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Does Darwinian Theory Make the Same Predictions as Intelligent Design?

Casey Luskin
Photo: Richard Dawkins, by Anders Hesselbom, Public domain, via Wikimedia Commons.

Editor’s note: We are delighted to present a series by geologist Casey Luskin on “The Positive Case for Intelligent Design.” This is the ninth 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 CosmosFind the full series so far here.

One potential objection to the positive case for intelligent design, developed in this series, is that Darwinian evolution might make some of the same predictions as ID, making it difficult to tell which theory has better explanatory power. For example, in systematics, ID predicted reuse of parts in different organisms, but neo-Darwinism also predicts different species may share similar traits either due to inheritance from a common ancestor, convergent evolution, or loss of function. Likewise, in genetics, ID predicted functionality for junk DNA, but evolutionists might argue noncoding DNA could evolve useful functions by mutation and selection. If neo-Darwinism makes the same predictions as ID, can we still make a positive argument for design? The answer is yes, and there are multiple responses to these objections.

First, not all the predictions generated by positive arguments for design are also made by Darwinian theory. For example, Michael Behe explains that irreducible complexity is predicted under design but predicted not to exist by Darwinism:

[I]rreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin’s and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design.1

The same could be said of high-CSI features like protein sequences, which require rare and finely tuned sequences of amino acids to function. These are predicted by ID but are not expected under a blind trial-and-error process of mutation and selection.2

What a “Positive Case” Means

Second, the fact that a different theory can explain some data does not negate ID’s ability to successfully make positive predictions. After all, a “positive case” means that the arguments for design stand on their own and do not depend merely on refuting other theories. While refuting competing hypotheses can certainly help solidify a theory’s status as the best explanation, a positive argument must be able to stand on its own. ID’s fulfilled predictions show there is positive evidence for design, regardless of what other models may or may not say. 

Third, it’s not clear that in any of these cases neo-Darwinian evolution (or other materialistic models) makes exactly the same predictions as ID. For example, in systematics, neo-Darwinism may predict the reuse of parts in different organisms, but it predicts that the distribution of parts will generally conform to a treelike pattern (or a nested hierarchy). Intelligent agents are not bound to distribute parts in a tree, and thus reuse of similar parts may be found even among very distantly related organisms. We can test among these different models. A 2018 paper by software engineer Winston Ewert in the journal BIO-Complexity proposed a model of common design called a dependency graph, which was “based on the technique used by software developers to reuse code among different software projects.”3 He compared the distribution of gene families reused in different organisms to a treelike pattern predicted by neo-Darwinism versus a dependency graph distribution used by computer programmers and predicted by ID. After analyzing the distribution of gene families in nine diverse types of animals, Ewert’s preliminary analysis found that a common design-based dependency graph model fit the data 103000 times better than a traditional Darwinian phylogenetic tree.4 His ID-based dependency graph model predicted reuse of parts much better than neo-Darwinism.  

Ewert tested the data against common descent. But even convergent evolution struggles to explain reuse of parts. Richard Dawkins acknowledges “it is vanishingly improbable that exactly the same evolutionary pathway should ever be traveled twice,”5 yet we often find striking similarities across distantly related organisms, such as the camera-like structure of the vertebrate eye and the octopus (cephalopod) eye. What evolutionary biology calls extreme convergence is better explained by common design. 

A Major Prediction of Evolutionary Theory

With junk DNA, it’s true that neo-Darwinian evolution predicts that functionality could sometimes evolve for noncoding DNA, and that finding function in a given case does not necessarily refute that model. Yet a major prediction of modern evolutionary theory is that neutral (neither harmful nor beneficial) mutations occur frequently and accumulate as useless genetic junk in genomes. For example, in 1972 the pioneering molecular evolutionary biologist Susumu Ohno published an article titled “So much ‘junk’ DNA in our genome.” Writing in a volume titled Evolution of Genetic Systems, he argued that “at the most, only 6% of our DNA” is functional genes, with the rest being “untranscribable and/or untranslatable DNA” representing “extinct genes” or “nature’s experiments which failed” — akin to “fossil remains of extinct species.”6 

