When I began college, I signed up for a premed major but quickly changed my course of study after my first biology class. Biology 101 introduced me to the fascinating molecular world inside the cell. At that point, I was hooked. All I wanted was to become a biochemist.

But there was another reason why I gave up on the prospects of becoming a physician. I didn’t think I had the mental wherewithal to make decisions with life and death consequences for patients. And to this day, I deeply admire men and women who do possess that mental fortitude.

The problem is that once someone dies, they don’t come back to life. I knew this reality would loom large for every decision I would make as a physician. Over 100,000 years of human experience teaches that when people die, they remain dead. And this experience is borne out by centuries of scientific study into human biology.

When It Comes to the Virgin Birth and the Resurrection, Christianity is Anti-Scientific

Yet at the heart of the Christian faith is the idea that Jesus Christ was raised from the dead. To be clear: This idea is counter to human experience and thoroughly anti-scientific.

On the other hand, a strong circumstantial case based on historical facts can be marshaled for the life, death, and resurrection of Jesus Christ. The historical evidence for the resurrection combined with the fact that this event transcends the laws of nature is clear evidence for Christians that God intervened in human history to perform a miracle—to act in a way that contravenes the laws of nature.

Even though alternative explanations for the facts surrounding the resurrection fall short, many skeptics remain unconvinced that the resurrection happened. Why? Because it defies scientific explanation—dead people don’t come back to life.

Yet, I don’t know of any evangelical or conservative Christian that would deny the resurrection. Nor would these same Christians deny the virgin birth—another event that also defies scientific explanation. As Christians, we readily embrace anti-scientific ideas when they are central to Christianity. We don’t view them as allegorical or as literary constructs that teach theological truths so that they can be accommodated to scientific truth. We regard them as real events in space and time, in which God discernibly acted in a miraculous way.

Not only are the resurrection and the virgin birth anti-scientific, but the explanations for these two events completely fly in the face of methodological naturalism—the philosophical idea undergirding contemporary science. According to this philosophical system, scientific explanations must rely on material causes—natural process mechanisms. Any explanation that appeals to the work of a supernatural agent—a Creator—or processes that defy known laws of nature can’t be part of the scientific construct. By definition, these types of explanations are forbidden. Yet when it comes to the resurrection and the virgin birth, Christians reject methodological naturalism without apology. We don’t try to force these events within the framework of methodological naturalism by arguing that God used the laws of nature to affect the virgin birth or the resurrection. Why? Because the explanations for these events go beyond nature’s laws—these events are transcendent miracles.

Adam and Eve’s Creation and Importance to the Christian Faith

Should we not be willing to do adopt the same posture when it comes to the question of origins, including the historicity of Adam and Eve?

Like the virgin birth and the resurrection, Adam and Eve’s existence and role as humanity’s founding couple impacts key doctrines of the Christian faith, such as inerrancy, the image of God, the fall, original sin, marriage, and the atonement.

Venema and McKnight’s Adam and the Genome

The importance of a historical Adam and Eve to the Christian faith explains why New testament scholar Scot McKnight (Northern Seminary) spent four chapters—half of a book—in Adam and the Genome trying to convince the reader that the existence of this primordial couple is not critical to the Christian faith. McKnight felt this exercise necessary because he concedes that comparative genomics and population genetics demonstrate the truth of human evolution and the impossibility that humanity arose from a primordial pair—an Adam and an Eve.

Coauthored along with biologist Dennis Venema (Trinity Western University), Adam and the Genome presents a scientific and theological case for evolutionary creationism—the idea that God employed evolutionary processes to bring about the design, origin, and history of life, including humanity.¹

The case Venema presents for human evolution serves as the motivation for McKnight’s contribution to the book. In fact, McKnight’s portion of Adam and the Genome is just the latest in a growing list of responses by evangelical and conservative Christian theologians to the specter of human evolution. Though this idea has been in play since the late 1800s with the publication of Darwin’s The Descent of Man, recently, Christian scholars, such as McKnight, feel compelled to sort through the theological fallout of this scientific explanation for human origins because of the emergence of genomics. Now that we have the capability to efficiently sequence and compare the entire genetic makeup of humans and other creatures, such as the great apes, the sense is that the case for human evolution has become undeniable.

So, have Venema and McKnight made their case? Is human evolution a fact? Are Adam and Eve merely theological constructs?

