Replacing Darwin on the Debate Stage: A Report on an Unusual, but Promising, Beginning for a Provocative Book

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Introduction and Overview

Forty years ago, the creation/evolution debates were in full swing. In more recent years, evolutionists have rarely taken the stage against creationists. Exceptions to this rule occur, such as the Ken Ham/Bill Nye debates. But evolutionists generally avoid sharing the lectern with creationists. On September 5, this rule was broken again.

At 8 p.m. Eastern time, I participated in the first formal oral debate on my recently published book, Replacing Darwin. My opponent was an evolutionary biologist at Marshall University, Dr. Herman Mays, and we exchanged ideas via an online, live-video forum.1 Since this forum isn’t known for supporting young-earth creation science, I was eager to present my views to a pro-evolution gathering. In other words, I was glad to present my views to the very audience for whom Replacing Darwin was written.

In the days since, I’ve discovered that much confusion arose during and after the debate. For example, I’ve found that many viewers, after watching the debate, left having learned little. Furthermore, since the debate, my opponent has doubled down on some of his claims and continued to challenge my position in various online forums. This has raised more questions in the minds of many. To complicate matters further, strong claims were—and are being—made on both sides: Dr. Mays asserted that I’m scientifically incompetent to make the claims that I do in Replacing Darwin. He also claimed that my book is full of errors and omissions. Conversely, during the debate, I contended that Dr. Mays was criticizing a book that he has not read. With stakes this high, as well as emotions that typically accompany them, it’s no surprise that confusion persists.

The goal of this report is to help clarify some of the lingering questions. My goal is not to attack Dr. Mays personally, criticize his competence, or hamper his career. I have much respect for him as a scientist and for the research he does. In fact, one of his papers for which I’m particularly grateful is his recent publication of the DNA sequence (the genome) of the Sumatran rhinoceros. Furthermore, his expertise and competence is one of the reasons I specifically asked him to publicly review my book. Instead of condemning him, my goal is to further our discussion.

Ultimately, my aim is to make the science in Replacing Darwin as accurate as possible. I actively seek out and invite criticism, and we publish it on our website (e.g., see criticism and response). I seek critical peer review because I know this is the best way to advance our scientific knowledge. My hope is that this article will make the conversation more productive, and will lead to stronger science in the end.

Before diving into the specifics of the debate, I think it’s helpful to review the events leading up to the debate. Again, my impression is that many viewing the debate walked away confused about the purpose, rather than challenged or edified. The background might alleviate some of this confusion.

Background to the Debate

In March of this year, a pro-evolution forum contacted me about having a debate on their platform. After two months of negotiations, we mutually agreed to a contract, which included the following:

Topic: Origin of species, primarily as covered in Nathaniel Jeanson’s book “Replacing Darwin: The New Origin of Species,” versus the prevailing explanation from current evolutionary thought

  1. The discussion will be a serious intellectual conversation between two PhD biologists, with both participants and subject matter to be treated seriously and respectfully.
  2. The topic will be confined to origins, primarily as covered in Dr. Jeanson’s book, “Replacing Darwin,” versus the prevailing explanation from current evolutionary thought.

(Again, several viewers of the live debate seemed to wonder why I emphasized my book so heavily during the debate.)

Shortly after the contract was signed, I emailed Dr. Mays, and included the following:

I do my best to accurately represent the other side, never demean or insult them, and generally apply the golden rule. I don’t see any value in treating my opponents as anything other than decent human beings. My goal is to be as respectful and professional as possible.

I’m also eager to make my science as accurate as possible. This is one of the reasons I’m thrilled you’ll be doing a chapter-by-chapter review of my book Replacing Darwin on September 5th. I wanted to make sure that you had a copy well in advance.

Dr. Mays responded positively and said he already possessed a copy of the book.

Several days before the debate, I discovered that the hosts of the evolutionary forum would be doing a pre-debate show with four people—the two regular hosts, plus an atheist and a critic of Answers in Genesis. On September 4, “Stated Clearly: The Science of ‘Replacing Darwin’”2 was aired. To their credit, all four participants strove to be as fair as possible, and they deliberately tried to withhold criticism of my book. Their explicitly stated goal was to introduce viewers to some of the genetic concepts in Replacing Darwin, in hopes that the debate on the following day would be more understandable. I was very pleased.

In fact, near the close of the show, one of the atheist participants made a very helpful exhortation3 to the audience:

I would very much encourage you to read the book if you are going to be critical. . . I fear that the actually underlying message that Nathaniel is trying to get out may be lost, and we run the risk of his position being straw-manned. . . To a certain degree, this message is to Dr. Mays to ensure that he has Nathaniel’s actual position nailed down going in and isn’t arguing against an assumption of a position.

On September 5, several hours before the debate, I chatted with one of the hosts to decide on the format of the debate. I expressed how much I appreciated the pre-debate show on September 4, and I asked if, perhaps, we could just pick one chapter from my book and go through it slowly during the debate, making sure everyone was following. In a sense, this would almost make the debate more of a discussion. The host liked the idea and said he would consult with Mays. We were unable to revisit this question before the debate went live.

Three hours before the debate, the hosts sent me the slides for Dr. Mays’ opening presentation. By 7pm, I was able to review Dr. Mays’ content. Having watched two of Dr. Mays’ previous debates with creationists, I immediately recognized many of the slides. In fact, the presentation drew heavily on material that Dr. Mays had presented in January4 of this year—two months before the online evolutionary forum would contact Dr. Mays and invite him to review Replacing Darwin. I also recognized that his arguments ascribed positions to my book that were in direct conflict with what Replacing Darwin actually said. In other words, in his slides Dr. Mays attributed to Replacing Darwin things that the book explicitly rejects. I was stunned. In 60 minutes, I was about to take the stage opposite someone who appeared to be unfamiliar with the very content he and I were supposed to debate.

Navigating the Debate: Points of Confusion

If you watch the debate, you’ll probably walk away with two observations. On one hand, you’ll see Dr. Mays advancing a position that (1) I don’t know what I’m talking about; and that (2) consequently, and not surprisingly, my book is full of factual errors and of errors of omission. On the other hand, you’ll see me mainly advancing a position that (1) Dr. Mays didn’t read my book; and that (2) consequently, and not surprisingly, his arguments represent refutations of straw men, rather than actual refutations of my book.

Which presenter was correct? Again, from the feedback that I’ve received from viewers, few seemed to reach any conclusion on the validity of either participant’s content. Several factors seem to have produced confusion:

  1. Much of the discussion was very technical and, therefore, hard to follow and evaluate. Thus, evaluating the competence of the participants, evaluating the levels of errors and omissions in Replacing Darwin, and evaluating relevance of Dr. Mays’ arguments to the actual content of Replacing Darwin was difficult because the subject matter was foreign.
  2. Instead of stating my position clearly, I used the Socratic method to make my point, asking questions of Dr. Mays in an attempt to draw out for the viewers what was happening. In retrospect, I see that I erroneously assumed viewers would have read the book and would, therefore, know the points that I was deriving via the Socratic method.
  3. Technological limitations rendered many exchanges unproductive. Since Dr. Mays and I joined one another virtually rather than in person on the same physical stage, we were dependent on sufficient internet speeds to hear one another’s points. We all knew going in that there would be a slight delay in transmission. I didn’t realize personally how much this impacted the debate until I re-watched the debate myself via the YouTube video. For me, it was the second viewing that revealed several instances of misunderstandings stemming from the audio delay. For example, I can recall making a point during the live debate, hearing Dr. Mays’ response, and thinking that he avoided my question and, therefore, denied a basic scientific fact. Re-watching uncovered the fact that he simply didn’t hear my point and, therefore, had no response. I saw the same scenario play out from his perspective. During the debate, I remember him advancing an argument, I remember responding to him, and I recall him denying my response and continuing his argument. Re-watching the exchange, I can see that he simply didn’t hear me. This became clear when, later in the debate, he endorsed the very point I had made earlier—the point I erroneously thought he had denied.
  4. The last 45 minutes were unstructured discussion. Though it was intended to be a naturally free-flowing exchange, our inability to hear one another in a timely manner made a free exchange even more erratic.