Biologists soon envisioned additional evolutionary mechanisms for filling our genomes with junk. In his influential 1976 book The Selfish Gene, Richard Dawkins predicted that “a large fraction” of our genomes has no function, because, “The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”7 In 1980, Nature published two papers by influential biologists furthering the concept of “selfish” junk DNA. The first article, “Selfish Genes, the Phenotype Paradigm and Genome Evolution,” by W. Ford Doolittle and Carmen Sapienza, maintained, “Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes.”8 A second paper, “Selfish DNA: the ultimate parasite,” was by Francis Crick, who won the Nobel Prize for determining the structure of DNA, and the eminent origin-of-life theorist Leslie Orgel. They concluded that “much DNA in higher organisms is little better than junk,” and “it would be folly in such cases to hunt obsessively for” its function.9 Since that time, Darwinian thinkers have been seduced by the idea that “parasitic” DNA and random mutations will spread junk throughout our genomes. In 1994, Kenneth Miller published an article claiming that “the human genome is littered with pseudogenes, gene fragments, ‘orphaned’ genes, ‘junk’ DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design.”10 Many similar quotes could be given showing that the idea of junk DNA was born, bred, and flourished from within an evolutionary paradigm. 

A Hindrance to Science

As might be expected from such statements, the literature admits that evolutionary thinking has hindered research into functions for junk DNA. A 2003 article in Scientific American noted that “introns,” a type of noncoding DNA found within genes, “were immediately assumed to be evolutionary junk” — a view that the article later called “one of the biggest mistakes in the history of molecular biology.”11 That same year, a paper in the journal Science observed that “[a]lthough catchy, the term ‘junk DNA’ for many years repelled mainstream researchers from studying noncoding DNA.”12 A striking admission came in a 2020 paper in Nature Reviews Genetics titled “Overcoming challenges and dogmas to understand the functions of pseudogenes,” which argues that “dogma” in biology causes “demotivation into exploring pseudogene function by the a priori assumption that they are functionless.” According to the paper, “[t]he dominant limitation in advancing the investigation of pseudogenes now lies in the trappings of the prevailing mindset that pseudogenic regions are intrinsically non-functional” and “there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.”13

ID’s Superior Predictions

The ID community’s view of junk DNA stands in stark contrast to the typical evolutionary view. Going back to some of ID theory’s early days in the 1990s, ID theorists have been predicting that noncoding DNA would turn out to have functions. In 1994, pro-ID scientist Forrest Mims submitted a letter to Science that warned against assuming that junk DNA was “useless.14 In 1998, William Dembski wrote that “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.”15 Many other ID theorists have made similar predictions over the years. What might have happened if their predictions had been heeded?

In 2021, the journal Nature acknowledged that prior to the Human Genome Project (HGP), which was completed in 2003, there was “great debate” over whether it was “worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome.” The article noted that over 130,000 “genomic elements, previously called junk DNA” have now been discovered, and highlighted how important these “junk” segments have turned out to be:

[I]t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

Under an ID paradigm, debates over whether to investigate junk DNA would have ended much sooner with an emphatic “Yes!,” furthering our knowledge of genetics and medicine. When it comes to junk DNA, ID has made superior predictions. 

Next, “Does Intelligent Design Make Predictions or Retrodictions?”


  1. Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press, 2006 reprint), 263-264.
  2. See Meyer, Darwin’s Doubt, 169-254; Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors”; Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds”; Steinar Thorvaldsen and Ola Hössjer, “Using statistical methods to model the fine-tuning of molecular machines and systems,” Journal of Theoretical Biology 501 (2020), 110352.
  3. Winston Ewert, “The Dependency Graph of Life,” BIO-Complexity 2018 (3).
  4. Ewert, “The Dependency Graph of Life.”
  5. Richard Dawkins, The Blind Watchmaker (New York: Norton, 1996), 94.
  6. Susumu Ohno, “So much ‘junk’ DNA in our genome,” Evolution of Genetic Systems, ed. H.H. Smith (New York: Gordon and Breach), 366-370.
  7. Richard Dawkins, The Selfish Gene (Oxford, UK: Oxford University Press, 1976), 44-45.
  8. W. F. Doolittle and Carmen Sapienza, “Selfish genes, the phenotype paradigm and genome evolution,” Nature, 284 (April 17, 1980), 601-603.
  9. Leslie Orgel and Francis Crick, “Selfish DNA: the ultimate parasite,” Nature, 284 (April 17, 1980), 604-706.
  10. Kenneth Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994), 24-32.
  11. Quoted in W. T. Gibbs, “Unseen Genome: Gems Among the Junk,” Scientific American (November 2003).
  12. Makalowski, “Not Junk After All.” 
  13. Cheetham et al., “Overcoming challenges and dogmas to understand the functions of pseudogenes.”
  14. Forrest Mims, “Rejected Letter to the Editor to Science” (Dec. 1, 1994), http://forrestmims.org/publications.html (accessed October 29, 2020).
  15. Dembski, “Intelligent Science and Design.”