Having left the theological response to McKnight in the hands of scholars such as Gavin Ortlund and Ken Keathley, in part 1 of this review, I offered my reflections on Venema’s intellectual journey from an antievolutionary intelligent design proponent to someone who embraces and now advocates for evolutionary creationism, concluding that it wasn’t scientific evidence alone that motivated Venema and many other evolutionary creationists to adopt this view. I contend that many evolutionary creationists adopt this view, in part, because they are reacting to the disappointment they felt when they realized that they had been unintentionally mislead (when they were young and scientifically naïve) by well-meaning Christians who taught them young-earth creationism. I argue that in abandoning young-earth creationism, many evolutionary creationists have moved to the opposite extreme, rejecting any science-faith model that doesn’t fully embrace mainstream scientific ideas—even if those ideas challenge key biblical doctrines.

In this second part of my review, I offer my thoughts on the core of Venema’s case for human evolution: namely, work in comparative genomics and population genetics, found in chapters two and three, respectively, of Adam and the Genome.

Venema’s goal in his contribution to Adam and the Genome is to communicate the “undeniable” evidence for human evolution. Specifically, Venema discusses recent work in comparative genomics with the hope of explaining to the motivated layperson why many biologists regard the shared features in genomes as evidence for common ancestry. Applying that insight to whole genome comparisons of humans, chimpanzees, and other great apes, Venema explains why biologists think humanity shares an evolutionary history with the great apes—in fact, with all life on Earth. Focusing on pseudogenes, Venema concludes the case for common descent by discussing the widespread occurrence of nonfunctional DNA sequences located throughout the genomes of humans and the great apes—usually in corresponding locations in these genomes. Venema argues that these one-time functional DNA sequence elements were rendered nonfunctional through mutational events and are retained in genomes as vestiges of evolutionary history.

Role of Methodological Naturalism in Venema’s Argument

Admittedly, the scientific case Venema presents for common descent is strong—at least at first glance. (Though, in making his case, he does overlook some significant scientific issues confronting evolutionary biologists, such as the incongruency of evolutionary trees. In other words, evolutionary biologists wind up with different evolutionary trees depending on the region of the genome they use to build the trees. This is certainly the case when the human genome is compared to the genomes of chimpanzees and gorillas. One-third of the human genome more closely aligns to the gorilla genome than to the chimpanzee genome, indicating that gorillas, not chimpanzees, are our closest evolutionary relative.)

Having acknowledged the strong case Venema makes for human evolution, I want to make sure that the reader recognizes the powerful, yet often unrecognized, role methodological naturalism plays, propping up the case for common descent, and, hence, human evolution. Because of the influence of methodological naturalism, the only permissible way to interpret shared genetic features within the mainstream scientific enterprise is from an evolutionary framework. Any explanation evoking a Creator’s involvement is off the table—even if a creation model can account for the data, and it can. However, this approach will never receive a hearing in the scientific community today because it violates the tenets of methodological naturalism. In other words, because of methodological naturalism’s sway, common descent, and, consequently, human evolution must be true by default. No other option is allowed. No other explanation, no matter how valid, is permitted.

Like most evolutionary creationists, Venema and McKnight embrace methodological naturalism when it comes to the question of human origins. Yet they readily reject this idea when it comes to the virgin birth and the resurrection. As a result, their approach to science is inconsistent. Why apply the principles of methodological naturalism to human origins but not to questions surrounding the resurrection or the virgin birth?

It is true that methodological naturalism has a demonstrated track record of success—when it guides investigation of secondary, proximal causes. But this scientific approach often comes up short when scientific questions focus on primary or ultimate causes, such as the origin of the universe or the origin of life.

In fact, I wonder if Christians should embrace methodological naturalism at all. At its essence, this philosophical approach to science is inherently atheistic. A Christian could justify embracing a limited or weak form of methodological naturalism because Scripture teaches that God has providentially instituted processes that operate within the creation to sustain it. When studying these types of phenomena, application of methodological naturalism appears to be justified because the focus is on identifying and characterizing secondary, proximal causes.

But what about the question of origins? Given the descriptions of God’s creative work in the creation accounts, it looks as if God intervened in a direct personal way when it comes to the origin of the universe and the origin and history of life—particularly when it comes to humanity’s beginnings. If so, then methodological naturalism becomes an impotent guide for scientific study because it insists that these events must have mechanistic causes—even if they may not. By default, an atheistic worldview is imposed on the scientific enterprise. Within the framework of methodological naturalism, science no longer becomes the quest for truth, but a game played, with the goal being to produce a material causes explanation for the universe and phenomena within the universe, even if material causes aren’t the true explanation—and even if the explanations leave something to be desired.

Adherents of methodological naturalism defend its restrictions by arguing that science can’t put God in a test tube. Yet it is a straightforward exercise to show that science does have the tool kit to detect the work of intelligent agents within nature and to characterize their capabilities. By extension, science should have no problem detecting a Creator’s handiwork—and even determining the Creator’s identity.

