Intelligent Design and the Death of the "Junk-DNA" Neo-Darwinian Paradigm

Casey Luskin
Fall, 2007

Two recent news articles are discussing the death of the junk-DNA icon of Neo-Darwinism. Wired Magazine has an article pejoratively titled "One Scientist's Junk Is a Creationist's Treasure" that emphasizes the positive point that intelligent design has made successful predictions on the question of "junk-DNA." The article reports: [A] surprising group is embracing the results: intelligent-design advocates. Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions.The Wired Magazine article then quotes Discovery Institute's Stephen Meyer explaining that this is a prediction of intelligent design that was largely unexpected under neo-Darwinian thought:"It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis," said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle. The Wired Magazine article openly and unashamedly confuses intelligent design with creationism, but it does admit that ID proponents are making positive predictions about the scientific data:Advocates like Meyer are increasingly latching onto scientific evidence to support the theory of intelligent design, a modern arm of creationism that claims life is not the result of natural selection but of an intelligent creator. Most scientists believe that intelligent design is not science. But Meyer says the opossum data supports intelligent design's prediction that junk DNA sequences aren't random, but important genetic material. It's an argument Meyer makes in his yet-to-be-published manuscript, The DNA Enigma.Another article in the Washington Post similarly discusses the death of the junk-DNA paradigm of Neo-Darwinism:The first concerted effort to understand all the inner workings of the DNA molecule is overturning a host of long-held assumptions about the nature of genes and their role in human health and evolution. ... The findings, from a project involving hundreds of scientists in 11 countries and detailed in 29 papers being published today, confirm growing suspicions that the stretches of "junk DNA" flanking hardworking genes are not junk at all. But the study goes further, indicating for the first time that the vast majority of the 3 billion "letters" of the human genetic code are busily toiling at an array of previously invisible tasks.

(Rick Weiss, "Intricate Toiling Found In Nooks of DNA Once Believed to Stand Idle," Washington Post, June 14, 2007) The Washington Post article explains that scientists are finally "being forced to pay attention to our non-gene DNA sequences." What were the consequences of their failure to suspect function for junk-DNA? The article explains how there may be real-world medical consequences of the failure to presume function for non-coding DNA:But much of it seems to be playing crucial roles: regulating genes, keeping chromosomes properly packaged or helping to control the spectacularly complicated process of cell division, which is key to life and also is at the root of cancer. .... [S]everal recent studies have found that people are more likely to have Type 2 diabetes and other diseases if they have small mutations in non-gene parts of their DNA that were thought to be medically irrelevant.Could neo-Darwinism have stopped science from investigating the causes of these medical problems?

Intelligent Design has Long Predicted This Day
Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk'." [4] Design theorists have thus been predicting the death of the junk-DNA paradigm for many years:

As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science[1] against assuming that 'junk' DNA was 'useless.'" Science wouldn't print Mims' letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things:[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. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.

(William Dembski, "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998))In 2002, Dr. Richard Sternberg surveyed the literature and found extensive evidence for function of certain types of junk-DNA and argued that "neo-Darwinian 'narratives' have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes."[1] Sternberg concluded that "the selfish DNA narrative and allied frameworks must join the other ‘icons’ of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.”[2] Then in 2004, pro-ID molecular biologist Jonathan Wells argued 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."[4]

The next year, Sternberg and leading geneticist James A. Shapiro conclude that “one day, we will think of what used to be called ‘junk DNA’ as a critical component of truly ‘expert’ cellular control regimes.”[5] It seems that day may have come.

It seems beyond dispute that the Neo-Darwinian paradigm led to a false presumption that non-coding DNA lacks function, and that this presumption has resulted in real-world negative consequences for molecular biology and even for medicine. Moreover, it can no longer seriously be maintained that intelligent design is a science stopper: under an intelligent design approach to investigating non-coding DNA, the false presumptions of Neo-Darwinism might have been avoided.

