As we mark the 30th anniversary of the Center for Science and Culture (CSC) and the publication of Darwin’s Black Box, I’m reviewing here how the evidence supporting intelligent design (ID) has come in during this period. In a post yesterday I described the remarkable phenomenon of “Third Way” evolution, and what it portends. Here I will cover the no less remarkable “unexpected genome” — i.e., new discoveries in genetics and genomics that were not anticipated by the evolutionary paradigm, but that were expected by intelligent design. One of the most successful ID predictions over this time anticipated function for junk DNA.
Junk DNA
The idea that the genome is largely functionless junk was developed out of the neutral theory of evolution, a mainstay evolutionary concept. Estimates vary, but evolutionary scientists made claims like:
- “Mammalian genomes are littered with [Repetitive DNA], with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.” (Francis Collins, 2006)
- “90 percent of your genome is junk” (Moran, 2023)
- “[T]he greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” (Dawkins, 2009)
- “As we discovered in 2003 with the conclusion of the Human Genome Project, a monumental 13-year-long research effort to sequence the entire human genome, approximately 98.8 percent of our DNA was categorized as junk.” (Mortola and Long, 2021)
Simultaneously, ID proponents bucked the trend and made very different sets of predictions. In 1994, the pro-ID scientist Forrest Mims submitted a letter to Science warning against assuming that “junk” DNA was “useless.” In 1998, William Dembski published an article in First Things predicting that function for junk DNA would be discovered:
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. … Design encourages scientists to look for function where evolution discourages it.
Then in 2004, pro-ID biologist Jonathan Wells noted that “The fact that ‘junk DNA’ is not junk has emerged not because of evolutionary theory but in spite of it. On the other hand, people asking research questions in an ID framework would presumably have been looking for the functions of non-coding regions of DNA all along, and we might now know considerably more about them.”
In 2012, something happened that showed ID’s predictions were correct, causing nothing less than a paradigm shift away from the idea of junk DNA. The ENCODE project published a series of papers showing that over 80 percent of the genome gave evidence of biochemical functionality. The journal Science immediately published an article stating that the project’s findings “sound the death knell for the idea that our DNA is mostly littered with useless bases.” Within three years, Francis Collins stated that “In terms of junk DNA we don’t use that term anymore,” calling it “hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn’t functional” (see Brunet and Doolittle, 2015).
So-called “junk DNA” performs a myriad of vital functional roles, including gene regulation, controlling cell differentiation, and helping to encode the basic blueprint for an organism’s body plan. By 2021 a paper in Genome Biology and Evolution declared “The days of ‘junk DNA’ are over” and papers in BioEssays in 2023 and Cell in 2026 explained we’ve witnessed a Kuhnian “paradigm shift” away from the idea of junk DNA. While there is still much we don’t know about the genome, ID predicted these trends, evolution did not, and the discovery of function for junk DNA represents a spectacularly fulfilled prediction for intelligent design.
The Unexpected Genome
Evolution failed to predict function or junk DNA. The standard paradigm also failed to anticipate modern discoveries in genomics and bioinformatics. Intelligent design, however, predicted not just function for junk DNA but a number of other key discoveries — what might be called the “unexpected genome.”
As more genomes are sequenced, it’s been discovered that large numbers of genes in every species are unique and unlike any other known genes — what are often called “orphan genes.” It is estimated that from 10 to 30 percent of a genome might consist of orphan genes (Wissler et al. 2013). According to evolution, genes evolve from other genes, and potential evolutionary gene sources are identified by finding other genes with similar DNA sequences. Yet orphan genes show genetic discontinuity among species, challenging standard evolutionary models because they have no gene-source from which to evolve.
At first, evolution-defenders were highly skeptical that orphan genes were real, and not an artifact of incomplete genome sequencing. They predicted that as more and more genomes were sequenced, the number of orphan genes would drop. Instead, the opposite has happened, showing that orphan genes are real and important elements of genomes that help define species. These orphans are expected under intelligent design because they show information in biology need not be connected to material antecedents. Information is discontinuous among material entities because it comes from a mind, not matter.
Another discovery in genomics predicted by ID is the presence of overlapping genes, where the same stretch of DNA encodes multiple genes. One strand of DNA might encode one protein while the opposite strand encodes an entirely different functional protein (see, e.g., Adelman et al., 1987 or Mehravar et al., 2021). Such an astonishing degree of information compression is only expected if a mind of genius encoded the information in DNA, not random mutation and blind natural selection.
