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Scientific Upset: More Functions for Pseudogenes

Long-held scientific consensus that pseudogenes are functionless genetic junk has been further discredited by the discovery that some pseudogenes code for proteins. Does this unexpected finding support the evolutionary paradigm—or creation models?

During the course of the football season, sports pundits fill the airwaves with predictions about the outcome of games to be played each week. Little agreement exists, and when the prognosticators do reach a consensus, invariably an upset occurs. No matter how much you know about the sport, it’s difficult to predict the outcome of a football contest. As the adage goes, “That’s why the game is played.”

Like armchair quarterbacks, scientists make predictions about the outcome of experiments and observational studies. In fact, making and evaluating predictions defines the scientific enterprise. As new work by researchers from Sweden attests, however, making successful predictions—particularly when they deal with so-called junk DNA—can be just as tricky as forecasting the results of a football game.1

Pseudogenes with Function

Evolutionary biologists long regarded pseudogenes as nonfunctional junk, a class of DNA elements that represents the remains of genes that lost their function due to mutations. Employing the evolutionary paradigm, biologists assumed that pseudogenes lack function solely based on their characteristics. For decades, this prediction was left unconfirmed experimentally—until the recent advent of genomics. Now, after nearly 10 years of research, molecular biologists and geneticists have delivered a scientific upset: pseudogenes display function. Specifically, they play a role in regulating gene expression.2 (As an example, see “Functional Pseudogenes Are Everywhere!”)

The researchers from Sweden have uncovered a second possible function for pseudogenes. They developed a new method of identifying and determining which genes are used to make proteins. Using their method, they discovered a number of previously unidentified genes in the human and mouse genomes. About 35 percent of the newly identified genes are pseudogenes that the cell’s machinery uses to produce proteins—a completely unexpected result. As one of the researchers noted, “Our study challenges the old theory that pseudogenes don’t code for proteins.”3

And that’s why experiments are performed.

Reflecting Common Design

The extent to which pseudogenes encode for useful protein products remains unknown at this point. Still, this study opens up the possibility that a significant fraction is translated. Moreover, the recognition that pseudogenes display a range of functions mitigates one of the most compelling arguments for common descent.

Many people believed these nonfunctional DNA sequences stood as a potent challenge to intelligent design and as powerful evidence for biological evolution. It didn’t make sense that a Creator would intentionally create genomes with junk sequences and then, on top of that, introduce identical (or nearly identical) versions of these sequences into the corresponding locations within the genomes of different organisms. A shared evolutionary history made better sense of shared pseudogenes.

But more and more genomics research implies that the shared pseudogene sequences in genomes could just as easily reflect common design. (For a more detailed discussion, see “Archetype or Ancestor? Sir Richard Owen and the Case for Design.”) While the evolutionary paradigm initially predicted that pseudogenes lack function, a creation model or intelligent design framework has long held to the expectation that most, if not all, of the genome, including pseudogenes, has purpose. (For an example, see “‘Junk’ DNA Not So Junky.”)

For a historical perspective on the key scientific discoveries demonstrating the central role pseudogenes play in gene expression, check out these articles:

  1. Rui M. M. Branca et al., “HiRIEF LC-MS Enables Deep Proteome Coverage and Unbiased Proteogenomics,” Nature Methods 11 (January 2014): 59–62.
  2. Karolinska Institutet, “Protein Coding ‘Junk Genes’ May Be Linked to Cancer,” ScienceDaily, posted November 17, 2013, http:/