So, what happens if we relax the restrictive requirements of methodological naturalism when we investigate the question of human origins? If we do, it becomes evident that human evolution isn’t unique in its capacity to explain shared genetic features. It becomes conceivable that the shared genetic features in the genomes of humans and the great apes could reflect similar designs employed by a Creator. To put it another way, the shared genetic features could reflect common design, not common descent.

Though this approach to the data is forbidden by contemporary mainstream science, this interpretative approach is not anti-scientific. In fact, there is a historical precedent for viewing shared genetic features as evidence for common design, not common descent. Prior to Darwin, distinguished biologist Sir Richard Owen interpreted shared (homologous) biological structures (and, consequently, related organisms) as manifestations of an archetype that originated in the mind of the First Cause, not the products of descent with modification. Darwin later replaced Owen’s archetype with a common ancestor. Again, the key point is that it is possible to conceive of an alternative interpretation of shared biological features, if one is willing to allow for the operation of a Creator within the history of life.

If the action of an intelligent agent becomes part of the construct of science, and hence, biology, then the shared molecular fossils in the genomes of humans and the great apes (such as pseudogenes) could be seen as shared design features. These sequence elements point to common descent only if certain assumptions are true:

1. the genomes’ shared structures and sequences are nonfunctional;
2. the events that created these features are rare, random, and nonrepeatable;
3. no mechanisms other than common descent (vertical gene transfer) can generate shared features in genomes.

However, recent studies raise questions about the validity of these assumptions. For example, in the last decade or so, molecular biologists and molecular geneticists have discovered that most classes of “junk DNA,” including pseudogenes, have function. (Interested readers can find references to the original scientific papers in the expanded second edition of Who Was Adam? and The Cell’s Design.) In fact, the recently proposed competitive endogenous RNA hypothesis explains why pseudogenes must display similar sequences to their functional counterparts in order to carry out their cellular function.

Moreover, as discussed in Who Was Adam?, researchers are now learning that many of the events that alter genomes’ structures and DNA sequences are not necessarily rare and random. For example, biochemists have known for quite some time that mutations occur in hotspots in genomes. Recent work also indicates that transposon insertion and intron insertion occur at hot spots, and gene loss is repeatable. New studies also reveal that horizontal gene transfer can mimic common descent. This phenomenon is not confined to bacteria and archaea but has been observed in higher plants and animals as well, via a vector-mediated pathway or organelle capture.

These advances serve to undermine key assumptions needed for a common descent argument. Considering these discoveries, is it possible to make sense of the shared genomic architecture and DNA sequences within the framework of a creation model?

A Scientific Creation Model for Common Design

What follows is a brief abstract of the RTB genomics model. A more detailed description and defense of our model can be found in the second expanded edition of Who Was Adam?

A key tenet of the model is the idea that organisms—and hence, their genomes—are the products of God’s direct creative activity. But once created, genomes are subjected to microevolutionary processes.

In brief, our model explains the similarities among organisms’ genomes in one of two ways:

1. Reflecting the work of a Creator who deliberately designed similar features in genomes according to: (1) a common function, or (2) a common blueprint.
2. Reflecting the outworking of physical, chemical, or biochemical processes that (1) occur frequently, (2) are nonrandom, and (3) are reproducible. These processes cause the independent origin of the same features in the genomes of different organisms. These features can be either functional or nonfunctional.

Our model also explains genomes’ differences in one of two ways:

1. Reflecting the work of a Creator who deliberately designed differences in genomes with distinct functions.
2. Reflecting the outworking of physical, chemical, or biochemical processes that reflect microevolutionary changes.

In principle, our model can account for similarities and differences in the genomes of organisms as either the deliberate work of a Creator or via natural-process mechanisms that alter the genomes after creation.

Were Adam and Eve Real?

Having argued for the reality of human evolution, Venema focuses attention on Adam and Eve’s historicity. If humanity arose through an evolutionary process, then Venema rightly points out that humanity must have begun as a population, not a primordial couple—by definition. According to evolutionary biologists: evolution is a population-level phenomenon. That being the case, if humanity arose via evolutionary processes, then there could never have been an Adam and an Eve. In support of this idea, Venema then discusses population genetics studies that indicate humanity began as an initial group of around 10,000 individuals. Based on these methods, the genetic diversity among humans today is too great to have come from just two individuals. Venema then goes on to explain how evolutionary biologists reconcile the existence of Mitochondrial Eve and Y-chromosomal Adam (understood to be an actual woman and man, respectively) with the idea that humanity began as a population.

