Shortly I’ll be debating Rutgers University biology professor Dr. Dan Stern Cardinale about junk DNA. That’s at 5:30 pm Pacific time. You can see it here. The question before us will be: “Is the Human Genome Largely Junk DNA?” The following are some key quotes on the subject that will be relevant to our conversation. They are divided into three categories: 

• Category 1: Quotes from evolutionists claiming (or recounting the widespread belief) that non-coding DNA is “junk” and has no function.
• Category 2: Early quotes from intelligent design theorists predicting function for non-coding “junk” DNA.
• Category 3: Quotes from mainstream scientific sources saying that we’ve experienced a shift in our thinking that junk DNA actually has function.

Many of these quotes are from mainstream scientific papers, books, or book chapters of a technical nature, while quite a few are from mainstream scientific or journalistic sources of a more popular style. The latter sources, while not peer-reviewed technical papers, are nonetheless quite valuable. 

Category 1

Quotes from evolutionists claiming (or repeating the widespread belief) that non-coding DNA is “junk” and has no function.

Note: Many of these quotes are from decades ago, showing how the idea of junk DNA was born and bred in the evolutionary paradigm. But some are more recent. 

• “While current evidence makes plausible the idea that all genetic material is DNA (with the possible exception of RNA viruses), it does not follow that all DNA is competent genetic material (viz. “junk” DNA)…” (Ehret and Haller, 1963) 
• Postulating: “99 percent of mammalian DNA is not true genetic material” (King and Jukes, 1969)
• “So much ‘junk’ DNA in our genome” (Ohno, 1972a)
• “At least 90% of the mammalian genomic DNA appears to represent ‘nonsense’ DNA base sequence of various kinds.” (Ohno, 1972b)
• “Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes.” (Doolittle and Sapienza, 1980)
• “Selfish DNA: the ultimate parasite … In summary, then, there is a large amount of evidence which suggests, but does not prove, that much DNA in higher organisms is little better than junk. … Thus, some selfish DNA may acquire a useful function and confer a selective advantage on the organism. Using the analogy of parasitism, slightly harmful infestation may ultimately be transformed into a symbiosis. What we would stress is that not all selfish DNA is likely to become useful. Much of it may have no specific function at all. It would be folly in such cases to hunt obsessively for one.” (Orgel and Crick, 1980)
• “These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution … In humans, about 97 percent of the genome is junk.” (Yam, 1995)
• “Mammalian genomes are littered with such AREs [ancient repetitive elements], with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.” (Collins, 2006)
• “The most striking feature of the genomic analyses we now have is how much apparently nonfunctional DNA there is … From the Darwinian perspective all this is explicable—the molecular equivalent of the tinkering that is pervasive in the history of life at the anatomical level.” (Kitcher, 2007)
• “50% of our genomes … are composed of non-functional, parasitic DNA, like transposons” (Alexander, 2008)
• “the 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)
• “There is, however, no way that I would admit to serving on a committee that designed the human genome. Not even a university committee could botch something that badly.” (David Penny, quoted in Graur et al., 2013)
• “For most of the history of genetics, the most prominent experts of the field have held that you, your mom, your great-great-uncle, Abraham Lincoln, all the emperors of Rome, and every one of Genghis Khan’s Mongol Army all inherited a vast amount of “junk DNA.” 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)
• “90 percent of your genome is junk” (Moran, 2023)

Category 2

Early quotes from intelligent design theorists predicting function for non-coding “junk” DNA. 

Note: There are many such quotes, but the most relevant ones are from the late 1990s and early 2000s before it was widely thought that junk DNA was functional. 

• “Science reports “Hints of a Language in Junk DNA” (25 November, p. 1320). Those supposedly meaningless strands of filler DNA that molecular biologists refer to as ‘junk’ don’t necessarily appear so useless to those of us who have designed and written code for digital controllers. They have always reminded me of strings of NOP (No OPeration) instructions. A do-nothing string of NOPs might appear as ‘junk code’ to the uninitiated, but, when inserted in a program loop, a string of NOPs can be used to achieve a precise time delay. Perhaps the ‘junk DNA’ puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology.” (Mims, 1994)
• “[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.” (Dembski, 1998)
• “[N]eo-Darwinian ‘narratives’ have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes. … 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.” (Sternberg, 2002)
• “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.” (Wells, 2004)

Category 3

Quotes from mainstream scientific sources saying that we’ve experienced a shift in our thinking that junk DNA actually has function.

Note: Some of these quotes also acknowledge that evolutionary thinking stopped science from discovering function for junk DNA. 