Consequently, the video of the debate can be hard to follow. I originally planned on walking through the debate minute-by-minute and offering clarifying commentary. Instead, in this report I will pick out the larger, big-picture points, and attempt to simplify and clarify them. Then, in light of this larger context, I will revisit some of the minor points. Hopefully, this clarification will simplify the viewing and understanding of the debate video.

Key Debate Points: What Does Replacing Darwin Say?

Again, one of the main points of feedback that I received from viewers was that I didn’t clearly state what Replacing Darwin actually claimed. To facilitate more productive discussion, let’s consider the background to the book and then the main claims of each chapter.

In October of 2017, I published Replacing Darwin. Its central thesis is that the progress of science has done more than rebut Darwin. One-hundred-fifty years of scientific advances have uncovered a full-fledged scientific alternative—one that is actively replacing his ideas.

This claim comes on the heels of a decades-old criticism of creation science by the evolutionary community. For 40 years, evolutionists have told creationists that it’s not enough to claim to have identified flaws in evolution. Instead, to have a place at the scientific table, evolutionists have insisted that creationists make predictions that can be tested—and, in principle, be disproven or falsified—in the laboratory or the field. Replacing Darwin contains many falsifiable predictions. Effectively, this resets the origins debate. Moreover, I argue in Replacing Darwin that, currently, the creation model is scientifically superior to evolution. Thus, in this historical context, the publication of Replacing Darwin represents a landmark in the creation/evolution debate.

In my opening presentation,5 I reviewed this history in hopes that my common ground with Dr. Mays would allow us to jump right into evaluating the predictions of Replacing Darwin. From a rhetorical perspective, I also designed my arguments to preemptively rebut potential objections from Dr. Mays. Since the main thesis of Replacing Darwin is that the creationist explanation for the origin of species makes better testable, falsifiable predictions than evolution, I wondered if Dr. Mays might eventually walk back the long-standing evolutionary emphasis on testable predictions. I laid out a lengthy history of the importance of this concept to make it harder for him to walk it back, should he eventually choose to go down this path.

Setting up the Argument

In Replacing Darwin, I derive and lay out these testable creationist predictions in a very deliberate manner. Chapter 1 (“Inevitable”) functions as an introduction and as a teaser, inviting the reader to explore the rest of the book. Chapters 2 (“The Secret of Life”) and 3 (“Cracking the Code”) review the history of modern genetics and its relationship to the origin of species. My main theses in Chapters 2 and 3 are that (1) genetics is the most important field of science in the debate over the origin of species; that (2) genetics wasn’t even a field of science when Darwin wrote On the Origin of Species; and that (3) therefore, Darwin took a massive risk when he published his evolutionary answer to this question. The summary section of Chapter 2 says as much:

We observed at the beginning of this chapter that species are ultimately defined by their traits.

We then observed that traits are defined by genetics. Therefore, the origin of species is a fundamentally genetic question. . . .

Yet the physical basis for heredity—the nature of the code of life—was not uncovered until nearly 100 years after Darwin wrote On the Origin of Species.

Consider the significance of this fact . . . Fossils aren’t inherited in sperm and egg. A miniature adult is not passed on through germ cells. A geographic location is not the substance of heredity. Instead, a set of instructions (encoded in DNA) is . . .

Without this genetic knowledge, could Darwin have speculated intelligently on the origin of species? If he had no idea how traits were coded and inherited each generation, could he have identified the origin of a particular trait? Before the advent of genetics, would his explanation have had any hope of being accurate?

The history of genetics poses a second set of questions to Darwin. Not only was his question a fundamentally genetic one, but his specific answers to the origin of species were also deeply tied to this field. For example, Darwin proposed that all species had one or a few common ancestors.

In other words, he said that the vast diversity of life belongs to one or a few family trees. Genealogical relationships are directly recorded in genetics—and nowhere else.

Furthermore, Darwin claimed that new species arose via the process of survival of the fittest, or natural selection. Natural selection is useful to evolution if—and only if—the survivors pass on their superior traits to offspring. In other words, the mechanism of evolution is inextricably tied to inheritance. Inheritance is directly recorded only in genetics.

Finally, Darwin placed the origin of species on a very long timescale. However, the process of inheritance also acts like a timekeeper, independently recording the length of time over which species appeared (a concept we’ll explore in detail in later chapters). How could Darwin have written On the Origin of Species without any genetic data to test his ideas? Since both his question and his hypotheses were deeply tied to inheritance, what prompted him, not only to pen, but also to vigorously argue for his proposal?

When Darwin wrote his most famous work, he took a scientific risk of massive proportions. (p. 38)6

Naturally, this raises the question of how Darwin was able to successfully persuade his peers of evolution. Chapters 4 (“The Riddle of Geography”) and 5 (“The Riddle of Ancestry”) seek to answer this question. In short, I argue that Darwin succeeded because the available (i.e., non-genetic) evidence successfully falsified the competing (and archaic, Bible-contradicting) creationist views of his day. Chapter 4 details how Darwin did this from the field of biogeography—the study of how species are distributed around the globe. Chapter 5 explores how Darwin disproved the 1859 creationist ideas with data from the fields of paleontology (i.e., the study of fossils), embryology, and anatomy and physiology.

If Darwin succeeded in 1859 against creation science, why revisit the question? In Chapters 4 and 5, I show that creation science has matured. Today, creation science makes different testable predictions in the fields of biogeography. For example, modern creationists agree that species have migrated to the present locations, and they posit that species within “kinds” have a common ancestor. I also show how creationists have honed their expectations from a design perspective in the fields of paleontology, embryology, and anatomy and physiology. For instance, from first principles, I derive a predictive method, which leads to the expectation that life would fall in a nested hierarchical pattern (i.e., groups-within-groups pattern). Chapter 5 derives other expectations from this same method. Consequently,

with respect to Darwin’s evidences for universal common ancestry, all fail to eliminate modern creationist views. His evidences do not distinguish between the hypothesis of common ancestry and the hypothesis of common design. Furthermore, though his breed-species comparison successfully eliminated the hypothesis that each and every species has been independently designed, his comparisons failed to eliminate the hypothesis that original ancestors of each family were designed. In other words, all of Darwin’s evidences fail to eliminate modern creationist views. (p. 149)

This fact has profound ramifications for the modern debate. For example, many of Darwin’s arguments for evolutionary common ancestry continue to be cited in modern textbooks as evidence for evolution. In Replacing Darwin, I argue that these evidences cannot distinguish between the expectations of the modern creationist view, and the expectations of evolution. Since these evidences do not favor one side over the other, they cannot advance the debate at present.

As a side note, in Replacing Darwin I am deliberately vague on where common ancestry stops, and where common design begins. While I give rough approximations of where I think “kinds” start and stop, I don’t have a chapter dedicated to definitive identification of “kind” relationships. The end of Chapter 5 explains why:

[With respect to the question of ancestry] beyond the level of family, uncertainty reigned. In light of the history of genetics, this uncertainty was natural. The only direct scientific record of a species’ ancestry is found in DNA. Since the DNA sequences of various species. . . weren’t available until recently, it’s no surprise that the debate over ancestry would persist to this day. (p. 149)

In other words, I argue that the scientific answer to the question of which species are related and which ones are not is still forthcoming. Genetics is the scientific arbiter of this debate, and these data are still being gathered. (I add more to this in Chapter 10.)

Chapter 6 (“A Stitch in Time”) adds a new twist to the origins debate. From Darwin’s own writings, I identify a neglected argument for common ancestry and take it to its logical conclusion. However, the conclusion doesn’t revolve around the question of genealogical relationships; it directly hits the question of the timescale over which species arose. In essence, Chapter 6 makes an argument for the recent origin of species, one that is derived independent of geology and paleontology—and is, therefore, an independent test of the evolutionary conclusions in the fields of geology and paleontology. This claim has large implications for the rate at which species form in the present, and much of Chapter 6 is devoted to mathematically exploring these implications. More importantly, Chapter 6 contains testable predictions about the average rates at which species have formed.

