Mayans and the High Stakes of Creationist Research

For almost 15 years, I had been hot on the trail of solving the genetics of human history. Slowly and steadily, the genetic echoes of the biblical record for humanity had begun to emerge. DNA had revealed the confirmation of creation, fall, and flood. Hints of Babel had beckoned me. Eventually, I had scored one of the biggest research prizes—the DNA confirmation of the history of civilization within a strictly young-earth timescale.

In the fall of 2024, I was poised to score an even bigger prize. Up to this point, much of my research had been rebutting and replacing evolutionary explanations. Now I was ready to penetrate fields that had confounded the mainstream community. I had just drafted a book on the pre-European history of North America. Soon, I thought, I could penetrate the world of the Aztecs, Maya, and Olmecs. On this historical front, I wanted to put creationists in the lead.

But I couldn’t shake a lingering contradiction—one that was intimately connected to the young-earth chronology.

Two Steps Forward

I had been working primarily with male-inherited DNA—the Y chromosome. From it, I had created a family tree. For indigenous Americans, the tree had revealed a startling history. I should say, it revealed a startling history, but only within a young-earth framework.

Mainstream science posits a single migration from Asia into the Americas about 15,000 years ago, followed by 14,500 years of isolation that was eventually shattered by Columbus. Within a young-earth framework, the Y chromosome DNA tree showed multiple migrations from Asia. The most recent migration was in the AD 900s. It brought members of the Algic language family—Algonquian peoples like the Cheyenne, Blackfeet, Shawnee, Potawatomi, Cree, and Delaware.

The same DNA tree also showed a massive migration in the AD 300s to 600s. I say massive, not because of the number of people arriving but because of the magnitude of the consequences. Apparently, these invaders wiped out whoever came before. I couldn’t find any family tree branches older than this anywhere in the Americas. Whoever was here prior disappeared genetically.

Or so I thought. The nongenetic history of Central America told another story.

Three Steps Back

The Aztecs, whose massive cities and pyramids had awed the first conquistadores, posed no problem for my genetic conclusions. It turned out that their own origins story1 began in AD 635. In other words, the timing of their history corresponded almost exactly to when genetics had identified a migration from Asia. Their ancestors had likely arrived with the Asian invaders.

The ancestors of another Central American group, the Maya, apparently did not.2 Like the Aztecs, the Maya had built stupendous cities and pyramids. They had also gained notoriety for their exquisite timekeeping and calendar. These two features revealed a much deeper history than that of the Aztecs.

However, it took nearly half a millennium to uncover it. When conquistadores had first set foot in Central America, they had sought the Aztecs, not the Maya. In the AD 1500s, evidence for great Mayan civilizations existed. But the conquistadores never found it.3 The Classic Mayan civilization was in ruins, buried deep in the jungles of Guatemala and the Yucatán. It took three centuries before the outside world became aware of the existence of these ruins.

“Ruins” naturally and immediately raise questions: Why didn’t the great Mayan civilizations still exist? What happened? The answers were slow in coming.

The Mayan ruins contained a script—one that looked like hieroglyphics. But it remained a silent testimony for more than a century. No one was able to read it for 100 years.4

Also recorded at these sites was another code. It turns out to have been the Mayan calendar. Once cracked, it revealed the rise of the Classic Mayan civilization in the centuries after Christ. It also revealed an inexplicable collapse around the AD 900s and 1000s.

But the jungle had more secrets to reveal. Last century, another Mayan era was discovered: the Preclassic. In the lowlands of Guatemala, the Maya appeared in 1000 BC and built great pyramids during the Preclassic. The Preclassic ended around AD 150. Like the Classic era, the Preclassic terminated with a civilizational collapse.

When I first began to gain genetic insights into the pre-European history of the Americas, I thought I had discovered an explanation for the Classic Mayan collapse. In 2020, I published my first paper on creationist Y chromosome DNA analysis and the pre-European history of the Americas.5 At that time, I had reconstructed a family tree from Y chromosome DNA. But I didn’t know where the beginning—the root—of the tree was. I had narrowed the possibilities to a range of candidates. From this range, I had calculated a range of arrival times for the Asian invaders of the Americas: AD 200s to 900s. The latter end of this range overlapped the time of the Classic Mayan collapse. Maybe the Asian invasion was the cause of the collapse.

If so, this would explain why I didn’t find any older branches on the family tree. The Asian invasion had wiped them out, along with the civilization (Mayan) that went with them.

The problem with this view? The Mayans didn’t die out. Archaeologically, there’s another period I haven’t told you about: the Postclassic. After the Classic collapse, the Maya continued to build cities and pyramids on the Yucatán Peninsula. One of the more famous Mayan ruins, Chichén Itzá, dates to the Postclassic.

More importantly, millions of Maya are still alive today. Most live in Guatemala and Mexico, speaking languages in the Mayan family. Some of them are in the United States. I know this fact personally. On Sunday nights in a park near my house in Northern Kentucky, I have played soccer with Mayan-speaking Guatemalans.

Why, then, did the Y chromosome DNA results suggest that they disappeared? I couldn’t find the answer.

In 2022, I published a book on the genetic history of the globe—again, within a strictly young-earth creationist framework.6 I had a full chapter on the pre-European history of the Americas. At the time, I thought more testing of Mayan Y chromosomes might reveal an older lineage.

