Reasons to Believe

Junk DNA Hotspots Connect to the Case for Intelligent Design

For many people, me included, looking for a Wi-Fi hotspot has become part of daily life.

The quest to find hotspots has also become part of molecular geneticists’ daily routine. But instead of looking in coffee shops, cafés, etc., these scientists search for hotspots in genomes.

View Image

As scientists search through genomes, they are discovering that the biochemical events that lead to the origin of junk DNA are not random but are highly reproducible, occurring at the same locations within the genome. These locations are referred to as “insertion hotspots.”

The growing recognition that the origin of junk DNA sequences is not random has profound implications for the creation/evolution debate, weakening one of the most powerful arguments for the evolutionary paradigm.

Junk DNA Evidence for Evolution?

According to evolutionary biologists, junk DNA results when undirected biochemical processes and random physicochemical events transform a functional DNA segment into a useless molecular artifact. They argue that pieces of junk DNA remain part of an organism’s genome solely because of its attachment to functional DNA. In this way, junk DNA persists from generation to generation.

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 segments reside in corresponding locations in these genomes. Because evolutionary biologists think the events that produce junk DNA are rare and random, the existence of shared junk DNA sequences only makes sense if these organisms arose from a common ancestor. As such, the segments emerged prior to the time the organisms diverged from their shared evolutionary ancestor.

Why would a Creator purposely introduce nonfunctional, junk DNA at the exact same location in the genomes of different, but seemingly related, organisms?


Junk DNA Function

Over the last five years or so, scientific advance has provided a partial answer to this question. As detailed in both The Cell’s Design and Who Was Adam?, biologists discovered that many classes of junk DNA possess function. (Go here and here to read articles on the functional importance of junk DNA.) The recognition of junk DNA’s utility weakens the argument for biological evolution and common descent. It may also explain why identical junk DNA sequences occur in corresponding regions of related organisms’ genomes. The location of these sequences may be critical for them to operate properly.

But what about the sequences that currently don’t appear to play useful roles? Do these sequence elements—which may be true junk— provide evidence for common descent, and consequently, biological evolution? How else can they be explained?


Not Rare or Random

The origin of junk DNA sequences may notbe random or rare. Instead, the mechanisms that generate these sequences appear to have regularity to them, which leads to predictable outcomes.

Researchers from Tel-Aviv University in Israel recently discovered that this is the case for a class of junk DNA called transposable elements.1 These pieces of DNA have the capacity to move around organisms’ genomes. There are three types of transposable elements.

  • Class 1 makes a copy of itself; then, the copy inserts into another location within the genome.
  • Class 2 moves from one location in the genome to another directly.
  • Retroviruses. These are infectious agents that insert themselves into organisms’ genomes.


Generally, scientists consider all of these mobile pieces of DNA destructive because if they insert into a gene, it will disrupt and result in a mutation.

Researchers long thought that the insertion of transposable elements into the genome took place at random locations. The scientists from Israel discovered that this is not the case at all. Instead transposable elements insert within specific locations (called hotspots). Interestingly, these hotspots are also located within transposable elements. The net result is that transposable elements are often found nested within each other. Specifically, the researchers discovered that transposable elements will preferentially insert into certain classes of transposable elements; they will insert with a specific orientation and at specific locations within the host transposable element sequence.

This result opens up the possibility that some classes of junk DNA may genuinely be junk, and yet reflect, not common ancestry, but reproducible, nonrandom biochemical events. Biochemists have known for years that mutations frequently occur in nonrandom fashion at hotspots. It is only reasonable to expect that other types of junk DNA have a nonrandom genesis.

So why do organisms possess identical junk DNA sequences at corresponding locations within their genomes? From a creation model standpoint there appears to be two facets to the response. One relates to the usefulness of junk DNA sequence elements designed by the Creator.  The other acknowledges that some sequences of junk DNA truly are garbage originating through natural processes. But the discovery of insertion hotspots for introns (as I wrote about previously) and transposable elements raises the possibility that other junk DNA sequences may arise by repeatable, nonrandom mechanisms and suggests that these shared sequences do not reflect common ancestry, but reproducible biochemical events.

I hope that after you read this article that you will look for a Wi-Fi hotspot and email this article describing these findings to someone else.

Subjects: Junk DNA

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana


  1. Asaf Levy et al., “Large-Scale Discovery of Insertion Hotspots and Preferential Integration Sites of Human Transposed Elements,” Nucleic Acids Research 38 (2010): 1515–30.