A Paradigm Shift

Chapters 7 (“Turning the (time)Tables”), 8 (“A Preexisting Answer”), 9 (“From DNA to Visible Traits”), and 10 (“On the Origin of Species”) of the book constitute Part III of Replacing Darwin. As such, they represent the heart of my argument for replacing Darwin instead of just rebutting him. In Chapter 7, I explore DNA in a small but significant compartment termed mitochondrial DNA (mtDNA). This mtDNA mutates, which suggests that it can be used a biological “clock” of sorts, ticking off time since species first arose. I show that the mitochondrial DNA clock indicates that species have formed recently. In fact, this conclusion is so strong that I make testable predictions about the rate of mutation in mitochondrial DNA across vast swaths of life. I also challenge competing views to publish testable predictions of their own.

In Chapter 8, I explore DNA clocks in another genetic compartment, the nucleus. This compartment contains the vast majority of our DNA, and I derive at least two arguments in favor of the creationist explanation for nuclear DNA clocks. In short, I argue that the vast majority of DNA differences were the result of divine creation, not mutation. This claim leads to testable predictions on DNA function. I also challenge competing views to publish testable predictions of their own.

Chapter 9 explores the implications of Chapter 8 with respect to the question of how species form. I show that the conclusions of Chapter 8 have massive implications for this field. In a nutshell, Chapter 9 reveals that the conclusions of Chapter 8 in combination with standard population-level natural processes are sufficient to explain the origin of species in a few thousand years.

Chapter 10 adds yet another line of evidence to support the conclusions from Chapters 8 and 9. From the pattern of speciation, I derive indirect evidence in support of Chapters 8 and 9. I also revisit the question of ancestry at the end of Chapter 10 and suggest that genetic clocks might ultimately reveal which species are related and which ones are not. In other words, I argue that testable genetic predictions will be the scientific arbiter of the question of common ancestry. Chapter 10 also suggests testable predictions about the relationship between the nuclear DNA and mitochondrial DNA compartments.

In sum, these are the claims that I expected to debate on the evening of September 5.

Key Debate Points: What Did Dr. Mays Criticize?

Instead, I debated something very different with Dr. Mays. Let’s consider his four key claims and explore their relationship to the claims of Replacing Darwin.

Dr. Mays First Key Argument

The first five minutes of Dr. Mays’ opening statement/presentation are very helpful to view.7 They set the context for his subsequent arguments, reveal insights into his debate strategy, and ironically foreshadow subsequent exchanges between Dr. Mays and myself. For example, Dr. Mays says, “The subject of Replacing Darwin is rooted in population genetics, biogeography, phylogeography, speciation, molecular evolution, and systematics—none of which are fields in which Jeanson possesses any professional expertise himself” (see the 0:34:10 mark in the video). Dr. Mays also asserted that my book is “mostly divorced from the actual primary literature in the fields it seeks to replace” (0:36:30). In addition, Dr. Mays insisted that science should build on prior discoveries. With respect to Replacing Darwin, Dr. Mays said I was not following this practice but, instead, following the maxim “I’ll make it up as I go along” (0:34:45). Thus, Dr. Mays’ first major argument was that I was scientifically incompetent to discuss the origin of species.

Having been in the creation/evolution debate for years, I have heard this line of reasoning before. However, after the debate, I was reminded of one of Dr. Mays’ blog posts from four years prior. In 2014, Dr. Mays published a blog post titled “In Praise of Ridicule: Our last weapon against the unintelligible.” Dr. Mays made a specific endorsement: “As purely articles of some particular sectarian religious conviction creationist ideas deserve the respect afforded to any religious ideology and should be debated alongside other theological positions, however when presented as if they are scientific propositions creationist ideas have earned our ridicule.” Had I recalled Dr. Mays’ position prior to the debate, I would have better anticipated Dr. Mays’ strategy.

(As a general response to this first key argument of Dr. Mays, I invite the reader to explore my professional training by reading the technical papers that I’ve published. With respect to Dr. Mays’ claim that my views are divorced from the relevant primary literature, I also invite the reader to consult the extensive list of citations to the primary literature in the Endnotes of Replacing Darwin. Finally, I invite the reader to test Dr. Mays’ assertions against the evidence uncovered below.)

Dr. Mays Second Key Argument

Arguing from 2016 Data

Dr. Mays’ second major argument was that Replacing Darwin had already been falsified. Most of his opening presentation was dedicated to this point (see approximately 0:37:50 to 0:59:00 of the debate video), and he advanced it from several angles. His first angle derived from a 2016 paper that discussed genetic differences between families or “kinds.” Dr. Mays argued that Replacing Darwin makes certain predictions about the number of DNA differences between “kinds” (roughly the 0:37:50 to the 0:51:00 marks in the video), and that the actual number of DNA differences is inconsistent with this prediction.

Unfortunately, as might be suggested by the date of the paper—published over a year before my book was released, Replacing Darwin makes no such prediction. It makes predictions on relative DNA patterns between “kinds” (Chapters 7 and 8); it makes predictions about rates of mutation within “kinds” (Chapter 7); and it makes predictions on DNA function between “kinds” (Chapters 7 and 8). But you will not find any predictions on the number of DNA differences between “kinds” in Replacing Darwin.

For the record, I would be delighted to possess the tools to make such predictions. In theory, these predictions would be a fantastic means by which to identify the “kinds,” which would directly address the question of which species are related and which ones are not—a research question that creationists have wrestled with for decades. In other words, I have a vested interest in being able to make such predictions. However, to date, I know of no methodology that would allow me to make them. Hence, Replacing Darwin does not contain predictions on the number of DNA differences between “kinds.”

Thus, Dr. Mays’ first angle represents an attack on a straw man of my position.

Nevertheless, Dr. Mays claimed that the 2016 “creationist predictions” were simply natural implications of the ideas that I outlined in Replacing Darwin (see the 1:23:05 mark in the video). He tried to justify his claim by citing a generic aspect of young-earth creation—the independent creation of “kinds.” Dr. Mays never showed how this generic element of young-earth creation leads to the very specific “predictions” he cites—predictions which are not found in Replacing Darwin.

Arguing from Even Older Data

In support of his contention that Replacing Darwin has been falsified, Dr. Mays’ next angle (slide 10 from his opening presentation in the debate video) derived from about six additional technical references (the seventh is a duplicate). Once again, all six of these papers 8 were published before my book was released. One was published over 35 years ago. Again, each of these papers never addresses the arguments in Replacing Darwin. For example, the Theobald 2010 paper attempted to test which explanation best fits the patterns of biological trees (i.e., graphical representations of DNA similarities and differences) that we see in nature. Theobald never attempted an explicit test of the trees predicted by my book (i.e., trees that result from the combination of divinely created DNA differences, plus DNA differences stemming from mutation). (The Theobald 2011 paper simply responded to evolutionary—not creationist—objections to his 2010 paper.)

Conversely, in the 2013 White, Zhong, and Penny paper, the authors claimed that creationist models predict no nested hierarchies above the level of “kind”; the 2016 Baum et al. paper and the 1982 Penny, Foulds, and Hendry paper made a similar claim.

In contrast, Chapters 5, 7, and 8 of Replacing Darwin predict the opposite. Specifically, Chapter 5 spends six pages (p. 135–140) explicitly deriving, from a design perspective, the prediction of nested hierarchies. For sake of space, I will not reprint the six pages here. However, Chapter 7 succinctly reiterates this claim:

In other words, the creation/design model predicts the fact of mtDNA nested hierarchies as much as evolution does.

If evolution were the only explanation for nested hierarchies, then we might conclude that all mammals—from echidnas to equids (Figure 7.2) and every mammal in between—have a common ancestor.

However, at least one other competing explanation exists. Again, as in chapter 5, the mtDNA hierarchy shows strong parallels with the hierarchy present within the Linnaean classification system.19 Since this system is based on biological function, the parallel between the mtDNA hierarchy and the Linnaean categories suggests that the mtDNA hierarchy has something to do with function. In other words, the creation/design model predicts the fact of mtDNA nested hierarchies as much as evolution does.

More specifically, I have taken these design expectations one step further and derived a very detailed, testable model on mtDNA genome function.20 For mtDNA differences among species within families, my model treats these as functionally neutral changes—the result of mutation over time. However, with respect to the differences between families—those mtDNA positions that are identical among species within a family but different to species outside of the family—my model views these as having been created. Thus, my model predicts that these mtDNA differences play a functional role specific to each family. (p. 171)

(Endnotes 19 and 20 reference a long, detailed, technical paper I published in 2013 in which I rigorously derive and justify these predictions.)