• “Geneticists have long focused on just the small part of DNA that contains blueprints for proteins. The remainder—in humans, 98 percent of the DNA—was often dismissed as junk. But the discovery of many hidden genes that work through RNA, rather than protein, has overturned that assumption.” (Gibbs, 2003)
• “Though long ago written off as irrelevant because they yield no proteins, many of these sections have been preserved mostly intact through millions of years of evolution. That suggests they do something indispensable. And indeed a large number are transcribed into varieties of RNA that perform a much wider range of functions than biologists had imagined possible. Some scientists now suspect that much of what makes one person, and one species, different from the next are variations in the gems hidden within our “junk” DNA.” (Gibbs, 2003)
• “Yet the introns within genes and the long stretches of intergenic DNA between genes, Mattick says, “were immediately assumed to be evolutionary junk.” That assumption was too hasty. “Increasingly we are realizing that there is a large collection of ‘genes’ that are clearly functional even though they do not code for any protein” but produce only RNA, Georges remarks. … “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology…. What was damned as junk because it was not understood may, in fact, turn out to be the very basis of human complexity” (Gibbs, 2003)
• “Our expectation is that, one day, we will think of what used to be called ‘junk DNA’ as a critical component of truly ‘expert’ cellular control regimes.” (Sternberg and Shapiro, 2005)
• “The idea that repetitive DNA is ‘junk’ without functional significance in the genome is simply not consistent with an extensive and growing literature, only a minor part of which is cited here” (Shapiro and Sternberg, 2005)
• “DNA previously written off as junk actually carries biological information.” (Pearson, 2006)
• “I will review here these discoveries and stress how they could change our view of the large component of the genome that was previously solely seen as selfish DNA, or using a more popular term as junk DNA, and of its importance for the organisms that carry it.” (Morgante, 2006)
• “Although very catchy, the term ‘junk DNA’ repelled mainstream researchers from studying noncoding genetic material for many years. After all, who would like to dig through genomic garbage? Thankfully, though, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. And it is because of them that in the early 1990s, the view of junk DNA, especially repetitive elements, began to change. In fact, more and more biologists now regard repetitive elements as genomic treasures. It appears that these transposable elements are not useless DNA. Instead, they interact with the surrounding genomic environment and increase the ability of the organism to evolve by serving as hot spots for genetic recombination and by providing new and important signals for regulating gene expression. … These and countless other examples demonstrate that repetitive elements are hardly “junk” but rather are important, integral components of eukaryotic genomes.” (Makalowski, 2007)
• “The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more “junk DNA”, think again.” (Collins, 2010)
• “Previously, the majority of the human genome was thought to be ‘junk’ DNA with no functional purpose. Over the past decade, the field of RNA research has rapidly expanded, with a concomitant increase in the number of non-protein coding RNA (ncRNA) genes identified in this ‘junk’. Many of the encoded ncRNAs have already been shown to be essential for a variety of vital functions… ” (Wright et al., 2011)
• “I have noticed that there are some creationists who are jumping on [the 2012 ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, is to find usefulness in the living world […] we thought only a minority of the genome was doing something, mainly that minority which only codes for protein, and now we find that actually the majority of it is doing something. What it’s doing is calling into action the protein coding genes. […] The program that’s calling them into action is the rest that had previously been written off as junk” (Dawkins, 2012)
• “The thought before the start of the [ENCODE] project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used. The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.” (NY Times—Kolata, 2012)
• “It’s likely that 80 percent [estimate of functional human DNA] will go to 100 percent. We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful” (Ewan Birney quoted in Yong, 2012)
• “I would say, in terms of junk DNA, we don’t use that term any more ’cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn’t functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu’s, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that’s where the epigenome gets involved, and is teaching us a lot.” (Francis Collins, at the 33rd Annual J.P. Morgan Healthcare Conference in San Francisco on January 13, 2015, requoted in Brunet and Doolittle, 2015)
• “The genomes of eukaryotic species are made up of large amounts of repeated sequences. Among them, the most abundant fraction is constituted of satellite DNA (satDNA) whose monomeric units are organized in tandem in long arrays  preferentially located at centromeric, pericentromeric, and subtelomeric regions but also at interstitial positions …  The functional significance of satDNA has been long debated. Because of the correspondence to the heterochromatic fraction, the absence of transcriptional activity as well as the high sequence divergence across species, this DNA was labeled as “junk”. However, several evidences have challenged this view assigning a role in genomic functions such as centromere structure, kinetochore assembly, chromosome pairing, and segregation. The evolution of repetitive DNA has been related to reproductive isolation and hence in the onset of new species; moreover, it has been suggested as force driving the genome integrity and karyotype evolution. Over the years, an increasing number of studies provided evidence that satDNA is also transcriptionally active in vertebrates, invertebrates, and plants. Indeed, in human, 97–98% of the genome produces stable RNAs, the so-called dark matter RNA. The major part of these transcripts are noncoding RNAs (ncRNAs) and are involved not only in heterochromatin maintenance, centromere, and kinetochore assembly but also in gene expression regulation in several biological contexts.” (Biscotti et al., 2015)
