people unto Himself; a one-world government would be risky in that there would be a loss of freedom of choice. God decided to stop the Enmerkar empire and did the following:

Genesis 11:6 And the LORD said, Behold, the people is one, and they have all one language; and this they begin to do: and now nothing will be restrained from them, which they have imagined to do. 

Genesis 11:7 Go to, let us go down, and there confound their language, that they may not understand one another’s speech.

Genesis 11:8 So the LORD scattered them abroad from thence upon the face of all the earth: and they left off to build the city.

The entire population of the world spoke one language and were of one mind. In the land of Sumer, there arose a mighty person who built the city of Uruk (Biblical Erech) and formed an empire. Because the people were of one mind, he had little trouble forming this empire without bloodshed. It was a sophisticated society with farming, the wheel, chariots, government, toilets, septic tanks, geometry, the “Roman” arch, irrigation, think tanks, and beer. The Empire planted outposts near trading partners, and everything was booming. Here are the scriptures about Nimrod:

Genesis 10:8 And Cush begat Nimrod: he began to be a mighty one in the earth.

Genesis 10:9 He was a mighty hunter before the LORD: wherefore it is said, Even as Nimrod the mighty hunter before the LORD.

Genesis 10:10 And the beginning of his kingdom was Babel, and Erech, and Accad, and Calneh, in the land of Shinar.

Genesis 10:11 Out of that land went forth Asshur, and builded Nineveh, and the city Rehoboth, and Calah,

Genesis 10:12 And Resen between Nineveh and Calah: the same is a great city.

These scriptures vividly point to the making of an empire with Nimrod as the emperor. Everything fits with the Bible except the carbon 14 dates. However, the secular carbon dates assume there was no flood. If the dates are corrected for flood effects, it all comes together. Here is our date assessment using the Flood Effects on Radio-Carbon Dating corrected dates.

Event                                               Corrected dates                                    Secular dates

The flood                                          2348 BC (Bible)                                   Didn’t happen

Oldest vineyard                              2150 BC                                                  6100 BC

Death of Noah                                 1998 BC                                                  He didn’t exist

Uruk Expansion Start                    1996 BC                                                  3700 BC

Confusion of Tongues                   1908 BC                                                  3000 BC

Jemdat Nassr period                      1930 BC -1892 BC                              3150 BC – 2900 BC
(transition period
Between the Uruk empire
and the dynastic era)

First writing                                          1908 BC                                                  3000 BC

Beginning of                                         1892 BC                                                  2900 BC
Dynastic Period
(End of Uruk Empire)

The obvious question is, “where was Noah when all this happened?” Notice in the above dates that the Uruk expansion did not start until Noah died. This makes sense in that Noah must have been considered an important influence on society, and maybe the Uruk expansion, which included the building of the Tower of Babel, could not have happened if Noah were alive.

Conclusion:

When merging the Biblical narrative with secular archaeology, it appears that Noah did, indeed, disembark from his famous Ark in the land of Ararat, i.e., Armenia. He planted a vineyard, which was the beginning of post-flood farming. His offspring migrated from the vineyard in all directions, but many settled in the Fertile Crescent. As the waters abated, those from the Eastern portion of the fertile crescent settled in the Biblical “Land of Shinar” (Mesopotamia). From the Land of Shinar, there arose a powerful man, Nimrod/Enmerkar, who built the city of Uruk (Erech) and from that city arose the Uruk/Erech empire. The empire spread to much of the ancient world, but the expansion was stopped by the confusion of languages. The emperor attempted to keep the empire intact by using an invention, writing; however, it didn’t work, and the empire collapsed, ushering in the dynastic period. The dynastic period stopped globalization, and the earth was divided by nations and languages as it has remained to this day.

References:

1. The Bible

2. Noah’s Wine Country

3. Radio Carbon Date Calculator

4. The Uruk World System The Dynamics of Expansion of Early Mesopotamian Civilization, by Algaze Guillermo