Chapter 8 underscores my predictions about nested hierarchies as well:

Twice in previous chapters we’ve engaged nested hierarchies. Twice we’ve come away without any new conclusions on the origin of species. Both at the anatomical level (chapter 5) and at the mtDNA level (chapter 7), we have discovered nested hierarchical patterns. And, at both levels, we have observed that both the evolutionary model and the creationist model expect nested hierarchies. For example, from the perspective of descent with modification, evolutionists have argued that a branching hierarchy is exactly what the process of evolution should produce. Similarly, creationists have pointed to the products of human design, which happen to fall in nested hierarchies. Creationists have argued that the matches between these designed hierarchies and the biological hierarchies is consistent with the hypothesis of design. In all of our previous attempts, nested hierarchies have failed to eliminate one of these two competing scientific explanations.

Similarly, in the realm of nuclear DNA comparisons, nested hierarchies cannot eliminate either explanation.

What, then, could nuclear DNA comparisons reveal about the origin of species? In chapter 7, we observed that the function of DNA differences strongly discriminates between the creationist and evolutionary models. Evolutionists ascribe the origin of all DNA differences ultimately to mutations. Thus, between two species that share similar genes [i.e., genes are subsections of DNA], they generally expect sequence differences between these genes to be functionally neutral.3 In contrast, among species from separate families, creationists predict high levels of function for DNA sequence differences.4

These contrasting predictions lay the foundation for a head-to-head comparison of these two models in the realm of nuclear genes. (p. 208, emphasis added)

(Endnote 3 references an evolutionary paper that suggests evolutionary predictions are being modified; endnote 4 again references a long, detailed, technical paper I published in 2013 in which I rigorously derive and justify these predictions.)

Thus, five of the six references that Dr. Mays cited refute a straw man of my position, not an actual element of my explanation for the origin of species.

The one remaining reference from Dr. Mays’ list of six references explores yet another angle of testing creationist predictions. The authors in the 2003 Penny, Hendy, and Poole study tested whether the specifics of the creatures in the various nested hierarchies in nature fit the expectations of creation science. (In contrast, most of the other papers simply explored whether a nested hierarchy exists; if it did, the authors/Dr. Mays considered this a refutation of creation.) Since Dr. Mays adopted the 2003 Penny, Hendy, and Poole line of reasoning in his own presentation (see slides 12–19), and since both Dr. Mays and the 2003 authors employed the same principle, I’ll deal with both together by explicitly addressing Dr. Mays’ example.

Dr. Mays began this angle by suggesting that a design/creation perspective would predict certain animals to fall in the same grouping. Dr. Mays (rightly) thought that function should determine the groupings. However, Dr. Mays’ application of this line of thinking quickly became a caricature. For instance, Dr. Mays thought a functional design/creation perspective predicts whales and sharks to be part of one biological grouping and land mammals as part of another biological grouping. Since whales are currently classified (biologically) as mammals and not as fish, Dr. Mays thought that this fact falsifies creation. Dr. Mays then showed several types of groupings that all yield the same conclusion.

The irony of this specific example is that it reveals Dr. Mays’ failure to engage not only my book, but hundreds of years of biology. For example, Carl Linnaeus lived 100 years before Darwin published On the Origin of Species. Linnaeus is the father of our modern classification system, and he was a strong creationist. In his landmark classification text, Systema Naturae, Linnaeus grouped whales with mammals, not fish. As a creationist, why would Linnaeus do this? Linnaeus based his classification on function. Superficially, since whales and fish live in the water, you might be tempted to group them together. However, despite their superficial outward similarity, they strongly diverge at the physiological levels. Linnaeus recognized this; Dr. Mays seems to have taken a very superficial approach to this question.

Thus, the entirety of Dr. Mays’ opening presentation “falsified” a version of creation that evolutionists invented. Dr. Mays’ presentation never addressed the arguments—or actual, explicitly-stated falsifiable predictions—in Replacing Darwin.

Dr. Mays’ Third Key Argument

“Coalescence” and Nuclear DNA

Dr. Mays’ alluded to his third key argument in the first five minutes of his opening presentation. He said that “the bulk of the errors in Replacing Darwin are errors of omission”—a theme to which he would return frequently in the open discussion section9 of the debate.

Understanding the Technical Background

In the free discussion section of the debate, Dr. Mays’ illustrated his claim in two major ways. Both illustrations revolved around the concept of tracing DNA differences back through time. The first illustration claimed that I omitted a key element of analysis of DNA in the compartment termed the nucleus. Since this argument is rather technical, let’s define key terms before exploring it further. Nuclear DNA is DNA found in the nucleus of the cell. Mitochondrial DNA is DNA found in another compartment in the cell—the mitochondria. DNA differences exist between species (and between groups within species) in both of these compartments; in fact, DNA differences in each of these compartments define major human ethnolinguistic groups.

The DNA differences in both compartments can be traced back to a common ancestor. This tracing process is the foundation of coalescent theory. Conversely, the time it takes to trace DNA differences back to a common ancestor (i.e., time = number of generations) is known as the coalescent time. As I mentioned early in the open discussion section of the debate, the process of tracing these differences back involves fairly complex statistics. These statistics reveal that the coalescent time for nuclear DNA differences is four times longer than the coalescent time for mitochondrial DNA differences.

Dr. Mays invoked this principle at least four times in the open discussion section (e.g., see the video at the 1:12:25 mark, the 1:14:20 mark, the 1:34:40 mark, and the 1:37:10 mark). He did so because Replacing Darwin claims that mitochondrial DNA in multiple species have coalescent times of only 6,000 years. Dr. Mays claimed that my book omits the necessary consequence of this claim—that the nuclear DNA coalescent times must be at least four times longer (i.e., 24,000 years or more), which would undermine my claim that species arose within the last 6,000 years. In fact, at one point (about the 1:35:35 mark), Dr. Mays said, “In the book, you generally avoid any discussion of any nuclear markers at all.”

Identifying the Straw Man

The problem with Dr. Mays’ argument is that it assumes all DNA differences are the result of mutation. (In the video, I attempt to make this point. Unfortunately, the audio delay leads to crosstalk, and it takes more than one attempt for me to successfully communicate this fact to Dr. Mays.) In contrast, Replacing Darwin rejects this assumption for nuclear DNA and explains the vast majority of nuclear DNA differences as having been created in the first humans and in the first “kinds.” (This explanation also makes testable predictions.) In technical terms, these differences existed in a heterozygous state in the ancestors. (The opposite of heterozygous is homozygous—a state of no genetic differences.)

This claim—the claim that most nuclear DNA differences are the result of created heterozygosity—is one of the most central elements of my explanation for the origin of species. It’s difficult to read Chapters 8 through 10 of Replacing Darwin and miss this point. For example, Chapter 8 alone contains six pages (p. 222–227) of text and graphs that together make this point repeatedly. Pages 227 through 231 of Chapter 8 explicitly derive the testable predictions that flow from this model. In addition, just to help the reader further understand the concept, the closing page of Chapter 8 deliberately contrasts my explanation for the origin of nuclear DNA differences to my explanation for the origin of mitochondrial DNA differences:

Together, the mtDNA and nuclear DNA results of the previous chapter and of this chapter severely constrained the possible explanations within the evolutionary model [i.e., in earlier pages, I showed how difficult it is for the evolutionary model to reconcile the data from nuclear DNA clocks with the data from mtDNA clocks]. In fact, pitting the results from the two compartments against one another raised the question of whether the evolutionary model would be able to connect these pieces of evidence into a coherent whole.

