Faith & Science
Et tu, Pseudogenes? Another Type of “Junk” DNA Betrays Darwinian Predictions
Evolutionists have long cited pseudogenes as a type of “junk” DNA that demonstrates an unguided evolutionary origin of the genome. Richard Dawkins typifies this view:
Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.
(Richard Dawkins, “The Information Challenge,” The Skeptic, Vol. 18 (4) (December, 1998). For a full rebuttal, see here.)
Sounding much like Dawkins, Francis Collins and Karl Giberson discuss pseudogenes to argue that is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” (Karl W. Giberson and Francis S. Collins, The Language of Science and Faith: Straight Answers to Genuine Questions, p. 43 (InterVarsity Press, 2011).)
But are pseudogenes actually “nonfunctional … faulty duplicates … that do nothing” (Dawkins) or “broken DNA” (Giberson and Collins)? Consider the abstract of a new review article in the decidedly non-pro-ID journal RNA which sounds decidedly different from atheistic evolutionist Dawkins and theistic evolutionists Giberson and Collins:
Pseudogenes have long been labeled as “junk” DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.
(Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, “Pseudogenes: Pseudo-functional or key regulators in health and disease?,” RNA, Vol. 17:792-798 (2011).)
According to the paper, one way to infer function for pseudogenes is to find degrees of similarity between pseudogenes that are higher than what would be expected if they were functionless DNA acquiring mutations at a neutral rate. If pseudogenes are functional, then that suggests they would tend to be intolerant to mutations that change DNA sequence. In such an instance, the sequence of a pseudogene is said to be “conserved.” The paper explains:
Pseudogenes are sometimes considered to represent ”neutral sequence,” in which mutations that accumulate are neither selected for or against (Li et al. 1981). However, this premise relies on the assumption that pseudogenes are functionally inert. There is recent evidence that some pseudogenes are functionally active, and therefore, studying their evolution and conservation could support a functional role and give insight into their potential mechanism of action.
The paper reports that one study compared pseudogenes found in mice and humans and found conserved sequence, implying function:
Interestingly, many of the pseudogenes examined were found to have very few mutations within the regulatory regions they shared with their parent genes, which might suggest that these regulatory regions are of importance to the pseudogene and that the pseudogene may be functional.
The paper closes with a warning against assuming that pseudogenes are “nonfunctional relics” and acknowledges that they have been “overlooked in the quest to understand the biology of health and disease”:
Caution must be exercised when interpreting the results of functional experiments on pseudogenes. In some cases, what appears to be a nontranslated pseudogene can, in fact, code for truncated proteins (Kandouz et al. 2004; Zhang et al. 2006). Nevertheless, the evidence that some pseudogenes can exert regulatory effects on their protein-coding cousins is mounting. Such functions appear to be mediated by noncoding RNAs produced from active pseudogenes. While not all pseudogenes (or even all transcribed pseudogenes) will have biological functions, it is likely that, where an unexpected regulatory benefit results from the formation of a pseudogene, the effect will be conserved. For the large part, pseudogenes have been overlooked in the quest to understand the biology of health and disease, to the extent that pseudogene probes are often absent from commercially available microarrays. As evidence emerges that pseudogenes are deregulated in disease, and indeed that their deregulation can contribute to diseases such as diabetes and cancer, the prevalent attitude that they are nonfunctional relics is slowly changing.
Perhaps the mindset of Dawkins, Giberson, and Collins is setting us up to miss important biological functions of pseudogenes. For a more complete discussion, see Jonathan Wells’ new book The Myth of Junk DNA.