An Unexpected Find

New research uncovers an unanticipated role for pseudogenes, undermines one of the best arguments for biological evolution

As I described last week, I love trolling about the aisles of club stores in search of free food samples. Usually all I find is the standard fare: a portion of a chicken nugget dipped in sweet-and-sour or barbeque sauce, a bite of pizza, a smear of cheese on a cracker, etc. But every once in a while I’ll happen upon a gourmet food item that is so delectable I have to concoct a way to sneak a second helping.

Recently a team of scientists happened upon a “delicious” new role for pseudogenes. It appears that this form of junk DNA helps to regulate gene expression. This unexpected discovery indicates that pseudogenes are functional elements, ebbing away support for one of evolution’s best arguments.

The challenge represented by junk DNA takes on a similar logical form to the problem of evil.
God is all-good.
God is all-powerful.
God is all-knowing.
Junk DNA exists.

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

For evolutionary biologists, shared junk DNA sequences clearly indicate that these organisms also shared a common ancestor. According to their interpretation, the junk DNA segment arose prior to the time that the organisms diverged from their mutual evolutionary ancestor.

Pseudogenes

Evolutionary biologists consider pseudogenes to be the dead, useless remains of once functional genes. According to this view, severe mutations destroyed the capacity of the cell’s machinery to “read” and process the information contained in these genes. Still, pseudogenes possess the tell-tale signatures that allow molecular biologists to recognize them as genes, albeit nonfunctional ones. Molecular biologists recognize several classes of pseudogenes.

Duplicated pseudogenes are the largest class. Molecular biologists posit that these DNA segments arose when a gene(s) underwent duplication in the genome. After this event, the duplicated copies experienced severe mutations that rendered them unrecognizable as a functional gene by the cell’s machinery. Loss of duplicated gene function has little, if any, effect on an organism’s fitness since an intact functional copy still exists.

Processed pseudogenes are another class. As conceived by molecular biologists, the pathway that produces processed pseudogenes is quite complex. The mechanism that generates processed pseudogenes overlaps with the one that the cell’s machinery uses to make proteins. Genes contain the information that the cell needs to make proteins. As the first step in protein synthesis, the cell’s machinery makes a copy of the gene in the form of RNA, a biomolecule class that structurally resembles DNA. The RNA message migrates to a subcellular particle, called a ribosome. Here the cell’s machinery “reads” the information stored in the RNA message to form the protein encoded by the messenger RNA.

Before the RNA message migrates to the ribosome, the cell’s machinery alters it in several ways. This includes removing segments in the RNA message that correspond to noncoding regions found in the gene (introns), splicing together the RNA segments that correspond to the gene’s coding regions (exons), and modifying and making additions to the ends of the RNA molecule. Processed pseudogenes are thought to arise when an enzyme, called reverse transcriptase, generates DNA from the processed RNA message. Once produced, this newly formed DNA inserts back into the genome. The newly inserted DNA, now called a processed pseudogene, resembles the gene from which it originated, yet also contains tell-tale signs that it has been processed. This type of pseudogene is nonfunctional because it lacks the regions that surround functional genes used by the cell’s machinery to initiate the production of the RNA message.

Pseudogenes Can Regulate Gene Expression Via an RNA Silencing Mechanism

Recent work by a team of scientists uncovered evidence that pseudogenes silence their corresponding homologous genes through the activity of small interfering (si) RNA molecules. These tiny RNA molecules are formed when an enzyme called dicer chops up double stranded RNA molecules into small fragments.

One of the strands of RNA from the resulting small double stranded fragments, called the guide strand, directs a large protein complex, called RISC, to chew up any messenger RNA in the cell with a complementary sequence to that of guide strand. The destruction of the messenger RNA is executed by a component of RISC, called argonaute.

In light of this mechanism, the sequence similarity between the pseudogene and the corresponding intact, functional gene makes sense. It’s this similarity that allows the guide sequences produced by the double-stranded RNA derived from the pseudogene to recognize the messenger RNA copied from the functional gene. In this sense, one could even argue that rather than arising as the outworkings of accidental events, pseudogenes could have been intentionally introduced into the genomes of organisms by the Creator as a regulatory device.

This new insight into the utility of pseudogenes is truly unexpected, and quite scrumptious. It makes me want to sneak back to the “snack table” of scientific discoveries for more. If pseudogenes stand as the work of a Creator there will be more opportunities to sample these types of breakthroughs in the future. I can hardly wait.