With respect to the YEC model, no such difficulty was found. Rather, the mtDNA and nuclear DNA results harmonized coherently. In short, it appears that mtDNA differences are due to a constant rate of mutation over 6,000 years, whereas the majority—if not vast majority—of nuclear DNA differences are due to preexisting DNA differences that were placed in the ancestors of modern species 6,000 years ago. This model for the origin of nuclear DNA differences even led to testable predictions on nuclear DNA function. (p. 232, emphasis added)

Conversely, Chapter 9 spends seven pages (p. 234–238, 240–241) drawing out in fine detail the genetic implications of my explanation for the origin of nuclear DNA differences. In fact, just to make my position even clearer, in the closing section of Chapter 9 I explicitly compare and contrast my explanation for nuclear DNA differences to the evolutionary explanation:

The 6,000-year model of speciation that I’ve just presented represents a sharp departure from the evolutionary model of speciation. Though the three steps of speciation [outlined earlier in Chapter 9] are the same under both models, the practical outworking of these steps looks very different under the evolutionary model.

Let’s set these two explanations side-by-side to highlight the major points of difference (Color Plate 84). For instance, according to evolution, the ultimate cause of genetic change is mutation. When mutations accumulate in a genome, recombination and gene conversion [i.e., recombination and gene conversion are two types of genetic change in addition to mutation] can reshuffle their original arrangement to produce new combinations. Consequently, in some generations the immediate cause of genetic distinctiveness might not be a mutational event. But, under the evolutionary model, mutations are the ultimate cause.23

The ramifications of this fact are clear. Today, millions of DNA differences separate species. Yet, each generation, mutations generate a trivial amount of variety. To generate millions of DNA differences via mutation, enormous amounts of time are required. Since the accumulation of these mutations must eventually produce the visible variety that we see among species, the first element of the speciation process—formation of genetic (and visible) distinctiveness—could not have occurred in just a few thousand years.

In contrast, if the ancestors of modern species had millions of heterozygous DNA sites from the start (as under the 6,000-year model), genetic (and visible) distinctiveness could have happened in a single generation. (p. 243–244, emphasis added)

(Endnote 23 is a clarifying comment about evolution.)

If this were not enough, Chapter 10 begins by reviewing the key elements of my model:

Since we began our quest to solve the puzzle of the origin of species, we’ve discovered many of the crucial pieces—the edge pieces and the corners. Specifically, species appear to have arisen recently, within the last few thousand years. Most of their traits seem to have been present in coded, genetically heterozygous form in their ancestors. In the descendants of these ancestors, shifts from heterozygosity to homozygosity would have been easy. These shifts would have revealed traits that were previously hidden. For example, the genes controlling zebra stripes likely come in dominant and recessive forms. As offspring arose with homozygous forms of one or the other,* distinct traits would have appeared—striped and unstriped individuals. Population subdivision via migration would have isolated these distinct traits and promoted the rise of new species, such as zebras and asses. These scientific pieces suggest a picture of species’ origins that is slowly coming together. (p. 247, emphasis added)

(The asterisk references a clarifying comment.)

The middle of Chapter 10 again reviews the key element of my model:

Recall what we’ve discussed about the mechanism by which species arise. If the ancestors to modern species possessed millions of heterozygous nuclear DNA sites, new species arise naturally (see chapters 8–9). Via the processes of recombination and gene conversion, new nuclear chromosome combinations arise each generation. When these processes involve millions of heterozygous sites, changes in visible traits are almost guaranteed to appear each generation.

To produce a new species, these traits and nuclear DNA combinations must be isolated. Small population sizes, inbreeding, and migration can lead to the founding of new, more homozygous populations. As these more homozygous groups grow to larger and larger sizes, they might eventually be recognized as new species. (p. 270, emphasis added)

In Chapter 10, this discussion extends for two pages (p. 270–271). Just a few pages later, the discussion is picked up again and expounded further (p. 275–280).

Finally, as another illustration of the repeated emphasis I put on this facet of my model, consider my references to other depictions of this same claim. This central element of my explanation for the origin of species was founded on a lengthy paper I published in 2016. The title itself reveals this facet: “On the Origin of Eukaryotic Species’ Genotypic and Phenotypic Diversity: Genetic Clocks, Population Growth Curves, and Comparative Nuclear Genome Analyses Suggest Created Heterozygosity in Combination with Natural Processes as a Major Mechanism” (emphasis added). Replacing Darwin references this paper—and gives the title for it—over 15 times.

In summary, Dr. Mays’ argument about nuclear versus mitochondrial DNA coalescent times doesn’t apply to my model. Furthermore, the fact that he emphasized it so frequently in the debate suggests that he is unfamiliar with large chunks of Chapters 8–10 of my book. In other words, this alleged “error of omission” on my part applies only if three chapters are omitted from Replacing Darwin.

“Coalescence” and mitochondrial DNA

In the open discussion section of the debate, Dr. Mays’ advanced a second major illustration of an “error of omission” in Replacing Darwin. Like the first illustration, this second one was also based on coalescent theory. Unlike the first, Dr. Mays’ second revolved primarily around mitochondrial DNA, not nuclear DNA.

Hitting mtDNA coalescence repeatedly

Specifically, Dr. Mays claimed that when I perform coalescence calculations for mitochondrial DNA, I do not follow the practices of the primary literature (see the 1:05:00 mark in the video). Dr. Mays especially found fault with my use of mutation rates based on pedigree studies. He also criticized my citation of a textbook (again the 1:05:00 mark) and implied that an enormous body of published literature refutes my practice. In addition, Dr. Mays claimed that there are numerous coalescent equations (the 1:05:50 mark) and that I throw out any that do not conform to my 6,000-year timescale. For instance, Dr. Mays asserted that I should be calibrating my equations on the (evolutionary) dates from the fossil record (the 1:37:30 mark). Dr. Mays said that I ignore ancient DNA (e.g., DNA from Neanderthals) because, according to Dr. Mays, “I [Jeanson] just don’t believe that it’s reliable” (the 1:38:35 mark). He also claimed that I ignore the role of natural selection (the 1:39:30 mark). (His claims about “substitution rates” and the need for calculations based on “neutral variation” are a form of this argument. See also the 1:53:15 mark.) Dr. Mays also said that I ignore the differences in relative rates of DNA change in the various sections of the mitochondrial DNA genome (the 1:53:35 mark).

Let’s make several observations that help clarify the main criticisms Dr. Mays leveled. First, when he criticized my use of a textbook, he was not objecting to the textbook itself. In the aftershow (titled “Post Podium: Mays vs Jeanson Debate”),10 Dr. Mays was asked for a list of recommended books, and the Evolution textbook by Futuyma (i.e., the one which I cite to justify my coalescence calculations, and the one that Dr. Mays criticizes) was part of Dr. Mays’ recommended stack (see the 0:23:25 mark in the Post Podium video). Therefore, it’s not that Dr. Mays found fault with Futuyma. Rather, Dr. Mays thought that I had not done justice to the additional research that goes beyond Futuyma.

Second, when Dr. Mays said that I do not follow the practices of the primary literature, he actually meant the practice of certain segments of the primary literature. To be sure, as Dr. Mays implied, a vast body of primary literature on human mitochondrial mutation and substitution rates exists. But Dr. Mays failed to tell the audience why this body of literature is so large.

Tracing the History of Pedigree Studies

A brief review of this history of this field illuminates key facts that Dr. Mays did not disclose. Let’s begin this history with one of the first major pedigree-based measurements of the human mitochondrial DNA mutation rate—a now famous paper in 1997 by Parsons and colleagues in the journal Nature Genetics (see The title of their paper immediately communicates how their results conformed (or failed to conform) to past evolutionary research: “A High Observed Substitution Rate in the Human Mitochondrial DNA Control Region [i.e., the control region is a subsection of the total mitochondrial DNA sequence].” The authors explained their use of “high” in the title: “Here, we report a direct measurement of the intergenerational substitution rate . . . of 1/33 generations. . . . This is roughly twenty-fold higher than estimates derived from phylogenetic analyses” (emphasis added). In other words, their results were much higher than expected from the mainstream timescale of human evolution.

(By the way, please note that the authors of the 1997 Nature Genetics paper referred to the pedigree-derived “mutation” rate as the “substitution” rate.)

