ENCODE and the Dark Matter of the Genome, Part Two

In part one I discussed the exciting discoveries of the ENCODE project on “junk” DNA. In part two I want to discuss the opposition of many evolutionists to the ENCODE findings.

Rather than put words in the evolutionists’ mouths, I will let them speak for themselves as to how they regard approximately 98 percent of human DNA, the so-called “junk” DNA. Only about two percent of DNA is thought to consist of coding DNA or genes (packets of information on how to make proteins).

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?

– Susumu Ohno (coined the term junk DNA).1

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.

– Leslie Orgel and Francis Crick (co-discoverer of the structure of DNA).2

Mammalian genomes are littered with such AREs [type of junk DNA], with roughly 45 percent of the human genomes made up of such genetic flotsam and jetsam [types of debris in the ocean].

– Francis Collins (Director of NIH and directed sequencing of human genome)3

Leaving pseudogenes aside, it is a remarkable fact that 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.

– Richard Dawkins (evolutionary biologist)4

These well known scientists make it clear that junk DNA is essentially a genetic graveyard representing our evolutionary past. But if evolution is true, then why do organisms still have so much unnecessary DNA? It’s a huge energy waste to replicate DNA that isn’t necessary or functional. The very presence of junk DNA in modern organisms seems inconsistent with an evolutionary worldview.

The findings of ENCODE provide the answer as to why junk DNA is there. A good portion of it appears to be functional. But did this finding change the mind of evolutionists regarding junk DNA as junk? No. Because this is not about the evidence; this is about worldviews. If the evidence is contrary, then rather than change their worldview, they will simply attempt to make the evidence “fit.” As I’ve reviewed the writings of many evolutionists about ENCODE, I see three main arguments being used to downplay or dismiss the idea that junk DNA is functional.

Argument One: ENCODE’s Definition of “Functional” Is Too Broad

ENCODE defined function as “specific biochemical activity.” This doesn’t necessarily mean they know the function of a given sequence of junk DNA, but that there is some activity associated with it. For example, ENCODE found that the majority of DNA is transcribed into RNA. Transcription is essentially copying the DNA into another form called RNA. This was thought to be exclusive to parts of the DNA that coded for proteins (the genes). The RNA would be “read” in the cell and the protein assembled from these instructions. Since junk DNA is non-coding DNA, why is it being transcribed into RNA? Many evolutionists think this RNA isn’t doing anything—that there is activity but not useful activity. Many believe it may be one of those “evolutionary leftovers” that hasn’t been eliminated from our DNA yet.

Again, it has not been shown yet that this RNA is non-functional. The evolutionists are saying this to accommodate the evidence within an evolutionary worldview. From a biblical creationist worldview, it would not be consistent with a logical, orderly designer God to design organisms with a lot of non-functional DNA. The finding that junk DNA has “activity” and will most likely be functional is consistent with a biblical worldview. Once again we see that observational science is consistent with God’s Word.

Of course, it is unlikely that all of the junk DNA will be functional. It has been affected by mutations since the Fall. It is also possible that the DNA had a function in the past but is no longer functional (possibly allowing for mediated design after the major environmental challenges following Noah’s Flood). Remember too that ENCODE only looked at 147 cell types of the many thousands that are in the human body. Also consider that they have not assessed function of the junk DNA during different developmental stages or under different environmental conditions. ENCODE is embarking on a third phase of research to further refine the activities and function of junk DNA.

Argument Two: The “Onion Test”

Many evolutionists have said that the ENCODE discovery of proposed function for the vast majority of junk DNA does not pass the so-called “onion test.” Evolutionary biologist, T. Ryan Gregory states,

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?5
In other words, the vast majority of junk DNA must not be functional if onions, which are less complex than humans, have a lot more junk DNA than humans. In my opinion, this is an argument from ignorance. How do scientists know that this “junk” DNA is not necessary for the onion? They would likely answer because of the variability in DNA amounts among different species of the onion family which can range widely. They conclude that if some onion species can grow, reproduce, and survive without that DNA then it must not be important or necessary.

