In The Myth of Junk DNA, Jonathan Wells predicted that “assuming that any feature of an organism has no function discourages further investigation. In this respect, the myth of junk DNA has become a science stopper.” (p. 107). Recently published literature has overwhelmingly confirmed Wells’ thesis, and evolutionary scientists who cling to the myth of junk DNA are being refuted by continual research publications.
We previously covered a May 2011 article in the journal RNA which reported functions for pseudogenes:
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) (emphases added).)
Another May, 2011 paper warned against presuming non-functionality for repetitive elements, including endogenous retroviral elements, in DNA:
Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms…
(G.C. Ferreri , J.D. Brown, C. Obergfell, N. Jue, C.E. Finn, M.J. O’Neill, R.J. O’Neill. “Recent amplification of the kangaroo endogenous retrovirus, KERV, limited to the centromere,” Journal of Virology, Vol. 85(10):4761-71. (May, 2011) (emphasis added).)
The paper went on to report expression patterns that hint at function for kangaroo endogenous retrovirus (KERV): “KERV’s sequence conservation, continued expression, localization to centromeres, breaks of synteny, and nearly ubiquitous distribution in the marsupial clade set it apart from previously observed ERVs.”
Some late 2010 articles also note the failure of the “junk DNA” concept. One noted that it’s no longer appropriate to call repetitive DNA “junk DNA”:
High-throughput sequencing of eukaryotic genomes has revived interest in the structure and function of repetitive genomic sequences, previously referred to as junk DNA. Repetitive sequences, including transposable elements, are now believed to play a significant role in genomic differentiation and evolution.
(Motonori Tomita, “Revolver and Superior: Novel Transposon-Like Gene Families of the Plant Kingdom,” Current Genomics, Vol. 11:62-69 (2010).)
Of course by saying that they play a “role” in evolution, what the paper simply means is that repetitive sequences perform useful functions that would be favored by natural selection. This article goes on to note:
These repetitive regions comprise >70% of the genomes and are often referred to as junk DNA. With the advent of high-throughput DNA sequencing, it has become apparent that transposable elements constitute a large proportion of the repetitive DNA component of most eukaryote genomes, that is, at least 45% of the human genome, and 50- 80% of some grass genomes. … a substantial proportion of the genome is expressed as regulatory noncoding RNAs, some of which are reconstructed from transposable elements.
Thus huge portions of the human, grass, and other genomes cannot be understood without studying the functions of this noncoding repetitive DNA.
Another paper from 2010 similarly found:
Genomic transposable elements, or transposons, are sequences of DNA that can move to different positions in the genome; in the process, they can cause chromosomal rearrengements and changes in gene expression. Despite their prevalence in the genomes of many species, their function is largely unknown: for this reason, they have been labelled “junk” DNA. … [This paper presents] a novel hypothesis on the biological role of transposons, according to which transposition in somatic cells during development drives cellular differentiation and transposition in germ cells is an indispensable tool to boost evolution. Thus, transposable elements, far from being “junk”, have one of the most important roles in multicellular biology.
(Alessandro Fontana, “A hypothesis on the role of transposons,” BioSystems, Vol. 101:187-193 (September, 2010) (emphasis added).)
Fontana’s article goes further:
Transposons represent a large genomic fraction (30-40% in mammals). Such amount of seemingly useless material initially led researchers to call it “junk DNA”, until further research hinted that it could in fact have a biological role.
Thus those who presumed that non-coding DNA is junk might have missed 30-40% of mammalian DNA which performs “one of the most important roles in biology.” Talk about stopping science!
Finally, another paper from the latter half of 2010 found that studying the functions of “junk DNA” could have important medical applications:
What was once considered “junk DNA” now holds the keys to many novel gene regulatory mechanisms, and genetic variation within these regions likely accounts for amajor portion of disease susceptibility. Until recently, the biochemical mechanisms linking noncoding DNA, which does not encode any proteins, to the pathogenesis of disease were largely unknown, but there has been a torrent of new information in this field that has the prospect of changing how we diagnose and treat patients.
(Kasey C. Vickers, Brian T. Palmisano, and Alan T. Remaley, “The Role of Noncoding ‘Junk DNA’ in Cardiovascular Disease,” Clinical Chemistry, Vol. 56(10):1518-1520 (2010) (emphasis added).)
Since noncoding DNA has important functions, a failure to seek function for junk DNA could cause medical researchers to miss important causes of diseases. This paper suggests that studying the functions of noncoding DNA could help us understand the causes of cardiovascular diseases.
The list of similar papers could go on and on, but the bottom line is this: Whether we’re talking about pseudogenes, ERVs, transposons, or other repetitive elements, the presumption that noncoding DNA is “junk” hinders biological and medical research from moving forward.