Are Pseudogenes Junk?

Are Pseudogenes Junk?

Evolutionary biologists regard “junk” DNA as one of the most potent pieces of evidence for biological evolution. Often identical (or nearly identical) segments of junk DNA occur in a wide range of related organisms. Frequently the identical junk DNA segments reside in corresponding locations in these genomes. For evolutionists, this clearly indicates that these organisms shared a common ancestor. According to this view, these junk DNA segments arose prior to the time when the organisms diverged from their shared evolutionary ancestor. Skeptics ask, “Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?”

Pseudogenes are one class of junk DNA. Evolutionary biologists consider pseudogenes to be the dead, useless remains of once-functional genes. Presumably, severe mutations destroyed the capacity of the cell’s machinery to “read” and process the information contained in these genes. Still, pseudogenes possess the telltale signatures that allow molecular biologists to identify them as one-time genes.

Formally, molecular biologists recognize pseudogenes in an organism’s genome by using two criteria: (1) sequence similarity to a known gene, and (2) evidence that the pseudogene is nonfunctional. Molecular biologists have traditionally viewed mutations to DNA sequences that appear to be catastrophic as evidence for nonfunctionality.

A recent perspectives article written by Deyou Zheng and Mark Gerstein, two molecular biologists from Yale University, published in Trends in Genetics casts aspersions on the criteria used to identify pseudogenes.1 In fact, recent discoveries—which motivated this article—raise questions as to whether pseudogenes are really junk at all.

Zheng and Gerstein point out that several research teams have reported that DNA sequences identified as pseudogenes play a critical role in regulating gene expression. The regulatory activity of pseudogenes seems to be related to the sequence similarity they share with their corresponding “functional” gene. They also highlight recent work that indicates that up to 50% of pseudogenes in some genomes appear to be transcriptionally active. (Transcription is the biochemical process that makes use of the information in the DNA sequences of genes.) This new insight runs contrary to the traditional view that regards pseudogenes as transcriptionally silent. Zheng and Gerstein also note that molecular biologists have also uncovered pseudogenes that appear to be under mutational constraints, meaning that they more than likely have function.

The authors conclude their perspectives piece by noting that nonfunctionality is not a legitimate criterion to use to categorize a DNA sequence as a pseudogene!

Pseudogenes appear to be functional, and, as Zheng and Gerstein point out, this class of “junk” DNA seemingly performs a wide range of biochemical functions. It seems premature to declare pseudogenes as the imperfect products of evolutionary processes.

For a detailed discussion of additional evidence that junk DNA is functional, see Who Was Adam?

  1. Deyou Zheng and Mark B. Gerstein, “The Ambiguous Boundary between Genes and Pseudogenes: The Dead Rise Up, or Do They?” Trends in Genetics 23 (2007): 219-24.