Some Thoughts on Methods Used to Estimate Humanity’s Initial Population Size

Did humanity originate from a primordial pair?

One point Venema fails to acknowledge is that, at best, the population sizes generated from genetic diversity data are merely estimates, not hard and fast values. The reason: the mathematical models these methods are based on are highly idealized, generating differing estimates based on several factors.

More significantly, recent studies focusing on birds and mammals, however, raise questions as to whether these models predict population size. As the author of one study states, “Analyses of mitochondrial DNA (mtDNA) have challenged the concept that genetic diversity within populations is governed by effective population size and mutation rate . . . the variation in the rate of mutation rather than in population size is the main explanation for variations in mtDNA diversity observed among bird species.”²

In fact, several studies—involving white-tail deer, mouflon sheep, Przewalski’s horses, white-tail eagles, the copper redhorse, and gray whales—in which the original population size was known, the measured genetic diversity generations later was much greater than expected based on the models. In turn, if this data was used to estimate initial population size, the numbers would be much greater than the models predicted.

Did humanity originate from a single pair? Even though population estimates indicate humanity originated from several hundred to several thousand individuals based on mathematical models, it could well be that these numbers overestimate the original numbers for the first humans. And given how poorly these population size models perform, it is hard to argue that science has falsified the notion that humanity descended from a primordial pair.

Final Thoughts

In Adam and the Genome, Venema makes a compelling case for human evolution, but he fails to tell the entire story. Venema overlooks a serious problem facing the evolutionary paradigm: namely, the incongruencies of evolutionary trees built from genetic data. He also neglects to communicate a legion of exciting discoveries made since the human genome sequence was completed—discoveries indicating that virtually every class of junk DNA has function. These discoveries undermine evolution’s case and make it apparent that we are in our infancy when it comes to understanding the structure and function of the human genome. The more we learn, the more evident its elegant and ingenious design.

At the end of the day, the case for human evolution is propped up by the restrictions of methodological naturalism. As we have demonstrated in Who Was Adam?, when this restriction is relaxed, it is possible to advance a competing creation model that can account for the data from comparative genomics.

One thing has become clear to me after reading Adam and the Genome. It is no longer effective for creationists and intelligent design proponents to focus our efforts on taking pot shots at human evolution. We must move beyond that type of critique and develop a philosophically robust framework for science that can compete with methodological naturalism and advance scientific models within that new framework with the capacity of explaining the data from comparative genomics and population genetics.

I am confident we can. We simply must roll up our sleeves and get to work.

Resources—Theological Reflections on Adam and the Genome

• Adam and the Genome: Some Thoughts from Ken Keathley
  by Ken Keathley (article)
• A Review of Adam and the Genome by Gavin Ortlund (article)

Resources—An Old-Earth Creationist Perspective on the Scientific Case for a Traditional Biblical View of Human Origins

• Who Was Adam? A Creation Model Approach to the Origin of Humanity by Fazale Rana with Hugh Ross (book)

Resources—The Problem of Incongruent Evolutionary Trees

• DNA Sequences: More Is Not Better by Fazale Rana (article)

Resources—Science Can Detect the Creator’s Handiwork in Nature

• Can Science Detect the Creator’s Fingerprints in Nature? by Fazale Rana (article)
• Can Science Identify the Intelligent Designer? by Fazale Rana (article)

Resources—Common Design as a Valid Scientific Model

• Archetype or Ancestor: Sir Richard Owen and the Case for Design by Fazale Rana (article)

Resources—Junk DNA is Functional

• ENCODE Junks Evolutionary Concept by Fazale Rana (article)
• Protein-Binding Sites ENCODEd into the Design of the Human Genome by Fazale Rana (article)

Resources—Pseudogenes are Functional

• Unitary Pseudogenes Have Function! Part 1 by Fazale Rana (article)
• Unitary Pseudogenes Have Function! Part 2 by Fazale Rana (article)

Resources—Mutational Hot Spots in Genomes

• Junk DNA Hot Spots Connect to the Case for Intelligent Design by Fazale Rana (article)
• Junk DNA Hot Spots Have Evolutionary Biologists Singing the Blues by Fazale Rana (article)
• Does Retroviral DNA Insert Randomly into Genomes? by Fazale Rana (article)

Resources—Adam and Eve’s Historicity

• Were They Real? The Scientific Case for Adam and Eve by Fazale Rana (article)
• Adam and Eve: A Primordial Pair or a Population? by Fazale Rana (article)
• Conservation Biology Studies Elicit Doubts about First Human Population Size by Fazale Rana (article)