Let’s examine more closely how they arrived at their conclusion. Near the close of their paper, they explored the significance of their findings: “Thus, our observation of the substitution rate, 2.5/site/Myr [i.e., 2.5 mutations per mitochondrial DNA position per million years], is roughly 20-fold higher than would be predicted from phylogenetic analyses. Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA [i.e., the mitochondrial DNA Most Recent Common Ancestor—the time at which modern Homo sapiens began] of only ~6,500 y.a. [i.e., years ago].” How did the authors calculate this ~6,500 y.a. date? The authors cited a previously published estimate of “an age for the mtDNA MRCA of 133,000 y.a.” Then they simply divided 133,000 (which is one of a range of estimates) by 20 (the fold-difference in the mutation rate measurement between the pedigree-based studies and the evolutionary timescale-based studies) to get the age of ~6,500 years ago.

But how did the earlier (i.e., 1992) paper—the one that claimed 133,000 years ago—derive their number? What equation did they use? From the earlier (1992) paper: “If we know the colonization time for PNG [i.e., Papua New Guinea], then the amount of sequence evolution to the origin of the PNG group, divided by the colonization time, provides an estimate of the rate of human mtDNA sequence evolution.” In other words, they calculated the human mutation rate by dividing the number of mtDNA sequence differences by the time of origin.

This calculation—this equation—is identical to the one that I used in my book. And it’s identical to the one which Futuyma used in his Evolution textbook, and is the very one that Dr. Mays criticizes.

Before diving deeper into this analysis, let’s recap what we’ve just observed. First, the field of human mtDNA pedigree-based mutation rate studies received its first big boost in 1997 with the publication of a large study. Second, this 1997 study made a discovery very much at odds with the evolutionary timescale. Third, the authors discovered this discrepancy by using the very equation that I used in my book—and they treated this equation as legitimate, as informative, and as a challenge to the evolutionary timescale. Thus, the mainstream primary literature does, in fact, use the equation that I use.

To understand why Dr. Mays objected so strongly to my use of this equation, let’s trace the history from 1997 onwards. Let’s begin by observing how the authors of the 1997 paper dealt with the straightforward implications of their study: They immediately rejected the 6,500-year date for the origin of humanity. Why? “It remains implausible to explain the known geographic distribution of mtDNA sequence variation by human migration that occurred only in the last ~6,500 years.” To support this conclusion, the authors cited two studies based on mainstream evolutionary archaeology.

Because of this conflict, the 1997 authors immediately sought other equations to reconcile their results with evolutionary archaeology: “What could account for the disparity between the observed substitution rate and those derived from phylogenetic analyses?” In the paper, they explored corrections to the equation based on “mutation ‘hot spots’,” based on “random genetic drift,” based on mutational reversion, and based on natural selection.

In other words, from the beginning of the pedigree-based human mtDNA mutation rate studies, evolutionists have rejected the straightforward application of the Futuyma equation because it disagrees with the evolutionary timescale.

Not surprisingly, from 1997 onward, the human mitochondrial DNA mutation rate literature is replete with attempts to find the “correct” equation. Some papers have called into question whether the results of the 1997 paper were real. Other papers have continued to explore avenues of explanation similar to the avenues explored by the 1997 authors—e.g., natural selection, etc.

To reiterate: My “non-standard” equation has been employed over and over again in the mainstream literature. However, its main use in the evolutionary literature is to show that multiple correction factors are needed to reconcile the results of the straightforward equation with the evolutionary timescale. Thus, the equation I used is not heavily employed because the equation does not conform to the evolutionary geological timescale.

I invite the reader to consult this history for themselves and verify that the equation is regularly employed.

What Did Replacing Darwin Omit?

Now let’s revisit how Replacing Darwin treats this history. First, let’s observe that Replacing Darwin actually covers this history. The details are documented in two of my published papers. Furthermore, these papers show how the pedigree-based mutation rate is, indeed, a real phenomenon. I show that, collectively, the 15+ pedigree-based studies have arrived at a consistent answer. Replacing Darwin cites these papers five (2015 paper) to seven (2013 paper) times.

Second, in the main text of Replacing Darwin, I derive this history for the reader. For example, on pages 180–183, I use the pedigree-derived mitochondrial mutation rate to show that it conflicts with the expectations derived from the evolutionary timescale for (1) the split between the human and chimpanzee lineages, (2) the split between the Neanderthal and modern human lineages, and (3) the evolutionary Out-of-Africa model for modern human origins. In other words, Replacing Darwin reiterates what the 1997 Nature Genetics paper (and a host of other papers since) already concluded.

Then, in Replacing Darwin I explicitly explore alternate equations and explanations. Dr. Mays fails to represent this key—and perhaps, most central and significant—aspect of my entire book. In considering how the simple coalescence equation for mitochondrial DNA (mtDNA) could be modified to fit the evolutionary timescale, Replacing Darwin reads as follows:

Can the [evolutionary] timescale itself be changed? In theory, perhaps this is possible. However, in practice, this would require significant reinterpretation of the conventional evolutionary geologic model—an action which could produce significant disarray in this discipline.

In a similar vein, perhaps the assumption of constant rates of change could be altered. However, as we observed above, evolutionists have insisted for years that changing rates must not be invoked to explain the majority of phenomena observed in geology and astronomy. Instead, they have claimed that present rates are the key to the past, and that the world we see today has arisen primarily by slow, constant rates over time. Invoking changing rates in genetics would be logically inconsistent with the practice of evolutionary geology and astronomy.

Perhaps the explanation involves natural selection. At first pass, this might seem plausible. After all, mtDNA encodes proteins with critical functions in the cell. If you interrupt basic metabolism, cellular death is sure to result. Surely most of the thousands of mtDNA mutations that have occurred over the last several million years of evolutionary time were lethal to the possessors of these mutations. Consequently, natural selection would surely have eliminated these mutations (and individuals) from the mtDNA pool.

How might we evaluate the natural selection hypothesis? The scientific community has a long-established practice of dealing with scientific controversies. We’ve already discussed in chapter 4 how to advance a scientific debate towards resolution. The scientific method operates like a process of elimination. When two hypotheses offer competing explanations for the same phenomenon, one must be eliminated before scientific inferences can be made.

Naturally, this logic assumes that two competing hypotheses actually make testable predictions. We assumed as much in our discussion of the history of genetics (chapter 2–3) and in our discussion of Darwin’s arguments from biogeography. For example, Mendel was successful as a scientist because he inferred rules that made testable, accurate predictions about the mathematical ratios of traits among offspring in each pea plant generation. As another example, in our discussion of whether DNA or proteins were the substance of heredity, we observed that both of these hypotheses made testable predictions. If proteins were the substance of heredity, their chemical elimination in the experiments of Avery and colleagues [i.e., the authors of a key paper in the field of genetics] should have eliminated the transforming ability of the heat-killed smooth cells. The same prediction follows from the hypothesis that DNA is substance of heredity. Conversely, if species were created in their present locations, then you might expect the fauna on islands to possess more terrestrial species. You wouldn’t expect the native fauna to be so skewed towards aquatic and aerial species. In other words, the hypothesis of the fixity of species’ geography makes testable predictions.

Hypotheses that fail to make predictions do not qualify as science. As evolutionists maintain to this day: “Science is . . . a process of acquiring an understanding of natural phenomena. This process consists largely of posing hypotheses and testing them with observational or experimental evidence. . . . Scientific research requires that we have some way of testing hypotheses based on experimental observational data. The most important feature of scientific hypotheses is that they are testable” [emphasis his].53

The importance of this fact to the evolutionary community is manifest in the way in which it has been applied to creationist ideas: “Science differs in this way [see quote above] from creationism, which does not use evidence to test its claims, does not allow evidence to shake its a priori commitment to certain beliefs, and does not grow in its capacity to explain the natural world. Unshakeable belief despite reason or evidence (i.e., faith) may be considered a virtue in a religious framework, but is precisely antithetical to the practice of science.”54

In other words, since the most important feature of a scientific hypothesis is that it is testable, the seeming un-testability of the existence of God, of the supernatural creation of various creatures, and of a global flood a few thousand years ago has typically removed creationist ideas from the realm of science.

Some evolutionists have even taken the criticism of the creation model one step further. They have summed up creationist views in a short phrase: “God did it.” Besides rejecting this phrase as unscientific, they have denounced it as anti-scientific. For example, let’s say that you were testing a potential anti-cancer drug in the lab. If you were laboring over a confounding experimental result, “God did it” wouldn’t seem to reveal an answer. At least, it wouldn’t lead to discoveries on how the natural world operated. Rather, testable hypotheses would be the only scientific way forward toward a solution.

