Reasons to Believe

Junk DNA: A Problem for the Evolutionary Paradigm?

New Discoveries Raise Questions about Molecular Evolution

One of the most significant challenges to the Christian faith comes from the problem of evil. If God is all-powerful, all-knowing and all-good, why do evil, pain, and suffering exist in the world? In logical terms:

God is all-good.

God is all-powerful.

Evil, pain, and suffering exist in the world.

For skeptics and atheists, the last statement is incompatible with the first two. This inconsistency translates into one of two possible conclusions: either God is not all-powerful or all-good, or God does not exist.

Could it be that a statement is missing from the syllogism? God could have a basis for allowing evil, pain, and suffering to exist. Christian apologists have identified several reasons why God might allow evil, pain, and suffering and still maintain His status as all-good and all-powerful. (See Ken Samples’ book Without a Doubt for a detailed Christian response to the problem of evil.)

While it is necessary to explain how God’s sovereignty and goodness cohere with the existence of evil in the world, a more fundamental consideration involves the absence of the categories of good and evil within an atheistic worldview and the philosophical position of naturalism. If God doesn’t exist, then nature is indifferent. There is no good and evil. When skeptics raise the problem of evil, they inadvertently undermine the very argument they’re trying to make because, for the atheist, evil cannot exist.

A couple of recent scientific discoveries expose a similar problem when skeptics bring up “junk” DNA as a challenge to intelligent design and creationism. These advances provide new insights into the behavior of junk (a noncoding type of) DNA that raise fundamental questions about the validity of molecular evolution.


Evolutionists also highlight the fact that in many instances identical (or nearly identical) segments of junk DNA appear in a wide range of related organisms. Frequently the identical noncoding DNA segments reside in corresponding locations in these genomes. For evolutionists, this clearly indicates that these organisms shared a common ancestor. Accordingly, the junk DNA segment arose prior to the time that the organisms diverged from their shared evolutionary ancestor.


God is all-good.

God is all-powerful.

Junk DNA exists.

For skeptics and atheists, the last statement is incompatible with the first two. Evolutionists ask, “Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?”

Proponents of intelligent design and creationism respond to this objection by highlighting recent discoveries that attribute function to junk DNA. The recognition that junk DNA has function weakens the best argument for biological evolution and common descent. It also explains why identical junk DNA sequences appear in corresponding regions of the genomes of related organisms.

Two recent studies raise much more fundamental questions about junk DNA and, as a consequence, the evolutionary paradigm. One study appeared in a recent issue of PLoS Biology. This work examined the functional significance of a class of junk DNA referred to as ultraconserved elements (UCEs). UCEs don’t code for proteins. Because they are noncoding, evolutionary biologists in the past would have considered these DNA elements to be junk. In the genomes of humans, rats, and mice, however, these DNA elements display virtually identical sequences. (There are approximately 480 UCEs in the human genome.)

Biologists immediately regarded this level of sequence identity as evidence that the UCEs must be functional, though they had no idea about the specific utility of these sequence elements. From an evolutionary standpoint, conservation of DNA sequences serves as a powerful indicator for function, since any change in these sequences via mutations would be weeded out by natural selection. From an evolutionary perspective, rats, mice, and humans share a common ancestor. As these lineages diverged from one another, the UCEs presumably remained unchanged because of their functional importance.

The idea that functional DNA sequences resist change and nonfunctional DNA sequences vary freely is one of the central tenets of molecular evolution. If the UCEs were nonfunctional, then mutational changes should be inconsequential. Over time, changes in the DNA sequences should accrue as rats, mice, and humans evolved along different evolutionary trajectories. As a consequence the sequences of the UCEs in these species should differ.

Biologists have speculated that UCEs regulate gene activity. For example, these sequence elements cluster near developmental genes. Researchers confirmed the functional importance of UCEs by deleting four carefully selected UCEs in the mouse genome. The deleted UCEs otherwise reside near key developmental genes. Presumably, their close proximity to these genes reflects the regulatory influence that these UCEs exert on the developmental genes.

To everyone’s surprise, the mice with deleted UCEs were perfectly healthy. This result suggests that UCEs are not functional.

It is still possible that UCEs are functional. For example, if the UCEs are redundant within the genome, disabling a limited number of them would not harm the mice, since back-up copies of the UCEs would take over the function of the deleted sequences. The experimental design did not take into account this possibility.

Apart from this caveat, taken at face value the deletion experiments indicate that UCEs are not functional. This, of course, is troubling for intelligent design and creationism models, which maintain that all of the classes of junk DNA will ultimately turn out to be functional. Ironically, however, this discovery is much more troubling for the evolutionary paradigm.

One of the cornerstone ideas supporting molecular evolution is the notion that conserved DNA sequences are functional. But this recent study raises the very real possibility that this is not the case at all. If so, then the deletion result makes absolutely no sense. Why would evolutionary processes preserve UCEs if their loss has no significant impact on the mice? Could it be that fundamental deficiencies exist in the evolutionary paradigm?

Equally problematic are the results from the pilot phase of the ENCODE project, published in the summer of 2007. The ENCODE project is a multi-million dollar international effort to catalog all of the functional sequences in the human genome. The initial stage of the project involved a detailed search for every functional element contained in a 1% sample of the human genome.

Based on this survey, researchers discovered that parts of the human genome previously viewed as nonfunctional junk are transcriptionally active, signifying function. Surprisingly, these sequences show little conservation in the genomes of other mammals. In other words, functional sequences freely vary without any evidence for evolutionary constraint.

This recognition runs contrary to the central ideas of molecular evolution and, too, raises fundamental questions about the validity of the evolutionary paradigm.

Consequently, junk DNA is not just a problem for intelligent design proponents and creationists. It is a problem for evolutionary biologists as well.

If skeptics bring up the problem of evil as a way to challenge God’s existence, they must also be willing to explain how the categories of good and evil fit within a naturalistic framework. In like manner, if evolutionary biologists bring up junk DNA as a challenge to the work of a Creator, they must be willing to explain the new understanding of junk DNA behavior within an evolutionary framework. Based on these new discoveries, the fundamental ideas about molecular evolution and the behavior of functional and nonfunctional DNA sequences no longer hold.


Dr. Fazale Rana