However, within a family of organisms a lot of variability in the amount of DNA can exist, and having less DNA does not necessarily equate to the non-functionality of the DNA of those that have more. The dog family is a perfect example of this. All dogs including wolves, coyotes, dingoes, foxes, and domestic dogs are part of the same family (Canidae). Most dogs have 78 chromosomes, however, foxes have a wide range in chromosome number from 34 in the red fox to 72 in the bat-eared fox. However, all foxes are considered part of the dog family by genetic studies6 and hybrid studies7 (two animals can mate and produce offspring). In some families (typically thought to be equivalent of the biblical kind) there seems to be a large range in chromosome number or amount of DNA. Would evolutionists argue that those chromosomes (that have DNA that codes for proteins and junk DNA) that are in wolves but not in foxes are not necessary because foxes don’t have them and they are fine? I doubt it.

Therefore, it is not a logical conclusion to say that because an onion has more junk DNA than a human that junk DNA is not functional. There have been no studies, to my knowledge, to support the idea that large amounts of junk DNA in some onion species are not necessary or important. As one scientist noted, “Those of you who still think junk DNA is junk, I invite you to take it out of your genome, and see what happens.”8

It’s possible the junk DNA is only necessary under certain environmental conditions, as onions don’t have the same choices as mobile organisms. It may be necessary for additional variation or speciation as environmental conditions change and onions adapt. For all we know about the genome, there is so much more that we don’t!

Argument Three: “We Never Said All Junk DNA Was Junk!”

Many evolutionists are “back-pedaling” and saying they never said all junk DNA was not functional. However, many seem to have different definitions of what does constitute “truly junk” DNA. Research has shown that for almost every type of DNA they classify as truly junk has been found to have function!

Richard Sternberg looked at a specific type of junk DNA called retroelements. He produced several tables in his paper showing the function of many of them (mainly in regulation). He said, “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.”9

Repetitive elements (sequences of DNA found many times throughout the human genome) are typically defined as junk. But as one group of scientists recently noted, “Historically, Alu elements were regarded as ‘junk DNA’ with no apparent function. However, studies in the past decade have revealed diverse roles for Alu elements in gene regulation and genome evolution.”10

The more we research junk DNA, the more we realize the reality of Ewan Birney’s (ENCODE Lead Analysis Coordinator) statement that, “It’s likely that 80 percent [percentage of junk DNA that is functional] will go to 100 percent.”11

While there are many things we still do not know about junk DNA and we look forward to more discovery in this area, there are some things we know for certain. Evidence will always be interpreted in light of a person’s worldview. God’s Word is true and it is clear from Genesis that He created by His spoken command in six literal, 24-hour days about 6,000 years ago. Observational science in the area of genetics is inconsistent with an evolutionary worldview but consistent with a biblical worldview.

Keep fighting the good fight of the faith!


  1. B. Kuska, “Should scientists scrap the notion of junk DNA?,” Journal of National Cancer Institute 90 (1988):1032-1033.
  2. L. E. Orgel and F. H. C. Crick, “Selfish DNA: the ultimate parasite,” Nature 284 (1980): 604-607.
  3. F. Collins, The Language of God (New York: Free Press, 2006), 136.
  4. R. Dawkins, The Greatest Show on Earth: The Evidence for Evolution (New York: Free Press, 2010), 333.
  5. T. R. Gregory, “The Onion Test,” Genomicron (blog), April 25, 2007, http://www.genomicron.evolverzone.com/2007/04/onion-test/.
  6. K. Lindblad-Toh et al., “Genome sequence, comparative analysis and haplotype structure of the domestic dog,” Nature 2005 (438): 803-819.
  7. R. G. Van Gelder, “Mammalian Hybrids and Generic Limits,” American Museum Novitates 1977 (2635):1-25.
  8. R. Lewis, “Founder populations fuel gene discovery: Isolated people-groups further genetic studyThe Scientist 15 (2001):8.
  9. R. von Sternberg and J. A. Shapiro, “How repeated retroelements format genome function,” Cytogenetic and Genome Research 110 (2005): 108-116.
  10. S. Shen et al., “Widespread establishment and regulatory impact of Alu exons in human genes,” PNAS 108 (2011): 2837-2842.
  11. E. Yong, “ENCODE: the rough guide to the human genome,” Discover Magazine, September 5, 2012.

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