In light of this historical practice, we can revisit the evolutionary explanation of natural selection. The elimination of thousands of mtDNA mutations by natural selection might seem plausible. But to be scientific, this explanation would have to make testable predictions. For example, the mtDNA mutation rate in the most divergent African people groups (San peoples, Biaka peoples, etc.) has not yet been measured. Can the evolutionary explanation of natural selection predict what this rate will be? In other words, before the rate is actually measured, will evolutionists publish a guess as to what it will be? If not, is the evolutionary explanation scientific? (p. 183–185, emphasis added)

Endnotes 53 and 54 cite Futuyma’s Evolution textbook—the very textbook that Dr. Mays recommends.

Next, on pages 185–186 of Replacing Darwin, I show that the straightforward application of Futuyma’s equation over a 6,000-year timescale captures the scope of mitochondrial DNA differences around the globe today. This success even leads me to a testable prediction:

As mentioned above, no direct measurement of the mtDNA mutation rate has been performed in the most divergent African people groups. I expect that the rate in these groups will be on the order of 1 mutation per 5 to 8 generations—or faster. In fact, I wouldn’t be surprised if these divergent African lineages mutate twice as fast as the non-African lineages—1 mutation per 2.5 to 4 generations. (p. 186)

On p.192, I extend these predictions even further:

Now let’s make the predictions of this model even more specific. If all modern human lineages trace their genetic differences to ancestors who lived only a few thousand years ago, then the history of civilization must be recorded in mtDNA. In other words, if what I’ve described is true, then the Roman and Mongol empires, the Greek conquests, the Persian Empire, and so many other events in recent history must have left their stamp in our mtDNA.

This hypothesis can be tested—and I’m just beginning to investigate this phenomenon. Some of these subnodes (Figure 7.8) might correspond to these recent historical events.

By way of aside, during the debate I specifically invited Dr. Mays to test this prediction with me (see the 1:33:35 and 1:41:10 marks). Along with two other collaborators, I’ve been exploring this prediction for quite some time. Unfortunately, Dr. Mays declined.

What about Neanderthal DNA? Replacing Darwin treats these data like any other:

Up to this point, you may have noticed that I have said nothing about the YEC [Young-Earth Creation] predictions for Neanderthal DNA. I did so deliberately. The explanation for these differences follows from what I just discussed. When Neanderthal and modern human sequences are visualized together in tree format, the Neanderthal sequences branch off of the sub-Saharan African lineages (Figure 7.12).75 From the YEC perspective that I’ve just outlined, it would appear that this lineage derived from ancient Africans. Since some African people groups might mutate their mtDNA faster than non-African people groups do, Neanderthal DNA might simply represent a hyper-mutating lineage—which eventually went extinct.

Alternatively, for technical reasons that I elaborate elsewhere,76 the Neanderthal sequences might be too degraded to be reliable. In short, when I perform DNA sequence analyses in the lab, I tend to throw away DNA sequences that are older than a year. Despite storing them at -20° C, being 12 months removed from their normal cellular environment appears to do irreversible damage to DNA. How much more so when DNA sequences sit in fluctuating temperatures and environmental conditions for thousands of years. (My evolutionary colleagues disagree with my assessment regarding DNA degradation—which is why I still made predictions for Neanderthal DNA under the evolutionary model.)

Regardless of the actual explanation for Neanderthal sequences, the way to investigate these hypotheses is clear. It’s the same method we would use to investigate any hypothesis. If someone thinks that they have an explanation for Neanderthal mtDNA, I would ask them what testable predictions their hypothesis makes. The hypothesis of an ancient timescale fails to make accurate predictions. My explanation of DNA degradation stems from the successful match between the predictions of the YEC timescale and mtDNA differences among modern humans. This may seem mundane. But can any other explanation do better? (p. 192–194, emphasis added)

(Endnotes 75 and 76 reference a lengthy paper I published in 2015 on mitochondrial DNA comparisons across a host of species.)

The Key Omission?
Straightforward mitochondrial DNA coalescence equations reject the evolutionary timescale and confirm the 6,000-year timescale.

To recap, with respect to mitochondrial DNA coalescence, the logic of Replacing Darwin is as follows: (1) Straightforward mitochondrial DNA coalescence equations reject the evolutionary timescale and confirm the 6,000-year timescale; (2) the latter result has led, from a 6,000-year perspective, to testable predictions for mitochondrial DNA mutation rates and to an active research program; (3) therefore, the 6,000-year timescale has no need for modified coalescence equations; (4) in addition, the evolutionary timescale requires a host of modified coalescence equations. However, until these modified equations make testable predictions—in the field of mitochondrial DNA—they remain pseudoscientific at best. I don’t mean pseudoscientific in a demeaning way. Rather, I’m simply applying labels that evolutionists themselves have employed, and I’m applying them consistently across both creation and evolutionary models.

This summary reveals that Dr. Mays did not grasp the main point of Chapter 7. When Dr. Mays claimed that I do not follow the practices of the primary literature, he was actually saying that I do not follow practices that assume the evolutionary timescale is correct. Since the validity of the evolutionary timescale is one of the main questions addressed by my entire book, Dr. Mays’ criticism represents a form of circular reasoning. Furthermore, Dr. Mays offered no testable predictions that flow from his corrected equations.

As a specific illustration of the circularity of his arguments, consider his claims about calibrating mitochondrial mutation rates. For example, at one point in the open discussion section, Dr. Mays seemed to argue that the evolutionary timescale assigned to the fossil record was an independent check on mitochondrial DNA mutation rates (see the 1:38:00 mark). Yes, geology can be an independent check on biology—but not when the geological timescale is the very point in question. (Pages 189–191 make it very clear that the evolutionary geological timescale is one of the points I am questioning in Replacing Darwin.) When Dr. Mays asserts that the mitochondrial DNA mutation rates/substitution rates must be calibrated on the evolutionary timescale, he assumes the point in question—a form of circular reasoning.

With respect to Dr. Mays’ claims that I ignore the differences in relative rates of DNA change in the various subsections of the mitochondrial DNA, this is factually incorrect. For the record, the pedigree studies I cite together examine the rates of change in all sections of mitochondrial DNA. I invite readers to examine and verify this for themselves.

Finally, just to reiterate, it should be obvious from the above discussion and quotes from Replacing Darwin that I do not “throw away” data and equations contrary to the 6,000-year timescale. I do not arbitrarily reject other coalescent equations. I do not arbitrarily reject the reliability of ancient DNA. I do not ignore the role of natural selection, the distinction between mutation rates and substitution rates, or the claims about the need for calculations based on “neutral variation.” Rather, I ask what testable predictions flow from each of these considerations. I have found only one model that makes testable, accurate retrodictions and predictions, and I have endeavored to explore and advance the predictions that flow from it.

Dr. Mays’ Fourth Key Argument

The closest that Dr. Mays came to engaging the actual predictions of Replacing Darwin was at the end of the debate. However, rather than engage the scientific predictions of Replacing Darwin, Dr. Mays attempted to show that the Answers in Genesis (AiG) statement of faith precludes me from making testable predictions. Specifically, the AiG statement in question reads as follows:

By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record. Of primary importance is the fact that evidence is always subject to interpretation by fallible people who do not possess all information.

Dr. Mays was convinced that this statement cannot possibly be compatible with a testable, falsifiable research program. In other words, Dr. Mays thought that the statement of faith forces me to fit scientific facts to predetermined conclusions.

However, the facts surrounding the development, publication, and release of Replacing Darwin are plain: When I was hired at Answers in Genesis (in 2015), I explicitly endorsed the statement of faith. I continue to endorse the statement, and I’ve published a book that contains printed testable, falsifiable predictions. Factually, these events are all real. Therefore, they must be compatible. The only way to claim that the statement of faith is not compatible with the scientific process is to omit certain facts from the discussion. Which participant in this debate is fitting facts to conclusions?

Summary of Key Debate Points

Let’s reflect on what we’ve observed thus far. In the debate, Dr. Mays never addressed the actual predictions of Replacing Darwin. He also provided no testable predictions of his own. Furthermore, when attempting to falsify Replacing Darwin, he resorted to straw men—caricatures of my position, whose falsification has no logical consequence for my book.