Will Darwinists Now try to Rewrite the History of Junk-DNA?
Now that we're witnessing the apparent death of the "Junk-DNA" Neo-Darwinian paradigm, some Darwinists are already trying to rewrite history by claiming that Neo-Darwinism never supported the "junk-DNA" hypothesis after all. As one Scienceblogger wrote, "If you read evolgen you know that the term ‘Junk DNA’ is crap. From an evolutionary viewpoint it also seemed a bit peculiar to relegate most of the genome to non-functional status..." But just how valid is that statement?

In 1995, Scientific American plainly expounded that under the Neo-Darwinian view, "[t]hese regions have traditionally been regarded as useless accumulations of material from millions of years of evolution." The view that non-coding DNA is "junk" has been adamantly promoted by TalkOrigins for years, as one leading contributor confidently asserted in 2001 that "[m]ost of human DNA is junk DNA." (Compare that claim with present discoveres which reveal that, "the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks.")

To be sure, over the years some rogue Darwinian biologists have bucked the consensus and promoted the view that non-coding DNA isn't mostly junk. But this doesn't change the fact that many leading Darwinists have had a long history of promoting the view that non-coding DNA is largely useless "junk." The comments above, and the quotes below document some examples of Darwinists asserting that non-coding DNA is thought to be "junk":

Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, "they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?"[6]

In 1994, the authoritative textbook, Molecular Biology of the Cell, co-authored by National Academy of Sciences president Bruce Alberts, suggested (incorrectly!) that introns are "largely genetic 'junk'":Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk”…[7]Soon thereafter, the 1995 edition of Voet & Voet's Biochemistry textbook explained that "a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome..."[8]

In 1996, leading origin of life theorist Christian de Duve wrote: "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."[9] Another leading biologist, Sydney Brenner argued in a biology journal in 1998 that: "The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it."[10] (Richard Dawkins makes similar pronouncements that DNA is junk in an article after 1998, here.)

Perhaps the most poignant example of how the neo-Darwinian paradigm opposed research into the function of "junk"-DNA was reported in 2003, when an article in Scientific American explained that “the introns within genes and the long stretches of intergenic DNA between genes ... ‘were immediately assumed to be evolutionary junk.’”[3] But once it was discovered that introns play vital cellular roles regulating gene production within the cell, John S. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland in Brisbane, Australia was thus quoted saying the failure to recognize function for introns might have been “one of the biggest mistakes in the history of molecular biology.”[3]

Even if some rogue biologists suspected function for "junk" DNA, this does nothing to change the fact that the false "junk"-DNA paradigm was born, bred, and sustained far beyond its reasonable lifetime under the Neo-Darwinian mindset. Some Darwinists do not want to admit this fact of history. Given the behavior of Darwinists regarding the film Flock of Dodos, where they have denied that Haeckel's faked embryo drawings have been misused in modern textbooks, it is not surprising that some Darwinists are now trying to rewrite history to claim their paradigm never called non-coding DNA "junk." It appears that junk-DNA is truly going the way of the dodo, in more way than one.

Citations:
[1] Forrest Mims, Rejected Letter to the Editor to Science, December 1, 1994.

[2] Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002).

[3] Wayt T. Gibbs, “The Unseen Genome: Gems Among the Junk,” Scientific American (Nov. 2003).

[4] Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research,” Progress in Complexity, Information, and Design, 3.1.2 (Nov. 2004).

[5] Richard v. Sternberg and James A. Shapiro, “How Repeated Retroelements format genome function,” Cytogenetic and Genome Research, Vol. 110: 108–116 (2005).

[6]. Susumu Ohno, "So much 'junk' DNA in our genome," Brook Haven Symposia in Biology, Vol. 23:366-370 (1972).

[7]. Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson, Molecular biology of the Cell, pg. 373 (3rd Ed., 1994).

[8]. Donald Voet & Judith Voet, Biochemistry, pg. 1138 (1995).

[9]. Christian de Duve, Vital Dust: Life as a Cosmic Imperative, Basic Books, pg., 222-223 (1996).

[10]. Sydney Brenner, "Refuge of spandrels," Current Biology, Vol. 8(19): R669 (1998).