• “The rest — 98.5 percent of DNA sequences — is so-called “junk DNA” that scientists long thought useless. The non-protein-coding stretches looked like gibberish sentences in a book draft — useless, perhaps forgotten, writing. But new research is revealing that the “junky” parts of our genome might play important roles nonetheless.” (Blanco, 2019)
• “Overcoming challenges and dogmas to understand the functions of pseudogenes … Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. … [A] broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that [] objective reassessment… [W]ith a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function….Where pseudogenes have been studied directly they are often found to have quantifiable biological roles…” (Cheetham et al., 2020)
• “This non-coding genome, once termed ‘junk’, was thought for decades to be inconsequential to the biology of an organism. It is now widely acknowledged that elements within the non-coding genome serve important gene-regulatory functions impacting when, where, and to what levels genes and their protein products are expressed.” (Farley et al., 2021)
• “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA. Consequently, these sequences were rarely studied. An international project has revealed that these DNA are far from junk.” (Mortola and Long, 2021)
• “Most protein-coding genes were discovered before the first draft of the Human Genome Project (HGP) in 2001. Many other genomic elements, previously called junk DNA, came in for scrutiny after that.” (Gates et al., 2021)
• “A great debate pre-dated the start of the HGP: was it worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome? Thanks in large part to the HGP, it 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.” (Gates et al., 2021)
• “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.” (Gates et al., 2021)
• “The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function. This view has fundamentally changed, and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.” (Stitz et al., 2021)
• “In his view, says co-author and University of Queensland researcher Tim Mercer, functional analysis of ncRNAs … has become well-established. … As matters shift from sweeping statements about junk and transcriptional noise, tasks shift to the practicalities of exploring functionality of ncRNAs to uncover their roles in differentiation, development and disease, says Mercer. He sees a new generation of scientists settling in to do the “hard work” of building on the field’s accomplishments, in which technology development and application have mattered. It will matter, for example, to combine methods — existing ones and new ones still to be developed. And it means being an explorer. Just as the Amazonian rain forest is sculpted on many levels by evolution, these forces have sculpted the human genome, including ncRNAs. Both rain forest and genome are abuzz with activity. The genome is constantly being transcribed; isoforms emerge; there’s splicing; genes interleave with other genes. The genome is far from what was once called ‘islands of genes among intergenic deserts.’” (Marx, 2022a)
• “How noncoding RNAs began to leave the junkyard … The research community focused on noncoding RNAs keeps growing. Skepticism about the field has some history. … To some, noncoding RNAs are junk. Over time they have left the proverbial junkyard.” (Marx, 2022b)
• “Junk. In the view of some, that’s what noncoding RNAs (ncRNAs) are — genes that are transcribed but not translated into proteins. With one of his ncRNA papers, University of Queensland researcher Tim Mercer recalls that two reviewers said, “this is good” and the third said, “this is all junk; noncoding RNAs aren’t functional.” Debates over ncRNAs, in Mercer’s view, have generally moved from ‘it’s all junk’ to ‘which ones are functional?’ and ‘what are they doing?’” (Marx, 2022b)
• “[O]ne of the most important reasons ncRNAs have transitioned from the realm of junk to importance is what labs have seen in loss-of-function experiments with lncRNAs and by using RNA interference (RNAi), among other methods. These experiments have been “key to show that lncRNAs have genuine cellular functions.” Few lncRNAs show strong phenotypes when mutated, but many have regulatory roles that can be assessed by studying how they alter gene expression. Orthogonal methods matter for getting such insight on ncRNAs, she says. “The lack of rigor in some studies has fed the skepticism of some researchers, and we face the challenge of producing the best possible evidence to overcome this prejudice.” (Marx, 2022b)
• “A further challenge to a gene-centered model of evolution is our growing appreciation of the fact that what was long considered to be irrelevant ‘junk DNA’—because it was repetitive, was noncoding for proteins, and therefore presumably not subject to natural selection—in fact plays an important role in shaping genome evolution, epigenetic development, and gene regulation.” (Corning et al., 2023)
• “A Kuhnian revolution in molecular biology:Most genes in complex organisms express regulatory RNAs … I]n simplified Kuhnian terms, the dominant paradigm in molecular biology since its foundation that “genes encode proteins and sequences that do not are mainly junk” should be replaced by “genes encode proteins and regulatory RNAs, the latter required for the epigenetic control of developmental trajectories”. RNA is not simply an intermediate between gene and protein, but a major player in gene regulation and a contributor to inheritance.” (Mattick, 2023)
• “While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory.” (Mattick and Amaral, 2023)