Junk DNA and ENCODE Revisited

The Newest Findings

A few months ago the ENCODE project (acronym for ENCyclopedia Of DNA Elements) consisting of 400 scientists in 32 different laboratories studying “junk” DNA released their findings in 30 papers published in several different scientific journals (see Encyclopedia of DNA Elements and Nature ENCODE for more information). The sheer volume of information is amazing, consisting of hundreds of terabytes of data.

The ENCODE project is devoted to making sense of the human genome. The sequence of the human genome was completed in 2000, but it only revealed the order of the individual components, called bases or nucleotides, in the DNA. The function of many of those components was still unknown. Some genes (packets of information in the DNA for making proteins) were known, but that only accounted for about two percent of the human genome. What about the other 98 percent? This became especially relevant when it was discovered that humans, as the most complex organism on the planet, only have about 20,000 genes and they are similar to genes in many other organisms. Scientists knew they had to look elsewhere for the differences in DNA among organisms.

In 2007 the ENCODE project released a series of papers explaining their findings from analyzing just one percent of the human genome (for more information see ‘Junk’ DNA: Evolutionary Discards or God’s Tools?, “Junk” DNA—Past, Present, and Future, Part 1, and “Junk” DNA—Past, Present, and Future, Part 2). One of the scientists involved in the research said, “We are now seeing the majority of the rest of the genome is active to some extent.”1 Fortunately, this prompted more extensive research of the remaining 99 percent of the genome over the last five years.

In the new study, ENCODE estimates that 80 percent of the genome is functional in the sense that it has “specific biochemical activity.” Mark Gerstein, an ENCODE researcher said, “It is like opening a wiring closet and seeing a hairball of wires. We tried to unravel this hairball and make it interpretable.”2

Most of the function is believed to be regulatory. In the simplest terms, the “junk” DNA is telling the genes when to produce their product (the protein) and when not to. The goal is to eventually figure out the function of each and every one of the three billion bases of human DNA. ENCODE researcher Tom Gingeras said, “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more.”3 ENCODE only studied 147 cell types, and considering the human body has a few thousand cell types, Ewan Birney, ENCODE’s Lead Analysis Coordinator, said, “It’s likely that 80 percent will go to 100 percent.”4 In light of this evidence, it’s obvious that a more appropriate term for “junk” DNA is needed.

The ENCODE findings will likely have significant impact on disease diagnosis and treatment. For many years scientists have known that certain variations in DNA (called single nucleotide polymorphisms, SNPs) are associated with risks for disease or with the disease itself. But 90 percent of those variations fall outside of genes (they are in the “junk” DNA). Up to this point no one really knew how that variation was causing the disease. The ENCODE study found that 60 percent of these variations fall in regions that affect the activity of genes. For example, the ENCODE study found five variations in patients with Crohn’s disease related to a specific factor that researchers weren’t even looking at.5 Of course, translating the basic lab science to clinical applications and treatments will take time, but it puts scientists one step closer in the battle against disease in this sin-cursed world.

A third phase of the ENCODE project is now beginning to further refine exactly what all the “junk” DNA is doing. Ewan Birney stated, “We are the most complex things we know about. It’s not surprising that the manual is huge. I think it’s going to take this century to fill in all the details.”6 Or will it take longer? Geneticist Rick Myers stated, “We’re far from finished. You might argue that this could go on forever.”7 The following verses seem appropriate in light of the ENCODE findings.

For You formed my inward parts;
You covered me in my mother’s womb.
I will praise You, for I am fearfully and wonderfully made;
Marvelous are Your works,
And that my soul knows very well (Psalm 139: 13–14).

Evolutionists’ Oppositions to the Findings

Although many scientists are thrilled about the newest ENCODE findings, there has also been opposition. For many evolutionists the finding that junk DNA is not junk is inconsistent with an evolutionary worldview. 98 percent of human DNA has been affectionately called “junk” because it did not code for proteins. It was assumed to be an evolutionary wasteland of sequences that were discarded as humans climbed the “tree of life” from a single-celled organism.

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?8
– Susumu Ohno (coined the term junk DNA).

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.9
– Leslie Orgel and Francis Crick (co-discoverer of the structure of DNA).

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].10
– Francis Collins (Director of the National Institute of Health and director of the human genome sequencing project)

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.11
– Richard Dawkins (evolutionary biologist)

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 may be functional. But will this finding change the mind of evolutionists regarding junk DNA as junk? Probably not because this is not about the evidence, this is about worldviews. If the evidence is contrary, rather than change their worldview, evolutionists will simply attempt to make the evidence “fit.” Three main arguments are being used to downplay or dismiss ENCODE’s findings 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 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 be inconsistent with a logical, orderly designer God to design organisms with a lot of non-functional DNA. The finding that junk DNA has “activity” and may be functional is consistent with a biblical worldview.

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 junk 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. They also 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?12

In other words, the vast majority of junk (or non-coding) DNA must not be functional if onions, which are less complex than humans, have a lot more junk DNA than humans. This is an argument from ignorance. Do scientists know that this “junk” DNA is not necessary for the onion? Many scientists claim it isn’t necessary because of the variability in DNA amounts among different species of the onion family. If onion species with small amounts of DNA can grow and survive as well as those with large amounts of DNA then some of the DNA must not be important or necessary.

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.

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 in 2001, “Those of you who still think junk DNA is junk, I invite you to take it out of your genome, and see what happens.”13

Argument Three: “We never said all junk DNA was junk!”

Many evolutionists are “back-pedaling” and claiming they never said all junk DNA was not functional. However, they 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 a function has been found!

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.”14

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 [a specific type of repetitive element] 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.”15

The more we research junk DNA, the more we realize the reality of Ewan Birney’s statement that, “It’s likely that 80 percent [junk DNA that may be functional] will go to 100 percent.”16

While there are many things unknown about junk DNA and more research is needed in this area, some things are known 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, including “junk” DNA, is consistent with a biblical worldview.