In fall of 2024, I finished a draft of a book on the pre-European history of North America.7 By this point, hundreds of Mayan Y chromosome test results were in the technical scientific literature. No ancient DNA branch had yet appeared. In the book draft, when I mentioned the Maya, I resorted again to the possibility that they might simply have disappeared after the Classic era collapse.

But they didn’t. Their languages persisted. This glaring problem was the strongest counterargument to the conclusions I had been reaching about the pre-European Americas.

Eventually, I resigned myself to the fact that I had a baffling problem in my creationist research. If I was going to dive deep into Central American history, I had to solve it.

But how?

A DNA Puzzle

In the earliest stages of my professional creation research career, I had worked with another type of DNA. From female-inherited mitochondrial DNA, I had reconstructed a family tree. This tree had uncovered critical confirmation of creation, fall, and flood. I was in the process of looking for Babel and for the young-earth stamps of the history of civilization when I switched to using male-inherited Y chromosome DNA.

Why? For big picture questions, the mitochondrial DNA–based tree had worked great. For detailed questions on the history of civilization, the mitochondrial DNA–based tree was befuddling. On the tree, I could clearly identify places where branches separated or came together. But I couldn’t reliably pin down dates. The statistical noise was too great.

For example, I knew that I could assign a date of, say, AD 500 for a particular branch point. But I also knew that my statistical uncertainty would be a millennium in either calendar direction—i.e., AD 500 might actually end up being 500 BC or AD 1500. Not exactly helpful.

For the Y chromosome DNA–based tree, I had no such problem.

But the Y chromosome DNA–based tree also ended up leaving me with the puzzle of the Maya.

In the fall of 2024, I returned to the mitochondrial DNA–based tree and determined to solve it. I decided to approach the mitochondrial tree in the same manner that I had initially approached the Y chromosome tree. For the latter, I had a burning question: How was time stamped on the tree?

For the Y chromosome tree, I also had used a specific method and a specific test population. My first revolutionary insights with the Y chromosome tree came from examining Native American history. But I hadn’t started in the pre-European era. I had begun in the present and worked my way backward. I knew that, after the arrival of Europeans, 80% to 90% of the indigenous population had disappeared. So I had looked for the genetic echo of this event first, before going backward in time to the pre-European era.

I applied the same method to the same populations in the mitochondrial DNA tree. In terms of time, I worked front to back—from the modern era backward in time through the pre-European era. I wanted to know: Was there a mitochondrial DNA echo of the indigenous population collapse?

Brute Force

Again, my main hurdle in answering this question was the statistical noisiness of mitochondrial DNA. But then I realized a new tool that I didn’t possess several years earlier. Back then, I was swimming in the dark. Now, I had already established and confirmed about 1,500 years of indigenous American history with the Y chromosome tree. From the AD 300s onward, I knew what indigenous American history should look like. I could test my mitochondrial results against the Y chromosome ones.

I began with brute force. I tried averages, medians, averages of distributions, and other statistical transformations on the mitochondrial DNA data. For each result, I tested its accuracy against the Y chromosome results. Eventually, a clear answer emerged—one that showed not only the post-European population collapse but also the pre-European Y chromosome history.

This was solid confirmation that useful information could be extracted from the mitochondrial DNA tree.

Critical Discoveries

And then the critical discoveries emerged. For the mitochondrial DNA tree, at least four clusters of Native American branches existed. For two of the clusters, I reconstructed a history that was virtually identical to the history in the Y chromosome tree. That is, I found two mitochondrial DNA clusters that revealed a migration from Asia into the Americas around the AD 300s.

The other cluster revealed a migration from Asia into the Americas in the 1000s BC—exactly the time that archaeology showed Mayan civilization in the Guatemalan lowlands.

But the two other clusters told a different story. Well, from the AD 300s to the present, both of these clusters told a story that matched Y chromosome history—except for the time of the original migration. One of these clusters revealed a migration from Asia into the Americas in the 100s BC—at least four centuries prior to the Y chromosome migration. More importantly, the other cluster revealed a migration from Asia into the Americas in the 1000s BC—exactly the time that archaeology showed Mayan civilization in the Guatemalan lowlands.8

Here, finally, was the long-lost Mayan branch.

High Stakes

What you’ve just read represents a successful creationist detective story—a scientific detective story. Creationists are now going out and solving scientific and historical mysteries.

Why does this matter? In the 1970s, creationists like Henry Morris and Duane Gish were doing regular debates in front of large audiences on college campuses across the United States.9 It was a real wave of enthusiasm for creation science. Unbelievers were exposed to a compelling scientific case against evolution that they hadn’t heard before.

Naturally, the evolutionary community refused to abide these inroads from creationists. Evolutionists stopped debating.10 In the 1980s, they also kicked creation science out of the public schools.11 Regular exposure of students to creation science was a bridge too far for evolutionists.

In the debates of the 1970s, creationists did a phenomenal job exposing the scientific shortcomings of evolution.12 Their cross-examination of the evidence for evolution was persuasive. I think the courts knew this.

So the courts shut down this lawyerly work. They decreed that lawyerlike analysis was not enough for creation science to be considered bona fide science. No, they said, creationists must also do detective work.13 They must go out and gather their own evidence and solve scientific mysteries.

The narrative you’ve just read fulfills this demand.