The Tree of Life
Yet another area where ID has predicted major trends in genomics and bioinformatics relates to efforts to construct the tree of life. Evolutionary theory claims that species are related through universal common descent, often represented in a “tree of life.” The theory predicts we should be able to reconstruct phylogenetic trees showing how different organisms are related. To be sure, if one assumes that biological similarity reflects common ancestry, such trees can be built. However, no matter how one formulates (or reformulates) a “tree,” it invariably turns out that various similarities across organisms cannot be explained by common ancestry. Thus, the Cambridge evolutionary biologist Simon Conway Morris has said that “convergence” (similarity that arises independently, rather than through common ancestry) is “ubiquitous” across living organisms.
Many evolutionary biologists hoped that DNA studies would finally settle these debates and show how organisms are related. Instead, what resulted was a major mess. Thus, we commonly find in the literature statements like:
- “[C]onflicting phylogenetic signal between genes is commonplace” (Schrempf and Szöllősi, 2020)
- “An immediate challenge is to address the pervasive phylogenetic conflict observed in whole genome data” (Adams et al., 2021)
- “Phylogenomic conflict, where gene trees disagree about species tree resolution, is common across genomes and throughout the Tree of Life” (Parins-Fukuchia et al., 2021)
- “[P]hylogenomics is adding another type of controversy never seen before in molecular phylogenetics: highly supported contradictory results” (Giribet, 2016)
- “[P]hylogenetic conflict is common, and frequently the norm rather than the exception” (Dávalos et al. 2012)
Intelligent design can make sense of this. It is not really a mess at all but a successful prediction. While ID allows for the possibility of common descent, it also predicts common design — where similarities can be the result of a designer re-using parts that work in different designs. In 2018, computer scientist Winston Ewert developed a “dependency graph” model of explaining the similarities and differences between organisms based upon their functional needs and his observation that programmers often re-use coding modules in different systems. Ewert compared the gene families in nine organisms and found that their distribution fit a common design-based “dependency graph” model 10^3000 times better than a Darwinian evolutionary tree.
In each of these burgeoning areas of biology research, we’re finding that information and discontinuity are prevalent throughout biology, often showing up in locations unexpected by evolution, but predicted by intelligent design.
Information and Codes Throughout Life
Intelligent design predicts we should find new layers of information, code, and control in biology. Thus, ID is very enthused that the past 20 years have witnessed an explosion of discovery of new sources information in biology apart from the DNA. Yes, DNA contains information that encodes proteins, and yes much of the non-protein coding DNA is turning out to have vital functions. But there’s also information outside of or on top of the DNA that plays vital roles.
The best-known example of this information comes from epigenetics. In epigenetics, chemical tags placed on DNA molecules can control gene expression — determining whether genes are turned on or off in cells, or how much of a particular protein should be produced. Under this coding scheme, methyl tags are added to DNA to silence genes, and adding acetyl tags can be added to activate genes. This creates a problem for neo-Darwinism. Neo-Darwinian processes operate by random mutations in the nucleotide sequence of DNA, but epigenetic information isn’t derived from the nucleotide sequence. It’s not at all clear how standard evolutionary theory can account for the origin of this epigenetic information.
And then there is information outside of genomes. Pro-ID biologist Jonathan Wells summarized this in a 2014 paper titled “Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA.” Wells reviewed information stored in gene regulatory networks, membranes (the “sugar code”), intracellular targeting or “zip codes,” and electric fields that help guide organismal development. As he concluded, “the fact that membrane patterns carry ontogenetic information that is not specified by DNA poses a problem for any theory of evolution (such as Neo-Darwinism) that attributes the origin of evolutionary novelties to changes in a genetic program.”
Wells’s review was important, but it only scratches the surface of information in biology outside of the DNA. A 2024 paper in Biological Theory found that “there are hundreds to thousands of biological codes, but only a fraction — although still a substantial number — have been explicitly described as such.” And that leaves aside even more radical ideas of an immaterial genome, developed by ID biologist Richard Sternberg and seconded by fascinating and unexpected sources, such as Tufts University biologist Michael Levin, totally outside the ID research community. As Levin recently wrote in a preprint article, he is arguing for “a radical Platonist view in which some of the causal input into mind and life originates outside the physical world.” Much, in short, remains to be studied and discovered in this area, and intelligent design is ideally poised to help biology make sense of these new codes.
Tomorrow, “Fossil Explosions Persist, and Other Confirmations of Intelligent Design.”