Editor’s note: We are delighted to present a series by geologist Casey Luskin on “The Positive Case for Intelligent Design.” This is the sixth entry in the series, a modified excerpt from the new book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. Find the full series so far here.

Observation (from previous studies): Intelligent agents generate structures that have a purpose or function: 

• “Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or ‘junk DNA.’ From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk.’”¹
• “[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term ‘junk DNA.’ Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function…Design encourages scientists to look for function where evolution discourages it.”²

Hypothesis (prediction): Cellular components were originally designed for a purpose, and “junk” DNA will generally turn out to perform valuable functions.

Experiment (data): Numerous studies have discovered function for “junk DNA,”³ including evidence of widespread biochemical function in the human genome discovered in the ENCODE project.⁴ Discover Magazine summarized ENCODE’s 2012 breakthrough report writing, “The key point is: It’s not ‘junk.’”⁵ Specific examples include functionality in pseudogenes, microRNAs, introns, endogenous retroviruses, and repetitive LINE, SINE, and Alu elements.⁶ Examples of unknown DNA functions persist, but ID encourages researchers to investigate functions, whereas neo-Darwinism has discouraged seeking such function.⁷

Conclusion: Functionality for junk DNA is prevalent, and was successfully predicted by intelligent design. 

Next, “The Positive Case for Design in Physics”

Notes

1. Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research,” Progress in Complexity, Information, and Design 3.1 (November 2004).
2. William Dembski, “Intelligent Science and Design,” First Things 86 (October 1998), 21-27.
3. See reviews in Jonathan Wells, The Myth of Junk DNA (Seattle, WA: Discovery Institute Press, 2011).
4. The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature 489 (September 6, 2012), 57-74.
5. Ed Yong, “ENCODE: the rough guide to the human genome,” Discover Magazine (Sept. 5, 2012), https://www.discovermagazine.com/the-sciences/encode-the-rough-guide-to-the-human-genome (accessed October 28, 2020).
6. See for example Richard Sternberg, “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System,” Annals of the NY Academy of Science, 981 (2002), 154-188; James A. Shapiro, and Richard Sternberg, “Why repetitive DNA is essential to genome function,” Biological Reviews of the Cambridge Philosophical Society, 80 (2005), 227-250; McIntosh, “Information and Entropy—Top-Down or Bottom-Up Development in Living Systems?”; S. Hirotsune et al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature 423 (2003), 91-96; G. Lev-Maor et al., “The birth of an alternatively spliced exon: 3’ splice-site selection in Alu exons,” Science 300 (May 23, 2003), 1288-1291; W.T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (November 2003); M.S. Hakimi et. al., “A chromatin remodelling complex that loads cohesin onto human chromosomes,” Nature 418 (2002), 994-998; T.A. Morrish et al., “DNA repair mediated by endonuclease-independent LINE-1 retrotransposition,” Nature Genetics 31 (June 2002), 159-165; E.S. Balakirev and F.J. Ayala, “Pseudogenes, Are They ‘Junk’ or Functional DNA?,” Annual Review of Genetics 37 (2003), 123-151; E. Pennisi, “Shining a Light on the Genome’s ‘Dark Matter,’” Science, 330 (December 2010), 1614; A.B. Conley et al., “Retroviral promoters in the human genome,” Bioinformatics 24 (2008), 1563-1567; G.J. Faulkner et al., “The regulated retrotransposon transcriptome of mammalian cells,” Nature Genetics 41 (April 19, 2009), 563-571.
7. W.T. Gibbs, “The Unseen Genome, Gems Among the Junk,” Scientific American (November 2003); W. Makalowski, “Not Junk After All,” Science300 (May 23, 2003), 1246-1247; Seth W. Cheetham et al., “Overcoming challenges and dogmas to understand the functions of pseudogenes,” Nature Reviews Genetics 21 (2020), 191-201.