In addition, during the open discussion section of the debate, the main arguments that Dr. Mays advanced revealed a troubling pattern. First, consider the fact that Dr. Mays’ primary arguments against Replacing Darwin stemmed from the fields of mitochondrial DNA and nuclear DNA. Second, recall the fact that Replacing Darwin covers these topics in Chapters 7–10. Third, consider the fact that my genetic data in Chapters 7–10 form the core of the arguments that I advance for replacing Darwin (rather than just rebutting him). Fourth, as we’ve just observed, Dr. Mays’ primary arguments against Replacing Darwin revealed his profound unfamiliarity with Chapters 7–10. Fifth, Dr. Mays claimed that my book contained numerous “errors of omission.” Which participant in the debate advanced his arguments with logic that was grounded in “errors of omission”?

Miscellaneous Additional Debate Points

With these clarifying concepts in mind, let’s explore a few remaining aspects of the debate. Besides the larger points that we’ve already discussed, Dr. Mays highlighted what he claims are basic factual errors with my presentation and my book.

For example, he claimed that my description of science with the term “inductive reasoning” was incorrect. (I also use the term in Replacing Darwin.) Instead, he said that the correct term is hypothetico-deductive.

To clarify, if you compare his description of the science process to mine (both in my presentation and in Replacing Darwin), you’ll see a close match. This is a critical point of agreement in order for him and me to have a productive discussion. However, the labels that Dr. Mays and I apply to the scientific process are obviously different.

Since the debate, I’ve revisited the primary sources from which I derived my use of these terms. During my opening presentation, my description of the nature of science leaned heavily on what I’ve gleaned from a leading evolutionist of the 20th Century, Ernst Mayr, and from philosopher of science David Hull. In particular, I have been heavily influenced by Mayr’s book The Growth of Biological Thought (Cambridge, MA: The Belknap Press, 1982), and by Hull’s book Darwin and His Critics: The Reception of Darwin's Theory of Evolution by the Scientific Community (Cambridge, MA: Harvard University Press, 1973). For some reason, I thought Mayr and Hull use the term inductive reasoning and the term hypothetico-deductive synonymously. I’ve re-checked the books above. While both my description of deductive reasoning—“science by thinking”—and my description of the current practice of science matches these authors, I cannot find them equating the terms inductive reasoning and the term hypothetico-deductive. I’m happy to stand corrected on my use of these terms. Dr. Mays and I agree on how science works; I erred on the terminology and am happy to employ the correct language.

Dr. Mays also claimed to have found two other factual errors in Replacing Darwin. Specifically, he said that I erroneously claimed that river otters are native to Hawaii, and he claimed my description of the similarity between rheas and ostriches is in error. With respect to river otters, Endnote 4 in Chapter 4 specifies that I gleaned my biogeographic information from the International Union for Conservation of Nature (IUCN) Red List database. The IUCN describes itself as “the world’s largest and most diverse environmental network” and “the global authority on the status of the natural world and the measures needed to safeguard it.”11 It harnesses the “input of some 13,000 experts.”12 Currently, the IUCN Red List still lists river otters as native to Hawaii,13 and the IUCN graphically depicts its range as still present in Hawaii.14 The river otter appears to be on the decline in Hawaii since IUCN describes it as “absent or rare” there.15 When IUCN changes the status of the river otter to absent/extinct in Hawaii, I will be happy to follow suit.

With respect to Dr. Mays’ claims about the similarity between rheas and ostriches, it’s not clear to me what he finds objectionable. Chapter 4 discusses these species in the following manner:

Flightless birds exist in both Africa (Figure 4.17) (e.g., two species of ostriches, Color Plates 21–22) and South America (Figure 4.18) (e.g., the three species of rheas, see Color Plates 23–24 for two of the species). All five species occupy similar habitats. Nevertheless, the species in closest geographic proximity (i.e., the three species of rheas or the two species of ostrich) look much more alike than species at a great geographic distance. (p. 122)

I’m still not sure what part of this Dr. Mays found in error.

In the future, I’m happy to correct any additional errors as they are found.


In light of the discussion above, what can we conclude from the debate between Dr. Mays and myself? What can we learn about the claims of Replacing Darwin—which was supposed to be the main focus of the debate? Given Dr. Mays unfamiliarity with large chunks of my book, I’m disappointed to say that his criticisms have little relevance to my book. I was hoping that the debate would supply helpful critical feedback on the science in Replacing Darwin.

Perhaps his stated commitment to ridiculing creationism precluded him from assessing my core arguments. Perhaps he will reconsider this approach and, in the future, evaluate Replacing Darwin in a more logically rational way. Again, my goal is not to condemn Dr. Mays; rather, my goal is to further our discussion in hopes of making the science in Replacing Darwin as accurate as possible. I seek critical peer review because I know this is the best way to advance our scientific knowledge, and Dr. Mays is eminently qualified to provide this peer review.

Despite the unproductiveness of my exchange with Dr. Mays, I think the facts of our debate can still inform the wider creation/evolution controversy. Consider again the following:

  • Dr. Mays, a skilled evolutionary biologist whose expertise is evolutionary genetics, had several months to review Replacing Darwin and to organize a strong critique.
  • In the debate, Dr. Mays was unable to demonstrate any flaws in the central arguments of Replacing Darwin, choosing instead to refute straw men.
  • Furthermore, Replacing Darwin contains many testable predictions that future observations could reveal to be true or false. Despite the passing of nearly a year since the publication of these predictions, Dr. Mays did not present a falsification of any of these predictions.
  • For forty years, evolutionists have insisted that creationists make falsifiable predictions. When given the opportunity to engage these predictions, Dr. Mays avoided interacting with them.

Together, these observations point toward a promising start for Replacing Darwin. To be sure, evolutionists are free to disagree with Replacing Darwin. Dr. Mays emphatically did. However, in light of my recent debate, evolutionists would not be justified in calling my book unscientific, nor can they claim that my book has been falsified. Since October 2017, evolutionists have had two chances to refute Replacing Darwin—once on September 5, and once previously in print (e.g., see here and here). Both times, the evolutionary critics of Replacing Darwin were unable to successfully challenge the main claims of my book.

I think this bodes well for the future.


The online evolutionary forum which hosted the debate is a non-Christian venue. As such, the main website for the evolutionary forum contains content that Christians would find morally objectionable. To avoid accidental clicks to undesired links, we have provided direct links to the relevant videos below.

Answers in Depth

2018 Volume 13


  1. See References at the end of this article.
  2. See References at the end of this article.
  3. Around the 1:20:00 mark in the “Stated Clearly: The Science of ‘Replacing Darwin’” video that is linked in the “References” section of this article.
  4. See References at the end of this article.
  5. Approximately 0:05:00 to 0:32:00 of the video.
  6. Page numbers refer to the print edition of Replacing Darwin.
  7. Approximately 0:33:00 to 0:38:00 of the debate video
  8. The papers are as follows:

    Theobald, D.L. 2010. “A Formal Test of the Theory of Universal Common Ancestry.” Nature 465(7295):219–222.

    White, W.T.J., Zhong, B., and Penny, D. 2013. “Beyond Reasonable Doubt: Evolution from DNA Sequences.” PLoS One 8(8): e69924.

    Baum, D.A. et al. 2016. “Statistical Evidence for Common Ancestry: Application to Primates.” Evolution 70(6):1354–63.

    Theobald, D.L. 2011. “On Universal Common Ancestry, Sequence Similarity, and Phylogenetic Structure: The Sins of P-Values and the Virtues of Bayesian Evidence.” Biol Direct 6(1):60.

    Penny, D., Hendy, M.D., and Poole, A.M. 2003. “Testing Fundamental Evolutionary Hypotheses.” J Theor Biol. 223(3):377–85.

    Penny, D., Foulds, L.R., and Hendy, M.D. 1982. “Testing the Theory of Evolution by Comparing Phylogenetic Trees Constructed from Five Different Protein Sequences.” Nature 297(5863):197–200.

  9. The free discussion section begins around the 0:58:15 mark and continues to the end of the video.
  10. See References at the end of this article.
  12. Ibid.


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